/*\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
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
e.printStackTrace();\r
}\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
+ i++)\r
{\r
- MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
- elementAt(\r
- i));\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
\r
- if (sg != null && sg.getSize(false)>0)\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
remove(groupMenu);\r
}\r
\r
- if (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
{\r
String id = seq.getName();\r
if (id.indexOf("|") > -1)\r
+ {\r
id = id.substring(id.lastIndexOf("|") + 1);\r
+ }\r
\r
url = link.substring(link.indexOf("|") + 1,\r
link.indexOf("$SEQUENCE_ID$"))\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
- ap.alignFrame.showURL(url, target);\r
- }\r
- });\r
- linkMenu.add(item);\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
+ if (seq != null)\r
+ {\r
seqMenu.add(linkMenu);\r
+ }\r
else\r
+ {\r
add(linkMenu);\r
+ }\r
}\r
- if(seq!=null)\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
+ 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
Object source = evt.getSource();\r
- if(source==clustalColour)\r
+ if (source == clustalColour)\r
+ {\r
clustalColour_actionPerformed();\r
- else if(source==zappoColour)\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
zappoColour_actionPerformed();\r
- else if(source==taylorColour)\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
taylorColour_actionPerformed();\r
- else if(source==hydrophobicityColour)\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
hydrophobicityColour_actionPerformed();\r
- else if(source==helixColour)\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
helixColour_actionPerformed();\r
- else if(source==strandColour)\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
strandColour_actionPerformed();\r
- else if(source==clustalColour)\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
turnColour_actionPerformed();\r
- else if(source==buriedColour)\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
buriedColour_actionPerformed();\r
- else if(source==nucleotideMenuItem)\r
+ }\r
+ else if (source == nucleotideMenuItem)\r
+ {\r
nucleotideMenuItem_actionPerformed();\r
+ }\r
\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
+ }\r
else if (source == noColourmenuItem)\r
+ {\r
noColourmenuItem_actionPerformed();\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 == pdb)\r
+ else if (source == sequenceName)\r
+ {\r
+ editName();\r
+ }\r
+ else if (source == pdb)\r
+ {\r
addPDB();\r
- else if(source == hideSeqs)\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
hideSequences(false);\r
- else if(source == repGroup)\r
+ }\r
+ else if (source == repGroup)\r
+ {\r
hideSequences(true);\r
- else if(source == revealAll)\r
+ }\r
+ else if (source == revealAll)\r
{\r
- ap.av.showAllHiddenSeqs();\r
- ap.repaint();\r
+ ap.av.showAllHiddenSeqs();\r
}\r
\r
- else if(source==copy)\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
- else if(source==cut)\r
+ }\r
+ else if (source == cut)\r
+ {\r
ap.alignFrame.cut_actionPerformed();\r
- else if(source==toUpper || source==toLower || source==toggleCase)\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
- for (int g = 0; g < sg.getSize(true); g++)\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
- 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
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
}\r
- ap.seqPanel.seqCanvas.repaint();\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 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
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
\r
Frame frame = new Frame();\r
frame.add(cap);\r
\r
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
e.getActionCommand(),\r
- vseqs,\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()\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
groupMenu.setLabel("Group");\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
hideSeqs.setLabel("Hide Sequences");\r
repGroup.setLabel("Represent Group with");\r
revealAll.setLabel("Reveal All");\r
-\r
+ menu1.setLabel("Group");\r
add(groupMenu);\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.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
+ groupMenu.add(menu1);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\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
\r
void refresh()\r
{\r
ap.seqPanel.seqCanvas.repaint();\r
- if(ap.overviewPanel!=null)\r
+ if (ap.overviewPanel != null)\r
+ {\r
ap.overviewPanel.updateOverviewImage();\r
+ }\r
}\r
\r
protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), 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.getSequences(true), 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.getSequences(true), 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.getSequences(true), 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.getSequences(true), 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
void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize(false)<1)\r
+ if (sg == null || sg.getSize() < 1)\r
{\r
- ap.av.hideSequence(seq);\r
+ ap.av.hideSequence(new SequenceI[]\r
+ {seq});\r
return;\r
}\r
\r
- int index = 0;\r
- while(index < sg.getSize(false))\r
- {\r
- if(representGroup && sg.getSequenceAt(index)!=seq)\r
- {\r
- seq.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- else if(!representGroup)\r
- {\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- index ++;\r
- }\r
+ ap.av.setSelectionGroup(null);\r
\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- refresh();\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