/*\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
CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
CheckboxMenuItem showText = new CheckboxMenuItem();\r
CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
+ Menu editMenu = new Menu("Edit");\r
+ MenuItem copy = new MenuItem("Copy (Jalview Only)");\r
+ MenuItem cut = new MenuItem("Cut (Jalview Only)");\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
+\r
+ Sequence seq;\r
+ MenuItem revealAll = new MenuItem();\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
- if (sg != null)\r
+\r
+ if (sg != null && sg.getSize(false)>0)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
- }\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
+ }\r
+ else\r
{\r
- groupMenu.remove(unGroupMenuItem);\r
+ remove(hideSeqs);\r
+ remove(groupMenu);\r
}\r
\r
- if (seq != null && links!=null)\r
+ if (links!=null)\r
{\r
Menu linkMenu = new Menu("Link");\r
MenuItem item;\r
link = links.elementAt(i).toString();\r
final String target = link.substring(0, link.indexOf("|"));\r
item = new MenuItem(target);\r
- String id = seq.getName();\r
- if(id.indexOf("|")>-1)\r
- id = id.substring(id.lastIndexOf("|")+1);\r
\r
- final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ final String url;\r
\r
+ if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+ {\r
+ String id = seq.getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+ url = link.substring(link.indexOf("|") + 1,\r
+ link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\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
});\r
linkMenu.add(item);\r
}\r
- add(linkMenu);\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
-\r
+ if(seq!=null)\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
\r
public void actionPerformed(ActionEvent evt)\r
{\r
- if(evt.getSource()==clustalColour)\r
+ Object source = evt.getSource();\r
+ if(source==clustalColour)\r
clustalColour_actionPerformed();\r
- else if(evt.getSource()==zappoColour)\r
+ else if(source==zappoColour)\r
zappoColour_actionPerformed();\r
- else if(evt.getSource()==taylorColour)\r
+ else if(source==taylorColour)\r
taylorColour_actionPerformed();\r
- else if(evt.getSource()==hydrophobicityColour)\r
+ else if(source==hydrophobicityColour)\r
hydrophobicityColour_actionPerformed();\r
- else if(evt.getSource()==helixColour)\r
+ else if(source==helixColour)\r
helixColour_actionPerformed();\r
- else if(evt.getSource()==strandColour)\r
+ else if(source==strandColour)\r
strandColour_actionPerformed();\r
- else if(evt.getSource()==clustalColour)\r
+ else if(source==turnColour)\r
turnColour_actionPerformed();\r
- else if(evt.getSource()==buriedColour)\r
+ else if(source==buriedColour)\r
buriedColour_actionPerformed();\r
- else if(evt.getSource()==nucleotideMenuItem)\r
+ else if(source==nucleotideMenuItem)\r
nucleotideMenuItem_actionPerformed();\r
\r
- else if(evt.getSource()==userDefinedColour)\r
- userDefinedColour_actionPerformed();\r
- else if(evt.getSource()==PIDColour)\r
- PIDColour_actionPerformed();\r
- else if(evt.getSource()==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(evt.getSource()==noColourmenuItem)\r
+ else if (source == noColourmenuItem)\r
noColourmenuItem_actionPerformed();\r
- else if(evt.getSource()==conservationMenuItem)\r
- conservationMenuItem_itemStateChanged();\r
- else if(evt.getSource()==unGroupMenuItem)\r
+ else if (source == conservationMenuItem)\r
+ conservationMenuItem_itemStateChanged();\r
+ else if (source == unGroupMenuItem)\r
unGroupMenuItem_actionPerformed();\r
\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==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
+ {\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\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
+\r
+ if (source == toggleCase)\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(start, end);\r
+ else\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == toUpper, 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
+ }\r
+ while (end < sg.getEndRes());\r
+ }\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ }\r
+ }\r
+ else\r
+ outputText(evt);\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+ Vector vseqs = new Vector();\r
+\r
+ String [] selection = ap.av.getViewAsString(true);\r
+ SequenceI [] seqs = ap.av.getSelectionAsNewSequence();\r
+ if (selection != null)\r
+ {\r
+ for (int i = 0; i < selection.length; i++)\r
+ {\r
+ Sequence seq = new Sequence(\r
+ seqs[i].getName(),\r
+ selection[i],\r
+ seqs[i].getStart(), seqs[i].getEnd());\r
+ seq.setDescription(seqs[i].getDescription());\r
+ vseqs.addElement( seq );\r
+ }\r
+ }\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
+ vseqs,\r
+ ap.av.showJVSuffix));\r
+\r
}\r
\r
- void addPDB(Sequence seq)\r
+ void addPDB()\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
cap.setText("Paste your PDB file here.");\r
- cap.setPDBImport(seq, ap.seqPanel.seqCanvas);\r
+ cap.setPDBImport(seq);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
throws Exception\r
{\r
groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Define");\r
+ groupMenu.setLabel("Selection");\r
\r
unGroupMenuItem.setLabel("Remove Group");\r
unGroupMenuItem.addActionListener(this);\r
showText.addItemListener(this);\r
showColourText.setLabel("Colour Text");\r
showColourText.addItemListener(this);\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
\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.addSeparator();\r
groupMenu.add(showBoxes);\r
groupMenu.add(showText);\r
groupMenu.add(showColourText);\r
BLOSUM62Colour.addActionListener(this);\r
conservationMenuItem.setLabel("Conservation");\r
\r
+ editMenu.add(copy);\r
+ copy.addActionListener(this);\r
+ editMenu.add(cut);\r
+ cut.addActionListener(this);\r
+ editMenu.add(toUpper);\r
+ toUpper.addActionListener(this);\r
+ editMenu.add(toLower);\r
+ toLower.addActionListener(this);\r
+ editMenu.add(toggleCase);\r
+ seqMenu.add(pdb);\r
+ seqMenu.add(repGroup);\r
+ toggleCase.addActionListener(this);\r
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\r
+\r
}\r
\r
void refresh()\r
{\r
- SequenceGroup sg = getGroup();\r
- if(sg!=null)\r
- {\r
- SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
- if (superG != null)\r
- {\r
- superG.setSuperGroupProperties(sg);\r
- }\r
- }\r
ap.seqPanel.seqCanvas.repaint();\r
if(ap.overviewPanel!=null)\r
ap.overviewPanel.updateOverviewImage();\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(true), 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(true), 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(true), 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(true), 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(true), 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(false)<1)\r
+ {\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
+ for(int i=0; i<gsize; i++)\r
+ {\r
+ if(representGroup && sg.getSequenceAt(i)!=seq)\r
+ {\r
+ seq.addHiddenSequence(sg.getSequenceAt(i));\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+ else if(!representGroup)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(index);\r
+ }\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+\r
+ ap.av.setSelectionGroup(null);\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff