/*\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
Menu groupMenu = new Menu();\r
+ MenuItem editGroupName = new MenuItem();\r
protected MenuItem clustalColour = new MenuItem();\r
protected MenuItem zappoColour = new MenuItem();\r
protected MenuItem taylorColour = new MenuItem();\r
MenuItem toUpper = new MenuItem("To Upper Case");\r
MenuItem toLower = new MenuItem("To Lower Case");\r
MenuItem toggleCase = new MenuItem("Toggle Case");\r
+ Menu outputmenu = new Menu();\r
+ Menu seqMenu = new Menu();\r
+ MenuItem pdb = new MenuItem();\r
+ MenuItem hideSeqs = new MenuItem();\r
+ MenuItem repGroup = new MenuItem();\r
+ MenuItem sequenceName = new MenuItem("Edit Name/Description");\r
+\r
+ Sequence seq;\r
+ MenuItem revealAll = new MenuItem();\r
+ Menu menu1 = new Menu();\r
\r
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
{\r
//////////////////////////////////////////////////////////\r
\r
this.ap = apanel;\r
+ this.seq = seq;\r
\r
try\r
{\r
e.printStackTrace();\r
}\r
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
+ item.addActionListener(this);\r
+ outputmenu.add(item);\r
+ }\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
if (sg != null && sg.getSize()>0)\r
{\r
+ editGroupName.setLabel(sg.getName());\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
}\r
else\r
{\r
+ remove(hideSeqs);\r
remove(groupMenu);\r
- remove(editMenu);\r
}\r
\r
if (links!=null)\r
});\r
linkMenu.add(item);\r
}\r
- add(linkMenu);\r
-\r
if(seq!=null)\r
- {\r
- item = new MenuItem("Show PDB Structure");\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addPDB(seq);\r
- }\r
- });\r
-\r
- add(item);\r
- }\r
+ seqMenu.add(linkMenu);\r
+ else\r
+ add(linkMenu);\r
}\r
+ if(seq!=null)\r
+ {\r
+ seqMenu.setLabel(seq.getName());\r
+ repGroup.setLabel("Represent Group with " + seq.getName());\r
+ }\r
+ else\r
+ remove(seqMenu);\r
+\r
+ if(!ap.av.hasHiddenRows)\r
+ remove(revealAll);\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\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==nucleotideMenuItem)\r
nucleotideMenuItem_actionPerformed();\r
\r
- else if(source==userDefinedColour)\r
- userDefinedColour_actionPerformed();\r
- else if(source==PIDColour)\r
- PIDColour_actionPerformed();\r
- else if(source==BLOSUM62Colour)\r
+ else if (source == userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if (source == PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if (source == BLOSUM62Colour)\r
BLOSUM62Colour_actionPerformed();\r
- else if(source==noColourmenuItem)\r
+ else if (source == noColourmenuItem)\r
noColourmenuItem_actionPerformed();\r
- else if(source==conservationMenuItem)\r
- conservationMenuItem_itemStateChanged();\r
- else if(source==unGroupMenuItem)\r
+ else if (source == conservationMenuItem)\r
+ conservationMenuItem_itemStateChanged();\r
+ else if (source == unGroupMenuItem)\r
unGroupMenuItem_actionPerformed();\r
\r
+ else if(source == sequenceName)\r
+ editName();\r
+ else if(source == pdb)\r
+ addPDB();\r
+ else if(source == hideSeqs)\r
+ hideSequences(false);\r
+ else if(source == repGroup)\r
+ hideSequences(true);\r
+ else if(source == revealAll)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ }\r
+\r
+ else if(source==editGroupName)\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ getGroup().getName(),\r
+ getGroup().getDescription(),\r
+ " Group Name",\r
+ "Group Description",\r
+ ap,\r
+ "Edit Group Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+\r
+ getGroup().setName(dialog.getName().replace(' ', '_'));\r
+ getGroup().setDescription(dialog.getDescription());\r
+ }\r
+\r
+ }\r
else if(source==copy)\r
ap.alignFrame.copy_actionPerformed();\r
else if(source==cut)\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(); g++)\r
+ if (ap.av.hasHiddenColumns)\r
{\r
- if (source == toggleCase)\r
- sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
- else\r
- sg.getSequenceAt(g).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(ap.av.hiddenRepSequences), 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
+ }\r
\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Selection output - " + e.getActionCommand(),\r
+ 600, 500);\r
+\r
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ new Alignment( ap.av.getSelectionAsNewSequence() ),\r
+ ap.av.showJVSuffix));\r
+\r
+ }\r
+\r
+ void editName()\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ seq.getName(),\r
+ seq.getDescription(),\r
+ " Sequence Name ",\r
+ "Sequence Description ",\r
+ ap,\r
+ "Edit Sequence Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+ seq.setName(dialog.getName());\r
+ seq.setDescription(dialog.getDescription());\r
+ ap.repaint();\r
+ }\r
}\r
\r
- void addPDB(Sequence seq)\r
+ void addPDB()\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
cap.setText("Paste your PDB file here.");\r
throws Exception\r
{\r
groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Define");\r
+ groupMenu.setLabel("Selection");\r
\r
+ editGroupName.addActionListener(this);\r
unGroupMenuItem.setLabel("Remove Group");\r
unGroupMenuItem.addActionListener(this);\r
\r
showBoxes.setLabel("Boxes");\r
showBoxes.setState(true);\r
showBoxes.addItemListener(this);\r
+ sequenceName.addActionListener(this);\r
\r
showText.setLabel("Text");\r
showText.addItemListener(this);\r
showColourText.setLabel("Colour Text");\r
showColourText.addItemListener(this);\r
-\r
+ outputmenu.setLabel("Output to Textbox...");\r
+ seqMenu.setLabel("Sequence");\r
+ pdb.setLabel("View PDB Structure");\r
+ hideSeqs.setLabel("Hide Sequences");\r
+ repGroup.setLabel("Represent Group with");\r
+ revealAll.setLabel("Reveal All");\r
+ menu1.setLabel("Group");\r
add(groupMenu);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
+ this.add(seqMenu);\r
+ this.add(hideSeqs);\r
+ this.add(revealAll);\r
+ groupMenu.add(editGroupName);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputmenu);\r
+ groupMenu.add(menu1);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
BLOSUM62Colour.addActionListener(this);\r
conservationMenuItem.setLabel("Conservation");\r
\r
- add(editMenu);\r
editMenu.add(copy);\r
copy.addActionListener(this);\r
editMenu.add(cut);\r
editMenu.add(toLower);\r
toLower.addActionListener(this);\r
editMenu.add(toggleCase);\r
+ seqMenu.add(sequenceName);\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
-\r
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\r
}\r
\r
void refresh()\r
protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
+ ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
\r
if (abovePIDColour.getState())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\r
\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(ap.av.hiddenRepSequences), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
refresh();\r
}\r
\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null || sg.getSize()<1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]{seq});\r
+ return;\r
+ }\r
+\r
+ ap.av.setSelectionGroup(null);\r
+\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(seq, sg);\r
+\r
+ return;\r
+ }\r
+\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
+\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff