X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=c71818e2dae8ab46be141ffdf76a1507b99a0e2a;hb=a90a2ca70e84c2923c682512a27e93785ad65557;hp=a932d66fc4ab8208f50bd23665e12cfd94ff18b8;hpb=6d6d6bc08bca95676a8175c634c03c163fb88684;p=jalview.git
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a932d66..c71818e 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,490 +1,1088 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
-import java.awt.*;
-import java.awt.event.*;
-
-public class APopupMenu extends java.awt.PopupMenu
-{
- Menu groupMenu = new Menu();
- protected MenuItem clustalColour = new MenuItem();
- protected MenuItem zappoColour = new MenuItem();
- protected MenuItem taylorColour = new MenuItem();
- protected MenuItem hydrophobicityColour = new MenuItem();
- protected MenuItem helixColour = new MenuItem();
- protected MenuItem strandColour = new MenuItem();
- protected MenuItem turnColour = new MenuItem();
- protected MenuItem buriedColour = new MenuItem();
- protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
- protected MenuItem userDefinedColour = new MenuItem();
- protected MenuItem PIDColour = new MenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
- MenuItem noColourmenuItem = new MenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-
-
- AlignmentPanel ap;
- Menu sequenceMenu = new Menu();
- MenuItem sequenceName = new MenuItem();
- Sequence sequence;
- MenuItem unGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
- Menu colourMenu = new Menu();
- CheckboxMenuItem showBoxes = new CheckboxMenuItem();
- CheckboxMenuItem showText = new CheckboxMenuItem();
- CheckboxMenuItem showColourText = new CheckboxMenuItem();
-
- public APopupMenu(AlignmentPanel ap, Sequence seq)
- {
- ///////////////////////////////////////////////////////////
- // If this is activated from the sequence panel, the user may want to
- // edit or annotate a particular residue. Therefore display the residue menu
- //
- // If from the IDPanel, we must display the sequence menu
- //////////////////////////////////////////////////////////
-
- this.ap = ap;
- sequence = seq;
-
- try
- { jbInit(); }
- catch(Exception e)
- { e.printStackTrace(); }
-
-
- SequenceGroup sg = ap.av.getSelectionGroup();
- if(sg!=null)
- {
- showText.setState(sg.getDisplayText());
- showColourText.setState(sg.getColourText());
- showBoxes.setState(sg.getDisplayBoxes());
- }
-
- if( !ap.av.alignment.getGroups().contains(sg))
- groupMenu.remove(unGroupMenuItem);
-
- if(seq==null)
- remove(sequenceMenu);
-
-
- }
- private void jbInit() throws Exception
- {
- groupMenu.setLabel("Group");
- groupMenu.setLabel("Define");
-
- sequenceMenu.setLabel("Sequence");
- sequenceName.setLabel("Edit name");
- unGroupMenuItem.setLabel("Remove Group");
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- unGroupMenuItem_actionPerformed(e);
- }
- });
-
-
- nucleotideMenuItem.setLabel("Nucleotide");
- nucleotideMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed(e);
- }
- });
- conservationMenuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent itemEvent)
- {
- conservationMenuItem_itemStateChanged(itemEvent);
- }
- });
- abovePIDColour.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent itemEvent)
- {
- abovePIDColour_itemStateChanged(itemEvent);
- }
- });
- colourMenu.setLabel("Group Colour");
- showBoxes.setLabel("Boxes");
- showBoxes.setState(true);
- showBoxes.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent itemEvent)
- {
- showBoxes_itemStateChanged(itemEvent);
- }
- });
-
- showText.setLabel("Text");
- showText.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent itemEvent)
- {
- showText_itemStateChanged(itemEvent);
- }
- });
- showColourText.setLabel("Colour Text");
- showColourText.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent itemEvent)
- {
- showColourText_itemStateChanged(itemEvent);
- }
- });
-
- add(groupMenu);
- this.add(sequenceMenu);
- groupMenu.add(unGroupMenuItem);
- groupMenu.add(colourMenu);
- groupMenu.addSeparator();
- groupMenu.add(showBoxes);
- groupMenu.add(showText);
- groupMenu.add(showColourText);
- sequenceMenu.add(sequenceName);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
-
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
-
- clustalColour.setLabel("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed(e);
- }
- });
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setLabel("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed(e);
- }
- });
- strandColour.setLabel("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed(e);
- }
- });
- turnColour.setLabel("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed(e);
- }
- });
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed(e);
- }
- });
- abovePIDColour.setLabel("Above % Identity");
-
- userDefinedColour.setLabel("User Defined");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed(e);
- }
- });
- BLOSUM62Colour.setLabel("BLOSUM62");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed(e);
- }
- });
- conservationMenuItem.setLabel("Conservation");
-
-
- }
-
- void refresh()
- {
- SequenceGroup sg = getGroup();
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
- if( superG !=null)
- superG.setSuperGroupProperties( sg );
-
- ap.seqPanel.seqCanvas.repaint();
- }
-
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
- refresh();
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
-
-
- protected void abovePIDColour_itemStateChanged(ItemEvent ie)
- {
- SequenceGroup sg = getGroup();
- if (abovePIDColour.getState())
- {
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
- if (sg.cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
- else if (sg.cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-
- SliderPanel.showPIDSlider();
-
-
- }
- else // remove PIDColouring
- {
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
- rcs.setThreshold(0);
- sg.cs = rcs;
- }
-
- refresh();
-
- }
-
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours( ap, getGroup());
- }
-
- protected void PIDColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
- refresh();
- }
-
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
- ap.av.alignment.getWidth()));
-
- refresh();
- }
-
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- getGroup().cs = null;
- refresh();
- }
-
- protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
- {
- SequenceGroup sg = getGroup();
-
- if(conservationMenuItem.getState())
- {
-
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, 0,
- ap.av.alignment.getWidth());
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-
- sg.cs = ccs;
-
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());
- SliderPanel.showConservationSlider();
- }
- else // remove ConservationColouring
- {
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
- sg.cs = ccs.cs;
- }
-
- refresh();
- }
-
-
- protected void analyze_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
- SequenceGroup sg = getGroup();
- StringBuffer sb = new StringBuffer();
-
- for(int i=0; iAnnotation for " + seq.getDisplayId(true)
+ + "
"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("
"); + } + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 600, 500); + cap.setText("" + contents.toString() + ""); + } + + void editName() + { + EditNameDialog dialog = new EditNameDialog(seq.getName(), + seq.getDescription(), " Sequence Name", + "Sequence Description", ap.alignFrame, + "Edit Sequence Name / Description", 500, 100, true); + + if (dialog.accept) + { + seq.setName(dialog.getName()); + seq.setDescription(dialog.getDescription()); + ap.paintAlignment(false); + } + } + + void addPDB() + { + if (seq.getPDBId() != null) + { + PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement(); + + if (ap.av.applet.jmolAvailable) + new jalview.appletgui.AppletJmol(entry, new Sequence[] + { seq }, null, ap, AppletFormatAdapter.URL); + else + new MCview.AppletPDBViewer(entry, new Sequence[] + { seq }, null, ap, AppletFormatAdapter.URL); + + } + else + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + cap.setText("Paste your PDB file here."); + cap.setPDBImport(seq); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Paste PDB file for sequence " + seq.getName(), 400, 300); + } + } + + private void jbInit() throws Exception + { + groupMenu.setLabel("Group"); + groupMenu.setLabel("Selection"); + sequenceFeature.addActionListener(this); + + editGroupName.addActionListener(this); + unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.addActionListener(this); + + nucleotideMenuItem.setLabel("Nucleotide"); + nucleotideMenuItem.addActionListener(this); + conservationMenuItem.addItemListener(this); + abovePIDColour.addItemListener(this); + colourMenu.setLabel("Group Colour"); + showBoxes.setLabel("Boxes"); + showBoxes.setState(true); + showBoxes.addItemListener(this); + sequenceName.addActionListener(this); + sequenceDetails.addActionListener(this); + selSeqDetails.addActionListener(this); + displayNonconserved.setLabel("Show Nonconserved"); + displayNonconserved.setState(false); + displayNonconserved.addItemListener(this); + showText.setLabel("Text"); + showText.addItemListener(this); + showColourText.setLabel("Colour Text"); + showColourText.addItemListener(this); + outputmenu.setLabel("Output to Textbox..."); + seqMenu.setLabel("Sequence"); + pdb.setLabel("View PDB Structure"); + hideSeqs.setLabel("Hide Sequences"); + repGroup.setLabel("Represent Group with"); + revealAll.setLabel("Reveal All"); + revealSeq.setLabel("Reveal Sequences"); + menu1.setLabel("Group"); + add(groupMenu); + this.add(seqMenu); + this.add(hideSeqs); + this.add(revealSeq); + this.add(revealAll); + // groupMenu.add(selSeqDetails); + groupMenu.add(editGroupName); + groupMenu.add(editMenu); + groupMenu.add(outputmenu); + groupMenu.add(sequenceFeature); + groupMenu.add(menu1); + + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + + clustalColour.setLabel("Clustalx colours"); + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + abovePIDColour.setLabel("Above % Identity"); + + userDefinedColour.setLabel("User Defined"); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62"); + BLOSUM62Colour.addActionListener(this); + conservationMenuItem.setLabel("Conservation"); + + editMenu.add(copy); + copy.addActionListener(this); + editMenu.add(cut); + cut.addActionListener(this); + + editMenu.add(editSequence); + editSequence.addActionListener(this); + + editMenu.add(toUpper); + toUpper.addActionListener(this); + editMenu.add(toLower); + toLower.addActionListener(this); + editMenu.add(toggleCase); + seqMenu.add(sequenceName); + // seqMenu.add(sequenceDetails); + + if (!ap.av.applet.useXtrnalSviewer) + { + seqMenu.add(pdb); + } + seqMenu.add(repGroup); + menu1.add(unGroupMenuItem); + menu1.add(colourMenu); + menu1.add(showBoxes); + menu1.add(showText); + menu1.add(showColourText); + menu1.add(displayNonconserved); + toggleCase.addActionListener(this); + pdb.addActionListener(this); + hideSeqs.addActionListener(this); + repGroup.addActionListener(this); + revealAll.addActionListener(this); + revealSeq.addActionListener(this); + } + + void refresh() + { + ap.paintAlignment(true); + } + + protected void clustalColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); + refresh(); + } + + protected void zappoColour_actionPerformed() + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + protected void strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + protected void abovePIDColour_itemStateChanged() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (abovePIDColour.getState()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); + + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + + } + else + // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + + refresh(); + + } + + protected void userDefinedColour_actionPerformed() + { + new UserDefinedColours(ap, getGroup()); + } + + protected void PIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); + refresh(); + } + + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); + + refresh(); + } + + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } + + protected void conservationMenuItem_itemStateChanged() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.getState()) + { + + sg.cs.setConservation(Conservation.calculateConservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment() + .getWidth(), false, ap.av.getConsPercGaps(), false)); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else + // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } + + SequenceGroup getGroup() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.getAlignment().addGroup(sg); + } + + return sg; + } + + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.getAlignment().deleteGroup(sg); + ap.av.setSelectionGroup(null); + ap.paintAlignment(true); + } + + public void showColourText_itemStateChanged() + { + getGroup().setColourText(showColourText.getState()); + refresh(); + } + + public void showText_itemStateChanged() + { + getGroup().setDisplayText(showText.getState()); + refresh(); + } + + public void showNonconserved_itemStateChanged() + { + getGroup().setShowNonconserved(this.displayNonconserved.getState()); + refresh(); + } + + public void showBoxes_itemStateChanged() + { + getGroup().setDisplayBoxes(showBoxes.getState()); + refresh(); + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) + { + ap.av.hideSequence(new SequenceI[] + { seq }); + return; + } + + ap.av.setSelectionGroup(null); + + if (representGroup) + { + ap.av.hideRepSequences(seq, sg); + + return; + } + + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); + } + + ap.av.hideSequence(hseqs); + ap.av.sendSelection(); + } + +}