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package jalview.gui; |
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import jalview.analysis.Conservation; |
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import jalview.binding.Annotation; |
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import jalview.binding.AnnotationElement; |
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import jalview.binding.Features; |
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import jalview.binding.JGroup; |
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import jalview.binding.JSeq; |
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import jalview.binding.JalviewModel; |
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import jalview.binding.JalviewModelSequence; |
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import jalview.binding.Pdbids; |
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import jalview.binding.Sequence; |
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import jalview.binding.SequenceSet; |
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import jalview.binding.Setting; |
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import jalview.binding.Tree; |
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import jalview.binding.UserColours; |
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import jalview.binding.Viewport; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.io.FileFormat; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemeProperty; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.MessageManager; |
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import jalview.util.jarInputStreamProvider; |
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import jalview.viewmodel.seqfeatures.FeatureRendererSettings; |
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import java.io.InputStreamReader; |
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import java.io.Reader; |
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import java.net.UnknownHostException; |
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import java.util.Hashtable; |
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import java.util.Vector; |
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import java.util.jar.JarEntry; |
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import java.util.jar.JarInputStream; |
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@author |
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@version |
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| 0% |
Uncovered Elements: 255 (255) |
Complexity: 49 |
Complexity Density: 0.28 |
|
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public class Jalview2XML_V1 |
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{ |
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boolean raiseGUI = true; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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public Jalview2XML_V1()... |
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{ |
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|
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}; |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public Jalview2XML_V1(boolean raiseGUI)... |
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{ |
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this.raiseGUI = raiseGUI; |
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}; |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
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jalview.schemes.UserColourScheme GetUserColourScheme(... |
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JalviewModelSequence jms, String id) |
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{ |
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UserColours[] uc = jms.getUserColours(); |
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UserColours colours = null; |
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for (int i = 0; i < uc.length; i++) |
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{ |
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if (uc[i].getId().equals(id)) |
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{ |
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colours = uc[i]; |
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|
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break; |
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} |
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} |
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int csize = colours.getUserColourScheme().getColourCount(); |
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java.awt.Color[] newColours = new java.awt.Color[csize]; |
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|
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for (int i = 0; i < csize; i++) |
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{ |
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newColours[i] = new java.awt.Color(Integer.parseInt( |
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colours.getUserColourScheme().getColour(i).getRGB(), 16)); |
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} |
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return new jalview.schemes.UserColourScheme(newColours); |
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} |
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@param |
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| 0% |
Uncovered Elements: 39 (39) |
Complexity: 9 |
Complexity Density: 0.33 |
|
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public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)... |
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{ |
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final String file = jprovider.getFilename(); |
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jalview.gui.AlignFrame af = null; |
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try |
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{ |
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JarInputStream jin = null; |
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JarEntry jarentry = null; |
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int entryCount = 1; |
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do |
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{ |
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jin = jprovider.getJarInputStream(); |
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for (int i = 0; i < entryCount; i++) |
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{ |
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jarentry = jin.getNextJarEntry(); |
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} |
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if (jarentry != null) |
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{ |
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entryCount++; |
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if (jarentry.getName().endsWith(".xml")) |
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{ |
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Reader in = new InputStreamReader(jin, "UTF-8"); |
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JalviewModel object = new JalviewModel(); |
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object = object.unmarshal(in); |
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af = LoadFromObject(object, file); |
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} |
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} |
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jin.close(); |
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} while (jarentry != null); |
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} catch (final UnknownHostException ex) |
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{ |
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ex.printStackTrace(); |
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if (raiseGUI) |
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{ |
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javax.swing.SwingUtilities.invokeLater(new Runnable() |
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{ |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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@Override... |
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public void run() |
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{ |
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|
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System.err.println( |
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"Couldn't locate Jalview XML file : " + ex + "\n"); |
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JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
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MessageManager.formatMessage("label.couldnt_locate", |
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new String[] |
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{ file }), |
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MessageManager.getString("label.url_not_found"), |
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JvOptionPane.WARNING_MESSAGE); |
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} |
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}); |
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} |
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; |
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} catch (Exception ex) |
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{ |
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System.err.println("Exception whilst loading jalview XML file : "); |
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ex.printStackTrace(); |
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if (raiseGUI) |
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{ |
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javax.swing.SwingUtilities.invokeLater(new Runnable() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public void run() |
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{ |
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|
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JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
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MessageManager.formatMessage( |
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"label.error_loading_file_params", new String[] |
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{ file }), |
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MessageManager |
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.getString("label.error_loading_jalview_file"), |
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JvOptionPane.WARNING_MESSAGE); |
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} |
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}); |
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} |
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} |
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|
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return af; |
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} |
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| 0% |
Uncovered Elements: 188 (188) |
Complexity: 32 |
Complexity Density: 0.25 |
|
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AlignFrame LoadFromObject(JalviewModel object, String file)... |
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{ |
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Vector seqids = new Vector(); |
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SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); |
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Sequence[] vamsasSeq = vamsasSet.getSequence(); |
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JalviewModelSequence jms = object.getJalviewModelSequence(); |
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jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length]; |
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JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); |
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for (int i = 0; i < vamsasSeq.length; i++) |
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{ |
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jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), |
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vamsasSeq[i].getSequence()); |
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jseqs[i].setStart(JSEQ[i].getStart()); |
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jseqs[i].setEnd(JSEQ[i].getEnd()); |
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seqids.add(jseqs[i]); |
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} |
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jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); |
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al.setDataset(null); |
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for (int i = 0; i < vamsasSeq.length; i++) |
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{ |
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if (JSEQ[i].getFeaturesCount() > 0) |
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{ |
227 |
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Features[] features = JSEQ[i].getFeatures(); |
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for (int f = 0; f < features.length; f++) |
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{ |
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SequenceFeature sf = new SequenceFeature(features[f].getType(), |
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features[f].getDescription(), features[f].getBegin(), |
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features[f].getEnd(), null); |
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sf.setStatus(features[f].getStatus()); |
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al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); |
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} |
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} |
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if (JSEQ[i].getPdbidsCount() > 0) |
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{ |
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Pdbids[] ids = JSEQ[i].getPdbids(); |
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for (int p = 0; p < ids.length; p++) |
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{ |
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jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); |
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entry.setId(ids[p].getId()); |
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if (ids[p].getType() != null) |
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{ |
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if (ids[p].getType().equalsIgnoreCase("PDB")) |
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{ |
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entry.setType(PDBEntry.Type.PDB); |
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} |
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else |
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{ |
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entry.setType(PDBEntry.Type.FILE); |
253 |
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} |
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} |
255 |
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al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); |
256 |
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StructureSelectionManager |
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.getStructureSelectionManager(Desktop.instance) |
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.registerPDBEntry(entry); |
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} |
260 |
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} |
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} |
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266 |
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267 |
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if (vamsasSet.getAnnotation() != null) |
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{ |
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Annotation[] an = vamsasSet.getAnnotation(); |
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271 |
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for (int i = 0; i < an.length; i++) |
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{ |
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AnnotationElement[] ae = an[i].getAnnotationElement(); |
274 |
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jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al |
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.getWidth()]; |
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|
277 |
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for (int aa = 0; aa < ae.length; aa++) |
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{ |
279 |
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anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( |
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ae[aa].getDisplayCharacter(), ae[aa].getDescription(), |
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ae[aa].getSecondaryStructure().charAt(0), |
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ae[aa].getValue()); |
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} |
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|
285 |
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jalview.datamodel.AlignmentAnnotation jaa = null; |
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|
287 |
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if (an[i].getGraph()) |
288 |
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{ |
289 |
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jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), |
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an[i].getDescription(), anot, 0, 0, |
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jalview.datamodel.AlignmentAnnotation.BAR_GRAPH); |
292 |
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} |
293 |
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else |
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{ |
295 |
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jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), |
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an[i].getDescription(), anot); |
297 |
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} |
298 |
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|
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al.addAnnotation(jaa); |
300 |
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} |
301 |
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} |
302 |
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305 |
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Viewport[] views = jms.getViewport(); |
306 |
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Viewport view = views[0]; |
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|
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AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); |
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|
310 |
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af.setFileName(file, FileFormat.Jalview); |
311 |
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312 |
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for (int i = 0; i < JSEQ.length; i++) |
313 |
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{ |
314 |
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af.viewport.setSequenceColour( |
315 |
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af.viewport.getAlignment().getSequenceAt(i), |
316 |
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new java.awt.Color(JSEQ[i].getColour())); |
317 |
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} |
318 |
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319 |
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320 |
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321 |
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|
322 |
0 |
if (jms.getJGroupCount() > 0) |
323 |
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{ |
324 |
0 |
JGroup[] groups = jms.getJGroup(); |
325 |
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|
326 |
0 |
for (int i = 0; i < groups.length; i++) |
327 |
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{ |
328 |
0 |
ColourSchemeI cs = null; |
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330 |
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if (groups[i].getColour() != null) |
331 |
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{ |
332 |
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if (groups[i].getColour().startsWith("ucs")) |
333 |
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{ |
334 |
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cs = GetUserColourScheme(jms, groups[i].getColour()); |
335 |
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} |
336 |
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else |
337 |
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{ |
338 |
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cs = ColourSchemeProperty.getColourScheme(al, |
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groups[i].getColour()); |
340 |
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} |
341 |
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} |
342 |
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int pidThreshold = groups[i].getPidThreshold(); |
