X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0d4e3e1203f641356ff28e07ddb8117d17040993;hb=4756b29312ca78d0975248c65e50157399e6ce39;hp=b85c7d205e1c7961dd258228ca6263b6d0bffa07;hpb=47a3f3d338d24f2a92d8249eede1ed0a6fd43d87;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index b85c7d2..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(); @@ -53,6 +55,22 @@ public class APopupMenu CheckboxMenuItem showBoxes = new CheckboxMenuItem(); CheckboxMenuItem showText = new CheckboxMenuItem(); CheckboxMenuItem showColourText = new CheckboxMenuItem(); + Menu editMenu = new Menu("Edit"); + MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem cut = new MenuItem("Cut (Jalview Only)"); + 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) { @@ -64,6 +82,7 @@ public class APopupMenu ////////////////////////////////////////////////////////// this.ap = apanel; + this.seq = seq; try { @@ -74,20 +93,35 @@ 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) + + if (sg != null && sg.getSize()>0) { + editGroupName.setLabel(sg.getName()); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - } + if (!ap.av.alignment.getGroups().contains(sg)) + { + groupMenu.remove(unGroupMenuItem); + } - if (!ap.av.alignment.getGroups().contains(sg)) + } + else { - groupMenu.remove(unGroupMenuItem); + remove(hideSeqs); + remove(groupMenu); } - if (seq != null && links!=null) + if (links!=null) { Menu linkMenu = new Menu("Link"); MenuItem item; @@ -97,13 +131,22 @@ public class APopupMenu link = links.elementAt(i).toString(); final String target = link.substring(0, link.indexOf("|")); item = new MenuItem(target); - String id = seq.getName(); - if(id.indexOf("|")>-1) - id = id.substring(id.lastIndexOf("|")+1); - final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) - + id + - link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + final String url; + + if (link.indexOf("$SEQUENCE_ID$") > -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + url = link.substring(link.lastIndexOf("|")+1); item.addActionListener(new java.awt.event.ActionListener() { @@ -114,21 +157,21 @@ public class APopupMenu }); linkMenu.add(item); } - add(linkMenu); - - item = new MenuItem("Show PDB Structure"); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addPDB(seq); - } - }); - - add(item); - - + if(seq!=null) + 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) @@ -145,41 +188,187 @@ public class APopupMenu public void actionPerformed(ActionEvent evt) { - if(evt.getSource()==clustalColour) + Object source = evt.getSource(); + if(source==clustalColour) clustalColour_actionPerformed(); - else if(evt.getSource()==zappoColour) + else if(source==zappoColour) zappoColour_actionPerformed(); - else if(evt.getSource()==taylorColour) + else if(source==taylorColour) taylorColour_actionPerformed(); - else if(evt.getSource()==hydrophobicityColour) + else if(source==hydrophobicityColour) hydrophobicityColour_actionPerformed(); - else if(evt.getSource()==helixColour) + else if(source==helixColour) helixColour_actionPerformed(); - else if(evt.getSource()==strandColour) + else if(source==strandColour) strandColour_actionPerformed(); - else if(evt.getSource()==clustalColour) + else if(source==turnColour) turnColour_actionPerformed(); - else if(evt.getSource()==buriedColour) + else if(source==buriedColour) buriedColour_actionPerformed(); - else if(evt.getSource()==nucleotideMenuItem) + else if(source==nucleotideMenuItem) nucleotideMenuItem_actionPerformed(); - else if(evt.getSource()==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(evt.getSource()==PIDColour) - PIDColour_actionPerformed(); - else if(evt.getSource()==BLOSUM62Colour) + else if (source == userDefinedColour) + userDefinedColour_actionPerformed(); + else if (source == PIDColour) + PIDColour_actionPerformed(); + else if (source == BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); - else if(evt.getSource()==noColourmenuItem) + else if (source == noColourmenuItem) noColourmenuItem_actionPerformed(); - else if(evt.getSource()==conservationMenuItem) - conservationMenuItem_itemStateChanged(); - else if(evt.getSource()==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(); + Vector regions = new Vector(); + if (sg != null) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + 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; + } + + 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."); @@ -193,8 +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); @@ -206,19 +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); @@ -265,6 +463,28 @@ public class APopupMenu BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); + editMenu.add(copy); + copy.addActionListener(this); + editMenu.add(cut); + cut.addActionListener(this); + editMenu.add(toUpper); + toUpper.addActionListener(this); + 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() @@ -277,7 +497,8 @@ public class APopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } @@ -337,7 +558,7 @@ public class APopupMenu if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 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()); @@ -365,7 +586,7 @@ public class APopupMenu { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); } @@ -376,7 +597,7 @@ public class APopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); @@ -399,7 +620,7 @@ public class APopupMenu Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -456,4 +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); + } + }