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package jalview.gui; |
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import jalview.analysis.AlignmentUtils; |
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import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureColourI; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.api.FeaturesDisplayedI; |
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import jalview.api.ViewStyleI; |
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import jalview.bin.Cache; |
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import jalview.commands.CommandI; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SearchResults; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.renderer.ResidueShader; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemeProperty; |
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import jalview.schemes.ResidueColourScheme; |
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import jalview.schemes.UserColourScheme; |
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import jalview.structure.SelectionSource; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.structure.VamsasSource; |
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import jalview.util.ColorUtils; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.AlignmentViewport; |
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import jalview.ws.params.AutoCalcSetting; |
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import java.awt.Container; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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import java.awt.FontMetrics; |
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import java.awt.Rectangle; |
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import java.util.ArrayList; |
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import java.util.Hashtable; |
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import java.util.Iterator; |
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import java.util.List; |
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import javax.swing.JInternalFrame; |
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@author |
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@version |
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| 70.1% |
Uncovered Elements: 126 (422) |
Complexity: 129 |
Complexity Density: 0.49 |
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public class AlignViewport extends AlignmentViewport |
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implements SelectionSource |
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{ |
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Font font; |
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boolean cursorMode = false; |
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boolean antiAlias = false; |
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private Rectangle explodedGeometry = null; |
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private String viewName = null; |
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private boolean gatherViewsHere = false; |
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private AnnotationColumnChooser annotationColumnSelectionState; |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public AlignViewport(AlignmentI al)... |
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{ |
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super(al); |
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init(); |
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} |
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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 AlignViewport(AlignmentI al, String seqsetid)... |
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{ |
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this(al, seqsetid, null); |
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} |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 7 |
Complexity Density: 0.88 |
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public AlignViewport(AlignmentI al, String seqsetid, String viewid)... |
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{ |
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super(al); |
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sequenceSetID = seqsetid; |
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viewId = viewid; |
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if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) |
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{ |
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Cache.log.debug( |
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"Setting viewport's sequence set id : " + sequenceSetID); |
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} |
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if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) |
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{ |
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Cache.log.debug("Setting viewport's view id : " + viewId); |
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} |
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init(); |
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} |
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@param |
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@param |
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| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)... |
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{ |
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super(al); |
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if (hiddenColumns != null) |
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{ |
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al.setHiddenColumns(hiddenColumns); |
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} |
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init(); |
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} |
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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 AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,... |
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String seqsetid) |
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{ |
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this(al, hiddenColumns, seqsetid, null); |
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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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| 87.5% |
Uncovered Elements: 2 (16) |
Complexity: 8 |
Complexity Density: 0.8 |
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public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,... |
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String seqsetid, String viewid) |
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{ |
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super(al); |
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sequenceSetID = seqsetid; |
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viewId = viewid; |
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if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) |
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{ |
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Cache.log.debug( |
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"Setting viewport's sequence set id : " + sequenceSetID); |
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} |
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if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) |
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{ |
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Cache.log.debug("Setting viewport's view id : " + viewId); |
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} |
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if (hiddenColumns != null) |
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{ |
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al.setHiddenColumns(hiddenColumns); |
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} |
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init(); |
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} |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
|
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private void applyViewProperties()... |
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{ |
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antiAlias = Cache.getDefault("ANTI_ALIAS", true); |
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viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); |
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setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); |
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setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); |
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setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); |
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autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); |
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setPadGaps(Cache.getDefault("PAD_GAPS", true)); |
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setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); |
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setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); |
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viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); |
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viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); |
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viewStyle.setShowUnconserved( |
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Cache.getDefault("SHOW_UNCONSERVED", false)); |
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sortByTree = Cache.getDefault("SORT_BY_TREE", false); |
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followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); |
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sortAnnotationsBy = SequenceAnnotationOrder |
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.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, |
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SequenceAnnotationOrder.NONE.name())); |
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showAutocalculatedAbove = Cache |
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.getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); |
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viewStyle.setScaleProteinAsCdna( |
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Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); |
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} |
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| 82.4% |
Uncovered Elements: 9 (51) |
Complexity: 10 |
Complexity Density: 0.29 |
|
238 |
294 |
void init()... |
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{ |
240 |
294 |
applyViewProperties(); |
241 |
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242 |
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String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); |
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294 |
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); |
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String fontSize = Cache.getDefault("FONT_SIZE", "10"); |
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int style = 0; |
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294 |
if (fontStyle.equals("bold")) |
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{ |
250 |
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style = 1; |
251 |
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} |
252 |
294 |
else if (fontStyle.equals("italic")) |
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{ |
254 |
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style = 2; |
255 |
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} |
256 |
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257 |
294 |
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); |
258 |
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259 |
294 |
alignment |
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.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); |
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262 |
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263 |
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264 |
294 |
if (hconsensus == null && !isDataset) |
265 |
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{ |
266 |
294 |
if (!alignment.isNucleotide()) |
267 |
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{ |
268 |
248 |
showConservation = Cache.getDefault("SHOW_CONSERVATION", true); |
269 |
248 |
showQuality = Cache.getDefault("SHOW_QUALITY", true); |
270 |
248 |
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", |
271 |
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false); |
272 |
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} |
273 |
294 |
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", |
274 |
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true); |
275 |
294 |
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); |
276 |
294 |
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", |
277 |
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false); |
278 |
294 |
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); |
279 |
294 |
showConsensus = Cache.getDefault("SHOW_IDENTITY", true); |
280 |
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|
281 |
294 |
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); |
282 |
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} |
283 |
294 |
initAutoAnnotation(); |
284 |
294 |
String colourProperty = alignment.isNucleotide() |
285 |
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? Preferences.DEFAULT_COLOUR_NUC |
286 |
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: Preferences.DEFAULT_COLOUR_PROT; |
287 |
294 |
String schemeName = Cache.getProperty(colourProperty); |
288 |
294 |
if (schemeName == null) |
289 |
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{ |
290 |
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291 |
286 |
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, |
292 |
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ResidueColourScheme.NONE); |
293 |
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} |
294 |
294 |
ColourSchemeI colourScheme = ColourSchemeProperty |
295 |
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.getColourScheme(this, alignment, schemeName); |
296 |
294 |
residueShading = new ResidueShader(colourScheme); |
297 |
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|
298 |
294 |
if (colourScheme instanceof UserColourScheme) |
299 |
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{ |
300 |
0 |
residueShading = new ResidueShader( |
301 |
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UserDefinedColours.loadDefaultColours()); |
302 |
0 |
residueShading.setThreshold(0, isIgnoreGapsConsensus()); |
303 |
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} |
304 |
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|
305 |
294 |
if (residueShading != null) |
306 |
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{ |
307 |
294 |
residueShading.setConsensus(hconsensus); |
308 |
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} |
309 |
294 |
setColourAppliesToAllGroups(true); |
310 |
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} |
311 |
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312 |
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boolean validCharWidth; |
