import jalview.analysis.*;\r
import jalview.io.*;\r
import jalview.ws.*;\r
-import MCview.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
import javax.swing.*;\r
import javax.swing.event.*;\r
import java.util.*;\r
-import jalview.datamodel.SequenceI;\r
+import java.awt.datatransfer.*;\r
+\r
\r
public class AlignFrame extends GAlignFrame\r
{\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
fontNameMenuItem.setText(viewport.getFont().getName());\r
fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
+\r
+ addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(InternalFrameEvent evt)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ { alignPanel.requestFocus(); }\r
+ });\r
+\r
+ }\r
+ });\r
+\r
+ AlignmentUtil.fetchSequenceFeatures(al, alignPanel);\r
}\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
+ JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
chooser.setToolTipText("Save");\r
int value = chooser.showSaveDialog(this);\r
if(value == JFileChooser.APPROVE_OPTION)\r
{\r
String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
try{\r
java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
alignPanel.RefreshPanels();\r
}\r
\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+ if (sg == null)\r
+ return;\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.sequences.contains(seq))\r
+ continue;\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+ if (sg.sequences.contains(temp))\r
+ continue;\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.sequences.contains(seq))\r
+ continue;\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+ if (sg.sequences.contains(temp))\r
+ continue;\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+\r
+\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getRubberbandGroup()==null)\r
+ return;\r
+\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ StringBuffer buffer= new StringBuffer();\r
+\r
+ for(int i=0; i<sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
+ +seq.findPosition( sg.getEndRes() )+ "\t"\r
+ +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
+ }\r
+ c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
+\r
+ }\r
+\r
+\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(false);\r
+ }\r
+\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try{\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+ if (contents == null)\r
+ return;\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ StringTokenizer st = new StringTokenizer(str);\r
+ ArrayList seqs = new ArrayList();\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
+\r
+ if(!newAlignment)\r
+ viewport.alignment.addSequence(sequence);\r
+ else\r
+ seqs.add(sequence);\r
+ }\r
+\r
+ if(newAlignment)\r
+ {\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ seqs.toArray(newSeqs);\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
+ if (newHeight > 500)\r
+ newHeight = 500;\r
+ Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
+ }\r
+ else\r
+ {\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ }catch(Exception ex){}// could be anything being pasted in here\r
+\r
+ }\r
+\r
+\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getRubberbandGroup() == null)\r
+ return;\r
+\r
+ SequenceGroup sg = viewport.getRubberbandGroup();\r
+ for (int i=0;i < sg.sequences.size(); i++)\r
+ viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
+\r
+ viewport.alignment.deleteGroup(sg);\r
+ viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
+ if(viewport.getAlignment().getHeight()<1)\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }catch(Exception ex){}\r
+ alignPanel.RefreshPanels();\r
+\r
+ }\r
+\r
+\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
{\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
+ viewport.getSelection().clear();\r
+\r
alignPanel.RefreshPanels();\r
}\r
\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ viewport.setRubberbandGroup(null);\r
viewport.getSelection().clear();\r
PaintRefresher.Refresh(null);\r
}\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
}\r
\r
\r
alignPanel.RefreshPanels();\r
}\r
\r
- public void secondaryStructure_actionPerformed(ActionEvent evt)\r
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
{\r
- alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());\r
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+ alignPanel.RefreshPanels();\r
}\r
\r
public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( null );\r
- changeColour();\r
+ changeColour( null );\r
}\r
\r
\r
- public void Colour_actionPerformed(ActionEvent e)\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
- conservationMenuItem.setSelected(false);\r
abovePIDThreshold.setSelected(false);\r
- changeColour();\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
- changeColour();\r
+ changeColour(new ZappoColourScheme());\r
}\r
\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
- changeColour();\r
+ changeColour(new TaylorColourScheme());\r
}\r
\r
\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
- changeColour();\r
+ changeColour( new HydrophobicColourScheme() );\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new HelixColourScheme() );\r
- changeColour();\r
+ changeColour(new HelixColourScheme() );\r
}\r
\r
\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new StrandColourScheme() );\r
- changeColour();\r
+ changeColour(new StrandColourScheme());\r
}\r
\r
\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new TurnColourScheme() );\r
- changeColour();\r
+ changeColour(new TurnColourScheme());\r
}\r
\r
\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
- changeColour();\r
+ changeColour(new BuriedColourScheme() );\r
}\r
\r
public void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
- changeColour();\r
+ changeColour(new NucleotideColourScheme());\r
}\r
\r
\r
- void changeColour()\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold_actionPerformed(null);\r
- else if(conservationMenuItem.isSelected())\r
- conservationMenuItem_actionPerformed(null);\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
\r
\r
- alignPanel.RefreshPanels();\r
- }\r
\r
- void addConservationOrPIDColour()\r
+ void changeColour(ColourSchemeI cs)\r
{\r
- int x=0, y=0, threshold = 70;\r
\r
- if(sliderFrame!=null)\r
- try\r
- {\r
- x = sliderFrame.getX();\r
- y = sliderFrame.getY();\r
- SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
- threshold = sp.getValue();\r
- sliderFrame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- { ex.printStackTrace(); }\r
+ if(viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ sg.cs = cs;\r
\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+ if(abovePIDThreshold.isSelected())\r
+ abovePIDThreshold_actionPerformed(null);\r
+ else if( viewport.getConservationSelected() )\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, sg.getStartRes(),\r
+ sg.getEndRes());\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+\r
+ sg.cs = ccs;\r
+ }\r
\r
- ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\r
+ }\r
+ }\r
\r
- if(conservationMenuItem.isSelected())\r
- {\r
- Alignment al = (Alignment)viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
\r
- c.calculate();\r
- c.verdict(false, 100);\r
+ if ( viewport.getAbovePIDThreshold())\r
+ {\r
+ int threshold = 0;\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
+ Desktop.hideConservationSlider();\r
\r
- if(ccs!=null)\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
- else\r
- ccs = new ConservationColourScheme(c, oldCs);\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold);\r
\r
- viewport.setGlobalColourScheme( ccs );\r
+ viewport.setGlobalColourScheme(cs);\r
\r
- }\r
- else if(oldCs instanceof ConservationColourScheme)\r
- {\r
- oldCs = ccs.cs;\r
- viewport.setGlobalColourScheme( oldCs );\r
- }\r
+ }\r
+ else\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(0);\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(0);\r
\r
\r
- if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
- {\r
- sliderFrame = new JInternalFrame();\r
- sliderFrame.setMaximizable(false);\r
- sliderFrame.setResizable(false);\r
\r
- SliderPanel sp = null;\r
- if (conservationMenuItem.isSelected())\r
- {\r
- if(threshold > 50)\r
- threshold = 30;\r
- sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
- Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);\r
- threshold = 0;\r
- }\r
- else if (abovePIDThreshold.isSelected())\r
- {\r
- sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
- sp.cs = oldCs;\r
- Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
- }\r
\r
- sliderFrame.setContentPane(sp);\r
- if(x!=0 && y!=0)\r
- sliderFrame.setLocation(x,y);\r
+if ( viewport.getConservationSelected() )\r
+ {\r
+ ConservationColourScheme ccs = null;\r
\r
- }\r
- else\r
- threshold = 0;\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
\r
- if (oldCs instanceof ResidueColourScheme)\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
- rcs.setThreshold(threshold);\r
- }\r
- else if (oldCs instanceof ScoreColourScheme)\r
- {\r
- ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
- scs.setThreshold(threshold);\r
- }\r
+ ccs = new ConservationColourScheme(c, cs);\r
+\r
+ int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
+ "Background");\r
+\r
+ ccs.inc = threshold;\r
\r
+ viewport.setGlobalColourScheme(ccs);\r
\r
}\r
+ else\r
+ viewport.setGlobalColourScheme( cs );\r
+\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold.setSelected(false);\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+ Desktop.hidePIDSlider();\r
+ if(!viewport.getConservationSelected())\r
+ Desktop.hideConservationSlider();\r
\r
- addConservationOrPIDColour();\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
}\r
\r
- JInternalFrame sliderFrame;\r
+\r
public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+ Desktop.hideConservationSlider();\r
+\r
+ if(!viewport.getAbovePIDThreshold())\r
+ Desktop.hidePIDSlider();\r
+\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
\r
- addConservationOrPIDColour();\r
}\r
\r
\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new PIDColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ changeColour( new PIDColourScheme() );\r
}\r
\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- alignPanel.setColourScheme();\r
+ changeColour(new Blosum62ColourScheme(viewport) );\r
}\r
\r
\r
\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
- Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
- }\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("sort");\r
\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
+ //are the sequences aligned?\r
+ if(!viewport.alignment.isAligned())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
+ "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
JInternalFrame frame = new javax.swing.JInternalFrame();\r
TreePanel tp=null;\r
if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
if (alignment != null)\r
{\r
AlignFrame af = new AlignFrame(new Alignment(alignment));\r
+ af.clustalColour.setSelected(true);\r
+ af.clustalColour_actionPerformed(null);\r
Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
700, 500); // JBPNote - is there a new window geom. property ?\r
}\r
g.setColor(Color.black);\r
g.drawString("Clustal Alignment Web Service running", 30,30);\r
}\r
-\r
-\r
- }\r
-\r
-\r
- public void pdbTest_actionPerformed(ActionEvent e)\r
- {\r
- String reply =\r
- JOptionPane.showInternalInputDialog(this, "Enter pdb code",\r
- "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
-\r
- String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
- if (reply.length()>1)\r
- url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
-\r
- try\r
- {\r
- PDBfile pdb = new PDBfile(url,\r
- "URL");\r
- Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
- seq.setPDBfile(pdb);\r
- ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
- ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
- // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
-\r
- rotCanvas rc = new rotCanvas(pdb);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame, url, 400,400);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
}\r
-\r
-\r
- public void doKeyPressed(KeyEvent evt)\r
- {\r
-\r
- System.out.println(evt.getKeyChar());\r
- if(evt.isControlDown() && evt.getKeyChar()=='f')\r
- findMenuItem_actionPerformed(null);\r
-\r
- }\r
-\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff