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package jalview.appletgui; |
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import java.awt.BorderLayout; |
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import java.awt.Canvas; |
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import java.awt.CheckboxMenuItem; |
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import java.awt.Color; |
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import java.awt.FlowLayout; |
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import java.awt.Font; |
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import java.awt.FontMetrics; |
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import java.awt.Frame; |
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import java.awt.Graphics; |
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import java.awt.Label; |
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import java.awt.Menu; |
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import java.awt.MenuBar; |
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import java.awt.MenuItem; |
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import java.awt.Panel; |
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import java.awt.Rectangle; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.FocusEvent; |
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import java.awt.event.FocusListener; |
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import java.awt.event.ItemEvent; |
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import java.awt.event.ItemListener; |
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import java.awt.event.KeyEvent; |
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import java.awt.event.KeyListener; |
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import java.awt.event.WindowAdapter; |
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import java.awt.event.WindowEvent; |
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import java.io.IOException; |
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import java.io.UnsupportedEncodingException; |
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import java.net.URL; |
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import java.net.URLEncoder; |
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import java.util.Arrays; |
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import java.util.Deque; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.StringTokenizer; |
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import java.util.Vector; |
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import org.jmol.viewer.Viewer; |
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import jalview.analysis.AlignmentSorter; |
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import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; |
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import jalview.analysis.TreeBuilder; |
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import jalview.analysis.scoremodels.PIDModel; |
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import jalview.analysis.scoremodels.ScoreModels; |
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import jalview.api.AlignViewControllerGuiI; |
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import jalview.api.AlignViewControllerI; |
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import jalview.api.AlignViewportI; |
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import jalview.api.FeatureColourI; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.FeatureSettingsControllerI; |
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import jalview.api.SequenceStructureBinding; |
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import jalview.bin.JalviewLite; |
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import jalview.commands.CommandI; |
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import jalview.commands.EditCommand; |
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import jalview.commands.EditCommand.Action; |
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import jalview.commands.OrderCommand; |
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import jalview.commands.RemoveGapColCommand; |
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import jalview.commands.RemoveGapsCommand; |
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import jalview.commands.SlideSequencesCommand; |
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import jalview.commands.TrimRegionCommand; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentOrder; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.AnnotationFile; |
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import jalview.io.AppletFormatAdapter; |
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import jalview.io.DataSourceType; |
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import jalview.io.FeaturesFile; |
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import jalview.io.FileFormat; |
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import jalview.io.FileFormatI; |
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import jalview.io.FileFormats; |
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import jalview.io.TCoffeeScoreFile; |
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import jalview.schemes.Blosum62ColourScheme; |
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import jalview.schemes.BuriedColourScheme; |
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import jalview.schemes.ClustalxColourScheme; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.HelixColourScheme; |
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import jalview.schemes.HydrophobicColourScheme; |
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import jalview.schemes.NucleotideColourScheme; |
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import jalview.schemes.PIDColourScheme; |
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import jalview.schemes.PurinePyrimidineColourScheme; |
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import jalview.schemes.RNAHelicesColour; |
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import jalview.schemes.StrandColourScheme; |
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import jalview.schemes.TCoffeeColourScheme; |
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import jalview.schemes.TaylorColourScheme; |
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import jalview.schemes.TurnColourScheme; |
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import jalview.schemes.ZappoColourScheme; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structures.models.AAStructureBindingModel; |
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import jalview.util.MappingUtils; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.AlignmentViewport; |
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import jalview.viewmodel.ViewportRanges; |
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| 0% |
Uncovered Elements: 2,499 (2,499) |
Complexity: 566 |
Complexity Density: 0.34 |
|
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public class AlignFrame extends EmbmenuFrame implements ActionListener, |
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ItemListener, KeyListener, AlignViewControllerGuiI |
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{ |
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public AlignViewControllerI avc; |
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public AlignmentPanel alignPanel; |
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public AlignViewport viewport; |
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int frameWidth = 700; |
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int frameHeight = 500; |
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String jalviewServletURL; |
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private boolean showAutoCalculatedAbove; |
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private SequenceAnnotationOrder annotationSortOrder; |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
155 |
0 |
public AlignFrame(AlignmentI al, JalviewLite applet, String title,... |
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boolean embedded) |
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{ |
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this(al, applet, title, embedded, true); |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public AlignFrame(AlignmentI al, JalviewLite applet, String title,... |
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boolean embedded, boolean addToDisplay) |
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{ |
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this(al, null, null, applet, title, embedded, addToDisplay); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,... |
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HiddenColumns hidden, JalviewLite applet, String title, |
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boolean embedded) |
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{ |
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this(al, hiddenSeqs, hidden, applet, title, embedded, true); |
182 |
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} |
183 |
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| 0% |
Uncovered Elements: 121 (121) |
Complexity: 21 |
Complexity Density: 0.24 |
|
184 |
0 |
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,... |
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HiddenColumns hidden, JalviewLite applet, String title, |
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boolean embedded, boolean addToDisplay) |
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{ |
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if (applet != null) |
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{ |
190 |
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jalviewServletURL = applet.getParameter("APPLICATION_URL"); |
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} |
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|
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0 |
try |
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{ |
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jbInit(); |
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} catch (Exception ex) |
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{ |
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ex.printStackTrace(); |
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} |
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|
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0 |
if (applet != null) |
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{ |
203 |
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String param; |
204 |
0 |
try |
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{ |
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0 |
param = applet.getParameter("windowWidth"); |
207 |
0 |
if (param != null) |
208 |
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{ |
209 |
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int width = Integer.parseInt(param); |
210 |
0 |
frameWidth = width; |
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} |
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param = applet.getParameter("windowHeight"); |
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if (param != null) |
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{ |
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int height = Integer.parseInt(param); |
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frameHeight = height; |
217 |
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} |
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} catch (Exception ex) |
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{ |
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} |
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} |
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viewport = new AlignViewport(al, applet); |
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if (hiddenSeqs != null && hiddenSeqs.length > 0) |
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{ |
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viewport.hideSequence(hiddenSeqs); |
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} |
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if (hidden != null) |
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{ |
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viewport.getAlignment().setHiddenColumns(hidden); |
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} |
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viewport.setScaleAboveWrapped(scaleAbove.getState()); |
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|
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alignPanel = new AlignmentPanel(this, viewport); |
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avc = new jalview.controller.AlignViewController(this, viewport, |
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alignPanel); |
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viewport.updateConservation(alignPanel); |
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viewport.updateConsensus(alignPanel); |
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|
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displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); |
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followMouseOverFlag.setState(viewport.isFollowHighlight()); |
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showGroupConsensus.setState(viewport.isShowGroupConsensus()); |
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0 |
showGroupConservation.setState(viewport.isShowGroupConservation()); |
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showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); |
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showSequenceLogo.setState(viewport.isShowSequenceLogo()); |
246 |
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normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); |
247 |
0 |
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); |
248 |
0 |
annotationPanelMenuItem.setState(viewport.isShowAnnotation()); |
249 |
0 |
showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
250 |
0 |
showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); |
251 |
0 |
showAlignmentAnnotations.setState(true); |
252 |
0 |
showSequenceAnnotations.setState(false); |
253 |
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|
254 |
0 |
seqLimits.setState(viewport.getShowJVSuffix()); |
255 |
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|
256 |
0 |
if (applet != null) |
257 |
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{ |
258 |
0 |
String param = applet.getParameter("sortBy"); |
259 |
0 |
if (param != null) |
260 |
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{ |
261 |
0 |
if (param.equalsIgnoreCase("Id")) |
262 |
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{ |
263 |
0 |
sortIDMenuItem_actionPerformed(); |
264 |
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} |
265 |
0 |
else if (param.equalsIgnoreCase("Pairwise Identity")) |
266 |
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{ |
267 |
0 |
sortPairwiseMenuItem_actionPerformed(); |
268 |
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} |
269 |
0 |
else if (param.equalsIgnoreCase("Length")) |
270 |
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{ |
271 |
0 |
sortLengthMenuItem_actionPerformed(); |
272 |
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} |
273 |
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} |
274 |
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|
275 |
0 |
param = applet.getParameter("wrap"); |
276 |
0 |
if (param != null) |
277 |
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{ |
278 |
0 |
if (param.equalsIgnoreCase("true")) |
279 |
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{ |
280 |
0 |
wrapMenuItem.setState(true); |
281 |
0 |
wrapMenuItem_actionPerformed(); |
282 |
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} |
283 |
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} |
284 |
0 |
param = applet.getParameter("centrecolumnlabels"); |
285 |
0 |
if (param != null) |
286 |
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{ |
287 |
0 |
centreColumnLabelFlag.setState(true); |
288 |
0 |
centreColumnLabelFlag_stateChanged(); |
289 |
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} |
290 |
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|
291 |
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} |
292 |
0 |
if (viewport.getAlignment().isNucleotide()) |
293 |
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{ |
294 |
0 |
conservationMenuItem.setEnabled(false); |
295 |
0 |
clustalColour.setEnabled(false); |
296 |
0 |
BLOSUM62Colour.setEnabled(false); |
297 |
0 |
zappoColour.setEnabled(false); |
298 |
0 |
taylorColour.setEnabled(false); |
299 |
0 |
hydrophobicityColour.setEnabled(false); |
300 |
0 |
helixColour.setEnabled(false); |
301 |
0 |
strandColour.setEnabled(false); |
302 |
0 |
turnColour.setEnabled(false); |
303 |
0 |
buriedColour.setEnabled(false); |
304 |
0 |
viewport.updateStrucConsensus(alignPanel); |
305 |
0 |
if (viewport.getAlignment().hasRNAStructure()) |
306 |
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{ |
307 |
0 |
RNAHelixColour.setEnabled(true); |
308 |
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} |
309 |
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else |
310 |
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{ |
311 |
0 |
RNAHelixColour.setEnabled(false); |
312 |
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} |
313 |
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} |
314 |
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else |
315 |
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{ |
316 |
0 |
RNAHelixColour.setEnabled(false); |
317 |
0 |
purinePyrimidineColour.setEnabled(false); |
318 |
0 |
nucleotideColour.setEnabled(false); |
319 |
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} |
320 |
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|
321 |
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|
322 |
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|
323 |
0 |
this.addKeyListener(this); |
324 |
0 |
alignPanel.seqPanel.seqCanvas.addKeyListener(this); |
325 |
0 |
alignPanel.idPanel.idCanvas.addKeyListener(this); |
326 |
0 |
alignPanel.scalePanel.addKeyListener(this); |
327 |
0 |
alignPanel.annotationPanel.addKeyListener(this); |
328 |
0 |
alignPanel.annotationPanelHolder.addKeyListener(this); |
329 |
0 |
alignPanel.annotationSpaceFillerHolder.addKeyListener(this); |
330 |
0 |
alignPanel.alabels.addKeyListener(this); |
331 |
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|
332 |
0 |
setAnnotationsVisibility(); |
333 |
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|
334 |
0 |
if (addToDisplay) |
335 |
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{ |
336 |
0 |
addToDisplay(embedded); |
337 |
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} |
338 |
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} |
339 |
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|
340 |
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|
341 |
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@param |
342 |
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|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
343 |
0 |
public void addToDisplay(boolean embedded)... |
344 |
|
{ |
345 |
0 |
createAlignFrameWindow(embedded); |
346 |
0 |
validate(); |
347 |
0 |
alignPanel.adjustAnnotationHeight(); |
348 |
0 |
alignPanel.paintAlignment(true, true); |
349 |
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} |
350 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
351 |
0 |
public AlignViewport getAlignViewport()... |
352 |
|
{ |
353 |
0 |
return viewport; |
354 |
|
} |
355 |
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|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
356 |
0 |
public SeqCanvas getSeqcanvas()... |
357 |
|
{ |
358 |
0 |
return alignPanel.seqPanel.seqCanvas; |
359 |
|
} |
360 |
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361 |
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362 |
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363 |
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|
364 |
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@param |
365 |
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366 |
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@param |
367 |
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|
368 |
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|
369 |
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
370 |
0 |
public boolean parseFeaturesFile(String file, DataSourceType type)... |
371 |
|
{ |
372 |
0 |
return parseFeaturesFile(file, type, true); |
373 |
|
} |
374 |
|
|
375 |
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|
376 |
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|
377 |
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|
378 |
|
@param |
379 |
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|
380 |
|
@param |
381 |
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|
382 |
|
@param |
383 |
|
|
384 |
|
|
385 |
|
@return |
386 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 6 |
Complexity Density: 0.35 |
|
387 |
0 |
public boolean parseFeaturesFile(String file, DataSourceType sourceType,... |
388 |
|
boolean autoenabledisplay) |
389 |
|
{ |
390 |
0 |
boolean featuresFile = false; |
391 |
0 |
try |
392 |
|
{ |
393 |
0 |
Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas |
394 |
|
.getFeatureRenderer().getFeatureColours(); |
395 |
0 |
boolean relaxedIdMatching = viewport.applet |
396 |
|
.getDefaultParameter("relaxedidmatch", false); |
397 |
0 |
featuresFile = new FeaturesFile(file, sourceType).parse( |
398 |
|
viewport.getAlignment(), colours, true, relaxedIdMatching); |
399 |
|
} catch (Exception ex) |
400 |
|
{ |
401 |
0 |
ex.printStackTrace(); |
402 |
|
} |
403 |
|
|
404 |
0 |
if (featuresFile) |
405 |
|
{ |
406 |
0 |
if (autoenabledisplay) |
407 |
|
{ |
408 |
0 |
viewport.setShowSequenceFeatures(true); |
409 |
0 |
sequenceFeatures.setState(true); |
410 |
|
} |
411 |
0 |
if (alignPanel.seqPanel.seqCanvas.fr != null) |
412 |
|
{ |
413 |
|
|
414 |
0 |
alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); |
415 |
|
} |
416 |
0 |
if (viewport.featureSettings != null) |
417 |
|
{ |
418 |
0 |
viewport.featureSettings.refreshTable(); |
419 |
|
} |
420 |
0 |
alignPanel.paintAlignment(true, true); |
421 |
0 |
setStatus(MessageManager |
422 |
|
.getString("label.successfully_added_features_alignment")); |
423 |
|
} |
424 |
0 |
return featuresFile; |
425 |
|
} |
426 |
|
|
|
|
| 0% |
Uncovered Elements: 207 (207) |
Complexity: 76 |
Complexity Density: 0.53 |
|
427 |
0 |
@Override... |
428 |
|
public void keyPressed(KeyEvent evt) |
429 |
|
{ |
430 |
0 |
ViewportRanges ranges = viewport.getRanges(); |
431 |
|
|
432 |
0 |
if (viewport.cursorMode |
433 |
|
&& ((evt.getKeyCode() >= KeyEvent.VK_0 |
434 |
|
&& evt.getKeyCode() <= KeyEvent.VK_9) |
435 |
|
|| (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 |
436 |
|
&& evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) |
437 |
|
&& Character.isDigit(evt.getKeyChar())) |
438 |
|
{ |
439 |
0 |
alignPanel.seqPanel.numberPressed(evt.getKeyChar()); |
440 |
|
} |
441 |
|
|
442 |
0 |
switch (evt.getKeyCode()) |
443 |
|
{ |
444 |
0 |
case 27: |
445 |
0 |
deselectAllSequenceMenuItem_actionPerformed(); |
446 |
|
|
447 |
0 |
alignPanel.alabels.cancelDrag(); |
448 |
0 |
break; |
449 |
0 |
case KeyEvent.VK_X: |
450 |
0 |
if (evt.isControlDown() || evt.isMetaDown()) |
451 |
|
{ |
452 |
0 |
cut_actionPerformed(); |
453 |
|
} |
454 |
0 |
break; |
455 |
0 |
case KeyEvent.VK_C: |
456 |
0 |
if (viewport.cursorMode && !evt.isControlDown()) |
457 |
|
{ |
458 |
0 |
alignPanel.seqPanel.setCursorColumn(); |
459 |
|
} |
460 |
0 |
if (evt.isControlDown() || evt.isMetaDown()) |
461 |
|
{ |
462 |
0 |
copy_actionPerformed(); |
463 |
|
} |
464 |
0 |
break; |
465 |
0 |
case KeyEvent.VK_V: |
466 |
0 |
if (evt.isControlDown()) |
467 |
|
{ |
468 |
0 |
paste(evt.isShiftDown()); |
469 |
|
} |
470 |
0 |
break; |
471 |
0 |
case KeyEvent.VK_A: |
472 |
0 |
if (evt.isControlDown() || evt.isMetaDown()) |
473 |
|
{ |
474 |
0 |
selectAllSequenceMenuItem_actionPerformed(); |
475 |
|
} |
476 |
0 |
break; |
477 |
0 |
case KeyEvent.VK_DOWN: |
478 |
0 |
if (viewport.cursorMode) |
479 |
|
{ |
480 |
0 |
alignPanel.seqPanel.moveCursor(0, 1); |
481 |
|
} |
482 |
|
else |
483 |
|
{ |
484 |
0 |
moveSelectedSequences(false); |
485 |
|
} |
486 |
0 |
break; |
487 |
|
|
488 |
0 |
case KeyEvent.VK_UP: |
489 |
0 |
if (viewport.cursorMode) |
490 |
|
{ |
491 |
0 |
alignPanel.seqPanel.moveCursor(0, -1); |
492 |
|
} |
493 |
|
else |
494 |
|
{ |
495 |
0 |
moveSelectedSequences(true); |
496 |
|
} |
497 |
0 |
break; |
498 |
|
|
499 |
0 |
case KeyEvent.VK_LEFT: |
500 |
0 |
if (evt.isAltDown() || !viewport.cursorMode) |
501 |
|
{ |
502 |
0 |
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); |
503 |
|
} |
504 |
|
else |
505 |
|
{ |
506 |
0 |
alignPanel.seqPanel.moveCursor(-1, 0); |
507 |
|
} |
508 |
0 |
break; |
509 |
|
|
510 |
0 |
case KeyEvent.VK_RIGHT: |
511 |
0 |
if (evt.isAltDown() || !viewport.cursorMode) |
512 |
|
{ |
513 |
0 |
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); |
514 |
|
} |
515 |
|
else |
516 |
|
{ |
517 |
0 |
alignPanel.seqPanel.moveCursor(1, 0); |
518 |
|
} |
519 |
0 |
break; |
520 |
|
|
521 |
0 |
case KeyEvent.VK_SPACE: |
522 |
0 |
if (viewport.cursorMode) |
523 |
|
{ |
524 |
0 |
alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() |
525 |
|
|| evt.isShiftDown() || evt.isAltDown()); |
526 |
|
} |
527 |
0 |
break; |
528 |
|
|
529 |
0 |
case KeyEvent.VK_DELETE: |
530 |
0 |
case KeyEvent.VK_BACK_SPACE: |
531 |
0 |
if (viewport.cursorMode) |
532 |
|
{ |
533 |
0 |
alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() |
534 |
|
|| evt.isShiftDown() || evt.isAltDown()); |
535 |
|
} |
536 |
|
else |
537 |
|
{ |
538 |
0 |
cut_actionPerformed(); |
539 |
0 |
alignPanel.seqPanel.seqCanvas.repaint(); |
540 |
|
} |
541 |
0 |
break; |
542 |
|
|
543 |
0 |
case KeyEvent.VK_S: |
544 |
0 |
if (viewport.cursorMode) |
545 |
|
{ |
546 |
0 |
alignPanel.seqPanel.setCursorRow(); |
547 |
|
} |
548 |
0 |
break; |
549 |
0 |
case KeyEvent.VK_P: |
550 |
0 |
if (viewport.cursorMode) |
551 |
|
{ |
552 |
0 |
alignPanel.seqPanel.setCursorPosition(); |
553 |
|
} |
554 |
0 |
break; |
555 |
|
|
556 |
0 |
case KeyEvent.VK_ENTER: |
557 |
0 |
case KeyEvent.VK_COMMA: |
558 |
0 |
if (viewport.cursorMode) |
559 |
|
{ |
560 |
0 |
alignPanel.seqPanel.setCursorRowAndColumn(); |
561 |
|
} |
562 |
0 |
break; |
563 |
|
|
564 |
0 |
case KeyEvent.VK_Q: |
565 |
0 |
if (viewport.cursorMode) |
566 |
|
{ |
567 |
0 |
alignPanel.seqPanel.setSelectionAreaAtCursor(true); |
568 |
|
} |
569 |
0 |
break; |
570 |
0 |
case KeyEvent.VK_M: |
571 |
0 |
if (viewport.cursorMode) |
572 |
|
{ |
573 |
0 |
alignPanel.seqPanel.setSelectionAreaAtCursor(false); |
574 |
|
} |
575 |
0 |
break; |
576 |
|
|
577 |
0 |
case KeyEvent.VK_F2: |
578 |
0 |
viewport.cursorMode = !viewport.cursorMode; |
579 |
0 |
setStatus(MessageManager.formatMessage("label.keyboard_editing_mode", |
580 |
|
new String[] |
581 |
0 |
{ (viewport.cursorMode ? "on" : "off") })); |
582 |
0 |
if (viewport.cursorMode) |
583 |
|
{ |
584 |
0 |
alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); |
585 |
0 |
alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq(); |
586 |
|
} |
587 |
0 |
break; |
588 |
|
|
589 |
0 |
case KeyEvent.VK_F: |
590 |
0 |
if (evt.isControlDown()) |
591 |
|
{ |
592 |
0 |
findMenuItem_actionPerformed(); |
593 |
|
} |
594 |
0 |
break; |
595 |
|
|
596 |
0 |
case KeyEvent.VK_H: |
597 |
|
{ |
598 |
0 |
boolean toggleSeqs = !evt.isControlDown(); |
599 |
0 |
boolean toggleCols = !evt.isShiftDown(); |
600 |
0 |
toggleHiddenRegions(toggleSeqs, toggleCols); |
601 |
0 |
break; |
602 |
|
} |
603 |
|
|
604 |
0 |
case KeyEvent.VK_PAGE_UP: |
605 |
0 |
ranges.pageUp(); |
606 |
0 |
break; |
607 |
|
|
608 |
0 |
case KeyEvent.VK_PAGE_DOWN: |
609 |
0 |
ranges.pageDown(); |
610 |
0 |
break; |
611 |
|
|
612 |
0 |
case KeyEvent.VK_Z: |
613 |
0 |
if (evt.isControlDown()) |
614 |
|
{ |
615 |
0 |
undoMenuItem_actionPerformed(); |
616 |
|
} |
617 |
0 |
break; |
618 |
|
|
619 |
0 |
case KeyEvent.VK_Y: |
620 |
0 |
if (evt.isControlDown()) |
621 |
|
{ |
622 |
0 |
redoMenuItem_actionPerformed(); |
623 |
|
} |
624 |
0 |
break; |
625 |
|
|
626 |
0 |
case KeyEvent.VK_L: |
627 |
0 |
if (evt.isControlDown()) |
628 |
|
{ |
629 |
0 |
trimAlignment(true); |
630 |
|
} |
631 |
0 |
break; |
632 |
|
|
633 |
0 |
case KeyEvent.VK_R: |
634 |
0 |
if (evt.isControlDown()) |
635 |
|
{ |
636 |
0 |
trimAlignment(false); |
637 |
|
} |
638 |
0 |
break; |
639 |
|
|
640 |
0 |
case KeyEvent.VK_E: |
641 |
0 |
if (evt.isControlDown()) |
642 |
|
{ |
643 |
0 |
if (evt.isShiftDown()) |
644 |
|
{ |
645 |
0 |
this.removeAllGapsMenuItem_actionPerformed(); |
646 |
|
} |
647 |
|
else |
648 |
|
{ |
649 |
0 |
removeGappedColumnMenuItem_actionPerformed(); |
650 |
|
} |
651 |
|
} |
652 |
0 |
break; |
653 |
0 |
case KeyEvent.VK_I: |
654 |
0 |
if (evt.isControlDown()) |
655 |
|
{ |
656 |
0 |
if (evt.isAltDown()) |
657 |
|
{ |
658 |
0 |
invertColSel_actionPerformed(); |
659 |
|
} |
660 |
|
else |
661 |
|
{ |
662 |
0 |
invertSequenceMenuItem_actionPerformed(); |
663 |
|
} |
664 |
|
} |
665 |
0 |
break; |
666 |
|
|
667 |
0 |
case KeyEvent.VK_G: |
668 |
0 |
if (evt.isControlDown()) |
669 |
|
{ |
670 |
0 |
if (evt.isShiftDown()) |
671 |
|
{ |
672 |
0 |
this.unGroup_actionPerformed(); |
673 |
|
} |
674 |
|
else |
675 |
|
{ |
676 |
0 |
this.createGroup_actionPerformed(); |
677 |
|
} |
678 |
|
} |
679 |
0 |
break; |
680 |
|
|
681 |
0 |
case KeyEvent.VK_U: |
682 |
0 |
if (evt.isControlDown()) |
683 |
|
{ |
684 |
0 |
this.deleteGroups_actionPerformed(); |
685 |
|
} |
686 |
0 |
break; |
687 |
|
|
688 |
0 |
case KeyEvent.VK_T: |
689 |
0 |
if (evt.isControlDown()) |
690 |
|
{ |
691 |
0 |
newView(null); |
692 |
|
} |
693 |
0 |
break; |
694 |
|
|
695 |
|
} |
696 |
|
|
697 |
0 |
alignPanel.paintAlignment(true, true); |
698 |
|
} |
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
|
@param |
704 |
|
@param |
705 |
|
|
|
|
| 0% |
Uncovered Elements: 45 (45) |
Complexity: 17 |
Complexity Density: 0.68 |
|
706 |
0 |
private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)... |
707 |
|
{ |
708 |
0 |
boolean hide = false; |
709 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
710 |
0 |
if (!toggleSeqs && !toggleCols) |
711 |
|
{ |
712 |
|
|
713 |
|
|
714 |
|
|
715 |
0 |
if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 |
716 |
|
&& sg.getStartRes() <= sg.getEndRes())) |
717 |
|
{ |
718 |
|
|
719 |
|
|
720 |
0 |
if (sg != null) |
721 |
|
{ |
722 |
0 |
invertSequenceMenuItem_actionPerformed(); |
723 |
0 |
sg = viewport.getSelectionGroup(); |
724 |
0 |
toggleSeqs = true; |
725 |
|
|
726 |
|
} |
727 |
0 |
viewport.expandColSelection(sg, true); |
728 |
|
|
729 |
|
|
730 |
0 |
invertColSel_actionPerformed(); |
731 |
0 |
toggleCols = true; |
732 |
|
} |
733 |
|
} |
734 |
|
|
735 |
0 |
if (toggleSeqs) |
736 |
|
{ |
737 |
0 |
if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) |
738 |
|
{ |
739 |
0 |
hide = true; |
740 |
0 |
viewport.hideAllSelectedSeqs(); |
741 |
|
} |
742 |
0 |
else if (!(toggleCols && viewport.hasSelectedColumns())) |
743 |
|
{ |
744 |
0 |
viewport.showAllHiddenSeqs(); |
745 |
|
} |
746 |
|
} |
747 |
|
|
748 |
0 |
if (toggleCols) |
749 |
|
{ |
750 |
0 |
if (viewport.hasSelectedColumns()) |
751 |
|
{ |
752 |
0 |
viewport.hideSelectedColumns(); |
753 |
0 |
if (!toggleSeqs) |
754 |
|
{ |
755 |
0 |
viewport.setSelectionGroup(sg); |
756 |
|
} |
757 |
|
} |
758 |
0 |
else if (!hide) |
759 |
|
{ |
760 |
0 |
viewport.showAllHiddenColumns(); |
761 |
|
} |
762 |
0 |
viewport.sendSelection(); |
763 |
|
} |
764 |
|
} |
765 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
766 |
0 |
@Override... |
767 |
|
public void keyReleased(KeyEvent evt) |
768 |
|
{ |
769 |
|
} |
770 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
771 |
0 |
@Override... |
772 |
|
public void keyTyped(KeyEvent evt) |
773 |
|
{ |
774 |
|
} |
775 |
|
|
|
|
| 0% |
Uncovered Elements: 145 (145) |
Complexity: 34 |
Complexity Density: 0.43 |
|
776 |
0 |
@Override... |
777 |
|
public void itemStateChanged(ItemEvent evt) |
778 |
|
{ |
779 |
0 |
final Object source = evt.getSource(); |
780 |
0 |
if (source == displayNonconservedMenuItem) |
781 |
|
{ |
782 |
0 |
displayNonconservedMenuItem_actionPerformed(); |
783 |
|
} |
784 |
0 |
else if (source == colourTextMenuItem) |
785 |
|
{ |
786 |
0 |
colourTextMenuItem_actionPerformed(); |
787 |
|
} |
788 |
0 |
else if (source == wrapMenuItem) |
789 |
|
{ |
790 |
0 |
wrapMenuItem_actionPerformed(); |
791 |
|
} |
792 |
0 |
else if (source == scaleAbove) |
793 |
|
{ |
794 |
0 |
viewport.setScaleAboveWrapped(scaleAbove.getState()); |
795 |
|
} |
796 |
0 |
else if (source == scaleLeft) |
797 |
|
{ |
798 |
0 |
viewport.setScaleLeftWrapped(scaleLeft.getState()); |
799 |
|
} |
800 |
0 |
else if (source == scaleRight) |
801 |
|
{ |
802 |
0 |
viewport.setScaleRightWrapped(scaleRight.getState()); |
803 |
|
} |
804 |
0 |
else if (source == seqLimits) |
805 |
|
{ |
806 |
0 |
seqLimits_itemStateChanged(); |
807 |
|
} |
808 |
0 |
else if (source == viewBoxesMenuItem) |
809 |
|
{ |
810 |
0 |
viewport.setShowBoxes(viewBoxesMenuItem.getState()); |
811 |
|
} |
812 |
0 |
else if (source == viewTextMenuItem) |
813 |
|
{ |
814 |
0 |
viewport.setShowText(viewTextMenuItem.getState()); |
815 |
|
} |
816 |
0 |
else if (source == renderGapsMenuItem) |
817 |
|
{ |
818 |
0 |
viewport.setRenderGaps(renderGapsMenuItem.getState()); |
819 |
|
} |
820 |
0 |
else if (source == annotationPanelMenuItem) |
821 |
|
{ |
822 |
0 |
boolean showAnnotations = annotationPanelMenuItem.getState(); |
823 |
0 |
showAlignmentAnnotations.setEnabled(showAnnotations); |
824 |
0 |
showSequenceAnnotations.setEnabled(showAnnotations); |
825 |
0 |
viewport.setShowAnnotation(showAnnotations); |
826 |
0 |
alignPanel.setAnnotationVisible(showAnnotations); |
827 |
|
} |
828 |
0 |
else if (source == sequenceFeatures) |
829 |
|
{ |
830 |
0 |
viewport.setShowSequenceFeatures(sequenceFeatures.getState()); |
831 |
0 |
alignPanel.seqPanel.seqCanvas.repaint(); |
832 |
|
} |
833 |
0 |
else if (source == showAlignmentAnnotations) |
834 |
|
{ |
835 |
0 |
setAnnotationsVisibility(); |
836 |
|
} |
837 |
0 |
else if (source == showSequenceAnnotations) |
838 |
|
{ |
839 |
0 |
setAnnotationsVisibility(); |
840 |
|
} |
841 |
0 |
else if (source == sortAnnBySequence) |
842 |
|
{ |
843 |
0 |
boolean newState = sortAnnBySequence.getState(); |
844 |
0 |
sortAnnByLabel.setState(false); |
845 |
0 |
setAnnotationSortOrder( |
846 |
0 |
newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL |
847 |
|
: SequenceAnnotationOrder.NONE); |
848 |
0 |
setViewportAnnotationOrder(); |
849 |
|
} |
850 |
0 |
else if (source == sortAnnByLabel) |
851 |
|
{ |
852 |
0 |
boolean newState = sortAnnByLabel.getState(); |
853 |
0 |
sortAnnBySequence.setState(false); |
854 |
0 |
setAnnotationSortOrder( |
855 |
0 |
newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE |
856 |
|
: SequenceAnnotationOrder.NONE); |
857 |
0 |
setViewportAnnotationOrder(); |
858 |
|
} |
859 |
0 |
else if (source == showAutoFirst) |
860 |
|
{ |
861 |
0 |
showAutoLast.setState(!showAutoFirst.getState()); |
862 |
0 |
setShowAutoCalculatedAbove(showAutoFirst.getState()); |
863 |
0 |
setViewportAnnotationOrder(); |
864 |
|
} |
865 |
0 |
else if (source == showAutoLast) |
866 |
|
{ |
867 |
0 |
showAutoFirst.setState(!showAutoLast.getState()); |
868 |
0 |
setShowAutoCalculatedAbove(showAutoFirst.getState()); |
869 |
0 |
setViewportAnnotationOrder(); |
870 |
|
} |
871 |
0 |
else if (source == conservationMenuItem) |
872 |
|
{ |
873 |
0 |
conservationMenuItem_actionPerformed(); |
874 |
|
} |
875 |
0 |
else if (source == abovePIDThreshold) |
876 |
|
{ |
877 |
0 |
abovePIDThreshold_actionPerformed(); |
878 |
|
} |
879 |
0 |
else if (source == applyToAllGroups) |
880 |
|
{ |
881 |
0 |
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); |
882 |
|
} |
883 |
0 |
else if (source == autoCalculate) |
884 |
|
{ |
885 |
0 |
viewport.autoCalculateConsensus = autoCalculate.getState(); |
886 |
|
} |
887 |
0 |
else if (source == sortByTree) |
888 |
|
{ |
889 |
0 |
viewport.sortByTree = sortByTree.getState(); |
890 |
|
} |
891 |
0 |
else if (source == this.centreColumnLabelFlag) |
892 |
|
{ |
893 |
0 |
centreColumnLabelFlag_stateChanged(); |
894 |
|
} |
895 |
0 |
else if (source == this.followMouseOverFlag) |
896 |
|
{ |
897 |
0 |
mouseOverFlag_stateChanged(); |
898 |
|
} |
899 |
0 |
else if (source == showGroupConsensus) |
900 |
|
{ |
901 |
0 |
showGroupConsensus_actionPerformed(); |
902 |
|
} |
903 |
0 |
else if (source == showGroupConservation) |
904 |
|
{ |
905 |
0 |
showGroupConservation_actionPerformed(); |
906 |
|
} |
907 |
0 |
else if (source == showSequenceLogo) |
908 |
|
{ |
909 |
0 |
showSequenceLogo_actionPerformed(); |
910 |
|
} |
911 |
0 |
else if (source == normSequenceLogo) |
912 |
|
{ |
913 |
0 |
normSequenceLogo_actionPerformed(); |
914 |
|
} |
915 |
0 |
else if (source == showConsensusHistogram) |
916 |
|
{ |
917 |
0 |
showConsensusHistogram_actionPerformed(); |
918 |
|
} |
919 |
0 |
else if (source == applyAutoAnnotationSettings) |
920 |
|
{ |
921 |
0 |
applyAutoAnnotationSettings_actionPerformed(); |
922 |
|
} |
923 |
|
|
924 |
0 |
alignPanel.paintAlignment(true, true); |
925 |
|
} |
926 |
|
|
927 |
|
|
928 |
|
|
929 |
|
|
930 |
|
|
931 |
|
@param |
932 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
933 |
0 |
private void setAnnotationsVisibility()... |
934 |
|
{ |
935 |
0 |
boolean showForAlignment = showAlignmentAnnotations.getState(); |
936 |
0 |
boolean showForSequences = showSequenceAnnotations.getState(); |
937 |
0 |
if (alignPanel.getAlignment().getAlignmentAnnotation() != null) |
938 |
|
{ |
939 |
0 |
for (AlignmentAnnotation aa : alignPanel.getAlignment() |
940 |
|
.getAlignmentAnnotation()) |
941 |
|
{ |
942 |
0 |
boolean visible = (aa.sequenceRef == null ? showForAlignment |
943 |
|
: showForSequences); |
944 |
0 |
aa.visible = visible; |
945 |
|
} |
946 |
|
} |
947 |
0 |
alignPanel.validateAnnotationDimensions(true); |
948 |
0 |
validate(); |
949 |
0 |
repaint(); |
950 |
|
} |
951 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
952 |
0 |
private void setAnnotationSortOrder(SequenceAnnotationOrder order)... |
953 |
|
{ |
954 |
0 |
this.annotationSortOrder = order; |
955 |
|
} |
956 |
|
|
957 |
|
|
958 |
|
|
959 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
960 |
0 |
private void setViewportAnnotationOrder()... |
961 |
|
{ |
962 |
0 |
this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder); |
963 |
0 |
this.alignPanel.av |
964 |
|
.setShowAutocalculatedAbove(this.showAutoCalculatedAbove); |
965 |
|
} |
966 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
967 |
0 |
private void setShowAutoCalculatedAbove(boolean showAbove)... |
968 |
|
{ |
969 |
0 |
this.showAutoCalculatedAbove = showAbove; |
970 |
|
} |
971 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
972 |
0 |
private void mouseOverFlag_stateChanged()... |
973 |
|
{ |
974 |
0 |
viewport.setFollowHighlight(followMouseOverFlag.getState()); |
975 |
|
|
976 |
|
|
977 |
|
} |
978 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
979 |
0 |
private void centreColumnLabelFlag_stateChanged()... |
980 |
|
{ |
981 |
0 |
viewport.centreColumnLabels = centreColumnLabelFlag.getState(); |
982 |
0 |
this.alignPanel.annotationPanel.repaint(); |
983 |
|
} |
984 |
|
|
|
|
| 0% |
Uncovered Elements: 358 (358) |
Complexity: 85 |
Complexity Density: 0.44 |
|
985 |
0 |
@Override... |
986 |
|
public void actionPerformed(ActionEvent evt) |
987 |
|
{ |
988 |
0 |
viewport.applet.currentAlignFrame = this; |
989 |
|
|
990 |
0 |
Object source = evt.getSource(); |
991 |
|
|
992 |
0 |