313 |
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314 |
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315 |
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@inheritDoc |
316 |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
317 |
439 |
@Override... |
318 |
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public void setFont(Font f, boolean setGrid) |
319 |
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{ |
320 |
439 |
font = f; |
321 |
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|
322 |
439 |
Container c = new Container(); |
323 |
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|
324 |
439 |
if (setGrid) |
325 |
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{ |
326 |
368 |
FontMetrics fm = c.getFontMetrics(font); |
327 |
368 |
int ww = fm.charWidth('M'); |
328 |
368 |
setCharHeight(fm.getHeight()); |
329 |
368 |
setCharWidth(ww); |
330 |
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} |
331 |
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viewStyle.setFontName(font.getName()); |
332 |
439 |
viewStyle.setFontStyle(font.getStyle()); |
333 |
439 |
viewStyle.setFontSize(font.getSize()); |
334 |
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|
335 |
439 |
validCharWidth = true; |
336 |
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} |
337 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
338 |
71 |
@Override... |
339 |
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public void setViewStyle(ViewStyleI settingsForView) |
340 |
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{ |
341 |
71 |
super.setViewStyle(settingsForView); |
342 |
71 |
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), |
343 |
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viewStyle.getFontSize()), false); |
344 |
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} |
345 |
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346 |
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347 |
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348 |
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349 |
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@return |
350 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
351 |
8015 |
public Font getFont()... |
352 |
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{ |
353 |
8015 |
return font; |
354 |
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} |
355 |
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356 |
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357 |
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358 |
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359 |
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@param |
360 |
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361 |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
362 |
396 |
@Override... |
363 |
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public void setAlignment(AlignmentI align) |
364 |
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{ |
365 |
396 |
replaceMappings(align); |
366 |
396 |
super.setAlignment(align); |
367 |
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} |
368 |
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369 |
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370 |
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371 |
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372 |
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373 |
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@param |
374 |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
375 |
402 |
public void replaceMappings(AlignmentI align)... |
376 |
|
{ |
377 |
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|
378 |
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|
379 |
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|
380 |
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|
381 |
402 |
deregisterMappings(); |
382 |
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383 |
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|
384 |
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385 |
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|
386 |
402 |
if (align != null) |
387 |
|
{ |
388 |
300 |
StructureSelectionManager ssm = StructureSelectionManager |
389 |
|
.getStructureSelectionManager(Desktop.instance); |
390 |
300 |
ssm.registerMappings(align.getCodonFrames()); |
391 |
|
} |
392 |
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393 |
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|
394 |
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|
395 |
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|
396 |
402 |
if (alignment != null && align != null) |
397 |
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{ |
398 |
6 |
alignment.setCodonFrames(align.getCodonFrames()); |
399 |
|
} |
400 |
|
} |
401 |
|
|
|
|
| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
402 |
402 |
protected void deregisterMappings()... |
403 |
|
{ |
404 |
402 |
AlignmentI al = getAlignment(); |
405 |
402 |
if (al != null) |
406 |
|
{ |
407 |
108 |
List<AlignedCodonFrame> mappings = al.getCodonFrames(); |
408 |
108 |
if (mappings != null) |
409 |
|
{ |
410 |
108 |
StructureSelectionManager ssm = StructureSelectionManager |
411 |
|
.getStructureSelectionManager(Desktop.instance); |
412 |
108 |
for (AlignedCodonFrame acf : mappings) |
413 |
|
{ |
414 |
69 |
if (noReferencesTo(acf)) |
415 |
|
{ |
416 |
15 |
ssm.deregisterMapping(acf); |
417 |
|
} |
418 |
|
} |
419 |
|
} |
420 |
|
} |
421 |
|
} |
422 |
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|
423 |
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|
424 |
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|
425 |
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|
426 |
|
@return |
427 |
|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
428 |
32 |
@Override... |
429 |
|
public char getGapCharacter() |
430 |
|
{ |
431 |
32 |
return getAlignment().getGapCharacter(); |
432 |
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} |
433 |
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|
434 |
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|
435 |
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|
436 |
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|
437 |
|
@param |
438 |
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|
439 |
|
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|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
440 |
0 |
public void setGapCharacter(char gap)... |
441 |
|
{ |
442 |
0 |
if (getAlignment() != null) |
443 |
|
{ |
444 |
0 |
getAlignment().setGapCharacter(gap); |
445 |
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} |
446 |
|
} |
447 |
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448 |
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|
449 |
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450 |
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|
451 |
|
@param |
452 |
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|
453 |
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|
454 |
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@return |
455 |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
456 |
1 |
public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)... |
457 |
|
{ |
458 |
1 |
int start = 0; |
459 |
1 |
int end = 0; |
460 |
1 |
if (selectedRegionOnly && selectionGroup != null) |
461 |
|
{ |
462 |
0 |
start = selectionGroup.getStartRes(); |
463 |
0 |
end = selectionGroup.getEndRes() + 1; |
464 |
|
} |
465 |
|
else |
466 |
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{ |
467 |
1 |
end = alignment.getWidth(); |
468 |
|
} |
469 |
1 |
return (alignment.getHiddenColumns().getVisContigsIterator(start, end, |
470 |
|
false)); |
471 |
|
} |
472 |
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|
473 |
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|
474 |
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|
475 |
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|
476 |
|
@return |
477 |
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|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
478 |
1 |
public long[] getUndoRedoHash()... |
479 |
|
{ |
480 |
|
|
481 |
1 |
if (historyList == null || redoList == null) |
482 |
|
{ |
483 |
0 |
return new long[] { -1, -1 }; |
484 |
|
} |
485 |
1 |
return new long[] { historyList.hashCode(), this.redoList.hashCode() }; |
486 |
|
} |
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
@param |
493 |
|
|
494 |
|
@return |
495 |
|
|
496 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 5 |
Complexity Density: 0.56 |
|
497 |
0 |
public boolean isUndoRedoHashModified(long[] undoredo)... |
498 |
|
{ |
499 |
0 |
if (undoredo == null) |
500 |
|
{ |
501 |
0 |
return true; |
502 |
|
} |
503 |
0 |
long[] cstate = getUndoRedoHash(); |
504 |
0 |
if (cstate.length != undoredo.length) |
505 |
|
{ |
506 |
0 |
return true; |
507 |
|
} |
508 |
|
|
509 |
0 |
for (int i = 0; i < cstate.length; i++) |
510 |
|
{ |
511 |
0 |
if (cstate[i] != undoredo[i]) |
512 |
|
{ |
513 |
0 |
return true; |
514 |
|
} |
515 |
|
} |
516 |
0 |
return false; |
517 |
|
} |
518 |
|
|
519 |
|
public boolean followSelection = true; |
520 |
|
|
521 |
|
|
522 |
|
@return |
523 |
|
|
524 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
525 |
0 |
public boolean getFollowSelection()... |
526 |
|
{ |
527 |
0 |
return followSelection; |
528 |
|
} |
529 |
|
|
530 |
|
|
531 |
|
|
532 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
533 |
21 |
@Override... |
534 |
|
public void sendSelection() |
535 |
|
{ |
536 |
21 |
jalview.structure.StructureSelectionManager |
537 |
|
.getStructureSelectionManager(Desktop.instance) |
538 |
|
.sendSelection(new SequenceGroup(getSelectionGroup()), |
539 |
|
new ColumnSelection(getColumnSelection()), |
540 |
|
new HiddenColumns(getAlignment().getHiddenColumns()), |
541 |
|
this); |
542 |
|
} |
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
@param |
549 |
|
@return |
550 |
|
|
551 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
552 |
431 |
public AlignmentPanel getAlignPanel()... |
553 |
|
{ |
554 |
431 |
AlignmentPanel[] aps = PaintRefresher |
555 |
|
.getAssociatedPanels(this.getSequenceSetId()); |
556 |
687 |
for (int p = 0; aps != null && p < aps.length; p++) |
557 |
|
{ |
558 |
451 |
if (aps[p].av == this) |
559 |
|
{ |
560 |
195 |
return aps[p]; |
561 |
|
} |
562 |
|
} |
563 |
236 |
return null; |
564 |
|
} |
565 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
566 |
11 |
public boolean getSortByTree()... |
567 |
|
{ |
568 |
11 |
return sortByTree; |
569 |
|
} |
570 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
571 |
2 |
public void setSortByTree(boolean sort)... |
572 |
|
{ |
573 |
2 |
sortByTree = sort; |
574 |
|
} |
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
579 |
1672 |
@Override... |
580 |
|
public StructureSelectionManager getStructureSelectionManager() |
581 |
|
{ |
582 |
1672 |
return StructureSelectionManager |
583 |
|
.getStructureSelectionManager(Desktop.instance); |
584 |
|
} |
585 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
586 |
1246 |
@Override... |
587 |
|
public boolean isNormaliseSequenceLogo() |
588 |
|
{ |
589 |
1246 |
return normaliseSequenceLogo; |
590 |
|
} |
591 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
592 |
70 |
public void setNormaliseSequenceLogo(boolean state)... |
593 |
|
{ |
594 |
70 |
normaliseSequenceLogo = state; |
595 |
|
} |
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
@return |
600 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
601 |
28735 |
@Override... |
602 |
|
public boolean isValidCharWidth() |
603 |
|
{ |
604 |
28735 |
return validCharWidth; |
605 |
|
} |
606 |
|
|
607 |
|
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>(); |
608 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
609 |
3 |
public AutoCalcSetting getCalcIdSettingsFor(String calcId)... |
610 |
|
{ |
611 |
3 |
return calcIdParams.get(calcId); |
612 |
|
} |
613 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
614 |
0 |
public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,... |
615 |
|
boolean needsUpdate) |
616 |
|
{ |
617 |
0 |
calcIdParams.put(calcId, settings); |
618 |
|
|
619 |
|
|
620 |
|
|
621 |
0 |
if (needsUpdate) |
622 |
|
{ |
623 |
0 |
Cache.log.debug("trigger update for " + calcId); |
624 |
|
} |
625 |
|
} |
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
@param |
642 |
|
@param |
643 |
|
@param |
644 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
|
645 |
0 |
@Override... |
646 |
|
public void mirrorCommand(CommandI command, boolean undo, |
647 |
|
StructureSelectionManager ssm, VamsasSource source) |
648 |
|
{ |
649 |
|
|
650 |
|
|
651 |
|
|
652 |
|
|
653 |
0 |
if (source instanceof AlignViewportI |
654 |
|
&& ((AlignViewportI) source).getCodingComplement() == this) |
655 |
|
{ |
656 |
|
|
657 |
|
} |
658 |
|
else |
659 |
|
{ |
660 |
0 |
return; |
661 |
|
} |
662 |
|
|
663 |
0 |
CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(), |
664 |
|
getGapCharacter()); |
665 |
0 |
if (mappedCommand != null) |
666 |
|
{ |
667 |
0 |
AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments(); |
668 |
0 |
mappedCommand.doCommand(views); |
669 |
0 |
getAlignPanel().alignmentChanged(); |
670 |
|
} |
671 |
|
} |
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
@param |
679 |
|
@param |
680 |
|
|
|
|
| 63.6% |
Uncovered Elements: 4 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
681 |
1 |
public void addAlignment(AlignmentI toAdd, String title)... |
682 |
|
{ |
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
|
691 |
|
|
692 |
|
|
693 |
|
|
694 |
|
|
695 |
|
|
696 |
|
|
697 |
1 |
toAdd.setDataset(null); |
698 |
|
|
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
1 |
getAlignment().realiseMappings(toAdd.getSequences()); |
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
|
709 |
1 |
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) |
710 |
|
{ |
711 |
1 |
if (AlignmentUtils.isMappable(toAdd, getAlignment())) |
712 |
|
{ |
713 |
0 |
openLinkedAlignment(toAdd, title); |
714 |
0 |
return; |
715 |
|
} |
716 |
|
} |
717 |
1 |
addDataToAlignment(toAdd); |
718 |
|
} |
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
|
@param |
724 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
725 |
1 |
void addDataToAlignment(AlignmentI toAdd)... |
726 |
|
{ |
727 |
|
|
728 |
|
|
729 |
|
|
730 |
1 |
AlignmentI al = getAlignment(); |
731 |
1 |
String gap = String.valueOf(al.getGapCharacter()); |
732 |
5 |
for (int i = 0; i < toAdd.getHeight(); i++) |
733 |
|
{ |
734 |
4 |
SequenceI seq = toAdd.getSequenceAt(i); |
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
|
742 |
4 |
if (true ) |
743 |
|
{ |
744 |
4 |
al.addSequence(seq); |
745 |
|
} |
746 |
|
} |
747 |
|
|
748 |
1 |
ranges.setEndSeq(getAlignment().getHeight() - 1); |
749 |
1 |
firePropertyChange("alignment", null, getAlignment().getSequences()); |
750 |
|
} |
751 |
|
|
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
@param |
759 |
|
@param |
760 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
761 |
0 |
protected void openLinkedAlignment(AlignmentI al, String title)... |
762 |
|
{ |
763 |
0 |
String[] options = new String[] { MessageManager.getString("action.no"), |
764 |
|
MessageManager.getString("label.split_window"), |
765 |
|
MessageManager.getString("label.new_window"), }; |
766 |
0 |
final String question = JvSwingUtils.wrapTooltip(true, |
767 |
|
MessageManager.getString("label.open_split_window?")); |
768 |
0 |
final AlignViewport us = this; |
769 |
|
|
770 |
|
|
771 |
|
|
772 |
|
|
773 |
|
|
774 |
|
|
775 |
0 |
JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop) |
776 |
|
.setResponseHandler(0, new Runnable() |
777 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
778 |
0 |
@Override... |
779 |
|
public void run() |
780 |
|
{ |
781 |
0 |
addDataToAlignment(al); |
782 |
|
} |
783 |
|
}).setResponseHandler(1, new Runnable() |
784 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
785 |
0 |
@Override... |
786 |
|
public void run() |
787 |
|
{ |
788 |
0 |
us.openLinkedAlignmentAs(al, title, true); |
789 |
|
} |
790 |
|
}).setResponseHandler(2, new Runnable() |
791 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
792 |
0 |
@Override... |
793 |
|
public void run() |
794 |
|
{ |
795 |
0 |
us.openLinkedAlignmentAs(al, title, false); |
796 |
|
} |
797 |
|
}); |
798 |
0 |
dialog.showDialog(question, |
799 |
|
MessageManager.getString("label.open_split_window"), |
800 |
|
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, |
801 |
|
options, options[0]); |
802 |
|
} |
803 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 7 |
Complexity Density: 0.47 |
|
804 |
0 |
protected void openLinkedAlignmentAs(AlignmentI al, String title,... |
805 |
|
boolean newWindowOrSplitPane) |
806 |
|
{ |
807 |
|
|
808 |
|
|
809 |
|
|
810 |
|
|
811 |
0 |
AlignmentI thisAlignment = newWindowOrSplitPane |
812 |
|
? new Alignment(getAlignment()) |
813 |
|
: getAlignment(); |
814 |
0 |
AlignmentI protein = al.isNucleotide() ? thisAlignment : al; |
815 |
0 |
final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; |
816 |
|
|
817 |
|
|
818 |
|
|
819 |
|
|
820 |
|
|
821 |
|
|
822 |
|
|
823 |
0 |
al.setDataset(null); |
824 |
0 |
AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna); |
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
|
829 |
|
|
830 |
0 |
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, |
831 |
|
AlignFrame.DEFAULT_HEIGHT); |
832 |
0 |
newAlignFrame.setTitle(title); |
833 |
0 |
newAlignFrame.setStatus(MessageManager |
834 |
|
.formatMessage("label.successfully_loaded_file", new Object[] |
835 |
|
{ title })); |
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
|
840 |
|
|
841 |
|
|
842 |
|
|
843 |
|
|
844 |
0 |
if (!newWindowOrSplitPane) |
845 |
|
{ |
846 |
0 |
Desktop.addInternalFrame(newAlignFrame, title, |
847 |
|
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
848 |
|
} |
849 |
|
|
850 |
0 |
try |
851 |
|
{ |
852 |
0 |
newAlignFrame.setMaximum( |
853 |
|
jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); |
854 |
|
} catch (java.beans.PropertyVetoException ex) |
855 |
|
{ |
856 |
|
} |
857 |
|
|
858 |
0 |
if (newWindowOrSplitPane) |
859 |
|
{ |
860 |
0 |
al.alignAs(thisAlignment); |
861 |
0 |
protein = openSplitFrame(newAlignFrame, thisAlignment); |
862 |
|
} |
863 |
|
} |
864 |
|
|
865 |
|
|
866 |
|
|
867 |
|
|
868 |
|
|
869 |
|
@param |
870 |
|
|
871 |
|
@param |
872 |
|
|
873 |
|
@return |
874 |
|
|
|
|
| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
875 |
1 |
protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,... |
876 |
|
AlignmentI complement) |
877 |
|
{ |
878 |
|
|
879 |
|
|
880 |
|
|
881 |
|
|
882 |
|
|
883 |
1 |
AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, |
884 |
|
AlignFrame.DEFAULT_HEIGHT); |
885 |
1 |
copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); |
886 |
|
|
887 |
1 |
AlignmentI al = newAlignFrame.viewport.getAlignment(); |
888 |
1 |
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe |
889 |
|
: newAlignFrame; |
890 |
1 |
final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe; |
891 |
1 |
cdnaFrame.setVisible(true); |
892 |
1 |
proteinFrame.setVisible(true); |
893 |
1 |
String linkedTitle = MessageManager |
894 |
|
.getString("label.linked_view_title"); |
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
|
899 |
1 |
JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); |
900 |
1 |
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); |
901 |
|
|
902 |
1 |
return proteinFrame.viewport.getAlignment(); |
903 |
|
} |
904 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
905 |
7 |
public AnnotationColumnChooser getAnnotationColumnSelectionState()... |
906 |
|
{ |
907 |
7 |
return annotationColumnSelectionState; |
908 |
|
} |
909 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
910 |
1 |
public void setAnnotationColumnSelectionState(... |
911 |
|
AnnotationColumnChooser currentAnnotationColumnSelectionState) |
912 |
|
{ |
913 |
1 |
this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; |
914 |
|
} |
915 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
916 |
247 |
@Override... |
917 |
|
public void setIdWidth(int i) |
918 |
|
{ |
919 |
247 |
super.setIdWidth(i); |
920 |
247 |
AlignmentPanel ap = getAlignPanel(); |
921 |
247 |
if (ap != null) |
922 |
|
{ |
923 |
|
|
924 |
11 |
Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize(); |
925 |
11 |
idw.width = i; |
926 |
11 |
ap.getIdPanel().getIdCanvas().setPreferredSize(idw); |
927 |
|
} |
928 |
|
} |
929 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
930 |
34 |
public Rectangle getExplodedGeometry()... |
931 |
|
{ |
932 |
34 |
return explodedGeometry; |
933 |
|
} |
934 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
935 |
49 |
public void setExplodedGeometry(Rectangle explodedPosition)... |
936 |
|
{ |
937 |
49 |
this.explodedGeometry = explodedPosition; |
938 |
|
} |
939 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
940 |
93 |
public boolean isGatherViewsHere()... |
941 |
|
{ |
942 |
93 |
return gatherViewsHere; |
943 |
|
} |
944 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
945 |
135 |
