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.formats.size()-1; i++)\r
+ {\r
+ MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
+ elementAt(\r
+ i));\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
+ if (sg != null && sg.getSize(false)>0)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
+\r
}\r
else\r
{\r
remove(groupMenu);\r
}\r
\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- groupMenu.remove(unGroupMenuItem);\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
item.addActionListener(new java.awt.event.ActionListener()\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
-\r
- add(item);\r
-\r
-\r
+ seqMenu.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
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 == 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
+ ap.repaint();\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)\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(); g++)\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
{\r
- sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),\r
- sg.getEndRes() + 1);\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
}\r
ap.seqPanel.seqCanvas.repaint();\r
}\r
}\r
- else if(source==toLower)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null)\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 g = 0; g < sg.getSize(); g++)\r
+ for (int i = 0; i < selection.length; i++)\r
{\r
- sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\r
- ap.seqPanel.seqCanvas.repaint();\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);\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
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
- add(editMenu);\r
editMenu.add(copy);\r
copy.addActionListener(this);\r
editMenu.add(cut);\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
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(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
+\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
+ refresh();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff