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
public AlignFrame(AlignmentI al)\r
{\r
super();\r
-\r
- AlignmentUtil.addUniprotFeatures(al);\r
-\r
viewport = new AlignViewport(al,true,true,true,false);\r
alignPanel = new AlignmentPanel(this, viewport);\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
}\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
htmlOutput = null;\r
}\r
\r
+ protected void createJPG_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
+ int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
+\r
+\r
+ if(!viewport.getWrapAlignment())\r
+ {\r
+ height = viewport.alignment.getHeight() * viewport.charHeight;\r
+ width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
+ }\r
+\r
+ alignPanel.makeJPG( width, height);\r
+ }\r
+\r
+\r
public void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
//Putting in a thread avoids Swing painting problems\r
}catch(Exception ex){}\r
}\r
\r
- ArrayList historyList = new ArrayList();\r
- ArrayList redoList = new ArrayList();\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
\r
void updateEditMenuBar()\r
{\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
+ addHistoryItem("Paste");\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
+ addHistoryItem("Delete");\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
public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+ if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
+ {\r
+ AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+ }\r
alignPanel.RefreshPanels();\r
}\r
\r
\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( null );\r
- changeColour();\r
+ changeColour( null );\r
}\r
\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(\r
- new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\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
-\r
- alignPanel.RefreshPanels();\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
}\r
\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ void changeColour(ColourSchemeI cs)\r
{\r
- if(abovePIDThreshold.isSelected())\r
- {\r
- abovePIDThreshold.setSelected(false);\r
- Desktop.hidePIDSlider();\r
- }\r
\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\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
+ 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
+ }\r
+ }\r
+\r
+\r
+ if ( viewport.getAbovePIDThreshold())\r
+ {\r
+ int threshold = 0;\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
+ Desktop.hideConservationSlider();\r
+\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(cs);\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
\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
\r
+if ( viewport.getConservationSelected() )\r
+ {\r
ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\r
\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth());\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
+ c.calculate();\r
+ c.verdict(false, 100);\r
\r
- if (ccs != null)\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
- else\r
- ccs = new ConservationColourScheme(c, oldCs);\r
+ ccs = new ConservationColourScheme(c, cs);\r
\r
+ int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
+ "Background");\r
\r
- int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
+ ccs.inc = threshold;\r
\r
- ccs.inc = threshold;\r
+ viewport.setGlobalColourScheme(ccs);\r
+\r
+ }\r
+ else\r
+ viewport.setGlobalColourScheme( cs );\r
\r
- if (ccs.cs instanceof ResidueColourScheme)\r
- ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
- else if (ccs.cs instanceof ScoreColourScheme)\r
- ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
+ alignPanel.RefreshPanels();\r
+ }\r
\r
- viewport.setGlobalColourScheme(ccs);\r
\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- }\r
- else if (oldCs instanceof ConservationColourScheme)\r
- {\r
- /// ie, if we remove ConservationColourScheme from backgroundColour\r
- oldCs = ccs.cs;\r
- viewport.setGlobalColourScheme(oldCs);\r
- Desktop.hideConservationSlider();\r
- }\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+ Desktop.hidePIDSlider();\r
+ if(!viewport.getConservationSelected())\r
+ Desktop.hideConservationSlider();\r
\r
- if(e!=null)\r
- alignPanel.RefreshPanels();\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
}\r
\r
\r
public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
- int threshold = 0;\r
- if (oldCs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
- oldCs = ccs.cs;\r
- }\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+ Desktop.hideConservationSlider();\r
\r
- if(abovePIDThreshold.isSelected())\r
- {\r
- threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
- Desktop.hideConservationSlider();\r
- }\r
- else\r
- Desktop.hidePIDSlider();\r
+ if(!viewport.getAbovePIDThreshold())\r
+ Desktop.hidePIDSlider();\r
\r
- if (oldCs instanceof ResidueColourScheme)\r
- ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
- else if (oldCs instanceof ScoreColourScheme)\r
- ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
\r
- viewport.setGlobalColourScheme(oldCs);\r
- if(e!=null)\r
- alignPanel.RefreshPanels();\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme )\r
+ changeColour( ((ConservationColourScheme)cs).cs );\r
+ else\r
+ changeColour( cs );\r
+\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
- changeColour();\r
+ changeColour(new Blosum62ColourScheme(viewport) );\r
}\r
\r
\r
\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
- JInternalFrame frame = new javax.swing.JInternalFrame();\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
TreePanel tp=null;\r
if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
{\r
tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
- viewport.getStartRes(), viewport.getEndRes());\r
+ 0, viewport.alignment.getWidth());\r
}\r
else\r
{\r
tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, viewport.getStartRes(),\r
- viewport.getEndRes());\r
+ type, pwType, 0, viewport.alignment.getWidth());\r
}\r
\r
- frame.setContentPane(tp);\r
- Desktop.addInternalFrame(frame, title, 600, 500);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
}\r
\r
\r
image = new Image[9];\r
for(int i=0; i<9; i++)\r
{\r
- java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
+ java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
if (url != null)\r
{\r
image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
g.drawString("Clustal Alignment Web Service running", 30,30);\r
}\r
}\r
-\r
-\r
- public void doKeyPressed(KeyEvent evt)\r
- {\r
- if(evt.isControlDown() && evt.getKeyChar()=='f')\r
- findMenuItem_actionPerformed(null);\r
- }\r
-\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff