X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0d4e3e1203f641356ff28e07ddb8117d17040993;hb=4756b29312ca78d0975248c65e50157399e6ce39;hp=a1e99ffe55772e2c74aca3f23f3835cad7c04cce;hpb=f63c96838e84bb6fd1d22fcf0197d49cee806470;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index a1e99ff..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(); @@ -71,10 +72,6 @@ public class APopupMenu MenuItem revealAll = new MenuItem(); Menu menu1 = new Menu(); - Dialog editNameDialog; - Button okDialog = new Button("Accept"); - Button cancelDialog = new Button("Cancel");; - public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { /////////////////////////////////////////////////////////// @@ -106,8 +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()); @@ -225,12 +223,6 @@ public class APopupMenu else if(source == sequenceName) editName(); - else if (source==okDialog || source==cancelDialog) - { - editNameDialog.setVisible(false); - if(source==cancelDialog) - editNameDialog = null; - } else if(source == pdb) addPDB(); else if(source == hideSeqs) @@ -242,6 +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) @@ -307,7 +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); @@ -326,22 +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); @@ -351,50 +345,25 @@ public class APopupMenu cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( e.getActionCommand(), - vseqs, + new Alignment( ap.av.getSelectionAsNewSequence() ), ap.av.showJVSuffix)); } void editName() { - TextField id = new TextField(seq.getName(), 40); - TextField description = new TextField(seq.getDescription(), 40); - Panel panel = new Panel(new BorderLayout()); - Panel panel2 = new Panel(new BorderLayout()); - panel2.add(new Label(" Sequence Name "), BorderLayout.WEST); - panel2.add(id, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.NORTH); - panel2 = new Panel(new BorderLayout()); - panel2.add(new Label("Sequence Description "), BorderLayout.WEST); - panel2.add(description, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.CENTER); - - panel2 = new Panel(new FlowLayout()); - - panel2.add(okDialog); - panel2.add(cancelDialog); - - panel.add(panel2, BorderLayout.SOUTH); - - editNameDialog = new Dialog(ap.alignFrame, - "Edit Sequence Name / Description", - true); - - editNameDialog.add(panel, BorderLayout.NORTH); - - editNameDialog.setBounds(ap.alignFrame.getBounds().x - +(ap.alignFrame.getSize().width-500)/2 , - ap.alignFrame.getBounds().y - +(ap.alignFrame.getSize().height-120)/2, - 500, 120); - - editNameDialog.show(); - - if (editNameDialog != null) + EditNameDialog dialog = new EditNameDialog( + seq.getName(), + seq.getDescription(), + " Sequence Name ", + "Sequence Description ", + ap, + "Edit Sequence Name / Description"); + + if (dialog.accept) { - seq.setName(id.getText()); - seq.setDescription(description.getText()); + seq.setName(dialog.getName()); + seq.setDescription(dialog.getDescription()); ap.repaint(); } } @@ -415,6 +384,7 @@ public class APopupMenu groupMenu.setLabel("Group"); groupMenu.setLabel("Selection"); + editGroupName.addActionListener(this); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); @@ -443,6 +413,7 @@ public class APopupMenu this.add(seqMenu); this.add(hideSeqs); this.add(revealAll); + groupMenu.add(editGroupName); groupMenu.add(editMenu); groupMenu.add(outputmenu); groupMenu.add(menu1); @@ -514,9 +485,6 @@ public class APopupMenu hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); - okDialog.addActionListener(this); - cancelDialog.addActionListener(this); - } void refresh() @@ -529,7 +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(); } @@ -589,7 +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()); @@ -617,7 +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(); } @@ -628,7 +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(); @@ -651,7 +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(); @@ -711,34 +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