343 |
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|
344 |
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Vector seqs = new Vector(); |
345 |
0 |
int[] ids = groups[i].getSeq(); |
346 |
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|
347 |
0 |
for (int s = 0; s < ids.length; s++) |
348 |
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{ |
349 |
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seqs.addElement(seqids.elementAt(ids[s])); |
350 |
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} |
351 |
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|
352 |
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jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( |
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seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), |
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groups[i].getDisplayText(), groups[i].getColourText(), |
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groups[i].getStart(), groups[i].getEnd()); |
356 |
0 |
sg.getGroupColourScheme().setThreshold(pidThreshold, true); |
357 |
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|
358 |
0 |
sg.setOutlineColour( |
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new java.awt.Color(groups[i].getOutlineColour())); |
360 |
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|
361 |
0 |
if (groups[i].getConsThreshold() != 0) |
362 |
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{ |
363 |
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Conservation c = new Conservation("All", sg.getSequences(null), 0, |
364 |
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sg.getWidth() - 1); |
365 |
0 |
c.calculate(); |
366 |
0 |
c.verdict(false, 25); |
367 |
0 |
sg.cs.setConservation(c); |
368 |
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} |
369 |
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|
370 |
0 |
al.addGroup(sg); |
371 |
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} |
372 |
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} |
373 |
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|
374 |
0 |
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), |
375 |
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view.getHeight()); |
376 |
0 |
af.viewport.getRanges().setStartRes(view.getStartRes()); |
377 |
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|
378 |
0 |
af.viewport.setShowAnnotation(view.getShowAnnotation()); |
379 |
0 |
af.viewport.setAbovePIDThreshold(view.getPidSelected()); |
380 |
0 |
af.viewport.setColourText(view.getShowColourText()); |
381 |
0 |
af.viewport.setConservationSelected(view.getConservationSelected()); |
382 |
0 |
af.viewport.setShowJVSuffix(view.getShowFullId()); |
383 |
0 |
af.viewport.setFont(new java.awt.Font(view.getFontName(), |
384 |
|
view.getFontStyle(), view.getFontSize()), true); |
385 |
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|
386 |
0 |
af.viewport.setRenderGaps(view.getRenderGaps()); |
387 |
0 |
af.viewport.setWrapAlignment(view.getWrapAlignment()); |
388 |
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|
389 |
0 |
af.viewport.setShowAnnotation(view.isShowAnnotation()); |
390 |
0 |
af.viewport.setShowBoxes(view.getShowBoxes()); |
391 |
0 |
af.viewport.setShowText(view.getShowText()); |
392 |
|
|
393 |
0 |
ColourSchemeI cs = null; |
394 |
|
|
395 |
0 |
if (view.getBgColour() != null) |
396 |
|
{ |
397 |
0 |
if (view.getBgColour().startsWith("ucs")) |
398 |
|
{ |
399 |
0 |
cs = GetUserColourScheme(jms, view.getBgColour()); |
400 |
|
} |
401 |
|
else |
402 |
|
{ |
403 |
0 |
cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); |
404 |
|
} |
405 |
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|
406 |
|
|
407 |
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|
408 |
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|
409 |
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|
410 |
|
|
411 |
|
} |
412 |
|
|
413 |
0 |
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(), |
414 |
|
true); |
415 |
0 |
af.viewport.getResidueShading() |
416 |
|
.setConsensus(af.viewport.getSequenceConsensusHash()); |
417 |
0 |
af.viewport.setColourAppliesToAllGroups(false); |
418 |
0 |
af.alignPanel.updateLayout(); |
419 |
0 |
af.changeColour(cs); |
420 |
0 |
if (view.getConservationSelected() && cs != null) |
421 |
|
{ |
422 |
0 |
af.viewport.getResidueShading() |
423 |
|
.setConservationInc(view.getConsThreshold()); |
424 |
|
} |
425 |
|
|
426 |
0 |
af.viewport.setColourAppliesToAllGroups(true); |
427 |
0 |
af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures()); |
428 |
|
|
429 |
0 |
if (jms.getFeatureSettings() != null) |
430 |
|
{ |
431 |
0 |
Hashtable featuresDisplayed = new Hashtable(); |
432 |
0 |
Hashtable featureColours = new Hashtable(); |
433 |
0 |
String[] renderOrder = new String[jms.getFeatureSettings() |
434 |
|
.getSettingCount()]; |
435 |
0 |
for (int fs = 0; fs < jms.getFeatureSettings() |
436 |
|
.getSettingCount(); fs++) |
437 |
|
{ |
438 |
0 |
Setting setting = jms.getFeatureSettings().getSetting(fs); |
439 |
|
|
440 |
0 |
featureColours.put(setting.getType(), |
441 |
|
new java.awt.Color(setting.getColour())); |
442 |
|
|
443 |
0 |
renderOrder[fs] = setting.getType(); |
444 |
|
|
445 |
0 |
if (setting.getDisplay()) |
446 |
|
{ |
447 |
0 |
featuresDisplayed.put(setting.getType(), |
448 |
|
new Integer(setting.getColour())); |
449 |
|
} |
450 |
|
} |
451 |
0 |
FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, |
452 |
|
new Hashtable(), featureColours, 1.0f, null); |
453 |
0 |
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() |
454 |
|
.transferSettings(frs); |
455 |
|
} |
456 |
|
|
457 |
0 |
af.setMenusFromViewport(af.viewport); |
458 |
|
|
459 |
0 |
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), |
460 |
|
view.getHeight()); |
461 |
|
|
462 |
|
|
463 |
|
|
464 |
0 |
if (jms.getTreeCount() > 0) |
465 |
|
{ |
466 |
0 |
try |
467 |
|
{ |
468 |
0 |
for (int t = 0; t < jms.getTreeCount(); t++) |
469 |
|
{ |
470 |
|
|
471 |
0 |
Tree tree = jms.getTree(t); |
472 |
|
|
473 |
0 |
TreePanel tp = af.showNewickTree( |
474 |
|
new jalview.io.NewickFile(tree.getNewick()), |
475 |
|
tree.getTitle(), tree.getWidth(), tree.getHeight(), |
476 |
|
tree.getXpos(), tree.getYpos()); |
477 |
|
|
478 |
0 |
tp.fitToWindow.setState(tree.getFitToWindow()); |
479 |
0 |
tp.fitToWindow_actionPerformed(null); |
480 |
|
|
481 |
0 |
if (tree.getFontName() != null) |
482 |
|
{ |
483 |
0 |
tp.setTreeFont(new java.awt.Font(tree.getFontName(), |
484 |
|
tree.getFontStyle(), tree.getFontSize())); |
485 |
|
} |
486 |
|
else |
487 |
|
{ |
488 |
0 |
tp.setTreeFont(new java.awt.Font(view.getFontName(), |
489 |
|
view.getFontStyle(), tree.getFontSize())); |
490 |
|
} |
491 |
|
|
492 |
0 |
tp.showPlaceholders(tree.getMarkUnlinked()); |
493 |
0 |
tp.showBootstrap(tree.getShowBootstrap()); |
494 |
0 |
tp.showDistances(tree.getShowDistances()); |
495 |
|
|
496 |
0 |
tp.treeCanvas.threshold = tree.getThreshold(); |
497 |
|
|
498 |
0 |
if (tree.getCurrentTree()) |
499 |
|
{ |
500 |
0 |
af.viewport.setCurrentTree(tp.getTree()); |
501 |
|
} |
502 |
|
} |
503 |
|
|
504 |
|
} catch (Exception ex) |
505 |
|
{ |
506 |
0 |
ex.printStackTrace(); |
507 |
|
} |
508 |
|
|
509 |
|
} |
510 |
|
|
511 |
0 |
return af; |
512 |
|
} |
513 |
|
} |