if (source == inputText) |
993 |
|
{ |
994 |
0 |
inputText_actionPerformed(); |
995 |
|
} |
996 |
0 |
else if (source == loadTree) |
997 |
|
{ |
998 |
0 |
loadTree_actionPerformed(); |
999 |
|
} |
1000 |
0 |
else if (source == loadApplication) |
1001 |
|
{ |
1002 |
0 |
launchFullApplication(); |
1003 |
|
} |
1004 |
0 |
else if (source == loadAnnotations) |
1005 |
|
{ |
1006 |
0 |
loadAnnotations(); |
1007 |
|
} |
1008 |
0 |
else if (source == outputAnnotations) |
1009 |
|
{ |
1010 |
0 |
outputAnnotations(true); |
1011 |
|
} |
1012 |
0 |
else if (source == outputFeatures) |
1013 |
|
{ |
1014 |
0 |
outputFeatures(true, "Jalview"); |
1015 |
|
} |
1016 |
0 |
else if (source == closeMenuItem) |
1017 |
|
{ |
1018 |
0 |
closeMenuItem_actionPerformed(); |
1019 |
|
} |
1020 |
0 |
else if (source == copy) |
1021 |
|
{ |
1022 |
0 |
copy_actionPerformed(); |
1023 |
|
} |
1024 |
0 |
else if (source == undoMenuItem) |
1025 |
|
{ |
1026 |
0 |
undoMenuItem_actionPerformed(); |
1027 |
|
} |
1028 |
0 |
else if (source == redoMenuItem) |
1029 |
|
{ |
1030 |
0 |
redoMenuItem_actionPerformed(); |
1031 |
|
} |
1032 |
0 |
else if (source == inputText) |
1033 |
|
{ |
1034 |
0 |
inputText_actionPerformed(); |
1035 |
|
} |
1036 |
0 |
else if (source == closeMenuItem) |
1037 |
|
{ |
1038 |
0 |
closeMenuItem_actionPerformed(); |
1039 |
|
} |
1040 |
0 |
else if (source == undoMenuItem) |
1041 |
|
{ |
1042 |
0 |
undoMenuItem_actionPerformed(); |
1043 |
|
} |
1044 |
0 |
else if (source == redoMenuItem) |
1045 |
|
{ |
1046 |
0 |
redoMenuItem_actionPerformed(); |
1047 |
|
} |
1048 |
0 |
else if (source == copy) |
1049 |
|
{ |
1050 |
0 |
copy_actionPerformed(); |
1051 |
|
} |
1052 |
0 |
else if (source == pasteNew) |
1053 |
|
{ |
1054 |
0 |
pasteNew_actionPerformed(); |
1055 |
|
} |
1056 |
0 |
else if (source == pasteThis) |
1057 |
|
{ |
1058 |
0 |
pasteThis_actionPerformed(); |
1059 |
|
} |
1060 |
0 |
else if (source == cut) |
1061 |
|
{ |
1062 |
0 |
cut_actionPerformed(); |
1063 |
|
} |
1064 |
0 |
else if (source == delete) |
1065 |
|
{ |
1066 |
0 |
delete_actionPerformed(); |
1067 |
|
} |
1068 |
0 |
else if (source == createGroup) |
1069 |
|
{ |
1070 |
0 |
createGroup_actionPerformed(); |
1071 |
|
} |
1072 |
0 |
else if (source == unGroup) |
1073 |
|
{ |
1074 |
0 |
unGroup_actionPerformed(); |
1075 |
|
} |
1076 |
0 |
else if (source == grpsFromSelection) |
1077 |
|
{ |
1078 |
0 |
makeGrpsFromSelection_actionPerformed(); |
1079 |
|
} |
1080 |
0 |
else if (source == deleteGroups) |
1081 |
|
{ |
1082 |
0 |
deleteGroups_actionPerformed(); |
1083 |
|
} |
1084 |
0 |
else if (source == selectAllSequenceMenuItem) |
1085 |
|
{ |
1086 |
0 |
selectAllSequenceMenuItem_actionPerformed(); |
1087 |
|
} |
1088 |
0 |
else if (source == deselectAllSequenceMenuItem) |
1089 |
|
{ |
1090 |
0 |
deselectAllSequenceMenuItem_actionPerformed(); |
1091 |
|
} |
1092 |
0 |
else if (source == invertSequenceMenuItem) |
1093 |
|
{ |
1094 |
0 |
invertSequenceMenuItem_actionPerformed(); |
1095 |
|
|
1096 |
|
|
1097 |
|
} |
1098 |
0 |
else if (source == invertColSel) |
1099 |
|
{ |
1100 |
0 |
viewport.invertColumnSelection(); |
1101 |
0 |
alignPanel.paintAlignment(false, false); |
1102 |
0 |
viewport.sendSelection(); |
1103 |
|
} |
1104 |
0 |
else if (source == remove2LeftMenuItem) |
1105 |
|
{ |
1106 |
0 |
trimAlignment(true); |
1107 |
|
} |
1108 |
0 |
else if (source == remove2RightMenuItem) |
1109 |
|
{ |
1110 |
0 |
trimAlignment(false); |
1111 |
|
} |
1112 |
0 |
else if (source == removeGappedColumnMenuItem) |
1113 |
|
{ |
1114 |
0 |
removeGappedColumnMenuItem_actionPerformed(); |
1115 |
|
} |
1116 |
0 |
else if (source == removeAllGapsMenuItem) |
1117 |
|
{ |
1118 |
0 |
removeAllGapsMenuItem_actionPerformed(); |
1119 |
|
} |
1120 |
0 |
else if (source == findMenuItem) |
1121 |
|
{ |
1122 |
0 |
findMenuItem_actionPerformed(); |
1123 |
|
} |
1124 |
0 |
else if (source == font) |
1125 |
|
{ |
1126 |
0 |
new FontChooser(alignPanel); |
1127 |
|
} |
1128 |
0 |
else if (source == newView) |
1129 |
|
{ |
1130 |
0 |
newView(null); |
1131 |
|
} |
1132 |
0 |
else if (source == showColumns) |
1133 |
|
{ |
1134 |
0 |
viewport.showAllHiddenColumns(); |
1135 |
0 |
alignPanel.paintAlignment(true, true); |
1136 |
0 |
viewport.sendSelection(); |
1137 |
|
} |
1138 |
0 |
else if (source == showSeqs) |
1139 |
|
{ |
1140 |
0 |
viewport.showAllHiddenSeqs(); |
1141 |
0 |
alignPanel.paintAlignment(true, true); |
1142 |
|
|
1143 |
|
|
1144 |
|
} |
1145 |
0 |
else if (source == hideColumns) |
1146 |
|
{ |
1147 |
0 |
viewport.hideSelectedColumns(); |
1148 |
0 |
alignPanel.paintAlignment(true, true); |
1149 |
0 |
viewport.sendSelection(); |
1150 |
|
} |
1151 |
0 |
else if (source == hideSequences |
1152 |
|
&& viewport.getSelectionGroup() != null) |
1153 |
|
{ |
1154 |
0 |
viewport.hideAllSelectedSeqs(); |
1155 |
0 |
alignPanel.paintAlignment(true, true); |
1156 |
|
|
1157 |
|
|
1158 |
|
} |
1159 |
0 |
else if (source == hideAllButSelection) |
1160 |
|
{ |
1161 |
0 |
toggleHiddenRegions(false, false); |
1162 |
0 |
alignPanel.paintAlignment(true, true); |
1163 |
0 |
viewport.sendSelection(); |
1164 |
|
} |
1165 |
0 |
else if (source == hideAllSelection) |
1166 |
|
{ |
1167 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
1168 |
0 |
viewport.expandColSelection(sg, false); |
1169 |
0 |
viewport.hideAllSelectedSeqs(); |
1170 |
0 |
viewport.hideSelectedColumns(); |
1171 |
0 |
alignPanel.paintAlignment(true, true); |
1172 |
0 |
viewport.sendSelection(); |
1173 |
|
} |
1174 |
0 |
else if (source == showAllHidden) |
1175 |
|
{ |
1176 |
0 |
viewport.showAllHiddenColumns(); |
1177 |
0 |
viewport.showAllHiddenSeqs(); |
1178 |
0 |
alignPanel.paintAlignment(true, true); |
1179 |
0 |
viewport.sendSelection(); |
1180 |
|
} |
1181 |
0 |
else if (source == showGroupConsensus) |
1182 |
|
{ |
1183 |
0 |
showGroupConsensus_actionPerformed(); |
1184 |
|
} |
1185 |
0 |
else if (source == showGroupConservation) |
1186 |
|
{ |
1187 |
0 |
showGroupConservation_actionPerformed(); |
1188 |
|
} |
1189 |
0 |
else if (source == showSequenceLogo) |
1190 |
|
{ |
1191 |
0 |
showSequenceLogo_actionPerformed(); |
1192 |
|
} |
1193 |
0 |
else if (source == normSequenceLogo) |
1194 |
|
{ |
1195 |
0 |
normSequenceLogo_actionPerformed(); |
1196 |
|
} |
1197 |
0 |
else if (source == showConsensusHistogram) |
1198 |
|
{ |
1199 |
0 |
showConsensusHistogram_actionPerformed(); |
1200 |
|
} |
1201 |
0 |
else if (source == applyAutoAnnotationSettings) |
1202 |
|
{ |
1203 |
0 |
applyAutoAnnotationSettings_actionPerformed(); |
1204 |
|
} |
1205 |
0 |
else if (source == featureSettings) |
1206 |
|
{ |
1207 |
0 |
showFeatureSettingsUI(); |
1208 |
|
} |
1209 |
0 |
else if (source == alProperties) |
1210 |
|
{ |
1211 |
0 |
StringBuffer contents = new jalview.io.AlignmentProperties( |
1212 |
|
viewport.getAlignment()).formatAsString(); |
1213 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); |
1214 |
0 |
cap.setText(contents.toString()); |
1215 |
0 |
Frame frame = new Frame(); |
1216 |
0 |
frame.add(cap); |
1217 |
0 |
jalview.bin.JalviewLite.addFrame(frame, MessageManager |
1218 |
|
.formatMessage("label.alignment_properties", new String[] |
1219 |
|
{ getTitle() }), 400, 250); |
1220 |
|
} |
1221 |
0 |
else if (source == overviewMenuItem) |
1222 |
|
{ |
1223 |
0 |
overviewMenuItem_actionPerformed(); |
1224 |
|
} |
1225 |
0 |
else if (source == noColourmenuItem) |
1226 |
|
{ |
1227 |
0 |
changeColour(null); |
1228 |
|
} |
1229 |
0 |
else if (source == clustalColour) |
1230 |
|
{ |
1231 |
0 |
abovePIDThreshold.setState(false); |
1232 |
0 |
changeColour(new ClustalxColourScheme(viewport.getAlignment(), null)); |
1233 |
|
} |
1234 |
0 |
else if (source == zappoColour) |
1235 |
|
{ |
1236 |
0 |
changeColour(new ZappoColourScheme()); |
1237 |
|
} |
1238 |
0 |
else if (source == taylorColour) |
1239 |
|
{ |
1240 |
0 |
changeColour(new TaylorColourScheme()); |
1241 |
|
} |
1242 |
0 |
else if (source == hydrophobicityColour) |
1243 |
|
{ |
1244 |
0 |
changeColour(new HydrophobicColourScheme()); |
1245 |
|
} |
1246 |
0 |
else if (source == helixColour) |
1247 |
|
{ |
1248 |
0 |
changeColour(new HelixColourScheme()); |
1249 |
|
} |
1250 |
0 |
else if (source == strandColour) |
1251 |
|
{ |
1252 |
0 |
changeColour(new StrandColourScheme()); |
1253 |
|
} |
1254 |
0 |
else if (source == turnColour) |
1255 |
|
{ |
1256 |
0 |
changeColour(new TurnColourScheme()); |
1257 |
|
} |
1258 |
0 |
else if (source == buriedColour) |
1259 |
|
{ |
1260 |
0 |
changeColour(new BuriedColourScheme()); |
1261 |
|
} |
1262 |
0 |
else if (source == nucleotideColour) |
1263 |
|
{ |
1264 |
0 |
changeColour(new NucleotideColourScheme()); |
1265 |
|
} |
1266 |
0 |
else if (source == purinePyrimidineColour) |
1267 |
|
{ |
1268 |
0 |
changeColour(new PurinePyrimidineColourScheme()); |
1269 |
|
} |
1270 |
|
|
1271 |
|
|
1272 |
|
|
1273 |
|
|
1274 |
0 |
else if (source == RNAHelixColour) |
1275 |
|
{ |
1276 |
0 |
changeColour(new RNAHelicesColour(viewport.getAlignment())); |
1277 |
|
|
1278 |
|
} |
1279 |
0 |
else if (source == modifyPID) |
1280 |
|
{ |
1281 |
0 |
modifyPID_actionPerformed(); |
1282 |
|
} |
1283 |
0 |
else if (source == modifyConservation) |
1284 |
|
{ |
1285 |
0 |
modifyConservation_actionPerformed(); |
1286 |
|
} |
1287 |
0 |
else if (source == userDefinedColour) |
1288 |
|
{ |
1289 |
0 |
new UserDefinedColours(alignPanel, null); |
1290 |
|
} |
1291 |
0 |
else if (source == PIDColour) |
1292 |
|
{ |
1293 |
0 |
changeColour(new PIDColourScheme()); |
1294 |
|
} |
1295 |
0 |
else if (source == BLOSUM62Colour) |
1296 |
|
{ |
1297 |
0 |
changeColour(new Blosum62ColourScheme()); |
1298 |
|
} |
1299 |
0 |
else if (source == tcoffeeColour) |
1300 |
|
{ |
1301 |
0 |
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); |
1302 |
|
} |
1303 |
0 |
else if (source == annotationColour) |
1304 |
|
{ |
1305 |
0 |
new AnnotationColourChooser(viewport, alignPanel); |
1306 |
|
} |
1307 |
0 |
else if (source == annotationColumnSelection) |
1308 |
|
{ |
1309 |
0 |
new AnnotationColumnChooser(viewport, alignPanel); |
1310 |
|
} |
1311 |
0 |
else if (source == sortPairwiseMenuItem) |
1312 |
|
{ |
1313 |
0 |
sortPairwiseMenuItem_actionPerformed(); |
1314 |
|
} |
1315 |
0 |
else if (source == sortIDMenuItem) |
1316 |
|
{ |
1317 |
0 |
sortIDMenuItem_actionPerformed(); |
1318 |
|
} |
1319 |
0 |
else if (source == sortLengthMenuItem) |
1320 |
|
{ |
1321 |
0 |
sortLengthMenuItem_actionPerformed(); |
1322 |
|
} |
1323 |
0 |
else if (source == sortGroupMenuItem) |
1324 |
|
{ |
1325 |
0 |
sortGroupMenuItem_actionPerformed(); |
1326 |
|
} |
1327 |
0 |
else if (source == removeRedundancyMenuItem) |
1328 |
|
{ |
1329 |
0 |
removeRedundancyMenuItem_actionPerformed(); |
1330 |
|
} |
1331 |
0 |
else if (source == pairwiseAlignmentMenuItem) |
1332 |
|
{ |
1333 |
0 |
pairwiseAlignmentMenuItem_actionPerformed(); |
1334 |
|
} |
1335 |
0 |
else if (source == PCAMenuItem) |
1336 |
|
{ |
1337 |
0 |
PCAMenuItem_actionPerformed(); |
1338 |
|
} |
1339 |
0 |
else if (source == averageDistanceTreeMenuItem) |
1340 |
|
{ |
1341 |
0 |
averageDistanceTreeMenuItem_actionPerformed(); |
1342 |
|
} |
1343 |
0 |
else if (source == neighbourTreeMenuItem) |
1344 |
|
{ |
1345 |
0 |
neighbourTreeMenuItem_actionPerformed(); |
1346 |
|
} |
1347 |
0 |
else if (source == njTreeBlosumMenuItem) |
1348 |
|
{ |
1349 |
0 |
njTreeBlosumMenuItem_actionPerformed(); |
1350 |
|
} |
1351 |
0 |
else if (source == avDistanceTreeBlosumMenuItem) |
1352 |
|
{ |
1353 |
0 |
avTreeBlosumMenuItem_actionPerformed(); |
1354 |
|
} |
1355 |
0 |
else if (source == documentation) |
1356 |
|
{ |
1357 |
0 |
documentation_actionPerformed(); |
1358 |
|
} |
1359 |
0 |
else if (source == about) |
1360 |
|
{ |
1361 |
0 |
about_actionPerformed(); |
1362 |
|
} |
1363 |
|
|
1364 |
|
} |
1365 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
1366 |
0 |
public void inputText_actionPerformed()... |
1367 |
|
{ |
1368 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1369 |
0 |
Frame frame = new Frame(); |
1370 |
0 |
frame.add(cap); |
1371 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
1372 |
|
MessageManager.getString("label.input_cut_paste"), 500, 500); |
1373 |
|
} |
1374 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
1375 |
0 |
protected void outputText_actionPerformed(ActionEvent e)... |
1376 |
|
{ |
1377 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1378 |
0 |
Frame frame = new Frame(); |
1379 |
0 |
frame.add(cap); |
1380 |
0 |
JalviewLite.addFrame(frame, MessageManager |
1381 |
|
.formatMessage("label.alignment_output_command", new Object[] |
1382 |
|
{ e.getActionCommand() }), 600, 500); |
1383 |
|
|
1384 |
0 |
FileFormatI fileFormat = FileFormats.getInstance() |
1385 |
|
.forName(e.getActionCommand()); |
1386 |
0 |
cap.setText( |
1387 |
|
new AppletFormatAdapter(alignPanel).formatSequences(fileFormat, |
1388 |
|
viewport.getAlignment(), viewport.getShowJVSuffix())); |
1389 |
|
} |
1390 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
1391 |
0 |
public void loadAnnotations()... |
1392 |
|
{ |
1393 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
1394 |
0 |
cap.setText(MessageManager |
1395 |
|
.getString("label.paste_features_annotations_Tcoffee_here")); |
1396 |
0 |
cap.setAnnotationImport(); |
1397 |
0 |
Frame frame = new Frame(); |
1398 |
0 |
frame.add(cap); |
1399 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
1400 |
|
MessageManager.getString("action.paste_annotations"), 400, 300); |
1401 |
|
|
1402 |
|
} |
1403 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
1404 |
0 |
public String outputAnnotations(boolean displayTextbox)... |
1405 |
|
{ |
1406 |
0 |
String annotation = new AnnotationFile() |
1407 |
|
.printAnnotationsForView(viewport); |
1408 |
|
|
1409 |
0 |
if (displayTextbox) |
1410 |
|
{ |
1411 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); |
1412 |
0 |
Frame frame = new Frame(); |
1413 |
0 |
frame.add(cap); |
1414 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
1415 |
|
MessageManager.getString("label.annotations"), 600, 500); |
1416 |
0 |
cap.setText(annotation); |
1417 |
|
} |
1418 |
|
|
1419 |
0 |
return annotation; |
1420 |
|
} |
1421 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1422 |
0 |
private Map<String, FeatureColourI> getDisplayedFeatureCols()... |
1423 |
|
{ |
1424 |
0 |
if (alignPanel.getFeatureRenderer() != null |
1425 |
|
&& viewport.getFeaturesDisplayed() != null) |
1426 |
|
{ |
1427 |
0 |
return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); |
1428 |
|
|
1429 |
|
} |
1430 |
0 |
return null; |
1431 |
|
} |
1432 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1433 |
0 |
private List<String> getDisplayedFeatureGroups()... |
1434 |
|
{ |
1435 |
0 |
if (alignPanel.getFeatureRenderer() != null |
1436 |
|
&& viewport.getFeaturesDisplayed() != null) |
1437 |
|
{ |
1438 |
0 |
return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups(); |
1439 |
|
|
1440 |
|
} |
1441 |
0 |
return null; |
1442 |
|
} |
1443 |
|
|
|
|
| 0% |
Uncovered Elements: 30 (30) |
Complexity: 7 |
Complexity Density: 0.35 |
|
1444 |
0 |
public String outputFeatures(boolean displayTextbox, String format)... |
1445 |
|
{ |
1446 |
0 |
String features; |
1447 |
0 |
FeaturesFile formatter = new FeaturesFile(); |
1448 |
0 |
if (format.equalsIgnoreCase("Jalview")) |
1449 |
|
{ |
1450 |
0 |
features = formatter.printJalviewFormat( |
1451 |
|
viewport.getAlignment().getSequencesArray(), |
1452 |
|
alignPanel.getFeatureRenderer(), true, false); |
1453 |
|
} |
1454 |
|
else |
1455 |
|
{ |
1456 |
0 |
features = formatter.printGffFormat( |
1457 |
|
viewport.getAlignment().getSequencesArray(), |
1458 |
|
alignPanel.getFeatureRenderer(), true, false); |
1459 |
|
} |
1460 |
|
|
1461 |
0 |
if (displayTextbox) |
1462 |
|
{ |
1463 |
0 |
boolean frimport = false; |
1464 |
0 |
if (features == null || features.equals("No Features Visible")) |
1465 |
|
{ |
1466 |
0 |
features = "# No features visible - paste some and import them here."; |
1467 |
0 |
frimport = true; |
1468 |
|
} |
1469 |
|
|
1470 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this); |
1471 |
0 |
if (frimport) |
1472 |
|
{ |
1473 |
0 |
cap.setAnnotationImport(); |
1474 |
|
} |
1475 |
0 |
Frame frame = new Frame(); |
1476 |
0 |
frame.add(cap); |
1477 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
1478 |
|
MessageManager.getString("label.features"), 600, 500); |
1479 |
0 |
cap.setText(features); |
1480 |
|
} |
1481 |
|
else |
1482 |
|
{ |
1483 |
0 |
if (features == null) |
1484 |
|
{ |
1485 |
0 |
features = ""; |
1486 |
|
} |
1487 |
|
} |
1488 |
|
|
1489 |
0 |
return features; |
1490 |
|
} |
1491 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 11 |
Complexity Density: 0.5 |
|
1492 |
0 |
void launchFullApplication()... |
1493 |
|
{ |
1494 |
0 |
StringBuffer url = new StringBuffer(jalviewServletURL); |
1495 |
|
|
1496 |
|
|
1497 |
0 |
String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&" |
1498 |
|
: "?"; |
1499 |
0 |
url.append(firstSep); |
1500 |
|
|
1501 |
0 |
url.append( |
1502 |
|
"open=" + appendProtocol(viewport.applet.getParameter("file"))); |
1503 |
|
|
1504 |
0 |
if (viewport.applet.getParameter("features") != null) |
1505 |
|
{ |
1506 |
0 |
url.append("&features="); |
1507 |
0 |
url.append(appendProtocol(viewport.applet.getParameter("features"))); |
1508 |
|
} |
1509 |
|
|
1510 |
0 |
if (viewport.applet.getParameter("annotations") != null) |
1511 |
|
{ |
1512 |
0 |
url.append("&annotations="); |
1513 |
0 |
url.append( |
1514 |
|
appendProtocol(viewport.applet.getParameter("annotations"))); |
1515 |
|
} |
1516 |
|
|
1517 |
0 |
if (viewport.applet.getParameter("jnetfile") != null |
1518 |
|
|| viewport.applet.getParameter("jpredfile") != null) |
1519 |
|
{ |
1520 |
0 |
url.append("&annotations="); |
1521 |
0 |
url.append(appendProtocol( |
1522 |
0 |
viewport.applet.getParameter("jnetfile") != null |
1523 |
|
? viewport.applet.getParameter("jnetfile") |
1524 |
|
: viewport.applet.getParameter("jpredfile"))); |
1525 |
|
} |
1526 |
|
|
1527 |
0 |
if (viewport.applet.getParameter("defaultColour") != null) |
1528 |
|
{ |
1529 |
0 |
url.append("&colour=" + removeWhiteSpace( |
1530 |
|
viewport.applet.getParameter("defaultColour"))); |
1531 |
|
} |
1532 |
|
|
1533 |
0 |
if (viewport.applet.getParameter("userDefinedColour") != null) |
1534 |
|
{ |
1535 |
0 |
url.append("&colour=" + removeWhiteSpace( |
1536 |
|
viewport.applet.getParameter("userDefinedColour"))); |
1537 |
|
} |
1538 |
0 |
if (viewport.applet.getParameter("tree") != null) |
1539 |
|
{ |
1540 |
0 |
url.append("&tree=" |
1541 |
|
+ appendProtocol(viewport.applet.getParameter("tree"))); |
1542 |
|
} |
1543 |
0 |
if (viewport.applet.getParameter("treeFile") != null) |
1544 |
|
{ |
1545 |
0 |
url.append("&tree=" |
1546 |
|
+ appendProtocol(viewport.applet.getParameter("treeFile"))); |
1547 |
|
} |
1548 |
|
|
1549 |
0 |
showURL(url.toString(), "FULL_APP"); |
1550 |
|
} |
1551 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1552 |
0 |
String removeWhiteSpace(String colour)... |
1553 |
|
{ |
1554 |
0 |
StringBuffer sb = new StringBuffer(); |
1555 |
0 |
for (int i = 0; i < colour.length(); i++) |
1556 |
|
{ |
1557 |
0 |
if (Character.isWhitespace(colour.charAt(i))) |
1558 |
|
{ |
1559 |
0 |
sb.append("%20"); |
1560 |
|
} |
1561 |
|
else |
1562 |
|
{ |
1563 |
0 |
sb.append(colour.charAt(i)); |
1564 |
|
} |
1565 |
|
} |
1566 |
|
|
1567 |
0 |
return sb.toString(); |
1568 |
|
} |
1569 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.43 |
|
1570 |
0 |
String appendProtocol(String url)... |
1571 |
|
{ |
1572 |
0 |
try |
1573 |
|
{ |
1574 |
0 |
new URL(url); |
1575 |
0 |
url = URLEncoder.encode(url, "UTF-8"); |
1576 |
|
} |
1577 |
|
|
1578 |
|
|
1579 |
|
|
1580 |
|
|
1581 |
|
|
1582 |
|
|
1583 |
|
|
1584 |
|
catch (java.net.MalformedURLException ex) |
1585 |
|
{ |
1586 |
0 |
url = viewport.applet.getCodeBase() + url; |
1587 |
|
} catch (UnsupportedEncodingException ex) |
1588 |
|
{ |
1589 |
0 |
jalview.bin.Console.errPrintln( |
1590 |
|
"WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR " |
1591 |
|
+ url); |
1592 |
0 |
ex.printStackTrace(); |
1593 |
|
} |
1594 |
0 |
return url; |
1595 |
|
} |
1596 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 9 |
Complexity Density: 0.75 |
|
1597 |
0 |
public void closeMenuItem_actionPerformed()... |
1598 |
|
{ |
1599 |
0 |
PaintRefresher.RemoveComponent(alignPanel); |
1600 |
0 |
if (alignPanel.seqPanel != null |
1601 |
|
&& alignPanel.seqPanel.seqCanvas != null) |
1602 |
|
{ |
1603 |
0 |
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); |
1604 |
|
} |
1605 |
0 |
if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null) |
1606 |
|
{ |
1607 |
0 |
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); |
1608 |
|
} |
1609 |
|
|
1610 |
0 |
if (PaintRefresher.components.size() == 0 && viewport.applet == null) |
1611 |
|
{ |
1612 |
0 |
System.exit(0); |
1613 |
|
} |
1614 |
|
|
1615 |
0 |
viewport = null; |
1616 |
0 |
if (alignPanel != null && alignPanel.overviewPanel != null) |
1617 |
|
{ |
1618 |
0 |
alignPanel.overviewPanel.dispose(); |
1619 |
|
} |
1620 |
0 |
alignPanel = null; |
1621 |
0 |
this.dispose(); |
1622 |
|
} |
1623 |
|
|
1624 |
|
|
1625 |
|
|
1626 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
1627 |
0 |
void updateEditMenuBar()... |
1628 |
|
{ |
1629 |
|
|
1630 |
0 |
if (viewport.getHistoryList().size() > 0) |
1631 |
|
{ |
1632 |
0 |
undoMenuItem.setEnabled(true); |
1633 |
0 |
CommandI command = viewport.getHistoryList().peek(); |
1634 |
0 |
undoMenuItem.setLabel(MessageManager |
1635 |
|
.formatMessage("label.undo_command", new Object[] |
1636 |
|
{ command.getDescription() })); |
1637 |
|
} |
1638 |
|
else |
1639 |
|
{ |
1640 |
0 |
undoMenuItem.setEnabled(false); |
1641 |
0 |
undoMenuItem.setLabel(MessageManager.getString("action.undo")); |
1642 |
|
} |
1643 |
|
|
1644 |
0 |
if (viewport.getRedoList().size() > 0) |
1645 |
|
{ |
1646 |
0 |
redoMenuItem.setEnabled(true); |
1647 |
|
|
1648 |
0 |
CommandI command = viewport.getRedoList().peek(); |
1649 |
0 |
redoMenuItem.setLabel(MessageManager |
1650 |
|
.formatMessage("label.redo_command", new Object[] |
1651 |
|
{ command.getDescription() })); |
1652 |
|
} |
1653 |
|
else |
1654 |
|
{ |
1655 |
0 |
redoMenuItem.setEnabled(false); |
1656 |
0 |
redoMenuItem.setLabel(MessageManager.getString("action.redo")); |
1657 |
|
} |
1658 |
|
} |
1659 |
|
|
1660 |
|
|
1661 |
|
|
1662 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1663 |
0 |
@Override... |
1664 |
|
public void addHistoryItem(CommandI command) |
1665 |
|
{ |
1666 |
0 |
if (command.getSize() > 0) |
1667 |
|
{ |
1668 |
0 |
viewport.addToHistoryList(command); |
1669 |
0 |
viewport.clearRedoList(); |
1670 |
0 |
updateEditMenuBar(); |
1671 |
0 |
viewport.updateHiddenColumns(); |
1672 |
|
} |
1673 |
|
} |
1674 |
|
|
1675 |
|
|
1676 |
|
|
1677 |
|
|
1678 |
|
@param |
1679 |
|
|
1680 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
1681 |
0 |
protected void undoMenuItem_actionPerformed()... |
1682 |
|
{ |
1683 |
0 |
if (viewport.getHistoryList().isEmpty()) |
1684 |
|
{ |
1685 |
0 |
return; |
1686 |
|
} |
1687 |
|
|
1688 |
0 |
CommandI command = viewport.getHistoryList().pop(); |
1689 |
0 |
viewport.addToRedoList(command); |
1690 |
0 |
command.undoCommand(null); |
1691 |
|
|
1692 |
0 |
AlignmentViewport originalSource = getOriginatingSource(command); |
1693 |
|
|
1694 |
0 |
if (originalSource != viewport) |
1695 |
|
{ |
1696 |
0 |
System.err |
1697 |
|
.println("Warning: Viewport object mismatch whilst undoing"); |
1698 |
|
} |
1699 |
0 |
originalSource.updateHiddenColumns(); |
1700 |
|
|
1701 |
|
|
1702 |
0 |
updateEditMenuBar(); |
1703 |
0 |
originalSource.firePropertyChange("alignment", null, |
1704 |
|
originalSource.getAlignment().getSequences()); |
1705 |
|
} |
1706 |
|
|
1707 |
|
|
1708 |
|
|
1709 |
|
|
1710 |
|
@param |
1711 |
|
|
1712 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
1713 |
0 |
protected void redoMenuItem_actionPerformed()... |
1714 |
|
{ |
1715 |
0 |
if (viewport.getRedoList().isEmpty()) |
1716 |
|
{ |
1717 |
0 |
return; |
1718 |
|
} |
1719 |
|
|
1720 |
0 |
CommandI command = viewport.getRedoList().pop(); |
1721 |
0 |
viewport.addToHistoryList(command); |
1722 |
0 |
command.doCommand(null); |
1723 |
|
|
1724 |
0 |
AlignmentViewport originalSource = getOriginatingSource(command); |
1725 |
|
|
1726 |
0 |
if (originalSource != viewport) |
1727 |
|
{ |
1728 |
0 |
System.err |
1729 |
|
.println("Warning: Viewport object mismatch whilst re-doing"); |
1730 |
|
} |
1731 |
0 |
originalSource.updateHiddenColumns(); |
1732 |
|
|
1733 |
|
|
1734 |
|
|
1735 |
0 |
updateEditMenuBar(); |
1736 |
0 |
originalSource.firePropertyChange("alignment", null, |
1737 |
|
originalSource.getAlignment().getSequences()); |
1738 |
|
} |
1739 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 7 |
Complexity Density: 0.44 |
|
1740 |
0 |
AlignmentViewport getOriginatingSource(CommandI command)... |
1741 |
|
{ |
1742 |
0 |
AlignmentViewport originalSource = null; |
1743 |
|
|
1744 |
|
|
1745 |
|
|
1746 |
0 |
AlignmentI al = null; |
1747 |
0 |
if (command instanceof EditCommand) |
1748 |
|
{ |
1749 |
0 |
EditCommand editCommand = (EditCommand) command; |
1750 |
0 |
al = editCommand.getAlignment(); |
1751 |
0 |
Vector comps = PaintRefresher.components |
1752 |
|
.get(viewport.getSequenceSetId()); |
1753 |
0 |
for (int i = 0; i < comps.size(); i++) |
1754 |
|
{ |
1755 |
0 |
if (comps.elementAt(i) instanceof AlignmentPanel) |
1756 |
|
{ |
1757 |
0 |
if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) |
1758 |
|
{ |
1759 |
0 |
originalSource = ((AlignmentPanel) comps.elementAt(i)).av; |
1760 |
0 |
break; |
1761 |
|
} |
1762 |
|
} |
1763 |
|
} |
1764 |
|
} |
1765 |
|
|
1766 |
0 |
if (originalSource == null) |
1767 |
|
{ |
1768 |
|
|
1769 |
|
|
1770 |
0 |
if (al != null) |
1771 |
|
{ |
1772 |
0 |
PaintRefresher.validateSequences(al, viewport.getAlignment()); |
1773 |
|
} |
1774 |
|
|
1775 |
0 |
originalSource = viewport; |
1776 |
|
} |
1777 |
|
|
1778 |
0 |
return originalSource; |
1779 |
|
} |
1780 |
|
|
1781 |
|
|
1782 |
|
|
1783 |
|
|
1784 |
|
|
1785 |
|
@param |
1786 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.5 |
|
1787 |
0 |
public void moveSelectedSequences(boolean up)... |
1788 |
|
{ |
1789 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
1790 |
0 |
if (sg == null) |
1791 |
|
{ |
1792 |
0 |
return; |
1793 |
|
} |
1794 |
0 |
viewport.getAlignment().moveSelectedSequencesByOne(sg, |
1795 |
0 |
up ? null : viewport.getHiddenRepSequences(), up); |
1796 |
0 |
alignPanel.paintAlignment(true, false); |
1797 |
|
|
1798 |
|
|
1799 |
|
|
1800 |
|
|
1801 |
0 |
AlignViewportI complement = viewport.getCodingComplement(); |
1802 |
0 |
if (complement != null) |
1803 |
|
{ |
1804 |
0 |
SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg, |
1805 |
|
viewport, complement); |
1806 |
0 |
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, |
1807 |
0 |
up ? null : complement.getHiddenRepSequences(), up); |
1808 |
0 |
getSplitFrame().getComplement(this).alignPanel.paintAlignment(true, |
1809 |
|
false); |
1810 |
|
} |
1811 |
|
} |
1812 |
|
|
|
|
| 0% |
Uncovered Elements: 66 (66) |
Complexity: 20 |
Complexity Density: 0.53 |
|
1813 |
0 |
synchronized void slideSequences(boolean right, int size)... |
1814 |
|
{ |
1815 |
0 |
List<SequenceI> sg = new Vector<>(); |
1816 |
0 |
if (viewport.cursorMode) |
1817 |
|
{ |
1818 |
0 |
sg.add(viewport.getAlignment() |
1819 |
|
.getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); |
1820 |
|
} |
1821 |
0 |
else if (viewport.getSelectionGroup() != null |
1822 |
|
&& viewport.getSelectionGroup().getSize() != viewport |
1823 |
|
.getAlignment().getHeight()) |
1824 |
|
{ |
1825 |
0 |
sg = viewport.getSelectionGroup() |
1826 |
|
.getSequences(viewport.getHiddenRepSequences()); |
1827 |
|
} |
1828 |
|
|
1829 |
0 |
if (sg.size() < 1) |
1830 |
|
{ |
1831 |
0 |
return; |
1832 |
|
} |
1833 |
|
|
1834 |
0 |
Vector<SequenceI> invertGroup = new Vector(); |
1835 |
|
|
1836 |
0 |
for (int i = 0; i < viewport.getAlignment().getHeight(); i++) |
1837 |
|
{ |
1838 |
0 |
if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) |
1839 |
|
{ |
1840 |
0 |
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); |
1841 |
|
} |
1842 |
|
} |
1843 |
|
|
1844 |
0 |
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); |
1845 |
|
|
1846 |
0 |
SequenceI[] seqs2 = invertGroup |
1847 |
|
.toArray(new SequenceI[invertGroup.size()]); |
1848 |
0 |
for (int i = 0; i < invertGroup.size(); i++) |
1849 |
|
{ |
1850 |
0 |
seqs2[i] = invertGroup.elementAt(i); |
1851 |
|
} |
1852 |
|
|
1853 |
0 |
SlideSequencesCommand ssc; |
1854 |
0 |
if (right) |
1855 |
|
{ |
1856 |
0 |
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, |
1857 |
|
viewport.getGapCharacter()); |
1858 |
|
} |
1859 |
|
else |
1860 |
|
{ |
1861 |
0 |
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, |
1862 |
|
viewport.getGapCharacter()); |
1863 |
|
} |
1864 |
|
|
1865 |
0 |
int groupAdjustment = 0; |
1866 |
0 |
if (ssc.getGapsInsertedBegin() && right) |
1867 |
|
{ |
1868 |
0 |
if (viewport.cursorMode) |
1869 |
|
{ |
1870 |
0 |
alignPanel.seqPanel.moveCursor(size, 0); |
1871 |
|
} |
1872 |
|
else |
1873 |
|
{ |
1874 |
0 |
groupAdjustment = size; |
1875 |
|
} |
1876 |
|
} |
1877 |
0 |
else if (!ssc.getGapsInsertedBegin() && !right) |
1878 |
|
{ |
1879 |
0 |
if (viewport.cursorMode) |
1880 |
|
{ |
1881 |
0 |
alignPanel.seqPanel.moveCursor(-size, 0); |
1882 |
|
} |
1883 |
|
else |
1884 |
|
{ |
1885 |
0 |
groupAdjustment = -size; |
1886 |
|
} |
1887 |
|
} |
1888 |
|
|
1889 |
0 |
if (groupAdjustment != 0) |
1890 |
|
{ |
1891 |
0 |
viewport.getSelectionGroup().setStartRes( |
1892 |
|
viewport.getSelectionGroup().getStartRes() + groupAdjustment); |
1893 |
0 |
viewport.getSelectionGroup().setEndRes( |
1894 |
|
viewport.getSelectionGroup().getEndRes() + groupAdjustment); |
1895 |
|
} |
1896 |
|
|
1897 |
0 |
boolean appendHistoryItem = false; |
1898 |
0 |
Deque<CommandI> historyList = viewport.getHistoryList(); |
1899 |
0 |
if (historyList != null && historyList.size() > 0 |
1900 |
|
&& historyList.peek() instanceof SlideSequencesCommand) |
1901 |
|
{ |
1902 |
0 |
appendHistoryItem = ssc.appendSlideCommand( |
1903 |
|
(SlideSequencesCommand) historyList.peek()); |
1904 |
|
} |
1905 |
|
|
1906 |
0 |
if (!appendHistoryItem) |
1907 |
|
{ |
1908 |
0 |
addHistoryItem(ssc); |
1909 |
|
} |
1910 |
|
|
1911 |
0 |
repaint(); |
1912 |
|
} |
1913 |
|
|
1914 |
|
static StringBuffer copiedSequences; |
1915 |
|
|
1916 |
|
static HiddenColumns copiedHiddenColumns; |
1917 |
|
|
|
|
| 0% |
Uncovered Elements: 51 (51) |
Complexity: 12 |
Complexity Density: 0.36 |
|
1918 |
0 |
protected void copy_actionPerformed()... |
1919 |
|
{ |
1920 |
0 |
if (viewport.getSelectionGroup() == null) |
1921 |
|
{ |
1922 |
0 |
return; |
1923 |
|
} |
1924 |
|
|
1925 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
1926 |
0 |
copiedSequences = new StringBuffer(); |
1927 |
0 |
Map<Integer, SequenceI> orderedSeqs = new HashMap<>(); |
1928 |
0 |
for (int i = 0; i < sg.getSize(); i++) |
1929 |
|
{ |
1930 |
0 |
SequenceI seq = sg.getSequenceAt(i); |
1931 |
0 |
int index = viewport.getAlignment().findIndex(seq); |
1932 |
0 |
orderedSeqs.put(index, seq); |
1933 |
|
} |
1934 |
|
|
1935 |
0 |
int index = 0, startRes, endRes; |
1936 |
0 |
char ch; |
1937 |
|
|
1938 |
0 |
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) |
1939 |
|
{ |
1940 |
0 |
int hiddenOffset = viewport.getSelectionGroup().getStartRes(); |
1941 |
0 |
int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); |
1942 |
|
|
1943 |
|
|
1944 |
|
|
1945 |
0 |
copiedHiddenColumns = new HiddenColumns( |
1946 |
|
viewport.getAlignment().getHiddenColumns(), hiddenOffset, |
1947 |
|
hiddenCutoff, hiddenOffset); |
1948 |
|
} |
1949 |
|
else |
1950 |
|
{ |
1951 |
0 |
copiedHiddenColumns = null; |
1952 |
|
} |
1953 |
|
|
1954 |
0 |
for (int i = 0; i < sg.getSize(); i++) |
1955 |
|
{ |
1956 |
0 |
SequenceI seq = null; |
1957 |
|
|
1958 |
0 |
while (seq == null) |
1959 |
|
{ |
1960 |
0 |
if (orderedSeqs.containsKey(index)) |
1961 |
|
{ |
1962 |
0 |
seq = orderedSeqs.get(index); |
1963 |
0 |
index++; |
1964 |
0 |
break; |
1965 |
|
} |
1966 |
|
else |
1967 |
|
{ |
1968 |
0 |
index++; |
1969 |
|
} |
1970 |
|
} |
1971 |
|
|
1972 |
|
|
1973 |
|
|
1974 |
0 |
startRes = seq.findPosition(sg.getStartRes()); |
1975 |
|
|
1976 |
|
|
1977 |
|
|
1978 |
0 |
endRes = 0; |
1979 |
|
|
1980 |
0 |
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) |
1981 |
|
{ |
1982 |
0 |
ch = seq.getCharAt(j); |
1983 |
0 |
if (!jalview.util.Comparison.isGap((ch))) |
1984 |
|
{ |
1985 |
0 |
endRes++; |
1986 |
|
} |
1987 |
|
} |
1988 |
|
|
1989 |
0 |
if (endRes > 0) |
1990 |
|
{ |
1991 |
0 |
endRes += seq.getStart() - 1; |
1992 |
|
} |
1993 |
|
|
1994 |
0 |
copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes |
1995 |
|
+ "\t" + seq.getSequenceAsString(sg.getStartRes(), |
1996 |
|
sg.getEndRes() + 1) |
1997 |
|
+ "\n"); |
1998 |
|
} |
1999 |
|
|
2000 |
|
} |
2001 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2002 |
0 |
protected void pasteNew_actionPerformed()... |
2003 |
|
{ |
2004 |
0 |
paste(true); |
2005 |
|
} |
2006 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2007 |
0 |
protected void pasteThis_actionPerformed()... |
2008 |
|
{ |
2009 |
0 |
paste(false); |
2010 |
|
} |
2011 |
|
|
|
|
| 0% |
Uncovered Elements: 32 (32) |
Complexity: 7 |
Complexity Density: 0.32 |
|
2012 |
0 |
void paste(boolean newAlignment)... |
2013 |
|
{ |
2014 |
0 |
try |
2015 |
|
{ |
2016 |
0 |
if (copiedSequences == null) |
2017 |
|
{ |
2018 |
0 |
return; |
2019 |
|
} |
2020 |
|
|
2021 |
0 |
StringTokenizer st = new StringTokenizer(copiedSequences.toString(), |
2022 |
|
"\t"); |
2023 |
0 |
Vector seqs = new Vector(); |
2024 |
0 |
while (st.hasMoreElements()) |
2025 |
|
{ |
2026 |
0 |
String name = st.nextToken(); |
2027 |
0 |
int start = Integer.parseInt(st.nextToken()); |
2028 |
0 |
int end = Integer.parseInt(st.nextToken()); |
2029 |
0 |
seqs.addElement(new Sequence(name, st.nextToken(), start, end)); |
2030 |
|
} |
2031 |
0 |
SequenceI[] newSeqs = new SequenceI[seqs.size()]; |
2032 |
0 |
for (int i = 0; i < seqs.size(); i++) |
2033 |
|
{ |
2034 |
0 |
newSeqs[i] = (SequenceI) seqs.elementAt(i); |
2035 |
|
} |
2036 |
|
|
2037 |
0 |
if (newAlignment) |
2038 |
|
{ |
2039 |
0 |
String newtitle = MessageManager |
2040 |
|
.getString("label.copied_sequences"); |
2041 |
0 |
if (getTitle().startsWith( |
2042 |
|
MessageManager.getString("label.copied_sequences"))) |
2043 |
|
{ |
2044 |
0 |
newtitle = getTitle(); |
2045 |
|
} |
2046 |
|
else |
2047 |
|
{ |
2048 |
0 |
newtitle = newtitle.concat(MessageManager |
2049 |
|
.formatMessage("label.from_msname", new String[] |
2050 |
|
{ getTitle() })); |
2051 |
|
} |
2052 |
0 |
AlignFrame af = new AlignFrame(new Alignment(newSeqs), |
2053 |
|
viewport.applet, newtitle, false); |
2054 |
0 |
af.viewport.setHiddenColumns(copiedHiddenColumns); |
2055 |
|
|
2056 |
0 |
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth, |
2057 |
|
frameHeight); |
2058 |
|
} |
2059 |
|
else |
2060 |
|
{ |
2061 |
0 |
addSequences(newSeqs); |
2062 |
|
} |
2063 |
|
|
2064 |
|
} catch (Exception ex) |
2065 |
|
{ |
2066 |
|
} |
2067 |
|
|
2068 |
|
} |
2069 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
2070 |
0 |
void addSequences(SequenceI[] seqs)... |
2071 |
|
{ |
2072 |
0 |
for (int i = 0; i < seqs.length; i++) |
2073 |
|
{ |
2074 |
0 |
viewport.getAlignment().addSequence(seqs[i]); |
2075 |
|
} |
2076 |
|
|
2077 |
|
|
2078 |
0 |
addHistoryItem(new EditCommand( |
2079 |
|
MessageManager.getString("label.add_sequences"), Action.PASTE, |
2080 |
|
seqs, 0, viewport.getAlignment().getWidth(), |
2081 |
|
viewport.getAlignment())); |
2082 |
|
|
2083 |
0 |
viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); |
2084 |
|
|
2085 |
0 |
viewport.getAlignment().getWidth(); |
2086 |
0 |
viewport.firePropertyChange("alignment", null, |
2087 |
|
viewport.getAlignment().getSequences()); |
2088 |
|
|
2089 |
|
} |
2090 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2091 |
0 |
protected void cut_actionPerformed()... |
2092 |
|
{ |
2093 |
0 |
copy_actionPerformed(); |
2094 |
0 |
delete_actionPerformed(); |
2095 |
|
} |
2096 |
|
|
|
|
| 0% |
Uncovered Elements: 49 (49) |
Complexity: 9 |
Complexity Density: 0.27 |
|
2097 |
0 |
protected void delete_actionPerformed()... |
2098 |
|
{ |
2099 |
|
|
2100 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
2101 |
0 |
if (sg == null) |
2102 |
|
{ |
2103 |
0 |
return; |
2104 |
|
} |
2105 |
|
|
2106 |
0 |
Vector seqs = new Vector(); |
2107 |
0 |
SequenceI seq; |
2108 |
0 |
for (int i = 0; i < sg.getSize(); i++) |
2109 |
|
{ |
2110 |
0 |
seq = sg.getSequenceAt(i); |
2111 |
0 |
seqs.addElement(seq); |
2112 |
|
} |
2113 |
|
|
2114 |
|
|
2115 |
|
|
2116 |
|
|
2117 |
0 |
if (sg.getSize() == viewport.getAlignment().getHeight()) |
2118 |
|
{ |
2119 |
0 |
boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) |
2120 |
|
+ 1) == viewport.getAlignment().getWidth()) ? true : false; |
2121 |
0 |
if (isEntireAlignWidth) |
2122 |
|
{ |
2123 |
0 |
String title = MessageManager.getString("label.delete_all"); |
2124 |
0 |
Panel infoPanel = new Panel(); |
2125 |
0 |
infoPanel.setLayout(new FlowLayout()); |
2126 |
0 |
infoPanel.add( |
2127 |
|
new Label(MessageManager.getString("warn.delete_all"))); |
2128 |
|
|
2129 |
0 |
final JVDialog dialog = new JVDialog(this, title, true, 400, 200); |
2130 |
0 |
dialog.setMainPanel(infoPanel); |
2131 |
0 |
dialog.ok.setLabel(MessageManager.getString("action.ok")); |
2132 |
0 |
dialog.cancel.setLabel(MessageManager.getString("action.cancel")); |
2133 |
0 |
dialog.setVisible(true); |
2134 |
|
|
2135 |
0 |
if (!dialog.accept) |
2136 |
|
{ |
2137 |
0 |
return; |
2138 |
|
} |
2139 |
|
} |
2140 |
0 |
viewport.getColumnSelection().removeElements(sg.getStartRes(), |
2141 |
|
sg.getEndRes() + 1); |
2142 |
|
} |
2143 |
|
|
2144 |
0 |
SequenceI[] cut = new SequenceI[seqs.size()]; |
2145 |
0 |
for (int i = 0; i < seqs.size(); i++) |
2146 |
|
{ |
2147 |
0 |
cut[i] = (SequenceI) seqs.elementAt(i); |
2148 |
|
} |
2149 |
|
|
2150 |
|
|
2151 |
|
|
2152 |
|
|
2153 |
0 |
addHistoryItem(new EditCommand( |
2154 |
|
MessageManager.getString("label.cut_sequences"), Action.CUT, |
2155 |
|
cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, |
2156 |
|
viewport.getAlignment())); |
2157 |
|
|
2158 |
0 |
viewport.setSelectionGroup(null); |
2159 |
0 |
viewport.getAlignment().deleteGroup(sg); |
2160 |
|
|
2161 |
0 |
viewport.firePropertyChange("alignment", null, |
2162 |
|
viewport.getAlignment().getSequences()); |
2163 |
|
|
2164 |
0 |
if (viewport.getAlignment().getHeight() < 1) |
2165 |
|
{ |
2166 |
0 |
this.setVisible(false); |
2167 |
|
} |
2168 |
0 |
viewport.sendSelection(); |
2169 |
|
} |
2170 |
|
|
2171 |
|
|
2172 |
|
|
2173 |
|
|
2174 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2175 |
0 |
protected void showGroupConsensus_actionPerformed()... |
2176 |
|
{ |
2177 |
0 |
viewport.setShowGroupConsensus(showGroupConsensus.getState()); |
2178 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2179 |
|
|
2180 |
|
} |
2181 |
|
|
2182 |
|
|
2183 |
|
|
2184 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2185 |
0 |
protected void showGroupConservation_actionPerformed()... |
2186 |
|
{ |
2187 |
0 |
viewport.setShowGroupConservation(showGroupConservation.getState()); |
2188 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2189 |
|
} |
2190 |
|
|
2191 |
|
|
2192 |
|
|
2193 |
|
|
2194 |
|
@see |
2195 |
|
|
2196 |
|
|
2197 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2198 |
0 |
protected void showConsensusHistogram_actionPerformed()... |
2199 |
|
{ |
2200 |
0 |
viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); |
2201 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2202 |
|
} |
2203 |
|
|
2204 |
|
|
2205 |
|
|
2206 |
|
|
2207 |
|
@see |
2208 |
|
|
2209 |
|
|
2210 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2211 |
0 |
protected void showSequenceLogo_actionPerformed()... |
2212 |
|
{ |
2213 |
0 |
viewport.setShowSequenceLogo(showSequenceLogo.getState()); |
2214 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2215 |
|
} |
2216 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2217 |
0 |
protected void normSequenceLogo_actionPerformed()... |
2218 |
|
{ |
2219 |
0 |
showSequenceLogo.setState(true); |
2220 |
0 |
viewport.setShowSequenceLogo(true); |
2221 |
0 |
viewport.setNormaliseSequenceLogo(normSequenceLogo.getState()); |
2222 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2223 |
|
} |
2224 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2225 |
0 |
protected void applyAutoAnnotationSettings_actionPerformed()... |
2226 |
|
{ |
2227 |
0 |
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); |
2228 |
|
} |
2229 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
2230 |
0 |
protected void makeGrpsFromSelection_actionPerformed()... |
2231 |
|
{ |
2232 |
0 |
if (avc.makeGroupsFromSelection()) |
2233 |
|
{ |
2234 |
0 |
PaintRefresher.Refresh(this, viewport.getSequenceSetId()); |
2235 |
0 |
alignPanel.updateAnnotation(); |
2236 |
0 |
alignPanel.paintAlignment(true, true); |
2237 |
|
} |
2238 |
|
} |
2239 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2240 |
0 |
protected void createGroup_actionPerformed()... |
2241 |
|
{ |
2242 |
0 |
avc.createGroup(); |
2243 |
|
} |
2244 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
2245 |
0 |
protected void unGroup_actionPerformed()... |
2246 |
|
{ |
2247 |
0 |
if (avc.unGroup()) |
2248 |
|
{ |
2249 |
0 |
alignPanel.alignmentChanged(); |
2250 |
|
} |
2251 |
|
} |
2252 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
2253 |
0 |
protected void deleteGroups_actionPerformed()... |
2254 |
|
{ |
2255 |
0 |
if (avc.deleteGroups()) |
2256 |
|
{ |
2257 |
0 |
alignPanel.alignmentChanged(); |
2258 |
|
} |
2259 |
|
} |
2260 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
2261 |
0 |
public void selectAllSequenceMenuItem_actionPerformed()... |
2262 |
|
{ |
2263 |
0 |
SequenceGroup sg = new SequenceGroup(); |
2264 |
0 |
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2265 |
|
{ |
2266 |
0 |
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); |
2267 |
|
} |
2268 |
0 |
sg.setEndRes(viewport.getAlignment().getWidth() - 1); |
2269 |
0 |
viewport.setSelectionGroup(sg); |
2270 |
|
|
2271 |
|
|
2272 |
|
|
2273 |
0 |
alignPanel.paintAlignment(false, false); |
2274 |
0 |
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2275 |
0 |
viewport.sendSelection(); |
2276 |
|
} |
2277 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
2278 |
0 |
public void deselectAllSequenceMenuItem_actionPerformed()... |
2279 |
|
{ |
2280 |
0 |
if (viewport.cursorMode) |
2281 |
|
{ |
2282 |
0 |
alignPanel.seqPanel.keyboardNo1 = null; |
2283 |
0 |
alignPanel.seqPanel.keyboardNo2 = null; |
2284 |
|
} |
2285 |
0 |
viewport.setSelectionGroup(null); |
2286 |
0 |
viewport.getColumnSelection().clear(); |
2287 |
0 |
viewport.setSelectionGroup(null); |
2288 |
0 |
alignPanel.idPanel.idCanvas.searchResults = null; |
2289 |
0 |
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); |
2290 |
|
|
2291 |
|
|
2292 |
|
|
2293 |
0 |
alignPanel.paintAlignment(false, false); |
2294 |
0 |
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2295 |
0 |
viewport.sendSelection(); |
2296 |
|
} |
2297 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
2298 |
0 |
public void invertSequenceMenuItem_actionPerformed()... |
2299 |
|
{ |
2300 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
2301 |
0 |
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) |
2302 |
|
{ |
2303 |
0 |
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); |
2304 |
|
} |
2305 |
|
|
2306 |
0 |
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2307 |
0 |
viewport.sendSelection(); |
2308 |
|
} |
2309 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2310 |
0 |
public void invertColSel_actionPerformed()... |
2311 |
|
{ |
2312 |
0 |
viewport.invertColumnSelection(); |
2313 |
0 |
alignPanel.paintAlignment(true, false); |
2314 |
0 |
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); |
2315 |
0 |
viewport.sendSelection(); |
2316 |
|
} |
2317 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 9 |
Complexity Density: 0.39 |
|
2318 |
0 |
void trimAlignment(boolean trimLeft)... |
2319 |
|
{ |
2320 |
0 |
AlignmentI al = viewport.getAlignment(); |
2321 |
0 |
ViewportRanges ranges = viewport.getRanges(); |
2322 |
0 |
ColumnSelection colSel = viewport.getColumnSelection(); |
2323 |
0 |
int column; |
2324 |
|
|
2325 |
0 |
if (!colSel.isEmpty()) |
2326 |
|
{ |
2327 |
0 |
if (trimLeft) |
2328 |
|
{ |
2329 |
0 |
column = colSel.getMin(); |
2330 |
|
} |
2331 |
|
else |
2332 |
|
{ |
2333 |
0 |
column = colSel.getMax(); |
2334 |
|
} |
2335 |
|
|
2336 |
0 |
SequenceI[] seqs; |
2337 |
0 |
if (viewport.getSelectionGroup() != null) |
2338 |
|
{ |
2339 |
0 |
seqs = viewport.getSelectionGroup() |
2340 |
|
.getSequencesAsArray(viewport.getHiddenRepSequences()); |
2341 |
|
} |
2342 |
|
else |
2343 |
|
{ |
2344 |
0 |
seqs = al.getSequencesArray(); |
2345 |
|
} |
2346 |
|
|
2347 |
0 |
TrimRegionCommand trimRegion; |
2348 |
0 |
if (trimLeft) |
2349 |
|
{ |
2350 |
0 |
trimRegion = new TrimRegionCommand("Remove Left", true, seqs, |
2351 |
|
column, al); |
2352 |
0 |
ranges.setStartRes(0); |
2353 |
|
} |
2354 |
|
else |
2355 |
|
{ |
2356 |
0 |
trimRegion = new TrimRegionCommand("Remove Right", false, seqs, |
2357 |
|
column, al); |
2358 |
|
} |
2359 |
|
|
2360 |
0 |
setStatus(MessageManager.formatMessage("label.removed_columns", |
2361 |
|
new String[] |
2362 |
|
{ Integer.valueOf(trimRegion.getSize()).toString() })); |
2363 |
0 |
addHistoryItem(trimRegion); |
2364 |
|
|
2365 |
0 |
for (SequenceGroup sg : al.getGroups()) |
2366 |
|
{ |
2367 |
0 |
if ((trimLeft && !sg.adjustForRemoveLeft(column)) |
2368 |
|
|| (!trimLeft && !sg.adjustForRemoveRight(column))) |
2369 |
|
{ |
2370 |
0 |
al.deleteGroup(sg); |
2371 |
|
} |
2372 |
|
} |
2373 |
|
|
2374 |
0 |
viewport.firePropertyChange("alignment", null, al.getSequences()); |
2375 |
|
} |
2376 |
|
} |
2377 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 2 |
Complexity Density: 0.12 |
|
2378 |
0 |
public void removeGappedColumnMenuItem_actionPerformed()... |
2379 |
|
{ |
2380 |
0 |
AlignmentI al = viewport.getAlignment(); |
2381 |
0 |
ViewportRanges ranges = viewport.getRanges(); |
2382 |
0 |
int start = 0; |
2383 |
0 |
int end = ranges.getAbsoluteAlignmentWidth() - 1; |
2384 |
|
|
2385 |
0 |
SequenceI[] seqs; |
2386 |
0 |
if (viewport.getSelectionGroup() != null) |
2387 |
|
{ |
2388 |
0 |
seqs = viewport.getSelectionGroup() |
2389 |
|
.getSequencesAsArray(viewport.getHiddenRepSequences()); |
2390 |
0 |
start = viewport.getSelectionGroup().getStartRes(); |
2391 |
0 |
end = viewport.getSelectionGroup().getEndRes(); |
2392 |
|
} |
2393 |
|
else |
2394 |
|
{ |
2395 |
0 |
seqs = viewport.getAlignment().getSequencesArray(); |
2396 |
|
} |
2397 |
|
|
2398 |
0 |
RemoveGapColCommand removeGapCols = new RemoveGapColCommand( |
2399 |
|
"Remove Gapped Columns", seqs, start, end, |
2400 |
|
viewport.getAlignment()); |
2401 |
|
|
2402 |
0 |
addHistoryItem(removeGapCols); |
2403 |
|
|
2404 |
0 |
setStatus(MessageManager.formatMessage("label.removed_empty_columns", |
2405 |
|
new String[] |
2406 |
|
{ Integer.valueOf(removeGapCols.getSize()).toString() })); |
2407 |
|
|
2408 |
|
|
2409 |
|
|
2410 |
0 |
SequenceI seq = al.getSequenceAt(0); |
2411 |
0 |
int startRes = seq.findPosition(ranges.getStartRes()); |
2412 |
|
|
2413 |
|
|
2414 |
|
|
2415 |
|
|
2416 |
|
|
2417 |
0 |
ranges.setStartRes(seq.findIndex(startRes) - 1); |
2418 |
0 |
viewport.firePropertyChange("alignment", null, al.getSequences()); |
2419 |
|
|
2420 |
|
} |
2421 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 2 |
Complexity Density: 0.13 |
|
2422 |
0 |
public void removeAllGapsMenuItem_actionPerformed()... |
2423 |
|
{ |
2424 |
0 |
AlignmentI al = viewport.getAlignment(); |
2425 |
0 |
ViewportRanges ranges = viewport.getRanges(); |
2426 |
0 |
int start = 0; |
2427 |
0 |
int end = ranges.getAbsoluteAlignmentWidth() - 1; |
2428 |
|
|
2429 |
0 |
SequenceI[] seqs; |
2430 |
0 |
if (viewport.getSelectionGroup() != null) |
2431 |
|
{ |
2432 |
0 |
seqs = viewport.getSelectionGroup() |
2433 |
|
.getSequencesAsArray(viewport.getHiddenRepSequences()); |
2434 |
0 |
start = viewport.getSelectionGroup().getStartRes(); |
2435 |
0 |
end = viewport.getSelectionGroup().getEndRes(); |
2436 |
|
} |
2437 |
|
else |
2438 |
|
{ |
2439 |
0 |
seqs = viewport.getAlignment().getSequencesArray(); |
2440 |
|
} |
2441 |
|
|
2442 |
|
|
2443 |
|
|
2444 |
0 |
SequenceI seq = al.getSequenceAt(0); |
2445 |
0 |
int startRes = seq.findPosition(ranges.getStartRes()); |
2446 |
|
|
2447 |
0 |
addHistoryItem( |
2448 |
|
new RemoveGapsCommand("Remove Gaps", seqs, start, end, al)); |
2449 |
|
|
2450 |
0 |
ranges.setStartRes(seq.findIndex(startRes) - 1); |
2451 |
|
|
2452 |
0 |
viewport.firePropertyChange("alignment", null, al.getSequences()); |
2453 |
|
|
2454 |
|
} |
2455 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2456 |
0 |
public void findMenuItem_actionPerformed()... |
2457 |
|
{ |
2458 |
0 |
new Finder(alignPanel); |
2459 |
|
} |
2460 |
|
|
2461 |
|
|
2462 |
|
|
2463 |
|
|
2464 |
|
@param |
2465 |
|
@return |
2466 |
|
|
|
|
| 0% |
Uncovered Elements: 45 (45) |
Complexity: 9 |
Complexity Density: 0.31 |
|
2467 |
0 |
public AlignFrame newView(String viewtitle)... |
2468 |
|
{ |
2469 |
0 |
AlignmentI newal; |
2470 |
0 |
if (viewport.hasHiddenRows()) |
2471 |
|
{ |
2472 |
0 |
newal = new Alignment(viewport.getAlignment().getHiddenSequences() |
2473 |
|
.getFullAlignment().getSequencesArray()); |
2474 |
|
} |
2475 |
|
else |
2476 |
|
{ |
2477 |
0 |
newal = new Alignment(viewport.getAlignment().getSequencesArray()); |
2478 |
|
} |
2479 |
|
|
2480 |
0 |
if (viewport.getAlignment().getAlignmentAnnotation() != null) |
2481 |
|
{ |
2482 |
0 |
for (int i = 0; i < viewport.getAlignment() |
2483 |
|
.getAlignmentAnnotation().length; i++) |
2484 |
|
{ |
2485 |
0 |
if (!viewport.getAlignment() |
2486 |
|
.getAlignmentAnnotation()[i].autoCalculated) |
2487 |
|
{ |
2488 |
0 |
newal.addAnnotation( |
2489 |
|
viewport.getAlignment().getAlignmentAnnotation()[i]); |
2490 |
|
} |
2491 |
|
} |
2492 |
|
} |
2493 |
|
|
2494 |
0 |
AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); |
2495 |
|
|
2496 |
0 |
newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId()); |
2497 |
0 |
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); |
2498 |
0 |
PaintRefresher.Register(newaf.alignPanel, |
2499 |
|
newaf.alignPanel.av.getSequenceSetId()); |
2500 |
|
|
2501 |
0 |
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, |
2502 |
|
newaf.alignPanel.av.getSequenceSetId()); |
2503 |
0 |
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, |
2504 |
|
newaf.alignPanel.av.getSequenceSetId()); |
2505 |
|
|
2506 |
0 |
Vector comps = PaintRefresher.components |
2507 |
|
.get(viewport.getSequenceSetId()); |
2508 |
0 |
int viewSize = -1; |
2509 |
0 |
for (int i = 0; i < comps.size(); i++) |
2510 |
|
{ |
2511 |
0 |
if (comps.elementAt(i) instanceof AlignmentPanel) |
2512 |
|
{ |
2513 |
0 |
viewSize++; |
2514 |
|
} |
2515 |
|
} |
2516 |
|
|
2517 |
0 |
String title = new String(this.getTitle()); |
2518 |
0 |
if (viewtitle != null) |
2519 |
|
{ |
2520 |
0 |
title = viewtitle + " ( " + title + ")"; |
2521 |
|
} |
2522 |
|
else |
2523 |
|
{ |
2524 |
0 |
if (title.indexOf("(View") > -1) |
2525 |
|
{ |
2526 |
0 |
title = title.substring(0, title.indexOf("(View")); |
2527 |
|
} |
2528 |
0 |
title += "(View " + viewSize + ")"; |
2529 |
|
} |
2530 |
|
|
2531 |
0 |
newaf.setTitle(title.toString()); |
2532 |
|
|
2533 |
0 |
newaf.viewport.setHistoryList(viewport.getHistoryList()); |
2534 |
0 |
newaf.viewport.setRedoList(viewport.getRedoList()); |
2535 |
0 |
return newaf; |
2536 |
|
} |
2537 |
|
|
2538 |
|
|
2539 |
|
|
2540 |
|
@return |
2541 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
2542 |
0 |
public String[] getFeatureGroups()... |
2543 |
|
{ |
2544 |
0 |
FeatureRenderer fr = null; |
2545 |
0 |
if (alignPanel != null |
2546 |
|
&& (fr = alignPanel.getFeatureRenderer()) != null) |
2547 |
|
{ |
2548 |
0 |
List<String> gps = fr.getFeatureGroups(); |
2549 |
0 |
String[] _gps = gps.toArray(new String[gps.size()]); |
2550 |
0 |
return _gps; |
2551 |
|
} |
2552 |
0 |
return null; |
2553 |
|
} |
2554 |
|
|
2555 |
|
|
2556 |
|
|
2557 |
|
|
2558 |
|
@param |
2559 |
|
|
2560 |
|
@return |
2561 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
2562 |
0 |
public String[] getFeatureGroupsOfState(boolean visible)... |
2563 |
|
{ |
2564 |
0 |
FeatureRenderer fr = null; |
2565 |
0 |
if (alignPanel != null |
2566 |
|
&& (fr = alignPanel.getFeatureRenderer()) != null) |
2567 |
|
{ |
2568 |
0 |
List<String> gps = fr.getGroups(visible); |
2569 |
0 |
String[] _gps = gps.toArray(new String[gps.size()]); |
2570 |
0 |
return _gps; |
2571 |
|
} |
2572 |
0 |
return null; |
2573 |
|
} |
2574 |
|
|
2575 |
|
|
2576 |
|
|
2577 |
|
|
2578 |
|
@param |
2579 |
|
|
2580 |
|
@param |
2581 |
|
|
2582 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
2583 |
0 |
public void setFeatureGroupState(String[] groups, boolean state)... |
2584 |
|
{ |
2585 |
0 |
FeatureRenderer fr = null; |
2586 |
0 |
this.sequenceFeatures.setState(true); |
2587 |
0 |
viewport.setShowSequenceFeatures(true); |
2588 |
0 |
if (alignPanel != null |
2589 |
|
&& (fr = alignPanel.getFeatureRenderer()) != null) |
2590 |
|
{ |
2591 |
|
|
2592 |
0 |
fr.setGroupVisibility(Arrays.asList(groups), state); |
2593 |
0 |
alignPanel.seqPanel.seqCanvas.repaint(); |
2594 |
0 |
if (alignPanel.overviewPanel != null) |
2595 |
|
{ |
2596 |
0 |
alignPanel.overviewPanel.updateOverviewImage(); |
2597 |
|
} |
2598 |
|
} |
2599 |
|
} |
2600 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
2601 |
0 |
public void seqLimits_itemStateChanged()... |
2602 |
|
{ |
2603 |
0 |
viewport.setShowJVSuffix(seqLimits.getState()); |
2604 |
0 |
alignPanel.fontChanged(); |
2605 |
0 |
alignPanel.paintAlignment(true, false); |
2606 |
|
} |
2607 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2608 |
0 |
protected void colourTextMenuItem_actionPerformed()... |
2609 |
|
{ |
2610 |
0 |
viewport.setColourText(colourTextMenuItem.getState()); |
2611 |
0 |
alignPanel.paintAlignment(false, false); |
2612 |
|
} |
2613 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2614 |
0 |
protected void displayNonconservedMenuItem_actionPerformed()... |
2615 |
|
{ |
2616 |
0 |
viewport.setShowUnconserved(displayNonconservedMenuItem.getState()); |
2617 |
0 |
alignPanel.paintAlignment(false, false); |
2618 |
|
} |
2619 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
2620 |
0 |
protected void wrapMenuItem_actionPerformed()... |
2621 |
|
{ |
2622 |
0 |
viewport.setWrapAlignment(wrapMenuItem.getState()); |
2623 |
0 |
alignPanel.setWrapAlignment(wrapMenuItem.getState()); |
2624 |
0 |
scaleAbove.setEnabled(wrapMenuItem.getState()); |
2625 |
0 |
scaleLeft.setEnabled(wrapMenuItem.getState()); |
2626 |
0 |
scaleRight.setEnabled(wrapMenuItem.getState()); |
2627 |
0 |
alignPanel.paintAlignment(true, false); |
2628 |
|
} |
2629 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 2 |
Complexity Density: 0.2 |
|
2630 |
0 |
public void overviewMenuItem_actionPerformed()... |
2631 |
|
{ |
2632 |
0 |
if (alignPanel.overviewPanel != null) |
2633 |
|
{ |
2634 |
0 |
return; |
2635 |
|
} |
2636 |
|
|
2637 |
0 |
Frame frame = new Frame(); |
2638 |
0 |
final OverviewPanel overview = new OverviewPanel(alignPanel); |
2639 |
0 |
frame.add(overview); |
2640 |
|
|
2641 |
0 |
jalview.bin.JalviewLite.addFrame(frame, MessageManager |
2642 |
|
.formatMessage("label.overview_params", new String[] |
2643 |
|
{ this.getTitle() }), overview.getPreferredSize().width, |
2644 |
|
overview.getPreferredSize().height + 50); |
2645 |
|
|
2646 |
0 |
frame.pack(); |
2647 |
0 |
final AlignmentPanel ap = alignPanel; |
2648 |
0 |
frame.addWindowListener(new WindowAdapter() |
2649 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
2650 |
0 |
@Override... |
2651 |
|
public void windowClosing(WindowEvent e) |
2652 |
|
{ |
2653 |
0 |
overview.dispose(); |
2654 |
0 |
if (ap != null) |
2655 |
|
{ |
2656 |
0 |
ap.setOverviewPanel(null); |
2657 |
|
} |
2658 |
|
}; |
2659 |
|
}); |
2660 |
|
|
2661 |
0 |
alignPanel.setOverviewPanel(overview); |
2662 |
|
|
2663 |
|
} |
2664 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2665 |
0 |
@Override... |
2666 |
|
public void changeColour(ColourSchemeI cs) |
2667 |
|
{ |
2668 |
0 |
viewport.setGlobalColourScheme(cs); |
2669 |
|
|
2670 |
0 |
alignPanel.paintAlignment(true, true); |
2671 |
|
} |
2672 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
2673 |
0 |
protected void modifyPID_actionPerformed()... |
2674 |
|
{ |
2675 |
0 |
if (viewport.getAbovePIDThreshold() |
2676 |
|
&& viewport.getGlobalColourScheme() != null) |
2677 |
|
{ |
2678 |
0 |
SliderPanel.setPIDSliderSource(alignPanel, |
2679 |
|
viewport.getResidueShading(), alignPanel.getViewName()); |
2680 |
0 |
SliderPanel.showPIDSlider(); |
2681 |
|
} |
2682 |
|
} |
2683 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
2684 |
0 |
protected void modifyConservation_actionPerformed()... |
2685 |
|
{ |
2686 |
0 |
if (viewport.getConservationSelected() |
2687 |
|
&& viewport.getGlobalColourScheme() != null) |
2688 |
|
{ |
2689 |
0 |
SliderPanel.setConservationSlider(alignPanel, |
2690 |
|
viewport.getResidueShading(), alignPanel.getViewName()); |
2691 |
0 |
SliderPanel.showConservationSlider(); |
2692 |
|
} |
2693 |
|
} |
2694 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
2695 |
0 |
protected void conservationMenuItem_actionPerformed()... |
2696 |
|
{ |
2697 |
0 |
boolean selected = conservationMenuItem.getState(); |
2698 |
0 |
modifyConservation.setEnabled(selected); |
2699 |
0 |
viewport.setConservationSelected(selected); |
2700 |
0 |
viewport.getResidueShading().setConservationApplied(selected); |
2701 |
|
|
2702 |
0 |
changeColour(viewport.getGlobalColourScheme()); |
2703 |
|
|
2704 |
0 |
if (selected) |
2705 |
|
{ |
2706 |
0 |
modifyConservation_actionPerformed(); |
2707 |
|
} |
2708 |
|
else |
2709 |
|
{ |
2710 |
0 |
SliderPanel.hideConservationSlider(); |
2711 |
|
} |
2712 |
|
} |
2713 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
2714 |
0 |
public void abovePIDThreshold_actionPerformed()... |
2715 |
|
{ |
2716 |
0 |
boolean selected = abovePIDThreshold.getState(); |
2717 |
0 |
modifyPID.setEnabled(selected); |
2718 |
0 |
viewport.setAbovePIDThreshold(selected); |
2719 |
0 |
if (!selected) |
2720 |
|
{ |
2721 |
0 |
viewport.getResidueShading().setThreshold(0, |
2722 |
|
viewport.isIgnoreGapsConsensus()); |
2723 |
|
} |
2724 |
|
|
2725 |
0 |
changeColour(viewport.getGlobalColourScheme()); |
2726 |
|
|
2727 |
0 |
if (selected) |
2728 |
|
{ |
2729 |
0 |
modifyPID_actionPerformed(); |
2730 |
|
} |
2731 |
|
else |
2732 |
|
{ |
2733 |
0 |
SliderPanel.hidePIDSlider(); |
2734 |
|
} |
2735 |
|
} |
2736 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2737 |
0 |
public void sortPairwiseMenuItem_actionPerformed()... |
2738 |
|
{ |
2739 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2740 |
0 |
AlignmentSorter.sortByPID(viewport.getAlignment(), |
2741 |
|
viewport.getAlignment().getSequenceAt(0)); |
2742 |
|
|
2743 |
0 |
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, |
2744 |
|
viewport.getAlignment())); |
2745 |
0 |
alignPanel.paintAlignment(true, false); |
2746 |
|
} |
2747 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2748 |
0 |
public void sortIDMenuItem_actionPerformed()... |
2749 |
|
{ |
2750 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2751 |
0 |
AlignmentSorter.sortByID(viewport.getAlignment()); |
2752 |
0 |
addHistoryItem( |
2753 |
|
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); |
2754 |
0 |
alignPanel.paintAlignment(true, false); |
2755 |
|
} |
2756 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2757 |
0 |
public void sortLengthMenuItem_actionPerformed()... |
2758 |
|
{ |
2759 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2760 |
0 |
AlignmentSorter.sortByLength(viewport.getAlignment()); |
2761 |
0 |
addHistoryItem(new OrderCommand("Length Sort", oldOrder, |
2762 |
|
viewport.getAlignment())); |
2763 |
0 |
alignPanel.paintAlignment(true, false); |
2764 |
|
} |
2765 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2766 |
0 |
public void sortGroupMenuItem_actionPerformed()... |
2767 |
|
{ |
2768 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2769 |
0 |
AlignmentSorter.sortByGroup(viewport.getAlignment()); |
2770 |
0 |
addHistoryItem(new OrderCommand("Group Sort", oldOrder, |
2771 |
|
viewport.getAlignment())); |
2772 |
0 |
alignPanel.paintAlignment(true, false); |
2773 |
|
|
2774 |
|
} |
2775 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2776 |
0 |
public void removeRedundancyMenuItem_actionPerformed()... |
2777 |
|
{ |
2778 |
0 |
new RedundancyPanel(alignPanel); |
2779 |
|
} |
2780 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
2781 |
0 |
public void pairwiseAlignmentMenuItem_actionPerformed()... |
2782 |
|
{ |
2783 |
0 |
if (viewport.getSelectionGroup() != null |
2784 |
|
&& viewport.getSelectionGroup().getSize() > 1) |
2785 |
|
{ |
2786 |
0 |
Frame frame = new Frame(); |
2787 |
0 |
frame.add(new PairwiseAlignPanel(alignPanel)); |
2788 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
2789 |
|
MessageManager.getString("action.pairwise_alignment"), 600, |
2790 |
|
500); |
2791 |
|
} |
2792 |
|
} |
2793 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 9 |
Complexity Density: 0.75 |
|
2794 |
0 |
public void PCAMenuItem_actionPerformed()... |
2795 |
|
{ |
2796 |
|
|
2797 |
0 |
if (!viewport.getAlignment().isAligned(false)) |
2798 |
|
{ |
2799 |
0 |
SequenceI current; |
2800 |
0 |
int Width = viewport.getAlignment().getWidth(); |
2801 |
|
|
2802 |
0 |
for (int i = 0; i < viewport.getAlignment().getSequences() |
2803 |
|
.size(); i++) |
2804 |
|
{ |
2805 |
0 |
current = viewport.getAlignment().getSequenceAt(i); |
2806 |
|
|
2807 |
0 |
if (current.getLength() < Width) |
2808 |
|
{ |
2809 |
0 |
current.insertCharAt(Width - 1, viewport.getGapCharacter()); |
2810 |
|
} |
2811 |
|
} |
2812 |
0 |
alignPanel.paintAlignment(false, false); |
2813 |
|
} |
2814 |
|
|
2815 |
0 |
if ((viewport.getSelectionGroup() != null |
2816 |
|
&& viewport.getSelectionGroup().getSize() < 4 |
2817 |
|
&& viewport.getSelectionGroup().getSize() > 0) |
2818 |
|
|| viewport.getAlignment().getHeight() < 4) |
2819 |
|
{ |
2820 |
0 |
return; |
2821 |
|
} |
2822 |
|
|
2823 |
0 |
try |
2824 |
|
{ |
2825 |
0 |
new PCAPanel(viewport); |
2826 |
|
} catch (java.lang.OutOfMemoryError ex) |
2827 |
|
{ |
2828 |
|
} |
2829 |
|
|
2830 |
|
} |
2831 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2832 |
0 |
public void averageDistanceTreeMenuItem_actionPerformed()... |
2833 |
|
{ |
2834 |
0 |
newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(), |
2835 |
|
"Average distance tree using PID"); |
2836 |
|
} |
2837 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2838 |
0 |
public void neighbourTreeMenuItem_actionPerformed()... |
2839 |
|
{ |
2840 |
0 |
newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(), |
2841 |
|
"Neighbour joining tree using PID"); |
2842 |
|
} |
2843 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2844 |
0 |
protected void njTreeBlosumMenuItem_actionPerformed()... |
2845 |
|
{ |
2846 |
0 |
newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, |
2847 |
|
ScoreModels.getInstance().getBlosum62().getName(), |
2848 |
|
"Neighbour joining tree using BLOSUM62"); |
2849 |
|
} |
2850 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2851 |
0 |
protected void avTreeBlosumMenuItem_actionPerformed()... |
2852 |
|
{ |
2853 |
0 |
newTreePanel(TreeBuilder.AVERAGE_DISTANCE, |
2854 |
|
ScoreModels.getInstance().getBlosum62().getName(), |
2855 |
|
"Average distance tree using BLOSUM62"); |
2856 |
|
} |
2857 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 7 |
Complexity Density: 0.58 |
|
2858 |
0 |
void newTreePanel(String type, String pwType, String title)... |
2859 |
|
{ |
2860 |
|
|
2861 |
0 |
if (!viewport.getAlignment().isAligned(false)) |
2862 |
|
{ |
2863 |
0 |
SequenceI current; |
2864 |
0 |
int Width = viewport.getAlignment().getWidth(); |
2865 |
|
|
2866 |
0 |
for (int i = 0; i < viewport.getAlignment().getSequences() |
2867 |
|
.size(); i++) |
2868 |
|
{ |
2869 |
0 |
current = viewport.getAlignment().getSequenceAt(i); |
2870 |
|
|
2871 |
0 |
if (current.getLength() < Width) |
2872 |
|
{ |
2873 |
0 |
current.insertCharAt(Width - 1, viewport.getGapCharacter()); |
2874 |
|
} |
2875 |
|
} |
2876 |
0 |
alignPanel.paintAlignment(false, false); |
2877 |
|
|
2878 |
|
} |
2879 |
|
|
2880 |
0 |
if ((viewport.getSelectionGroup() != null |
2881 |
|
&& viewport.getSelectionGroup().getSize() > 1) |
2882 |
|
|| (viewport.getAlignment().getHeight() > 1)) |
2883 |
|
{ |
2884 |
0 |
final TreePanel tp = new TreePanel(alignPanel, type, pwType); |
2885 |
|
|
2886 |
0 |
addTreeMenuItem(tp, title); |
2887 |
|
|
2888 |
0 |
jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); |
2889 |
|
} |
2890 |
|
} |
2891 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
2892 |
0 |
void loadTree_actionPerformed()... |
2893 |
|
{ |
2894 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); |
2895 |
0 |
cap.setText(MessageManager.getString("label.paste_newick_tree_file")); |
2896 |
0 |
cap.setTreeImport(); |
2897 |
0 |
Frame frame = new Frame(); |
2898 |
0 |
frame.add(cap); |
2899 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
2900 |
|
MessageManager.getString("label.paste_newick_file"), 400, 300); |
2901 |
|
} |
2902 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
2903 |
0 |
public void loadTree(jalview.io.NewickFile tree, String treeFile)... |
2904 |
|
{ |
2905 |
0 |
TreePanel tp = new TreePanel(alignPanel, treeFile, |
2906 |
|
MessageManager.getString("label.load_tree_from_file"), tree); |
2907 |
0 |
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); |
2908 |
0 |
addTreeMenuItem(tp, treeFile); |
2909 |
|
} |
2910 |
|
|
2911 |
|
|
2912 |
|
|
2913 |
|
|
2914 |
|
@param |
2915 |
|
|
2916 |
|
@param |
2917 |
|
|
2918 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2919 |
0 |
public void sortByTree(TreePanel treePanel, String title)... |
2920 |
|
{ |
2921 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2922 |
0 |
AlignmentSorter.sortByTree(viewport.getAlignment(), |
2923 |
|
treePanel.getTree()); |
2924 |
|
|
2925 |
|
|
2926 |
0 |
addHistoryItem(new OrderCommand(MessageManager |
2927 |
|
.formatMessage("label.order_by_params", new String[] |
2928 |
|
{ title }), oldOrder, viewport.getAlignment())); |
2929 |
0 |
alignPanel.paintAlignment(true, false); |
2930 |
|
} |
2931 |
|
|
2932 |
|
|
2933 |
|
|
2934 |
|
|
2935 |
|
|
2936 |
|
@param |
2937 |
|
@param |
2938 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2939 |
0 |
protected void addTreeMenuItem(final TreePanel treePanel,... |
2940 |
|
final String title) |
2941 |
|
{ |
2942 |
0 |
final MenuItem item = new MenuItem(title); |
2943 |
0 |
sortByTreeMenu.add(item); |
2944 |
0 |
item.addActionListener(new java.awt.event.ActionListener() |
2945 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2946 |
0 |
@Override... |
2947 |
|
public void actionPerformed(ActionEvent evt) |
2948 |
|
{ |
2949 |
0 |
sortByTree(treePanel, title); |
2950 |
|
} |
2951 |
|
}); |
2952 |
|
|
2953 |
0 |
treePanel.addWindowListener(new WindowAdapter() |
2954 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
2955 |
0 |
@Override... |
2956 |
|
public void windowOpened(WindowEvent e) |
2957 |
|
{ |
2958 |
0 |
if (viewport.sortByTree) |
2959 |
|
{ |
2960 |
0 |
sortByTree(treePanel, title); |
2961 |
|
} |
2962 |
0 |
super.windowOpened(e); |
2963 |
|
} |
2964 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2965 |
0 |
@Override... |
2966 |
|
public void windowClosing(WindowEvent e) |
2967 |
|
{ |
2968 |
0 |
sortByTreeMenu.remove(item); |
2969 |
|
}; |
2970 |
|
}); |
2971 |
|
} |
2972 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
2973 |
0 |
public boolean sortBy(AlignmentOrder alorder, String undoname)... |
2974 |
|
{ |
2975 |
0 |
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); |
2976 |
0 |
if (viewport.applet.debug) |
2977 |
|
{ |
2978 |
0 |
jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size() |
2979 |
|
+ " in alignment '" + getTitle() + "'"); |
2980 |
|
} |
2981 |
0 |
AlignmentSorter.sortBy(viewport.getAlignment(), alorder); |
2982 |
0 |
if (undoname != null) |
2983 |
|
{ |
2984 |
0 |
addHistoryItem(new OrderCommand(undoname, oldOrder, |
2985 |
|
viewport.getAlignment())); |
2986 |
|
} |
2987 |
0 |
alignPanel.paintAlignment(true, false); |
2988 |
0 |
return true; |
2989 |
|
} |
2990 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2991 |
0 |
protected void documentation_actionPerformed()... |
2992 |
|
{ |
2993 |
0 |
alignPanel.av.applet.openJalviewHelpUrl(); |
2994 |
|
} |
2995 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
2996 |
0 |
protected void about_actionPerformed()... |
2997 |
|
{ |
2998 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 2 |
Complexity Density: 0.09 |
|
2999 |
|
class AboutPanel extends Canvas |
3000 |
|
{ |
3001 |
|
String version; |
3002 |
|
|
3003 |
|
String builddate; |
3004 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
3005 |
0 |
public AboutPanel(String version, String builddate)... |
3006 |
|
{ |
3007 |
0 |
this.version = version; |
3008 |
0 |
this.builddate = builddate; |
3009 |
|
} |
3010 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 1 |
Complexity Density: 0.05 |
|
3011 |
0 |
@Override... |
3012 |
|
public void paint(Graphics g) |
3013 |
|
{ |
3014 |
0 |
g.setColor(Color.white); |
3015 |
0 |
g.fillRect(0, 0, getSize().width, getSize().height); |
3016 |
0 |
g.setFont(new Font("Helvetica", Font.PLAIN, 12)); |
3017 |
0 |
FontMetrics fm = g.getFontMetrics(); |
3018 |
0 |
int fh = fm.getHeight(); |
3019 |
0 |
int y = 5, x = 7; |
3020 |
0 |
g.setColor(Color.black); |
3021 |
|
|
3022 |
|
|
3023 |
0 |
g.setFont(new Font("Helvetica", Font.BOLD, 14)); |
3024 |
0 |
g.drawString(MessageManager |
3025 |
|
.formatMessage("label.jalviewLite_release", new String[] |
3026 |
|
{ version }), x, y += fh); |
3027 |
0 |
g.setFont(new Font("Helvetica", Font.BOLD, 12)); |
3028 |
0 |
g.drawString(MessageManager.formatMessage("label.jaview_build_date", |
3029 |
|
new String[] |
3030 |
|
{ builddate }), x, y += fh); |
3031 |
0 |
g.setFont(new Font("Helvetica", Font.PLAIN, 12)); |
3032 |
0 |
g.drawString(MessageManager.getString("label.jalview_authors_1"), x, |
3033 |
|
y += fh * 1.5); |
3034 |
0 |
g.drawString(MessageManager.getString("label.jalview_authors_2"), |
3035 |
|
x + 50, y += fh + 8); |
3036 |
0 |
g.drawString(MessageManager.getString("label.jalview_dev_managers"), |
3037 |
|
x, y += fh); |
3038 |
0 |
g.drawString(MessageManager |
3039 |
|
.getString("label.jalview_distribution_lists"), x, y += fh); |
3040 |
0 |
g.drawString(MessageManager.getString("label.jalview_please_cite"), |
3041 |
|
x, y += fh + 8); |
3042 |
0 |
g.drawString( |
3043 |
|
MessageManager.getString("label.jalview_cite_1_authors"), x, |
3044 |
|
y += fh); |
3045 |
0 |
g.drawString(MessageManager.getString("label.jalview_cite_1_title"), |
3046 |
|
x, y += fh); |
3047 |
0 |
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"), |
3048 |
|
x, y += fh); |
3049 |
|
} |
3050 |
|
} |
3051 |
|
|
3052 |
0 |
Frame frame = new Frame(); |
3053 |
0 |
frame.add(new AboutPanel(JalviewLite.getVersion(), |
3054 |
|
JalviewLite.getBuildDate())); |
3055 |
0 |
jalview.bin.JalviewLite.addFrame(frame, |
3056 |
|
MessageManager.getString("label.jalview"), 580, 220); |
3057 |
|
|
3058 |
|
} |
3059 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
3060 |
0 |
public void showURL(String url, String target)... |
3061 |
|
{ |
3062 |
0 |
if (viewport.applet == null) |
3063 |
|
{ |
3064 |
0 |
jalview.bin.Console |
3065 |
|
.outPrintln("Not running as applet - no browser available."); |
3066 |
|
} |
3067 |
|
else |
3068 |
|
{ |
3069 |
0 |
viewport.applet.showURL(url, target); |
3070 |
|
} |
3071 |
|
} |
3072 |
|
|
3073 |
|
|
3074 |
|
|
3075 |
|
|
3076 |
|
MenuBar alignFrameMenuBar = new MenuBar(); |
3077 |
|
|
3078 |
|
Menu fileMenu = new Menu(MessageManager.getString("action.file")); |
3079 |
|
|
3080 |
|
MenuItem loadApplication = new MenuItem( |
3081 |
|
MessageManager.getString("label.view_full_application")); |
3082 |
|
|
3083 |
|
MenuItem loadTree = new MenuItem( |
3084 |
|
MessageManager.getString("label.load_associated_tree")); |
3085 |
|
|
3086 |
|
MenuItem loadAnnotations = new MenuItem( |
3087 |
|
MessageManager.getString("label.load_features_annotations")); |
3088 |
|
|
3089 |
|
MenuItem outputFeatures = new MenuItem( |
3090 |
|
MessageManager.getString("label.export_features")); |
3091 |
|
|
3092 |
|
MenuItem outputAnnotations = new MenuItem( |
3093 |
|
MessageManager.getString("label.export_annotations")); |
3094 |
|
|
3095 |
|
MenuItem closeMenuItem = new MenuItem( |
3096 |
|
MessageManager.getString("action.close")); |
3097 |
|
|
3098 |
|
MenuItem selectAllSequenceMenuItem = new MenuItem( |
3099 |
|
MessageManager.getString("action.select_all")); |
3100 |
|
|
3101 |
|
MenuItem deselectAllSequenceMenuItem = new MenuItem( |
3102 |
|
MessageManager.getString("action.deselect_all")); |
3103 |
|
|
3104 |
|
MenuItem invertSequenceMenuItem = new MenuItem( |
3105 |
|
MessageManager.getString("action.invert_selection")); |
3106 |
|
|
3107 |
|
MenuItem remove2LeftMenuItem = new MenuItem(); |
3108 |
|
|
3109 |
|
MenuItem remove2RightMenuItem = new MenuItem(); |
3110 |
|
|
3111 |
|
MenuItem removeGappedColumnMenuItem = new MenuItem(); |
3112 |
|
|
3113 |
|
MenuItem removeAllGapsMenuItem = new MenuItem(); |
3114 |
|
|
3115 |
|
CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); |
3116 |
|
|
3117 |
|
CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); |
3118 |
|
|
3119 |
|
MenuItem sortPairwiseMenuItem = new MenuItem(); |
3120 |
|
|
3121 |
|
MenuItem sortIDMenuItem = new MenuItem(); |
3122 |
|
|
3123 |
|
MenuItem sortLengthMenuItem = new MenuItem(); |
3124 |
|
|
3125 |
|
MenuItem sortGroupMenuItem = new MenuItem(); |
3126 |
|
|
3127 |
|
MenuItem removeRedundancyMenuItem = new MenuItem(); |
3128 |
|
|
3129 |
|
MenuItem pairwiseAlignmentMenuItem = new MenuItem(); |
3130 |
|
|
3131 |
|
MenuItem PCAMenuItem = new MenuItem(); |
3132 |
|
|
3133 |
|
MenuItem averageDistanceTreeMenuItem = new MenuItem(); |
3134 |
|
|
3135 |
|
MenuItem neighbourTreeMenuItem = new MenuItem(); |
3136 |
|
|
3137 |
|
BorderLayout borderLayout1 = new BorderLayout(); |
3138 |
|
|
3139 |
|
public Label statusBar = new Label(); |
3140 |
|
|
3141 |
|
MenuItem clustalColour = new MenuItem(); |
3142 |
|
|
3143 |
|
MenuItem zappoColour = new MenuItem(); |
3144 |
|
|
3145 |
|
MenuItem taylorColour = new MenuItem(); |
3146 |
|
|
3147 |
|
MenuItem hydrophobicityColour = new MenuItem(); |
3148 |
|
|
3149 |
|
MenuItem helixColour = new MenuItem(); |
3150 |
|
|
3151 |
|
MenuItem strandColour = new MenuItem(); |
3152 |
|
|
3153 |
|
MenuItem turnColour = new MenuItem(); |
3154 |
|
|
3155 |
|
MenuItem buriedColour = new MenuItem(); |
3156 |
|
|
3157 |
|
MenuItem purinePyrimidineColour = new MenuItem(); |
3158 |
|
|
3159 |
|
|
3160 |
|
|
3161 |
|
MenuItem RNAHelixColour = new MenuItem(); |
3162 |
|
|
3163 |
|
MenuItem userDefinedColour = new MenuItem(); |
3164 |
|
|
3165 |
|
MenuItem PIDColour = new MenuItem(); |
3166 |
|
|
3167 |
|
MenuItem BLOSUM62Colour = new MenuItem(); |
3168 |
|
|
3169 |
|
MenuItem tcoffeeColour = new MenuItem(); |
3170 |
|
|
3171 |
|
MenuItem njTreeBlosumMenuItem = new MenuItem(); |
3172 |
|
|
3173 |
|
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); |
3174 |
|
|
3175 |
|
CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); |
3176 |
|
|
3177 |
|
CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); |
3178 |
|
|
3179 |
|
CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); |
3180 |
|
|
3181 |
|
MenuItem alProperties = new MenuItem( |
3182 |
|
MessageManager.getString("label.alignment_props")); |
3183 |
|
|
3184 |
|
MenuItem overviewMenuItem = new MenuItem(); |
3185 |
|
|
3186 |
|
MenuItem undoMenuItem = new MenuItem(); |
3187 |
|
|
3188 |
|
MenuItem redoMenuItem = new MenuItem(); |
3189 |
|
|
3190 |
|
CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); |
3191 |
|
|
3192 |
|
MenuItem noColourmenuItem = new MenuItem(); |
3193 |
|
|
3194 |
|
CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); |
3195 |
|
|
3196 |
|
CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); |
3197 |
|
|
3198 |
|
MenuItem findMenuItem = new MenuItem(); |
3199 |
|
|
3200 |
|
CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); |
3201 |
|
|
3202 |
|
MenuItem nucleotideColour = new MenuItem(); |
3203 |
|
|
3204 |
|
MenuItem deleteGroups = new MenuItem(); |
3205 |
|
|
3206 |
|
MenuItem grpsFromSelection = new MenuItem(); |
3207 |
|
|
3208 |
|
MenuItem createGroup = new MenuItem(); |
3209 |
|
|
3210 |
|
MenuItem unGroup = new MenuItem(); |
3211 |
|
|
3212 |
|
MenuItem delete = new MenuItem(); |
3213 |
|
|
3214 |
|
MenuItem copy = new MenuItem(); |
3215 |
|
|
3216 |
|
MenuItem cut = new MenuItem(); |
3217 |
|
|
3218 |
|
Menu pasteMenu = new Menu(); |
3219 |
|
|
3220 |
|
MenuItem pasteNew = new MenuItem(); |
3221 |
|
|
3222 |
|
MenuItem pasteThis = new MenuItem(); |
3223 |
|
|
3224 |
|
CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); |
3225 |
|
|
3226 |
|
MenuItem font = new MenuItem(); |
3227 |
|
|
3228 |
|
CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); |
3229 |
|
|
3230 |
|
CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); |
3231 |
|
|
3232 |
|
CheckboxMenuItem scaleRight = new CheckboxMenuItem(); |
3233 |
|
|
3234 |
|
MenuItem modifyPID = new MenuItem(); |
3235 |
|
|
3236 |
|
MenuItem modifyConservation = new MenuItem(); |
3237 |
|
|
3238 |
|
CheckboxMenuItem autoCalculate = null; |
3239 |
|
|
3240 |
|
CheckboxMenuItem sortByTree = new CheckboxMenuItem( |
3241 |
|
"Sort Alignment With New Tree", true); |
3242 |
|
|
3243 |
|
Menu sortByTreeMenu = new Menu(); |
3244 |
|
|
3245 |
|
MenuItem inputText = new MenuItem(); |
3246 |
|
|
3247 |
|
MenuItem documentation = new MenuItem(); |
3248 |
|
|
3249 |
|
MenuItem about = new MenuItem(); |
3250 |
|
|
3251 |
|
CheckboxMenuItem seqLimits = new CheckboxMenuItem(); |
3252 |
|
|
3253 |
|
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); |
3254 |
|
|
3255 |
|
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); |
3256 |
|
|
3257 |
|
CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem(); |
3258 |
|
|
3259 |
|
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); |
3260 |
|
|
3261 |
|
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); |
3262 |
|
|
3263 |
|
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); |
3264 |
|
|
3265 |
|
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); |
3266 |
|
|
3267 |
|
CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem(); |
3268 |
|
|
3269 |
|
|
3270 |
|
|
3271 |
|
|
3272 |
|
@throws |
3273 |
|
|
|
|
| 0% |
Uncovered Elements: 382 (382) |
Complexity: 2 |
Complexity Density: 0.01 |
|
3274 |
0 |
private void jbInit() throws Exception... |
3275 |
|
{ |
3276 |
0 |
setMenuBar(alignFrameMenuBar); |
3277 |
|
|
3278 |
|
|
3279 |
|
|
3280 |
|
|
3281 |
0 |
inputText |
3282 |
|
.setLabel(MessageManager.getString("label.input_from_textbox")); |
3283 |
0 |
inputText.addActionListener(this); |
3284 |
0 |
Menu outputTextboxMenu = new Menu( |
3285 |
|
MessageManager.getString("label.out_to_textbox")); |
3286 |
0 |
for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
3287 |
|
{ |
3288 |
0 |
MenuItem item = new MenuItem(ff); |
3289 |
|
|
3290 |
0 |
item.addActionListener(new java.awt.event.ActionListener() |
3291 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3292 |
0 |
@Override... |
3293 |
|
public void actionPerformed(ActionEvent e) |
3294 |
|
{ |
3295 |
0 |
outputText_actionPerformed(e); |
3296 |
|
} |
3297 |
|
}); |
3298 |
|
|
3299 |
0 |
outputTextboxMenu.add(item); |
3300 |
|
} |
3301 |
0 |
closeMenuItem.addActionListener(this); |
3302 |
0 |
loadApplication.addActionListener(this); |
3303 |
0 |
loadTree.addActionListener(this); |
3304 |
0 |
loadAnnotations.addActionListener(this); |
3305 |
0 |
outputFeatures.addActionListener(this); |
3306 |
0 |
outputAnnotations.addActionListener(this); |
3307 |
|
|
3308 |
|
|
3309 |
|
|
3310 |
|
|
3311 |
0 |
undoMenuItem.setEnabled(false); |
3312 |
0 |
undoMenuItem.setLabel(MessageManager.getString("action.undo")); |
3313 |
0 |
undoMenuItem.addActionListener(this); |
3314 |
0 |
redoMenuItem.setEnabled(false); |
3315 |
0 |
redoMenuItem.setLabel(MessageManager.getString("action.redo")); |
3316 |
0 |
redoMenuItem.addActionListener(this); |
3317 |
0 |
copy.setLabel(MessageManager.getString("action.copy")); |
3318 |
0 |
copy.addActionListener(this); |
3319 |
0 |
cut.setLabel(MessageManager.getString("action.cut")); |
3320 |
0 |
cut.addActionListener(this); |
3321 |
0 |
delete.setLabel(MessageManager.getString("action.delete")); |
3322 |
0 |
delete.addActionListener(this); |
3323 |
0 |
pasteMenu.setLabel(MessageManager.getString("action.paste")); |
3324 |
0 |
pasteNew.setLabel(MessageManager.getString("label.to_new_alignment")); |
3325 |
0 |
pasteNew.addActionListener(this); |
3326 |
0 |
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment")); |
3327 |
0 |
pasteThis.addActionListener(this); |
3328 |
0 |
remove2LeftMenuItem |
3329 |
|
.setLabel(MessageManager.getString("action.remove_left")); |
3330 |
0 |
remove2LeftMenuItem.addActionListener(this); |
3331 |
0 |
remove2RightMenuItem |
3332 |
|
.setLabel(MessageManager.getString("action.remove_right")); |
3333 |
0 |
remove2RightMenuItem.addActionListener(this); |
3334 |
0 |
removeGappedColumnMenuItem.setLabel( |
3335 |
|
MessageManager.getString("action.remove_empty_columns")); |
3336 |
0 |
removeGappedColumnMenuItem.addActionListener(this); |
3337 |
0 |
removeAllGapsMenuItem |
3338 |
|
.setLabel(MessageManager.getString("action.remove_all_gaps")); |
3339 |
0 |
removeAllGapsMenuItem.addActionListener(this); |
3340 |
0 |
removeRedundancyMenuItem |
3341 |
|
.setLabel(MessageManager.getString("action.remove_redundancy")); |
3342 |
0 |
removeRedundancyMenuItem.addActionListener(this); |
3343 |
|
|
3344 |
|
|
3345 |
|
|
3346 |
|
|
3347 |
0 |
findMenuItem.setLabel(MessageManager.getString("action.find")); |
3348 |
0 |
findMenuItem.addActionListener(this); |
3349 |
0 |
selectAllSequenceMenuItem.addActionListener(this); |
3350 |
0 |
deselectAllSequenceMenuItem.addActionListener(this); |
3351 |
0 |
invertSequenceMenuItem.setLabel( |
3352 |
|
MessageManager.getString("action.invert_sequence_selection")); |
3353 |
0 |
invertSequenceMenuItem.addActionListener(this); |
3354 |
0 |
invertColSel.setLabel( |
3355 |
|
MessageManager.getString("action.invert_column_selection")); |
3356 |
0 |
invertColSel.addActionListener(this); |
3357 |
0 |
deleteGroups |
3358 |
|
.setLabel(MessageManager.getString("action.undefine_groups")); |
3359 |
0 |
deleteGroups.addActionListener(this); |
3360 |
0 |
grpsFromSelection.setLabel( |
3361 |
|
MessageManager.getString("action.make_groups_selection")); |
3362 |
0 |
grpsFromSelection.addActionListener(this); |
3363 |
0 |
createGroup.setLabel(MessageManager.getString("action.create_group")); |
3364 |
0 |
createGroup.addActionListener(this); |
3365 |
0 |
unGroup.setLabel(MessageManager.getString("action.remove_group")); |
3366 |
0 |
unGroup.addActionListener(this); |
3367 |
|
|
3368 |
0 |
annotationColumnSelection.setLabel( |
3369 |
|
MessageManager.getString("action.select_by_annotation")); |
3370 |
0 |
annotationColumnSelection.addActionListener(this); |
3371 |
|
|
3372 |
|
|
3373 |
|
|
3374 |
|
|
3375 |
0 |
newView.setLabel(MessageManager.getString("action.new_view")); |
3376 |
0 |
newView.addActionListener(this); |
3377 |
0 |
Menu showMenu = new Menu(MessageManager.getString("action.show")); |
3378 |
0 |
showColumns.setLabel(MessageManager.getString("label.all_columns")); |
3379 |
0 |
showSeqs.setLabel(MessageManager.getString("label.all_sequences")); |
3380 |
0 |
Menu hideMenu = new Menu(MessageManager.getString("action.hide")); |
3381 |
0 |
hideColumns |
3382 |
|
.setLabel(MessageManager.getString("label.selected_columns")); |
3383 |
0 |
hideSequences |
3384 |
|
.setLabel(MessageManager.getString("label.selected_sequences")); |
3385 |
0 |
hideAllButSelection.setLabel( |
3386 |
|
MessageManager.getString("label.all_but_selected_region")); |
3387 |
0 |
hideAllSelection |
3388 |
|
.setLabel(MessageManager.getString("label.selected_region")); |
3389 |
0 |
showAllHidden.setLabel( |
3390 |
|
MessageManager.getString("label.all_sequences_columns")); |
3391 |
0 |
showColumns.addActionListener(this); |
3392 |
0 |
showSeqs.addActionListener(this); |
3393 |
0 |
hideColumns.addActionListener(this); |
3394 |
0 |
hideSequences.addActionListener(this); |
3395 |
0 |
hideAllButSelection.addActionListener(this); |
3396 |
0 |
hideAllSelection.addActionListener(this); |
3397 |
0 |
showAllHidden.addActionListener(this); |
3398 |
0 |
featureSettings |
3399 |
|
.setLabel(MessageManager.getString("action.feature_settings")); |
3400 |
0 |
featureSettings.addActionListener(this); |
3401 |
0 |
sequenceFeatures.setLabel( |
3402 |
|
MessageManager.getString("label.show_sequence_features")); |
3403 |
0 |
sequenceFeatures.addItemListener(this); |
3404 |
0 |
sequenceFeatures.setState(false); |
3405 |
0 |
followMouseOverFlag.setLabel( |
3406 |
|
MessageManager.getString("label.automatic_scrolling")); |
3407 |
0 |
followMouseOverFlag.addItemListener(this); |
3408 |
0 |
alProperties.addActionListener(this); |
3409 |
0 |
overviewMenuItem |
3410 |
|
.setLabel(MessageManager.getString("label.overview_window")); |
3411 |
0 |
overviewMenuItem.addActionListener(this); |
3412 |
|
|
3413 |
|
|
3414 |
|
|
3415 |
|
|
3416 |
0 |
annotationPanelMenuItem |
3417 |
|
.setLabel(MessageManager.getString("label.show_annotations")); |
3418 |
0 |
annotationPanelMenuItem.addItemListener(this); |
3419 |
0 |
showGroupConsensus |
3420 |
|
.setLabel(MessageManager.getString("label.group_consensus")); |
3421 |
0 |
showGroupConservation |
3422 |
|
.setLabel(MessageManager.getString("label.group_conservation")); |
3423 |
0 |
showConsensusHistogram.setLabel( |
3424 |
|
MessageManager.getString("label.show_consensus_histogram")); |
3425 |
0 |
showSequenceLogo.setLabel( |
3426 |
|
MessageManager.getString("label.show_consensus_logo")); |
3427 |
0 |
normSequenceLogo.setLabel( |
3428 |
|
MessageManager.getString("label.norm_consensus_logo")); |
3429 |
0 |
applyAutoAnnotationSettings |
3430 |
|
.setLabel(MessageManager.getString("label.apply_all_groups")); |
3431 |
0 |
applyAutoAnnotationSettings.setState(true); |
3432 |
0 |
Menu autoAnnMenu = new Menu( |
3433 |
|
MessageManager.getString("label.autocalculated_annotation")); |
3434 |
|
|
3435 |
0 |
Menu selectSS = new Menu(MessageManager |
3436 |
|
.getString("label.select_secondary_structure_source")); |
3437 |
0 |
showGroupConsensus.addItemListener(this); |
3438 |
0 |
showGroupConservation.addItemListener(this); |
3439 |
0 |
showConsensusHistogram.addItemListener(this); |
3440 |
0 |
showSequenceLogo.addItemListener(this); |
3441 |
0 |
normSequenceLogo.addItemListener(this); |
3442 |
0 |
applyAutoAnnotationSettings.addItemListener(this); |
3443 |
0 |
showAlignmentAnnotations = new CheckboxMenuItem( |
3444 |
|
MessageManager.getString("label.show_all_al_annotations")); |
3445 |
0 |
showSequenceAnnotations = new CheckboxMenuItem( |
3446 |
|
MessageManager.getString("label.show_all_seq_annotations")); |
3447 |
0 |
sortAnnBySequence = new CheckboxMenuItem( |
3448 |
|
MessageManager.getString("label.sort_annotations_by_sequence")); |
3449 |
0 |
sortAnnByLabel = new CheckboxMenuItem( |
3450 |
|
MessageManager.getString("label.sort_annotations_by_label")); |
3451 |
0 |
showAutoFirst = new CheckboxMenuItem( |
3452 |
|
MessageManager.getString("label.show_first")); |
3453 |
0 |
showAutoFirst.setState(false); |
3454 |
0 |
setShowAutoCalculatedAbove(showAutoFirst.getState()); |
3455 |
0 |
showAutoLast = new CheckboxMenuItem( |
3456 |
|
MessageManager.getString("label.show_last")); |
3457 |
0 |
showAutoLast.setState(!showAutoFirst.getState()); |
3458 |
0 |
showAlignmentAnnotations.addItemListener(this); |
3459 |
0 |
showSequenceAnnotations.addItemListener(this); |
3460 |
0 |
sortAnnBySequence.addItemListener(this); |
3461 |
0 |
sortAnnByLabel.addItemListener(this); |
3462 |
0 |
showAutoFirst.addItemListener(this); |
3463 |
0 |
showAutoLast.addItemListener(this); |
3464 |
|
|
3465 |
|
|
3466 |
|
|
3467 |
|
|
3468 |
0 |
font.setLabel(MessageManager.getString("action.font")); |
3469 |
0 |
font.addActionListener(this); |
3470 |
0 |
scaleAbove.setLabel(MessageManager.getString("action.scale_above")); |
3471 |
0 |
scaleAbove.setState(true); |
3472 |
0 |
scaleAbove.setEnabled(false); |
3473 |
0 |
scaleAbove.addItemListener(this); |
3474 |
0 |
scaleLeft.setEnabled(false); |
3475 |
0 |
scaleLeft.setState(true); |
3476 |
0 |
scaleLeft.setLabel(MessageManager.getString("action.scale_left")); |
3477 |
0 |
scaleLeft.addItemListener(this); |
3478 |
0 |
scaleRight.setEnabled(false); |
3479 |
0 |
scaleRight.setState(true); |
3480 |
0 |
scaleRight.setLabel(MessageManager.getString("action.scale_right")); |
3481 |
0 |
scaleRight.addItemListener(this); |
3482 |
0 |
viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes")); |
3483 |
0 |
viewBoxesMenuItem.setState(true); |
3484 |
0 |
viewBoxesMenuItem.addItemListener(this); |
3485 |
0 |
viewTextMenuItem.setLabel(MessageManager.getString("action.text")); |
3486 |
0 |
viewTextMenuItem.setState(true); |
3487 |
0 |
viewTextMenuItem.addItemListener(this); |
3488 |
0 |
colourTextMenuItem |
3489 |
|
.setLabel(MessageManager.getString("label.colour_text")); |
3490 |
0 |
colourTextMenuItem.addItemListener(this); |
3491 |
0 |
displayNonconservedMenuItem |
3492 |
|
.setLabel(MessageManager.getString("label.show_non_conserved")); |
3493 |
0 |
displayNonconservedMenuItem.addItemListener(this); |
3494 |
0 |
wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); |
3495 |
0 |
wrapMenuItem.addItemListener(this); |
3496 |
0 |
renderGapsMenuItem |
3497 |
|
.setLabel(MessageManager.getString("action.show_gaps")); |
3498 |
0 |
renderGapsMenuItem.setState(true); |
3499 |
0 |
renderGapsMenuItem.addItemListener(this); |
3500 |
0 |
centreColumnLabelFlag.setLabel( |
3501 |
|
MessageManager.getString("label.centre_column_labels")); |
3502 |
0 |
centreColumnLabelFlag.addItemListener(this); |
3503 |
0 |
seqLimits.setState(true); |
3504 |
0 |
seqLimits.setLabel( |
3505 |
|
MessageManager.getString("label.show_sequence_limits")); |
3506 |
0 |
seqLimits.addItemListener(this); |
3507 |
|
|
3508 |
|
|
3509 |
|
|
3510 |
|
|
3511 |
0 |
applyToAllGroups.setLabel( |
3512 |
|
MessageManager.getString("label.apply_colour_to_all_groups")); |
3513 |
0 |
applyToAllGroups.setState(true); |
3514 |
0 |
applyToAllGroups.addItemListener(this); |
3515 |
0 |
clustalColour.setLabel( |
3516 |
|
MessageManager.getString("label.colourScheme_clustal")); |
3517 |
0 |
clustalColour.addActionListener(this); |
3518 |
0 |
zappoColour |
3519 |
|
.setLabel(MessageManager.getString("label.colourScheme_zappo")); |
3520 |
0 |
zappoColour.addActionListener(this); |
3521 |
0 |
taylorColour.setLabel( |
3522 |
|
MessageManager.getString("label.colourScheme_taylor")); |
3523 |
0 |
taylorColour.addActionListener(this); |
3524 |
0 |
hydrophobicityColour.setLabel( |
3525 |
|
MessageManager.getString("label.colourScheme_hydrophobic")); |
3526 |
0 |
hydrophobicityColour.addActionListener(this); |
3527 |
0 |
helixColour.setLabel( |
3528 |
|
MessageManager.getString("label.colourScheme_helixpropensity")); |
3529 |
0 |
helixColour.addActionListener(this); |
3530 |
0 |
strandColour.setLabel(MessageManager |
3531 |
|
.getString("label.colourScheme_strandpropensity")); |
3532 |
0 |
strandColour.addActionListener(this); |
3533 |
0 |
turnColour.setLabel( |
3534 |
|
MessageManager.getString("label.colourScheme_turnpropensity")); |
3535 |
0 |
turnColour.addActionListener(this); |
3536 |
0 |
buriedColour.setLabel( |
3537 |
|
MessageManager.getString("label.colourScheme_buriedindex")); |
3538 |
0 |
buriedColour.addActionListener(this); |
3539 |
0 |
purinePyrimidineColour.setLabel(MessageManager |
3540 |
|
.getString("label.colourScheme_purine/pyrimidine")); |
3541 |
0 |
purinePyrimidineColour.addActionListener(this); |
3542 |
|
|
3543 |
|
|
3544 |
|
|
3545 |
0 |
RNAHelixColour.setLabel( |
3546 |
|
MessageManager.getString("label.colourScheme_rnahelices")); |
3547 |
0 |
RNAHelixColour.addActionListener(this); |
3548 |
0 |
userDefinedColour |
3549 |
|
.setLabel(MessageManager.getString("action.user_defined")); |
3550 |
0 |
userDefinedColour.addActionListener(this); |
3551 |
0 |
PIDColour.setLabel( |
3552 |
|
MessageManager.getString("label.colourScheme_%identity")); |
3553 |
0 |
PIDColour.addActionListener(this); |
3554 |
0 |
BLOSUM62Colour.setLabel( |
3555 |
|
MessageManager.getString("label.colourScheme_blosum62")); |
3556 |
0 |
BLOSUM62Colour.addActionListener(this); |
3557 |
0 |
tcoffeeColour.setLabel( |
3558 |
|
MessageManager.getString("label.colourScheme_t-coffeescores")); |
3559 |
|
|
3560 |
0 |
tcoffeeColour.setEnabled(false); |
3561 |
0 |
tcoffeeColour.addActionListener(this); |
3562 |
0 |
conservationMenuItem |
3563 |
|
.setLabel(MessageManager.getString("action.by_conservation")); |
3564 |
0 |
conservationMenuItem.addItemListener(this); |
3565 |
0 |
noColourmenuItem.setLabel(MessageManager.getString("label.none")); |
3566 |
0 |
noColourmenuItem.addActionListener(this); |
3567 |
0 |
abovePIDThreshold.setLabel( |
3568 |
|
MessageManager.getString("label.above_identity_threshold")); |
3569 |
0 |
abovePIDThreshold.addItemListener(this); |
3570 |
0 |
nucleotideColour.setLabel( |
3571 |
|
MessageManager.getString("label.colourScheme_nucleotide")); |
3572 |
0 |
nucleotideColour.addActionListener(this); |
3573 |
0 |
modifyPID.setLabel( |
3574 |
|
MessageManager.getString("label.modify_identity_threshold")); |
3575 |
0 |
modifyPID.setEnabled(abovePIDThreshold.getState()); |
3576 |
0 |
modifyPID.addActionListener(this); |
3577 |
0 |
modifyConservation.setLabel(MessageManager |
3578 |
|
.getString("label.modify_conservation_threshold")); |
3579 |
0 |
modifyConservation.setEnabled(conservationMenuItem.getState()); |
3580 |
0 |
modifyConservation.addActionListener(this); |
3581 |
0 |
annotationColour |
3582 |
|
.setLabel(MessageManager.getString("action.by_annotation")); |
3583 |
0 |
annotationColour.addActionListener(this); |
3584 |
|
|
3585 |
|
|
3586 |
|
|
3587 |
|
|
3588 |
0 |
sortPairwiseMenuItem |
3589 |
|
.setLabel(MessageManager.getString("action.by_pairwise_id")); |
3590 |
0 |
sortPairwiseMenuItem.addActionListener(this); |
3591 |
0 |
sortIDMenuItem.setLabel(MessageManager.getString("action.by_id")); |
3592 |
0 |
sortIDMenuItem.addActionListener(this); |
3593 |
0 |
sortLengthMenuItem |
3594 |
|
.setLabel(MessageManager.getString("action.by_length")); |
3595 |
0 |
sortLengthMenuItem.addActionListener(this); |
3596 |
0 |
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group")); |
3597 |
0 |
sortGroupMenuItem.addActionListener(this); |
3598 |
0 |
pairwiseAlignmentMenuItem.setLabel( |
3599 |
|
MessageManager.getString("action.pairwise_alignment")); |
3600 |
0 |
pairwiseAlignmentMenuItem.addActionListener(this); |
3601 |
0 |
PCAMenuItem.setLabel( |
3602 |
|
MessageManager.getString("label.principal_component_analysis")); |
3603 |
0 |
PCAMenuItem.addActionListener(this); |
3604 |
0 |
autoCalculate = new CheckboxMenuItem( |
3605 |
|
MessageManager.getString("label.autocalculate_consensus"), |
3606 |
|
true); |
3607 |
0 |
averageDistanceTreeMenuItem.setLabel( |
3608 |
|
MessageManager.getString("label.average_distance_identity")); |
3609 |
0 |
averageDistanceTreeMenuItem.addActionListener(this); |
3610 |
0 |
neighbourTreeMenuItem.setLabel( |
3611 |
|
MessageManager.getString("label.neighbour_joining_identity")); |
3612 |
0 |
neighbourTreeMenuItem.addActionListener(this); |
3613 |
0 |
avDistanceTreeBlosumMenuItem.setLabel( |
3614 |
|
MessageManager.getString("label.average_distance_blosum62")); |
3615 |
0 |
avDistanceTreeBlosumMenuItem.addActionListener(this); |
3616 |
0 |
njTreeBlosumMenuItem |
3617 |
|
.setLabel(MessageManager.getString("label.neighbour_blosum62")); |
3618 |
0 |
njTreeBlosumMenuItem.addActionListener(this); |
3619 |
0 |
sortByTreeMenu |
3620 |
|
.setLabel(MessageManager.getString("action.by_tree_order")); |
3621 |
0 |
Menu sortMenu = new Menu(MessageManager.getString("action.sort")); |
3622 |
0 |
Menu calculateTreeMenu = new Menu( |
3623 |
|
MessageManager.getString("action.calculate_tree")); |
3624 |
0 |
autoCalculate.addItemListener(this); |
3625 |
0 |
sortByTree.addItemListener(this); |
3626 |
|
|
3627 |
|
|
3628 |
|
|
3629 |
|
|
3630 |
0 |
Menu helpMenu = new Menu(MessageManager.getString("action.help")); |
3631 |
0 |
documentation.setLabel(MessageManager.getString("label.documentation")); |
3632 |
0 |
documentation.addActionListener(this); |
3633 |
0 |
about.setLabel(MessageManager.getString("label.about")); |
3634 |
0 |
about.addActionListener(this); |
3635 |
|
|
3636 |
|
|
3637 |
|
|
3638 |
|
|
3639 |
0 |
alignFrameMenuBar.add(fileMenu); |
3640 |
0 |
Menu editMenu = new Menu(MessageManager.getString("action.edit")); |
3641 |
0 |
alignFrameMenuBar.add(editMenu); |
3642 |
0 |
Menu selectMenu = new Menu(MessageManager.getString("action.select")); |
3643 |
0 |
alignFrameMenuBar.add(selectMenu); |
3644 |
0 |
Menu viewMenu = new Menu(MessageManager.getString("action.view")); |
3645 |
0 |
alignFrameMenuBar.add(viewMenu); |
3646 |
0 |
Menu annotationsMenu = new Menu( |
3647 |
|
MessageManager.getString("action.annotations")); |
3648 |
0 |
alignFrameMenuBar.add(annotationsMenu); |
3649 |
0 |
Menu formatMenu = new Menu(MessageManager.getString("action.format")); |
3650 |
0 |
alignFrameMenuBar.add(formatMenu); |
3651 |
0 |
Menu colourMenu = new Menu(MessageManager.getString("action.colour")); |
3652 |
0 |
alignFrameMenuBar.add(colourMenu); |
3653 |
0 |
Menu calculateMenu = new Menu( |
3654 |
|
MessageManager.getString("action.calculate")); |
3655 |
0 |
alignFrameMenuBar.add(calculateMenu); |
3656 |
0 |
alignFrameMenuBar.add(helpMenu); |
3657 |
|
|
3658 |
|
|
3659 |
|
|
3660 |
|
|
3661 |
0 |
fileMenu.add(inputText); |
3662 |
0 |
fileMenu.add(loadTree); |
3663 |
0 |
fileMenu.add(loadAnnotations); |
3664 |
0 |
fileMenu.addSeparator(); |
3665 |
0 |
fileMenu.add(outputTextboxMenu); |
3666 |
0 |
fileMenu.add(outputFeatures); |
3667 |
0 |
fileMenu.add(outputAnnotations); |
3668 |
0 |
if (jalviewServletURL != null) |
3669 |
|
{ |
3670 |
0 |
fileMenu.add(loadApplication); |
3671 |
|
} |
3672 |
0 |
fileMenu.addSeparator(); |
3673 |
0 |
fileMenu.add(closeMenuItem); |
3674 |
|
|
3675 |
|
|
3676 |
|
|
3677 |
|
|
3678 |
0 |
editMenu.add(undoMenuItem); |
3679 |
0 |
editMenu.add(redoMenuItem); |
3680 |
0 |
editMenu.add(cut); |
3681 |
0 |
editMenu.add(copy); |
3682 |
0 |
pasteMenu.add(pasteNew); |
3683 |
0 |
pasteMenu.add(pasteThis); |
3684 |
0 |
editMenu.add(pasteMenu); |
3685 |
0 |
editMenu.add(delete); |
3686 |
0 |
editMenu.addSeparator(); |
3687 |
0 |
editMenu.add(remove2LeftMenuItem); |
3688 |
0 |
editMenu.add(remove2RightMenuItem); |
3689 |
0 |
editMenu.add(removeGappedColumnMenuItem); |
3690 |
0 |
editMenu.add(removeAllGapsMenuItem); |
3691 |
0 |
editMenu.add(removeRedundancyMenuItem); |
3692 |
|
|
3693 |
|
|
3694 |
|
|
3695 |
|
|
3696 |
0 |
selectMenu.add(findMenuItem); |
3697 |
0 |
selectMenu.addSeparator(); |
3698 |
0 |
selectMenu.add(selectAllSequenceMenuItem); |
3699 |
0 |
selectMenu.add(deselectAllSequenceMenuItem); |
3700 |
0 |
selectMenu.add(invertSequenceMenuItem); |
3701 |
0 |
selectMenu.add(invertColSel); |
3702 |
0 |
selectMenu.add(createGroup); |
3703 |
0 |
selectMenu.add(unGroup); |
3704 |
0 |
selectMenu.add(grpsFromSelection); |
3705 |
0 |
selectMenu.add(deleteGroups); |
3706 |
0 |
selectMenu.add(annotationColumnSelection); |
3707 |
|
|
3708 |
|
|
3709 |
|
|
3710 |
|
|
3711 |
0 |
viewMenu.add(newView); |
3712 |
0 |
viewMenu.addSeparator(); |
3713 |
0 |
showMenu.add(showColumns); |
3714 |
0 |
showMenu.add(showSeqs); |
3715 |
0 |
showMenu.add(showAllHidden); |
3716 |
0 |
viewMenu.add(showMenu); |
3717 |
0 |
hideMenu.add(hideColumns); |
3718 |
0 |
hideMenu.add(hideSequences); |
3719 |
0 |
hideMenu.add(hideAllSelection); |
3720 |
0 |
hideMenu.add(hideAllButSelection); |
3721 |
0 |
viewMenu.add(hideMenu); |
3722 |
0 |
viewMenu.addSeparator(); |
3723 |
0 |
viewMenu.add(followMouseOverFlag); |
3724 |
0 |
viewMenu.addSeparator(); |
3725 |
0 |
viewMenu.add(sequenceFeatures); |
3726 |
0 |
viewMenu.add(featureSettings); |
3727 |
0 |
viewMenu.addSeparator(); |
3728 |
0 |
viewMenu.add(alProperties); |
3729 |
0 |
viewMenu.addSeparator(); |
3730 |
0 |
viewMenu.add(overviewMenuItem); |
3731 |
|
|
3732 |
|
|
3733 |
|
|
3734 |
|
|
3735 |
0 |
annotationsMenu.add(annotationPanelMenuItem); |
3736 |
0 |
annotationsMenu.addSeparator(); |
3737 |
0 |
annotationsMenu.add(showAlignmentAnnotations); |
3738 |
0 |
annotationsMenu.add(showSequenceAnnotations); |
3739 |
0 |
annotationsMenu.add(sortAnnBySequence); |
3740 |
0 |
annotationsMenu.add(sortAnnByLabel); |
3741 |
0 |
annotationsMenu.addSeparator(); |
3742 |
0 |
autoAnnMenu.add(showAutoFirst); |
3743 |
0 |
autoAnnMenu.add(showAutoLast); |
3744 |
0 |
autoAnnMenu.addSeparator(); |
3745 |
0 |
autoAnnMenu.add(applyAutoAnnotationSettings); |
3746 |
0 |
autoAnnMenu.add(showConsensusHistogram); |
3747 |
0 |
autoAnnMenu.add(showSequenceLogo); |
3748 |
0 |
autoAnnMenu.add(normSequenceLogo); |
3749 |
0 |
autoAnnMenu.addSeparator(); |
3750 |
0 |
autoAnnMenu.add(showGroupConservation); |
3751 |
0 |
autoAnnMenu.add(showGroupConsensus); |
3752 |
0 |
annotationsMenu.add(autoAnnMenu); |
3753 |
|
|
3754 |
|
|
3755 |
|
|
3756 |
|
|
3757 |
0 |
formatMenu.add(font); |
3758 |
0 |
formatMenu.add(seqLimits); |
3759 |
0 |
formatMenu.add(wrapMenuItem); |
3760 |
0 |
formatMenu.add(scaleAbove); |
3761 |
0 |
formatMenu.add(scaleLeft); |
3762 |
0 |
formatMenu.add(scaleRight); |
3763 |
0 |
formatMenu.add(viewBoxesMenuItem); |
3764 |
0 |
formatMenu.add(viewTextMenuItem); |
3765 |
0 |
formatMenu.add(colourTextMenuItem); |
3766 |
0 |
formatMenu.add(displayNonconservedMenuItem); |
3767 |
0 |
formatMenu.add(renderGapsMenuItem); |
3768 |
0 |
formatMenu.add(centreColumnLabelFlag); |
3769 |
|
|
3770 |
|
|
3771 |
|
|
3772 |
|
|
3773 |
0 |
colourMenu.add(applyToAllGroups); |
3774 |
0 |
colourMenu.addSeparator(); |
3775 |
0 |
colourMenu.add(noColourmenuItem); |
3776 |
0 |
colourMenu.add(clustalColour); |
3777 |
0 |
colourMenu.add(BLOSUM62Colour); |
3778 |
0 |
colourMenu.add(PIDColour); |
3779 |
0 |
colourMenu.add(zappoColour); |
3780 |
0 |
colourMenu.add(taylorColour); |
3781 |
0 |
colourMenu.add(hydrophobicityColour); |
3782 |
0 |
colourMenu.add(helixColour); |
3783 |
0 |
colourMenu.add(strandColour); |
3784 |
0 |
colourMenu.add(turnColour); |
3785 |
0 |
colourMenu.add(buriedColour); |
3786 |
0 |
colourMenu.add(nucleotideColour); |
3787 |
0 |
colourMenu.add(purinePyrimidineColour); |
3788 |
|
|
3789 |
0 |
colourMenu.add(tcoffeeColour); |
3790 |
0 |
colourMenu.add(userDefinedColour); |
3791 |
0 |
colourMenu.addSeparator(); |
3792 |
0 |
colourMenu.add(conservationMenuItem); |
3793 |
0 |
colourMenu.add(modifyConservation); |
3794 |
0 |
colourMenu.add(abovePIDThreshold); |
3795 |
0 |
colourMenu.add(modifyPID); |
3796 |
0 |
colourMenu.add(annotationColour); |
3797 |
0 |
colourMenu.add(RNAHelixColour); |
3798 |
|
|
3799 |
|
|
3800 |
|
|
3801 |
|
|
3802 |
0 |
sortMenu.add(sortIDMenuItem); |
3803 |
0 |
sortMenu.add(sortLengthMenuItem); |
3804 |
0 |
sortMenu.add(sortByTreeMenu); |
3805 |
0 |
sortMenu.add(sortGroupMenuItem); |
3806 |
0 |
sortMenu.add(sortPairwiseMenuItem); |
3807 |
0 |
calculateMenu.add(sortMenu); |
3808 |
0 |
calculateTreeMenu.add(averageDistanceTreeMenuItem); |
3809 |
0 |
calculateTreeMenu.add(neighbourTreeMenuItem); |
3810 |
0 |
calculateTreeMenu.add(avDistanceTreeBlosumMenuItem); |
3811 |
0 |
calculateTreeMenu.add(njTreeBlosumMenuItem); |
3812 |
0 |
calculateMenu.add(calculateTreeMenu); |
3813 |
0 |
calculateMenu.addSeparator(); |
3814 |
0 |
calculateMenu.add(pairwiseAlignmentMenuItem); |
3815 |
0 |
calculateMenu.add(PCAMenuItem); |
3816 |
0 |
calculateMenu.add(autoCalculate); |
3817 |
0 |
calculateMenu.add(sortByTree); |
3818 |
|
|
3819 |
|
|
3820 |
|
|
3821 |
|
|
3822 |
0 |
helpMenu.add(documentation); |
3823 |
0 |
helpMenu.add(about); |
3824 |
|
|
3825 |
|
|
3826 |
|
|
3827 |
|
|
3828 |
0 |
statusBar.setBackground(Color.white); |
3829 |
0 |
statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
3830 |
0 |
setStatus(MessageManager.getString("label.status_bar")); |
3831 |
0 |
this.add(statusBar, BorderLayout.SOUTH); |
3832 |
|
} |
3833 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3834 |
0 |
@Override... |
3835 |
|
public void setStatus(String string) |
3836 |
|
{ |
3837 |
0 |
statusBar.setText(string); |
3838 |
|
}; |
3839 |
|
|
3840 |
|
MenuItem featureSettings = new MenuItem(); |
3841 |
|
|
3842 |
|
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); |
3843 |
|
|
3844 |
|
MenuItem annotationColour = new MenuItem(); |
3845 |
|
|
3846 |
|
MenuItem annotationColumnSelection = new MenuItem(); |
3847 |
|
|
3848 |
|
MenuItem invertColSel = new MenuItem(); |
3849 |
|
|
3850 |
|
MenuItem showColumns = new MenuItem(); |
3851 |
|
|
3852 |
|
MenuItem showSeqs = new MenuItem(); |
3853 |
|
|
3854 |
|
MenuItem hideColumns = new MenuItem(); |
3855 |
|
|
3856 |
|
MenuItem hideSequences = new MenuItem(); |
3857 |
|
|
3858 |
|
MenuItem hideAllButSelection = new MenuItem(); |
3859 |
|
|
3860 |
|
MenuItem hideAllSelection = new MenuItem(); |
3861 |
|
|
3862 |
|
MenuItem showAllHidden = new MenuItem(); |
3863 |
|
|
3864 |
|
MenuItem newView = new MenuItem(); |
3865 |
|
|
3866 |
|
private CheckboxMenuItem showAlignmentAnnotations; |
3867 |
|
|
3868 |
|
private CheckboxMenuItem showSequenceAnnotations; |
3869 |
|
|
3870 |
|
private CheckboxMenuItem sortAnnBySequence; |
3871 |
|
|
3872 |
|
private CheckboxMenuItem sortAnnByLabel; |
3873 |
|
|
3874 |
|
private CheckboxMenuItem showAutoFirst; |
3875 |
|
|
3876 |
|
private CheckboxMenuItem showAutoLast; |
3877 |
|
|
3878 |
|
private SplitFrame splitFrame; |
3879 |
|
|
3880 |
|
|
3881 |
|
|
3882 |
|
|
3883 |
|
|
3884 |
|
|
3885 |
|
@param |
3886 |
|
|
3887 |
|
|
3888 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
3889 |
0 |
public void createAlignFrameWindow(boolean reallyEmbedded)... |
3890 |
|
{ |
3891 |
0 |
if (reallyEmbedded) |
3892 |
|
{ |
3893 |
0 |
embedAlignFrameInApplet(viewport.applet); |
3894 |
|
} |
3895 |
|
else |
3896 |
|
{ |
3897 |
|
|
3898 |
|
|
3899 |
|
|
3900 |
0 |
if (embedMenuIfNeeded(alignPanel)) |
3901 |
|
{ |
3902 |
|
|
3903 |
|
|
3904 |
|
|
3905 |
|
|
3906 |
0 |
alignPanel.setSize(getSize().width, |
3907 |
|
getSize().height - statusBar.getHeight()); |
3908 |
|
} |
3909 |
0 |
add(statusBar, BorderLayout.SOUTH); |
3910 |
0 |
add(alignPanel, BorderLayout.CENTER); |
3911 |
|
|
3912 |
0 |
jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth, |
3913 |
|
frameHeight); |
3914 |
|
} |
3915 |
|
} |
3916 |
|
|
3917 |
|
|
3918 |
|
|
3919 |
|
|
3920 |
|
@param |
3921 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
|
3922 |
0 |
public void embedAlignFrameInApplet(final JalviewLite theApplet)... |
3923 |
|
{ |
3924 |
|
|
3925 |
|
|
3926 |
|
|
3927 |
|
|
3928 |
0 |
fileMenu.remove(closeMenuItem); |
3929 |
0 |
fileMenu.remove(3); |
3930 |
|
|
3931 |
0 |
embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false); |
3932 |
|
|
3933 |
0 |
theApplet.setLayout(new BorderLayout()); |
3934 |
0 |
theApplet.add(embeddedMenu, BorderLayout.NORTH); |
3935 |
0 |
theApplet.add(statusBar, BorderLayout.SOUTH); |
3936 |
|
|
3937 |
0 |
alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height |
3938 |
|
- embeddedMenu.getHeight() - statusBar.getHeight()); |
3939 |
0 |
theApplet.add(alignPanel, BorderLayout.CENTER); |
3940 |
0 |
final AlignFrame me = this; |
3941 |
0 |
theApplet.addFocusListener(new FocusListener() |
3942 |
|
{ |
3943 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
3944 |
0 |
@Override... |
3945 |
|
public void focusLost(FocusEvent e) |
3946 |
|
{ |
3947 |
0 |
if (theApplet.currentAlignFrame == me) |
3948 |
|
{ |
3949 |
0 |
theApplet.currentAlignFrame = null; |
3950 |
|
} |
3951 |
|
} |
3952 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3953 |
0 |
@Override... |
3954 |
|
public void focusGained(FocusEvent e) |
3955 |
|
{ |
3956 |
0 |
theApplet.currentAlignFrame = me; |
3957 |
|
} |
3958 |
|
}); |
3959 |
0 |
theApplet.validate(); |
3960 |
|
} |
3961 |
|
|
3962 |
|
|
3963 |
|
|
3964 |
|
|
3965 |
|
|
3966 |
|
|
3967 |
|
|
3968 |
|
|
3969 |
|
|
3970 |
|
@param |
3971 |
|
|
3972 |
|
@param |
3973 |
|
|
3974 |
|
|
|
|
| 0% |
Uncovered Elements: 39 (39) |
Complexity: 10 |
Complexity Density: 0.4 |
|
3975 |
0 |
public SequenceStructureBinding addStructureViewInstance(... |
3976 |
|
Object jmolviewer, String[] sequenceIds) |
3977 |
|
{ |
3978 |
0 |
Viewer viewer = null; |
3979 |
0 |
try |
3980 |
|
{ |
3981 |
0 |
viewer = (Viewer) jmolviewer; |
3982 |
|
} catch (ClassCastException ex) |
3983 |
|
{ |
3984 |
0 |
jalview.bin.Console.errPrintln( |
3985 |
|
"Unsupported viewer object :" + jmolviewer.getClass()); |
3986 |
|
} |
3987 |
0 |
if (viewer == null) |
3988 |
|
{ |
3989 |
0 |
jalview.bin.Console |
3990 |
|
.errPrintln("Can't use this object as a structure viewer:" |
3991 |
|
+ jmolviewer.getClass()); |
3992 |
0 |
return null; |
3993 |
|
} |
3994 |
0 |
SequenceI[] seqs = null; |
3995 |
0 |
if (sequenceIds == null || sequenceIds.length == 0) |
3996 |
|
{ |
3997 |
0 |
seqs = viewport.getAlignment().getSequencesArray(); |
3998 |
|
} |
3999 |
|
else |
4000 |
|
{ |
4001 |
0 |
Vector sqi = new Vector(); |
4002 |
0 |
AlignmentI al = viewport.getAlignment(); |
4003 |
0 |
for (int sid = 0; sid < sequenceIds.length; sid++) |
4004 |
|
{ |
4005 |
0 |
SequenceI sq = al.findName(sequenceIds[sid]); |
4006 |
0 |
if (sq != null) |
4007 |
|
{ |
4008 |
0 |
sqi.addElement(sq); |
4009 |
|
} |
4010 |
|
} |
4011 |
0 |
if (sqi.size() > 0) |
4012 |
|
{ |
4013 |
0 |
seqs = new SequenceI[sqi.size()]; |
4014 |
0 |
for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) |
4015 |
|
{ |
4016 |
0 |
seqs[sid] = (SequenceI) sqi.elementAt(sid); |
4017 |
|
} |
4018 |
|
} |
4019 |
|
else |
4020 |
|
{ |
4021 |
0 |
return null; |
4022 |
|
} |
4023 |
|
} |
4024 |
0 |
AAStructureBindingModel jmv = null; |
4025 |
|
|
4026 |
0 |
if (jmv == null) |
4027 |
|
{ |
4028 |
0 |
jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs }); |
4029 |
|
} |
4030 |
0 |
return jmv; |
4031 |
|
|
4032 |
|
} |
4033 |
|
|
4034 |
|
|
4035 |
|
|
4036 |
|
|
4037 |
|
@param |
4038 |
|
|
4039 |
|
@param |
4040 |
|
|
4041 |
|
@param |
4042 |
|
|
4043 |
|
@return |
4044 |
|
|
4045 |
|
|
4046 |
|
|
|
|
| 0% |
Uncovered Elements: 38 (38) |
Complexity: 10 |
Complexity Density: 0.42 |
|
4047 |
0 |
public boolean addPdbFile(String sequenceId, String pdbEntryString,... |
4048 |
|
String pdbFile) |
4049 |
|
{ |
4050 |
0 |
SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); |
4051 |
0 |
boolean needtoadd = false; |
4052 |
0 |
if (toaddpdb != null) |
4053 |
|
{ |
4054 |
0 |
Vector pdbe = toaddpdb.getAllPDBEntries(); |
4055 |
0 |
PDBEntry pdbentry = null; |
4056 |
0 |
if (pdbe != null && pdbe.size() > 0) |
4057 |
|
{ |
4058 |
0 |
for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) |
4059 |
|
{ |
4060 |
0 |
pdbentry = (PDBEntry) pdbe.elementAt(pe); |
4061 |
0 |
if (!pdbentry.getId().equals(pdbEntryString) |
4062 |
|
&& !pdbentry.getFile().equals(pdbFile)) |
4063 |
|
{ |
4064 |
0 |
pdbentry = null; |
4065 |
|
} |
4066 |
|
else |
4067 |
|
{ |
4068 |
0 |
continue; |
4069 |
|
} |
4070 |
|
} |
4071 |
|
} |
4072 |
0 |
if (pdbentry == null) |
4073 |
|
{ |
4074 |
0 |
pdbentry = new PDBEntry(); |
4075 |
0 |
pdbentry.setId(pdbEntryString); |
4076 |
0 |
pdbentry.setFile(pdbFile); |
4077 |
0 |
needtoadd = true; |
4078 |
|
} |
4079 |
|
|
4080 |
|
|
4081 |
0 |
DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile, |
4082 |
|
FileFormat.PDB); |
4083 |
0 |
if (protocol == null) |
4084 |
|
{ |
4085 |
0 |
return false; |
4086 |
|
} |
4087 |
0 |
if (needtoadd) |
4088 |
|
{ |
4089 |
0 |
pdbentry.setProperty("protocol", protocol); |
4090 |
0 |
toaddpdb.addPDBId(pdbentry); |
4091 |
0 |
alignPanel.getStructureSelectionManager() |
4092 |
|
.registerPDBEntry(pdbentry); |
4093 |
|
} |
4094 |
|
} |
4095 |
0 |
return true; |
4096 |
|
} |
4097 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 6 |
Complexity Density: 0.5 |
|
4098 |
0 |
private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)... |
4099 |
|
{ |
4100 |
0 |
if (seqs != null) |
4101 |
|
{ |
4102 |
0 |
Vector sequences = new Vector(); |
4103 |
0 |
for (int i = 0; i < seqs.length; i++) |
4104 |
|
{ |
4105 |
0 |
if (seqs[i] != null) |
4106 |
|
{ |
4107 |
0 |
sequences |
4108 |
|
.addElement(new Object[] |
4109 |
0 |
{ seqs[i], (chains != null) ? chains[i] : null }); |
4110 |
|
} |
4111 |
|
} |
4112 |
0 |
seqs = new SequenceI[sequences.size()]; |
4113 |
0 |
chains = new String[sequences.size()]; |
4114 |
0 |
for (int i = 0, isize = sequences.size(); i < isize; i++) |
4115 |
|
{ |
4116 |
0 |
Object[] oj = (Object[]) sequences.elementAt(i); |
4117 |
|
|
4118 |
0 |
seqs[i] = (SequenceI) oj[0]; |
4119 |
0 |
chains[i] = (String) oj[1]; |
4120 |
|
} |
4121 |
|
} |
4122 |
0 |
return new Object[] { seqs, chains }; |
4123 |
|
|
4124 |
|
} |
4125 |
|
|
|
|
| 0% |
Uncovered Elements: 52 (52) |
Complexity: 14 |
Complexity Density: 0.44 |
|
4126 |
0 |
public void newStructureView(JalviewLite applet, PDBEntry pdb,... |
4127 |
|
SequenceI[] seqs, String[] chains, DataSourceType protocol) |
4128 |
|
{ |
4129 |
|
|
4130 |
0 |
Object[] sqch = cleanSeqChainArrays(seqs, chains); |
4131 |
0 |
seqs = (SequenceI[]) sqch[0]; |
4132 |
0 |
chains = (String[]) sqch[1]; |
4133 |
0 |
if (seqs == null || seqs.length == 0) |
4134 |
|
{ |
4135 |
0 |
jalview.bin.Console.errPrintln( |
4136 |
|
"JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); |
4137 |
|
} |
4138 |
0 |
if (protocol == null) |
4139 |
|
{ |
4140 |
0 |
String sourceType = (String) pdb.getProperty("protocol"); |
4141 |
0 |
try |
4142 |
|
{ |
4143 |
0 |
protocol = DataSourceType.valueOf(sourceType); |
4144 |
|
} catch (IllegalArgumentException e) |
4145 |
|
{ |
4146 |
|
|
4147 |
|
} |
4148 |
0 |
if (protocol == null) |
4149 |
|
{ |
4150 |
0 |
jalview.bin.Console |
4151 |
|
.errPrintln("Couldn't work out protocol to open structure: " |
4152 |
|
+ pdb.getId()); |
4153 |
0 |
return; |
4154 |
|
} |
4155 |
|
} |
4156 |
0 |
if (applet.useXtrnalSviewer) |
4157 |
|
{ |
4158 |
|
|
4159 |
0 |
if (StructureSelectionManager.getStructureSelectionManager(applet) |
4160 |
|
.setMapping(seqs, chains, pdb.getFile(), protocol, |
4161 |
|
null) == null) |
4162 |
|
{ |
4163 |
0 |
jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() |
4164 |
|
+ " (" + protocol + ") to any sequences"); |
4165 |
|
} |
4166 |
0 |
return; |
4167 |
|
} |
4168 |
0 |
if (applet.isAlignPdbStructures() && applet.jmolAvailable) |
4169 |
|
{ |
4170 |
|
|
4171 |
|
|
4172 |
0 |
AppletJmol ajm = null, tajm; |
4173 |
0 |
Vector jmols = applet.getAppletWindow(AppletJmol.class); |
4174 |
0 |
for (int i = 0, iSize = jmols.size(); i < iSize; i++) |
4175 |
|
{ |
4176 |
0 |
tajm = (AppletJmol) jmols.elementAt(i); |
4177 |
0 |
if (tajm.ap.alignFrame == this) |
4178 |
|
{ |
4179 |
0 |
ajm = tajm; |
4180 |
0 |
break; |
4181 |
|
} |
4182 |
|
} |
4183 |
0 |
if (ajm != null) |
4184 |
|
{ |
4185 |
0 |
jalview.bin.Console.errPrintln( |
4186 |
|
"Incremental adding and aligning structure to existing Jmol view not yet implemented."); |
4187 |
|
|
4188 |
|
|
4189 |
0 |
ajm = null; |
4190 |
|
} |
4191 |
|
} |
4192 |
|
|
4193 |
0 |
if (applet.jmolAvailable) |
4194 |
|
{ |
4195 |
0 |
new AppletJmol(pdb, seqs, chains, alignPanel, protocol); |
4196 |
0 |
applet.lastFrameX += 40; |
4197 |
0 |
applet.lastFrameY += 40; |
4198 |
|
} |
4199 |
|
else |
4200 |
|
{ |
4201 |
0 |
new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); |
4202 |
|
} |
4203 |
|
|
4204 |
|
} |
4205 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4206 |
0 |
public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,... |
4207 |
|
SequenceI[][] seqs, String[][] chains, String[] protocols) |
4208 |
|
{ |
4209 |
|
|
4210 |
0 |
jalview.bin.Console |
4211 |
|
.errPrintln("Aligned Structure View: Not yet implemented."); |
4212 |
|
} |
4213 |
|
|
4214 |
|
|
4215 |
|
|
4216 |
|
|
4217 |
|
|
4218 |
|
@param |
4219 |
|
|
4220 |
|
@param |
4221 |
|
|
4222 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4223 |
0 |
public void select(SequenceGroup sel, ColumnSelection csel,... |
4224 |
|
HiddenColumns hidden) |
4225 |
|
{ |
4226 |
0 |
alignPanel.seqPanel.selection(sel, csel, hidden, null); |
4227 |
|
} |
4228 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4229 |
0 |
public void scrollTo(int row, int column)... |
4230 |
|
{ |
4231 |
0 |
alignPanel.seqPanel.scrollTo(row, column); |
4232 |
|
} |
4233 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4234 |
0 |
public void scrollToRow(int row)... |
4235 |
|
{ |
4236 |
0 |
alignPanel.seqPanel.scrollToRow(row); |
4237 |
|
} |
4238 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4239 |
0 |
public void scrollToColumn(int column)... |
4240 |
|
{ |
4241 |
0 |
alignPanel.seqPanel.scrollToColumn(column); |
4242 |
|
} |
4243 |
|
|
4244 |
|
|
4245 |
|
@return |
4246 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4247 |
0 |
public String getSequenceSetId()... |
4248 |
|
{ |
4249 |
0 |
return viewport.getSequenceSetId(); |
4250 |
|
} |
4251 |
|
|
4252 |
|
|
4253 |
|
|
4254 |
|
|
4255 |
|
@param |
4256 |
|
|
4257 |
|
@throws |
4258 |
|
@return |
4259 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 7 |
Complexity Density: 0.41 |
|
4260 |
0 |
public boolean loadScoreFile(String source) throws IOException... |
4261 |
|
{ |
4262 |
|
|
4263 |
0 |
TCoffeeScoreFile file = new TCoffeeScoreFile(source, |
4264 |
|
AppletFormatAdapter.checkProtocol(source)); |
4265 |
0 |
if (!file.isValid()) |
4266 |
|
{ |
4267 |
|
|
4268 |
0 |
jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: " |
4269 |
|
+ file.getWarningMessage()); |
4270 |
0 |
jalview.bin.Console.errPrintln("Origin was:\n" + source); |
4271 |
0 |
return false; |
4272 |
|
} |
4273 |
|
|
4274 |
|
|
4275 |
|
|
4276 |
|
|
4277 |
0 |
AlignmentI aln; |
4278 |
0 |
if ((aln = viewport.getAlignment()) != null |
4279 |
|
&& (aln.getHeight() != file.getHeight() |
4280 |
|
|| aln.getWidth() != file.getWidth())) |
4281 |
|
{ |
4282 |
|
|
4283 |
0 |
jalview.bin.Console.errPrintln( |
4284 |
|
"The scores matrix does not match the alignment dimensions"); |
4285 |
|
|
4286 |
|
} |
4287 |
|
|
4288 |
|
|
4289 |
0 |
if (file.annotateAlignment(alignPanel.getAlignment(), false)) |
4290 |
|
{ |
4291 |
0 |
alignPanel.fontChanged(); |
4292 |
0 |
tcoffeeColour.setEnabled(true); |
4293 |
|
|
4294 |
0 |
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); |
4295 |
0 |
return true; |
4296 |
|
} |
4297 |
|
else |
4298 |
|
{ |
4299 |
0 |
jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:"); |
4300 |
0 |
if (file.getWarningMessage() != null) |
4301 |
|
{ |
4302 |
0 |
jalview.bin.Console.errPrintln(file.getWarningMessage()); |
4303 |
|
} |
4304 |
|
} |
4305 |
0 |
return false; |
4306 |
|
} |
4307 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4308 |
0 |
public SplitFrame getSplitFrame()... |
4309 |
|
{ |
4310 |
0 |
return this.splitFrame; |
4311 |
|
} |
4312 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4313 |
0 |
public void setSplitFrame(SplitFrame sf)... |
4314 |
|
{ |
4315 |
0 |
this.splitFrame = sf; |
4316 |
|
} |
4317 |
|
|
4318 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4319 |
0 |
@Override... |
4320 |
|
public void setShowSeqFeatures(boolean b) |
4321 |
|
{ |
4322 |
|
|
4323 |
0 |
viewport.setShowSequenceFeatures(b); |
4324 |
|
|
4325 |
|
} |
4326 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
4327 |
0 |
@Override... |
4328 |
|
public void setMenusForViewport() |
4329 |
|
{ |
4330 |
|
|
4331 |
|
|
4332 |
|
} |
4333 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
4334 |
0 |
@Override... |
4335 |
|
public void refreshFeatureUI(boolean enableIfNecessary) |
4336 |
|
{ |
4337 |
0 |
if (enableIfNecessary) |
4338 |
|
{ |
4339 |
0 |
sequenceFeatures.setState(true); |
4340 |
0 |
alignPanel.av.setShowSequenceFeatures(true); |
4341 |
|
} |
4342 |
|
} |
4343 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4344 |
0 |
@Override... |
4345 |
|
public FeatureSettingsControllerI getFeatureSettingsUI() |
4346 |
|
{ |
4347 |
0 |
return alignPanel.av.featureSettings; |
4348 |
|
} |
4349 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4350 |
0 |
@Override... |
4351 |
|
public FeatureSettingsControllerI showFeatureSettingsUI() |
4352 |
|
{ |
4353 |
0 |
return new FeatureSettings(alignPanel); |
4354 |
|
} |
4355 |
|
|
4356 |
|
private Rectangle fs_bounds = null; |
4357 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4358 |
0 |
@Override... |
4359 |
|
public void setFeatureSettingsGeometry(Rectangle bounds) |
4360 |
|
{ |
4361 |
0 |
fs_bounds = bounds; |
4362 |
|
} |
4363 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4364 |
0 |
@Override... |
4365 |
|
public Rectangle getFeatureSettingsGeometry() |
4366 |
|
{ |
4367 |
0 |
return fs_bounds; |
4368 |
|
} |
4369 |
|
|
4370 |
|
} |