/*\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
import MCview.*;\r
\r
import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
-\r
-\r
import jalview.schemes.*;\r
+import jalview.commands.ChangeCaseCommand;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
\r
import java.util.Vector;\r
+import jalview.io.FormatAdapter;\r
\r
\r
/**\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
+ JMenuItem sequenceFeature = new JMenuItem();\r
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
\r
/**\r
* Creates a new PopupMenu object.\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
+ sequenceMenu.setText(sequence.getName());\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\r
- && ap.av.getSelectionGroup().getSize(false)>1)\r
+ && ap.av.getSelectionGroup().getSize()>1)\r
{\r
menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
if (ap.av.adjustForHiddenSeqs(index) -\r
ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
{\r
- menuItem = new JMenuItem("Reveal");\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
- ap.repaint();\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
}\r
});\r
- sequenceMenu.add(menuItem);\r
+ add(menuItem);\r
}\r
\r
menuItem = new JMenuItem("Reveal All");\r
public void actionPerformed(ActionEvent e)\r
{\r
ap.av.showAllHiddenSeqs();\r
- ap.repaint();\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
- }\r
+ }\r
});\r
\r
- sequenceMenu.add(menuItem);\r
-\r
-\r
-\r
+ add(menuItem);\r
}\r
\r
\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
\r
if(links != null && links.size()>0)\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("Group");\r
+ groupMenu.setText("Selection");\r
groupName.setText("Name");\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- upperCase_actionPerformed(e);\r
+ changeCase(e);\r
}\r
});\r
copy.setText("Copy");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- lowerCase_actionPerformed(e);\r
+ changeCase(e);\r
}\r
});\r
toggle.setText("Toggle Case");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- toggle_actionPerformed(e);\r
+ changeCase(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
+ sequenceFeature.setText("Create Sequence Feature");\r
+ sequenceFeature.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceFeature_actionPerformed(e);\r
+ }\r
+ });\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setText("Group");\r
add(groupMenu);\r
- add(sequenceMenu);\r
- this.add(editMenu);\r
- groupMenu.add(groupName);\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
- groupMenu.addSeparator();\r
- groupMenu.add(outline);\r
- sequenceMenu.add(sequenceName);\r
- colourMenu.add(noColourmenuItem);\r
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(jMenu1);\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(textColour);\r
+ colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.add(PIDColour);\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
+ jMenu1.add(groupName);\r
+ jMenu1.add(unGroupMenuItem);\r
+ jMenu1.add(colourMenu);\r
+ jMenu1.add(showBoxes);\r
+ jMenu1.add(showText);\r
+ jMenu1.add(showColourText);\r
+ jMenu1.add(outline);\r
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\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.getSequences(true),\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
if (abovePIDColour.isSelected())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
\r
sg.cs = udc;\r
}\r
+ refresh();\r
}\r
/**\r
* DOCUMENT ME!\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth());\r
+ sg.getSequences(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
groupName.setText(reply);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
-\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\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
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
}\r
\r
s = s.replace(' ', '_');\r
- sequence.getDatasetSequence().setName(s);\r
sequence.setName(s);\r
ap.repaint();\r
}\r
\r
- sequence.getDatasetSequence().setDescription(description.getText());\r
sequence.setDescription(description.getText());\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
\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(sequence);\r
+ ap.av.hideSequence(new SequenceI[]{sequence});\r
return;\r
}\r
\r
- int index = 0;\r
- while(index < sg.getSize(false))\r
- {\r
- if(representGroup && sg.getSequenceAt(index)!=sequence)\r
- {\r
- sequence.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
- refresh();\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(sequence, 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
public void copy_actionPerformed(ActionEvent e)\r
ap.alignFrame.cut_actionPerformed(null);\r
}\r
\r
- public void upperCase_actionPerformed(ActionEvent e)\r
+ void changeCase(ActionEvent e)\r
{\r
+ Object source = e.getSource();\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null)\r
- return;\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
+ start = ap.av.colSel.adjustForHiddenColumns(start);\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
+ 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
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if(source==toggle)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if(source==upperCase)\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
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
+ }\r
+ }\r
+\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+\r
+ String [] omitHidden = null;\r
\r
- for(int g=0; g<sg.getSize(true); g++)\r
+ if(ap.av.hasHiddenColumns)\r
{\r
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
+ System.out.println("PROMPT USER HERE");\r
+ omitHidden = ap.av.getViewAsString(true);\r
}\r
- ap.repaint();\r
+\r
+ cap.setText(new FormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ ap.av.getSelectionAsNewSequence(),\r
+ omitHidden));\r
}\r
\r
- public void lowerCase_actionPerformed(ActionEvent e)\r
+\r
+ public void pdbFromFile_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null)\r
- return;\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
- for(int g=0; g<sg.getSize(true); g++)\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
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id);\r
+ sequence.getDatasetSequence()\r
+ .addPDBId(entry);\r
}\r
- ap.repaint();\r
}\r
\r
- public void toggle_actionPerformed(ActionEvent e)\r
+ public void discoverPDB_actionPerformed(ActionEvent e)\r
+ {\r
+ new jalview.io.DBRefFetcher(\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+ }\r
+\r
+ public void sequenceFeature_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
+ if(sg==null)\r
return;\r
\r
- for (int g = 0; g < sg.getSize(true); g++)\r
+ int gSize= sg.getSize();\r
+ SequenceI [] seqs = new SequenceI[gSize];\r
+ SequenceFeature [] features = new SequenceFeature[gSize];\r
+\r
+ for (int i = 0; i < gSize; i++)\r
{\r
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+ seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
+ int end = sg.findEndRes(sg.getSequenceAt(i));\r
+ features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
}\r
\r
- ap.repaint();\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
+ .createNewFeatures(seqs, features))\r
+ {\r
+ ap.alignFrame.showSeqFeatures.setSelected(true);\r
+ ap.av.setShowSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
}\r
\r
+ public void textColour_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg != null)\r
+ new TextColourChooser().chooseColour(ap, sg);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff