/*\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) 2007 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
\r
package jalview.appletgui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.Vector;\r
\r
import jalview.analysis.*;\r
+import jalview.commands.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
\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
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
+ 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;\r
+ i++)\r
+ {\r
+ MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.\r
+ 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() > 0)\r
{\r
+ editGroupName.setLabel(sg.getName());\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
String link;\r
- for(int i=0; i<links.size(); i++)\r
+ for (int i = 0; i < links.size(); i++)\r
{\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
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.alignFrame.showURL(url, target);\r
- }\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
+ final String url;\r
+\r
+ if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+ {\r
+ String id = seq.getName();\r
+ if (id.indexOf("|") > -1)\r
+ {\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+ }\r
\r
- add(item);\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
+ {\r
+ url = link.substring(link.lastIndexOf("|") + 1);\r
+ }\r
\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
+ }\r
+ if (seq != null)\r
+ {\r
+ seqMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
+ }\r
+ if (seq != null)\r
+ {\r
+ seqMenu.setLabel(seq.getName());\r
+ repGroup.setLabel("Represent Group with " + seq.getName());\r
+ }\r
+ else\r
+ {\r
+ remove(seqMenu);\r
+ }\r
\r
+ if (!ap.av.hasHiddenRows)\r
+ {\r
+ remove(revealAll);\r
}\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
{\r
- if(evt.getSource()==abovePIDColour)\r
+ if (evt.getSource() == abovePIDColour)\r
+ {\r
abovePIDColour_itemStateChanged();\r
- else if(evt.getSource()==showColourText)\r
+ }\r
+ else if (evt.getSource() == showColourText)\r
+ {\r
showColourText_itemStateChanged();\r
- else if(evt.getSource()==showText)\r
+ }\r
+ else if (evt.getSource() == showText)\r
+ {\r
showText_itemStateChanged();\r
- else if(evt.getSource()==showBoxes)\r
- showBoxes_itemStateChanged() ;\r
+ }\r
+ else if (evt.getSource() == showBoxes)\r
+ {\r
+ showBoxes_itemStateChanged();\r
+ }\r
}\r
\r
public void actionPerformed(ActionEvent evt)\r
{\r
- if(evt.getSource()==clustalColour)\r
+ Object source = evt.getSource();\r
+ if (source == clustalColour)\r
+ {\r
clustalColour_actionPerformed();\r
- else if(evt.getSource()==zappoColour)\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
zappoColour_actionPerformed();\r
- else if(evt.getSource()==taylorColour)\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
taylorColour_actionPerformed();\r
- else if(evt.getSource()==hydrophobicityColour)\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
hydrophobicityColour_actionPerformed();\r
- else if(evt.getSource()==helixColour)\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
helixColour_actionPerformed();\r
- else if(evt.getSource()==strandColour)\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
strandColour_actionPerformed();\r
- else if(evt.getSource()==clustalColour)\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
turnColour_actionPerformed();\r
- else if(evt.getSource()==buriedColour)\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
buriedColour_actionPerformed();\r
- else if(evt.getSource()==nucleotideMenuItem)\r
+ }\r
+ else if (source == nucleotideMenuItem)\r
+ {\r
nucleotideMenuItem_actionPerformed();\r
+ }\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
+ {\r
+ userDefinedColour_actionPerformed();\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ PIDColour_actionPerformed();\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
BLOSUM62Colour_actionPerformed();\r
- else if(evt.getSource()==noColourmenuItem)\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
noColourmenuItem_actionPerformed();\r
- else if(evt.getSource()==conservationMenuItem)\r
- conservationMenuItem_itemStateChanged();\r
- else if(evt.getSource()==unGroupMenuItem)\r
+ }\r
+ else if (source == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_itemStateChanged();\r
+ }\r
+ else if (source == unGroupMenuItem)\r
+ {\r
unGroupMenuItem_actionPerformed();\r
+ }\r
+\r
+ else if (source == sequenceName)\r
+ {\r
+ editName();\r
+ }\r
+ else if (source == pdb)\r
+ {\r
+ addPDB();\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
+ hideSequences(false);\r
+ }\r
+ else if (source == repGroup)\r
+ {\r
+ hideSequences(true);\r
+ }\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
+ {\r
+ ap.alignFrame.copy_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed();\r
+ }\r
+ else if (source == toUpper || source == toLower || source == toggleCase)\r
+ {\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
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ if (start == 0)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(start);\r
+ }\r
+\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ if (end > sg.getEndRes())\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ }\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
+ 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),\r
+ startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ outputText(evt);\r
+ }\r
\r
}\r
\r
- void addPDB(Sequence seq)\r
+ void outputText(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);\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.paintAlignment(false);\r
+ }\r
+ }\r
+\r
+ void addPDB()\r
+ {\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
+ 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
+ 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(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
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\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
+ ap.paintAlignment(true);\r
}\r
\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
protected void abovePIDColour_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
+ if (sg.cs == null)\r
+ {\r
+ return;\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.\r
+ 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.\r
+ 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.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\r
protected void conservationMenuItem_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
\r
if (conservationMenuItem.getState())\r
{\r
\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
refresh();\r
}\r
\r
-\r
SequenceGroup getGroup()\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
// this method won't add a new group if it already exists\r
- if(sg!=null)\r
+ if (sg != null)\r
+ {\r
ap.av.alignment.addGroup(sg);\r
+ }\r
\r
return sg;\r
}\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
ap.av.alignment.deleteGroup(sg);\r
ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ ap.paintAlignment(true);\r
}\r
\r
public void showColourText_itemStateChanged()\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[]\r
+ {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