X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0d4e3e1203f641356ff28e07ddb8117d17040993;hb=4756b29312ca78d0975248c65e50157399e6ce39;hp=3401cc4b31d676978eb35fa75ec243603051d7ee;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 3401cc4..0d4e3e1 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -26,11 +26,13 @@ import java.util.Vector; import jalview.analysis.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.commands.ChangeCaseCommand; 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(); @@ -59,6 +61,16 @@ public class APopupMenu MenuItem toUpper = new MenuItem("To Upper Case"); MenuItem toLower = new MenuItem("To Lower Case"); MenuItem toggleCase = new MenuItem("Toggle Case"); + Menu outputmenu = new Menu(); + Menu seqMenu = new Menu(); + 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(); + Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { @@ -70,6 +82,7 @@ public class APopupMenu ////////////////////////////////////////////////////////// this.ap = apanel; + this.seq = seq; try { @@ -80,10 +93,19 @@ public class APopupMenu e.printStackTrace(); } + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + { + MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] ); + + item.addActionListener(this); + outputmenu.add(item); + } + 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()); @@ -95,8 +117,8 @@ public class APopupMenu } else { + remove(hideSeqs); remove(groupMenu); - remove(editMenu); } if (links!=null) @@ -135,22 +157,21 @@ public class APopupMenu }); linkMenu.add(item); } - add(linkMenu); - if(seq!=null) - { - item = new MenuItem("Show PDB Structure"); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addPDB(seq); - } - }); - - add(item); - } + seqMenu.add(linkMenu); + else + add(linkMenu); } + if(seq!=null) + { + seqMenu.setLabel(seq.getName()); + repGroup.setLabel("Represent Group with " + seq.getName()); + } + else + remove(seqMenu); + + if(!ap.av.hasHiddenRows) + remove(revealAll); } public void itemStateChanged(ItemEvent evt) @@ -180,52 +201,174 @@ public class APopupMenu helixColour_actionPerformed(); else if(source==strandColour) strandColour_actionPerformed(); - else if(source==clustalColour) + else if(source==turnColour) turnColour_actionPerformed(); else if(source==buriedColour) buriedColour_actionPerformed(); else if(source==nucleotideMenuItem) nucleotideMenuItem_actionPerformed(); - else if(source==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(source==PIDColour) - PIDColour_actionPerformed(); - else if(source==BLOSUM62Colour) + else if (source == userDefinedColour) + userDefinedColour_actionPerformed(); + else if (source == PIDColour) + PIDColour_actionPerformed(); + else if (source == BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); - else if(source==noColourmenuItem) + else if (source == noColourmenuItem) noColourmenuItem_actionPerformed(); - else if(source==conservationMenuItem) - conservationMenuItem_itemStateChanged(); - else if(source==unGroupMenuItem) + else if (source == conservationMenuItem) + conservationMenuItem_itemStateChanged(); + else if (source == unGroupMenuItem) unGroupMenuItem_actionPerformed(); + else if(source == sequenceName) + editName(); + else if(source == pdb) + addPDB(); + else if(source == hideSeqs) + hideSequences(false); + else if(source == repGroup) + hideSequences(true); + else if(source == revealAll) + { + 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) ap.alignFrame.cut_actionPerformed(); else if(source==toUpper || source==toLower || source==toggleCase) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do { - for (int g = 0; g < sg.getSize(true); g++) + if (ap.av.hasHiddenColumns) { - if (source == toggleCase) - ((SequenceI) sg.getSequences(true).elementAt(g)) - .toggleCase(sg.getStartRes(), sg.getEndRes() + 1); - else - ((SequenceI) sg.getSequences(true).elementAt(g)) - .changeCase(source == toUpper, sg.getStartRes(), - sg.getEndRes() + 1); + if(start==0) + start = ap.av.colSel.adjustForHiddenColumns(start); + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; } - ap.seqPanel.seqCanvas.repaint(); + + regions.addElement(new int[] + {start, end}); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + } + while (end < sg.getEndRes()); + + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } + + + String description; + int caseChange; + + if(source==toggleCase) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if(source==toUpper) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + + } } + else + outputText(evt); + + } + void outputText(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Selection output - " + e.getActionCommand(), + 600, 500); + + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + 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(Sequence seq) + void addPDB() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); cap.setText("Paste your PDB file here."); @@ -239,8 +382,9 @@ public class APopupMenu throws Exception { groupMenu.setLabel("Group"); - groupMenu.setLabel("Define"); + groupMenu.setLabel("Selection"); + editGroupName.addActionListener(this); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); @@ -252,19 +396,27 @@ public class APopupMenu showBoxes.setLabel("Boxes"); showBoxes.setState(true); showBoxes.addItemListener(this); + sequenceName.addActionListener(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"); + menu1.setLabel("Group"); add(groupMenu); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.addSeparator(); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); + this.add(seqMenu); + this.add(hideSeqs); + this.add(revealAll); + groupMenu.add(editGroupName); + groupMenu.add(editMenu); + groupMenu.add(outputmenu); + groupMenu.add(menu1); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -311,7 +463,6 @@ public class APopupMenu BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); - add(editMenu); editMenu.add(copy); copy.addActionListener(this); editMenu.add(cut); @@ -321,8 +472,19 @@ public class APopupMenu editMenu.add(toLower); toLower.addActionListener(this); editMenu.add(toggleCase); + seqMenu.add(sequenceName); + seqMenu.add(pdb); + seqMenu.add(repGroup); + menu1.add(unGroupMenuItem); + menu1.add(colourMenu); + menu1.add(showBoxes); + menu1.add(showText); + menu1.add(showColourText); toggleCase.addActionListener(this); - + pdb.addActionListener(this); + hideSeqs.addActionListener(this); + repGroup.addActionListener(this); + revealAll.addActionListener(this); } void refresh() @@ -335,7 +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(); } @@ -395,7 +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()); @@ -423,7 +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(); } @@ -434,7 +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(); @@ -457,7 +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(); @@ -514,4 +677,36 @@ public class APopupMenu 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); + } + }