public void setGatherViewsHere(boolean gatherViewsHere)... |
946 |
|
{ |
947 |
135 |
this.gatherViewsHere = gatherViewsHere; |
948 |
|
} |
949 |
|
|
950 |
|
|
951 |
|
|
952 |
|
|
953 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
954 |
402 |
public void scrollComplementaryAlignment()... |
955 |
|
{ |
956 |
|
|
957 |
|
|
958 |
|
|
959 |
|
|
960 |
|
|
961 |
402 |
SearchResultsI sr = new SearchResults(); |
962 |
402 |
int verticalOffset = findComplementScrollTarget(sr); |
963 |
402 |
if (!sr.isEmpty()) |
964 |
|
{ |
965 |
|
|
966 |
4 |
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) |
967 |
|
.getAlignPanel(); |
968 |
4 |
complementPanel.setToScrollComplementPanel(false); |
969 |
4 |
complementPanel.scrollToCentre(sr, verticalOffset); |
970 |
4 |
complementPanel.setToScrollComplementPanel(true); |
971 |
|
} |
972 |
|
} |
973 |
|
|
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
@param |
978 |
|
@return |
979 |
|
|
|
|
| 93.8% |
Uncovered Elements: 1 (16) |
Complexity: 5 |
Complexity Density: 0.5 |
|
980 |
69 |
protected boolean noReferencesTo(AlignedCodonFrame acf)... |
981 |
|
{ |
982 |
69 |
AlignFrame[] frames = Desktop.getAlignFrames(); |
983 |
69 |
if (frames == null) |
984 |
|
{ |
985 |
12 |
return true; |
986 |
|
} |
987 |
57 |
for (AlignFrame af : frames) |
988 |
|
{ |
989 |
64 |
if (!af.isClosed()) |
990 |
|
{ |
991 |
64 |
for (AlignmentViewPanel ap : af.getAlignPanels()) |
992 |
|
{ |
993 |
64 |
AlignmentI al = ap.getAlignment(); |
994 |
64 |
if (al != null && al.getCodonFrames().contains(acf)) |
995 |
|
{ |
996 |
54 |
return false; |
997 |
|
} |
998 |
|
} |
999 |
|
} |
1000 |
|
} |
1001 |
3 |
return true; |
1002 |
|
} |
1003 |
|
|
1004 |
|
|
1005 |
|
|
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
|
|
1010 |
|
@param |
1011 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1012 |
17 |
@Override... |
1013 |
|
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings) |
1014 |
|
{ |
1015 |
17 |
transferFeaturesStyles(featureSettings, false); |
1016 |
|
} |
1017 |
|
|
1018 |
|
|
1019 |
|
|
1020 |
|
|
1021 |
|
|
1022 |
|
|
1023 |
|
|
1024 |
|
@param |
1025 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1026 |
2 |
@Override... |
1027 |
|
public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings) |
1028 |
|
{ |
1029 |
2 |
transferFeaturesStyles(featureSettings, true); |
1030 |
|
} |
1031 |
|
|
1032 |
|
|
1033 |
|
|
1034 |
|
|
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
@param |
1039 |
|
@param |
1040 |
|
|
|
|
| 92.3% |
Uncovered Elements: 3 (39) |
Complexity: 14 |
Complexity Density: 0.56 |
|
1041 |
19 |
private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,... |
1042 |
|
boolean mergeOnly) |
1043 |
|
{ |
1044 |
19 |
if (featureSettings == null) |
1045 |
|
{ |
1046 |
0 |
return; |
1047 |
|
} |
1048 |
|
|
1049 |
19 |
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas |
1050 |
|
.getFeatureRenderer(); |
1051 |
19 |
List<String> origRenderOrder = new ArrayList(), |
1052 |
|
origGroups = new ArrayList(); |
1053 |
|
|
1054 |
19 |
origRenderOrder.addAll(fr.getRenderOrder()); |
1055 |
19 |
origGroups.addAll(fr.getFeatureGroups()); |
1056 |
|
|
1057 |
19 |
fr.findAllFeatures(true); |
1058 |
19 |
List<String> renderOrder = fr.getRenderOrder(); |
1059 |
19 |
FeaturesDisplayedI displayed = fr.getFeaturesDisplayed(); |
1060 |
19 |
if (!mergeOnly) |
1061 |
|
{ |
1062 |
|
|
1063 |
17 |
displayed.clear(); |
1064 |
|
} |
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
|
1069 |
|
|
1070 |
|
|
1071 |
|
|
1072 |
|
|
1073 |
19 |
for (String type : renderOrder) |
1074 |
|
{ |
1075 |
33 |
FeatureColourI preferredColour = featureSettings |
1076 |
|
.getFeatureColour(type); |
1077 |
33 |
FeatureColourI origColour = fr.getFeatureStyle(type); |
1078 |
33 |
if (!mergeOnly || (!origRenderOrder.contains(type) |
1079 |
|
|| origColour == null |
1080 |
|
|| (!origColour.isGraduatedColour() |
1081 |
|
&& origColour.getColour() != null |
1082 |
|
&& origColour.getColour().equals( |
1083 |
|
ColorUtils.createColourFromName(type))))) |
1084 |
|
{ |
1085 |
|
|
1086 |
|
|
1087 |
29 |
if (preferredColour != null) |
1088 |
|
{ |
1089 |
12 |
fr.setColour(type, preferredColour); |
1090 |
|
} |
1091 |
29 |
if (featureSettings.isFeatureDisplayed(type)) |
1092 |
|
{ |
1093 |
25 |
displayed.setVisible(type); |
1094 |
|
} |
1095 |
|
} |
1096 |
|
} |
1097 |
|
|
1098 |
|
|
1099 |
|
|
1100 |
|
|
1101 |
19 |
for (String group : fr.getFeatureGroups()) |
1102 |
|
{ |
1103 |
37 |
if (!mergeOnly || !origGroups.contains(group)) |
1104 |
|
{ |
1105 |
|
|
1106 |
29 |
fr.setGroupVisibility(group, |
1107 |
|
featureSettings.isGroupDisplayed(group)); |
1108 |
|
} |
1109 |
|
} |
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
|
|
1114 |
19 |
if (featureSettings.optimiseOrder()) |
1115 |
|
{ |
1116 |
|
|
1117 |
|
} |
1118 |
|
else |
1119 |
|
{ |
1120 |
19 |
fr.orderFeatures(featureSettings); |
1121 |
|
} |
1122 |
19 |
fr.setTransparency(featureSettings.getTransparency()); |
1123 |
|
} |
1124 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1125 |
1521 |
public String getViewName()... |
1126 |
|
{ |
1127 |
1521 |
return viewName; |
1128 |
|
} |
1129 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1130 |
66 |
public void setViewName(String viewName)... |
1131 |
|
{ |
1132 |
66 |
this.viewName = viewName; |
1133 |
|
} |
1134 |
|
} |