X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0d4e3e1203f641356ff28e07ddb8117d17040993;hb=4756b29312ca78d0975248c65e50157399e6ce39;hp=dad22cb64ec3e1a48145f6e6d3af212e8b719c55;hpb=07c1edb779cfa11d19ea6e5dc731333e5dfd2250;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index dad22cb..0d4e3e1 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -32,6 +32,7 @@ public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener { Menu groupMenu = new Menu(); + MenuItem editGroupName = new MenuItem(); protected MenuItem clustalColour = new MenuItem(); protected MenuItem zappoColour = new MenuItem(); protected MenuItem taylorColour = new MenuItem(); @@ -65,10 +66,10 @@ public class APopupMenu MenuItem pdb = new MenuItem(); MenuItem hideSeqs = new MenuItem(); MenuItem repGroup = new MenuItem(); + MenuItem sequenceName = new MenuItem("Edit Name/Description"); Sequence seq; MenuItem revealAll = new MenuItem(); - MenuItem menuItem1 = new MenuItem(); Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) @@ -102,8 +103,9 @@ public class APopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null && sg.getSize(false)>0) + if (sg != null && sg.getSize()>0) { + editGroupName.setLabel(sg.getName()); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); @@ -219,6 +221,8 @@ public class APopupMenu else if (source == unGroupMenuItem) unGroupMenuItem_actionPerformed(); + else if(source == sequenceName) + editName(); else if(source == pdb) addPDB(); else if(source == hideSeqs) @@ -230,6 +234,24 @@ public class APopupMenu ap.av.showAllHiddenSeqs(); } + else if(source==editGroupName) + { + EditNameDialog dialog = new EditNameDialog( + getGroup().getName(), + getGroup().getDescription(), + " Group Name", + "Group Description", + ap, + "Edit Group Name / Description"); + + if (dialog.accept) + { + + getGroup().setName(dialog.getName().replace(' ', '_')); + getGroup().setDescription(dialog.getDescription()); + } + + } else if(source==copy) ap.alignFrame.copy_actionPerformed(); else if(source==cut) @@ -295,7 +317,7 @@ public class APopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand( - description, sg.getSequencesAsArray(true), startEnd, caseChange + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange ); ap.alignFrame.addHistoryItem(caseCommand); @@ -314,22 +336,6 @@ public class APopupMenu void outputText(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); - Vector vseqs = new Vector(); - - String [] selection = ap.av.getViewAsString(true); - SequenceI [] seqs = ap.av.getSelectionAsNewSequence(); - if (selection != null) - { - for (int i = 0; i < selection.length; i++) - { - Sequence seq = new Sequence( - seqs[i].getName(), - selection[i], - seqs[i].getStart(), seqs[i].getEnd()); - seq.setDescription(seqs[i].getDescription()); - vseqs.addElement( seq ); - } - } Frame frame = new Frame(); frame.add(cap); @@ -339,11 +345,29 @@ public class APopupMenu cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( e.getActionCommand(), - vseqs, + new Alignment( ap.av.getSelectionAsNewSequence() ), ap.av.showJVSuffix)); } + void editName() + { + EditNameDialog dialog = new EditNameDialog( + seq.getName(), + seq.getDescription(), + " Sequence Name ", + "Sequence Description ", + ap, + "Edit Sequence Name / Description"); + + if (dialog.accept) + { + seq.setName(dialog.getName()); + seq.setDescription(dialog.getDescription()); + ap.repaint(); + } + } + void addPDB() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); @@ -360,6 +384,7 @@ public class APopupMenu groupMenu.setLabel("Group"); groupMenu.setLabel("Selection"); + editGroupName.addActionListener(this); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); @@ -371,6 +396,7 @@ public class APopupMenu showBoxes.setLabel("Boxes"); showBoxes.setState(true); showBoxes.addItemListener(this); + sequenceName.addActionListener(this); showText.setLabel("Text"); showText.addItemListener(this); @@ -382,15 +408,14 @@ public class APopupMenu hideSeqs.setLabel("Hide Sequences"); repGroup.setLabel("Represent Group with"); revealAll.setLabel("Reveal All"); - menuItem1.setLabel("Create Sequence Feature"); menu1.setLabel("Group"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); this.add(revealAll); + groupMenu.add(editGroupName); groupMenu.add(editMenu); groupMenu.add(outputmenu); - groupMenu.add(menuItem1); groupMenu.add(menu1); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -447,6 +472,7 @@ public class APopupMenu editMenu.add(toLower); toLower.addActionListener(this); editMenu.add(toggleCase); + seqMenu.add(sequenceName); seqMenu.add(pdb); seqMenu.add(repGroup); menu1.add(unGroupMenuItem); @@ -459,7 +485,6 @@ public class APopupMenu hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); - } void refresh() @@ -472,7 +497,8 @@ public class APopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } @@ -532,7 +558,7 @@ public class APopupMenu if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -560,7 +586,7 @@ public class APopupMenu { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); } @@ -571,7 +597,7 @@ public class APopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); @@ -594,7 +620,7 @@ public class APopupMenu Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), 0, + sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -654,34 +680,33 @@ public class APopupMenu void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize(false)<1) + if(sg==null || sg.getSize()<1) { ap.av.hideSequence(new SequenceI[]{seq}); return; } - int gsize = sg.getSize(false); - SequenceI [] hseqs; + ap.av.setSelectionGroup(null); - hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ]; + if (representGroup) + { + ap.av.hideRepSequences(seq, sg); - int index = 0; - for(int i=0; i