/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
+import jalview.commands.ChangeCaseCommand;\r
\r
public class APopupMenu\r
extends java.awt.PopupMenu implements ActionListener, ItemListener\r
\r
Sequence seq;\r
MenuItem revealAll = new MenuItem();\r
+ MenuItem menuItem1 = new MenuItem();\r
+ Menu menu1 = new Menu();\r
\r
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
{\r
e.printStackTrace();\r
}\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
- MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
- elementAt(\r
- i));\r
+ MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
item.addActionListener(this);\r
outputmenu.add(item);\r
}\r
else\r
url = link.substring(link.lastIndexOf("|")+1);\r
\r
- System.out.println("add "+url +" "+target);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
helixColour_actionPerformed();\r
else if(source==strandColour)\r
strandColour_actionPerformed();\r
- else if(source==clustalColour)\r
+ else if(source==turnColour)\r
turnColour_actionPerformed();\r
else if(source==buriedColour)\r
buriedColour_actionPerformed();\r
else if(source == revealAll)\r
{\r
ap.av.showAllHiddenSeqs();\r
- ap.repaint();\r
}\r
\r
else if(source==copy)\r
ap.alignFrame.cut_actionPerformed();\r
else if(source==toUpper || source==toLower || source==toggleCase)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null)\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
{\r
- for (int g = 0; g < sg.getSize(true); g++)\r
+ if (ap.av.hasHiddenColumns)\r
{\r
- if (source == toggleCase)\r
- ((SequenceI) sg.getSequences(true).elementAt(g))\r
- .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
- else\r
- ((SequenceI) sg.getSequences(true).elementAt(g))\r
- .changeCase(source == toUpper, sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
+ if(start==0)\r
+ start = ap.av.colSel.adjustForHiddenColumns(start);\r
+\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ end = sg.getEndRes() + 1;\r
+ if (end > sg.getEndRes())\r
+ end = sg.getEndRes() + 1;\r
}\r
- ap.seqPanel.seqCanvas.repaint();\r
+\r
+ regions.addElement(new int[]\r
+ {start, end});\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+ }\r
+ while (end < sg.getEndRes());\r
+\r
+ int[][] startEnd = new int[regions.size()][2];\r
+ for (int i = 0; i < regions.size(); i++)\r
+ {\r
+ startEnd[i] = (int[]) regions.elementAt(i);\r
+ }\r
+\r
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if(source==toggleCase)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if(source==toUpper)\r
+ {\r
+ description = "To Upper Case";\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
}\r
+ else\r
+ {\r
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
+ }\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
+ }\r
}\r
else\r
outputText(evt);\r
\r
void outputText(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
Vector vseqs = new Vector();\r
\r
String [] selection = ap.av.getViewAsString(true);\r
hideSeqs.setLabel("Hide Sequences");\r
repGroup.setLabel("Represent Group with");\r
revealAll.setLabel("Reveal All");\r
-\r
+ menuItem1.setLabel("Create Sequence Feature");\r
+ menu1.setLabel("Group");\r
add(groupMenu);\r
this.add(seqMenu);\r
this.add(hideSeqs);\r
this.add(revealAll);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputmenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
+ groupMenu.add(menuItem1);\r
+ groupMenu.add(menu1);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
editMenu.add(toggleCase);\r
seqMenu.add(pdb);\r
seqMenu.add(repGroup);\r
+ menu1.add(unGroupMenuItem);\r
+ menu1.add(colourMenu);\r
+ menu1.add(showBoxes);\r
+ menu1.add(showText);\r
+ menu1.add(showColourText);\r
toggleCase.addActionListener(this);\r
pdb.addActionListener(this);\r
hideSeqs.addActionListener(this);\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
if(sg==null || sg.getSize(false)<1)\r
{\r
- ap.av.hideSequence(seq);\r
+ ap.av.hideSequence(new SequenceI[]{seq});\r
return;\r
}\r
\r
+ int gsize = sg.getSize(false);\r
+ SequenceI [] hseqs;\r
+\r
+ hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
int index = 0;\r
- while(index < sg.getSize(false))\r
+ for(int i=0; i<gsize; i++)\r
{\r
- if(representGroup && sg.getSequenceAt(index)!=seq)\r
+ if(representGroup && sg.getSequenceAt(i)!=seq)\r
{\r
- seq.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ seq.addHiddenSequence(sg.getSequenceAt(i));\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
}\r
else if(!representGroup)\r
{\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
}\r
- index ++;\r
- }\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
\r
ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- refresh();\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff