/*\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
\r
import javax.swing.*;\r
\r
+import java.util.Vector;\r
+import jalview.io.FormatAdapter;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
-\r
- /**\r
+ JMenu editMenu = new JMenu();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem upperCase = new JMenuItem();\r
+ JMenuItem lowerCase = new JMenuItem();\r
+ JMenuItem toggle = new JMenuItem();\r
+ JMenu pdbMenu = new JMenu();\r
+ JMenuItem pdbFromFile = new JMenuItem();\r
+ JMenuItem enterPDB = new JMenuItem();\r
+ JMenuItem discoverPDB = new JMenuItem();\r
+ JMenu outputMenu = new JMenu();\r
+\r
+ /**\r
* Creates a new PopupMenu object.\r
*\r
* @param ap DOCUMENT ME!\r
* @param seq DOCUMENT ME!\r
*/\r
- public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputMenu.add(item);\r
+ }\r
+\r
+\r
try\r
{\r
jbInit();\r
\r
if (seq != null)\r
{\r
+ int start = Math.max(sequence.getName().length()-15, 0);\r
+ sequenceMenu.setText(sequence.getName().substring(start));\r
+\r
JMenuItem menuItem;\r
if( seq.getDatasetSequence().getPDBId() != null)\r
{\r
java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
elements();\r
+\r
while (e.hasMoreElements())\r
{\r
final PDBEntry pdb = (PDBEntry) e.nextElement();\r
hideSequences(false);\r
}\r
});\r
- sequenceMenu.add(menuItem);\r
+ add(menuItem);\r
\r
- if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)\r
+ if(ap.av.getSelectionGroup() !=null\r
+ && ap.av.getSelectionGroup().getSize(false)>1)\r
{\r
menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
sequenceMenu.add(menuItem);\r
}\r
\r
+ if (ap.av.hasHiddenRows)\r
+ {\r
+ final int index = ap.av.alignment.findIndex(seq);\r
+\r
+ if (ap.av.adjustForHiddenSeqs(index) -\r
+ ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
+ {\r
+ menuItem = new JMenuItem("Reveal Sequences");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showSequence(index);\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+ add(menuItem);\r
+ }\r
+\r
+ menuItem = new JMenuItem("Reveal All");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+\r
+ add(menuItem);\r
+ }\r
+\r
\r
}\r
\r
showColourText.setSelected(sg.getColourText());\r
showBoxes.setSelected(sg.getDisplayBoxes());\r
}\r
+ else\r
+ {\r
+ groupMenu.setVisible(false);\r
+ editMenu.setVisible(false);\r
+ }\r
\r
if (!ap.av.alignment.getGroups().contains(sg))\r
{\r
unGroupMenuItem.setVisible(false);\r
}\r
- else\r
- {\r
- groupMenu.insertSeparator(3);\r
- }\r
+\r
\r
if (seq == null)\r
{\r
sequenceMenu.setVisible(false);\r
+ pdbMenu.setVisible(false);\r
}\r
- else\r
- {\r
- java.util.Vector links = Preferences.sequenceURLLinks;\r
\r
+ if(links != null && links.size()>0)\r
+ {\r
JMenu linkMenu = new JMenu("Link");\r
JMenuItem item;\r
for(int i=0; i<links.size(); i++)\r
{\r
String link = links.elementAt(i).toString();\r
+ final String label = link.substring(0, link.indexOf("|"));\r
+ item = new JMenuItem(label);\r
+ final String url;\r
\r
- item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
- String id = sequence.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
+ 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
\r
item.addActionListener(new java.awt.event.ActionListener()\r
\r
linkMenu.add(item);\r
}\r
- add(linkMenu);\r
+ if(sequence!=null)\r
+ sequenceMenu.add(linkMenu);\r
+ else\r
+ add(linkMenu);\r
}\r
}\r
\r
private void jbInit() throws Exception\r
{\r
groupMenu.setText("Group");\r
- groupMenu.setText("Define");\r
+ groupMenu.setText("Selection");\r
groupName.setText("Name");\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
showColourText_actionPerformed(e);\r
}\r
});\r
- add(groupMenu);\r
- add(sequenceMenu);\r
- groupMenu.add(groupName);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ upperCase_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ lowerCase_actionPerformed(e);\r
+ }\r
+ });\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ toggle_actionPerformed(e);\r
+ }\r
+ });\r
+ pdbMenu.setText("Associate Structure with Sequence");\r
+ pdbFromFile.setText("From File");\r
+ pdbFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pdbFromFile_actionPerformed(e);\r
+ }\r
+ });\r
+ enterPDB.setText("Enter PDB Id");\r
+ enterPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ enterPDB_actionPerformed(e);\r
+ }\r
+ });\r
+ discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ discoverPDB_actionPerformed(e);\r
+ }\r
+ });\r
+ outputMenu.setText("Output to Textbox...");\r
+ add(groupMenu);\r
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(groupName);\r
+ groupMenu.add(unGroupMenuItem);\r
groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
+ groupMenu.add(showBoxes);\r
groupMenu.add(showText);\r
groupMenu.add(showColourText);\r
- groupMenu.addSeparator();\r
- groupMenu.add(outline);\r
+ groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
- colourMenu.add(noColourmenuItem);\r
+ sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.add(PIDColour);\r
colourMenu.addSeparator();\r
colourMenu.add(abovePIDColour);\r
colourMenu.add(conservationMenuItem);\r
- noColourmenuItem.setText("None");\r
+ editMenu.add(copy);\r
+ editMenu.add(cut);\r
+ editMenu.add(upperCase);\r
+ editMenu.add(lowerCase);\r
+ editMenu.add(toggle);\r
+ pdbMenu.add(pdbFromFile);\r
+ pdbMenu.add(enterPDB);\r
+ pdbMenu.add(discoverPDB);\r
+ noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
\r
- ap.seqPanel.repaint();\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
}\r
\r
/**\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences,\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
if (abovePIDColour.isSelected())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\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
if (conservationMenuItem.isSelected())\r
{\r
Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(true), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
SequenceGroup sg = getGroup();\r
StringBuffer sb = new StringBuffer();\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
- Sequence tmp = (Sequence) sg.sequences.get(i);\r
+ Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
sb.append("\n");\r
}\r
void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize()<1)\r
+ if(sg==null || sg.getSize(false)<1)\r
{\r
- ap.av.hideSequence(sequence);\r
+ ap.av.hideSequence(new SequenceI[]{sequence});\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
- while(index < sg.sequences.size())\r
+ while(index < gsize)\r
{\r
if(representGroup && sg.getSequenceAt(index)!=sequence)\r
{\r
sequence.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ hseqs[index] = sg.getSequenceAt(index);\r
}\r
else if(!representGroup)\r
{\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
+ hseqs[index] = sg.getSequenceAt(index);\r
}\r
index ++;\r
}\r
\r
+ ap.av.hideSequence(hseqs);\r
+\r
ap.av.setSelectionGroup(null);\r
- refresh();\r
}\r
\r
+ public void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed(null);\r
+ }\r
+\r
+ public void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed(null);\r
+ }\r
+\r
+ public void upperCase_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
+\r
+ public void lowerCase_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
+\r
+ public void toggle_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
+\r
+ void changeCase(Object source)\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 == toggle)\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(start, end);\r
+ else\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == upperCase, 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
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ }\r
+ }\r
+\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+\r
+ String [] omitHidden = null;\r
+\r
+ if(ap.av.hasHiddenColumns)\r
+ {\r
+ System.out.println("PROMPT USER HERE");\r
+ omitHidden = ap.av.getViewAsString(true);\r
+ }\r
+\r
+ cap.setText(new FormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ ap.av.getSelectionAsNewSequence(),\r
+ omitHidden));\r
+ }\r
+\r
+\r
+ public void pdbFromFile_actionPerformed(ActionEvent e)\r
+ {\r
+ jalview.io.JalviewFileChooser chooser\r
+ = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Select a PDB file");\r
+ chooser.setToolTipText("Load a PDB file");\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ PDBEntry entry = new PDBEntry();\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ try\r
+ {\r
+ MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
+ jalview.io.AppletFormatAdapter.FILE);\r
+\r
+ if (pdbfile.id == null)\r
+ {\r
+ String reply = JOptionPane.showInternalInputDialog(\r
+ Desktop.desktop,\r
+ "Couldn't find a PDB id in the file supplied."\r
+ + "Please enter an Id to identify this structure.",\r
+ "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
+ if (reply == null)\r
+ return;\r
+\r
+ entry.setId(reply);\r
+ }\r
+ else\r
+ entry.setId(pdbfile.id);\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ entry.setFile(choice);\r
+ sequence.getDatasetSequence().addPDBId(entry);\r
+ }\r
+\r
+ }\r
+\r
+ public void enterPDB_actionPerformed(ActionEvent e)\r
+ {\r
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (id != null && id.length() > 0)\r
+ {\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id);\r
+ sequence.getDatasetSequence()\r
+ .addPDBId(entry);\r
+ }\r
+ }\r
+\r
+ public void discoverPDB_actionPerformed(ActionEvent e)\r
+ {\r
+ new jalview.io.DBRefFetcher(\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff