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(false)>0)\r
else\r
{\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
}\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.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);\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
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
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