import javax.swing.*;\r
import javax.swing.event.*;\r
import java.util.*;\r
-import java.awt.datatransfer.*;\r
+import java.awt.datatransfer.*;\r
\r
\r
public class AlignFrame extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
final AlignViewport viewport;\r
+ public static final int NEW_WINDOW_WIDTH = 700;\r
+ public static final int NEW_WINDOW_HEIGHT = 500;\r
+ public String currentFileFormat = "Jalview";\r
+\r
public AlignFrame(AlignmentI al)\r
{\r
- super();\r
- viewport = new AlignViewport(al,true,true,true,false);\r
-\r
- String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
- String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
- String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
- if(fontName!=null && fontStyle!=null && fontSize!=null)\r
- viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
-\r
-\r
+ viewport = new AlignViewport(al);\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+ alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
+\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
\r
addInternalFrameListener(new InternalFrameAdapter()\r
\r
}\r
\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
{\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
+ , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
+ new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},\r
+ currentFileFormat);\r
+\r
+ chooser.setAcceptAllFileFilterUsed(false);\r
chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
+ chooser.setDialogTitle("Save Alignment to file");\r
chooser.setToolTipText("Save");\r
int value = chooser.showSaveDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
+ if(value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+\r
+ if (currentFileFormat.equals("Jalview"))\r
+ {\r
+ String shortName = title.replace('/', '_');\r
+ title = title.replace('\\', '_');\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,\r
+ choice);\r
+ // USE Jalview2XML to save this file\r
+ return;\r
+ }\r
+\r
String choice = chooser.getSelectedFile().getPath();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
+ String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());\r
try{\r
java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
out.println(output);\r
cap.formatForOutput();\r
frame.setContentPane(cap);\r
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
- cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+ cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
}\r
\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
htmlOutput = null;\r
}\r
\r
- protected void createJPG_actionPerformed(ActionEvent e)\r
+ protected void createPNG_actionPerformed(ActionEvent e)\r
{\r
+ alignPanel.makePNG();\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
+ protected void epsFile_actionPerformed(ActionEvent e)\r
+ {\r
+ alignPanel.makeEPS();\r
}\r
\r
\r
{\r
// must make sure we add new sequence objects her, not refs to the existing sequences\r
redoList.clear();\r
+\r
SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
{\r
viewport.getAlignment().getSequenceAt(i).getSequence());\r
}\r
\r
+\r
historyList.add(0, new Object[]{type, seq} );\r
updateEditMenuBar();\r
}\r
redoList.add(0, new Object[] {history[0], seq});\r
\r
seq = (SequenceI[]) history[1];\r
+ AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
viewport.setAlignment( new Alignment(seq) );\r
+ viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
updateEditMenuBar();\r
- alignPanel.RefreshPanels();\r
+ for(int i=0; i<old.length; i++)\r
+ viewport.alignment.addAnnotation(old[i]);\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
}\r
}\r
\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
\r
\r
protected void copy_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
+ if(viewport.getSelectionGroup()==null)\r
+ return;\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
StringBuffer buffer= new StringBuffer();\r
\r
- for(int i=0; i<sg.getSize(); i++)\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for(int i=0; i<sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index+"", seq);\r
+ }\r
+\r
+ int index=0;\r
+ for(int i=0; i<sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+ while( seq == null )\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
+ if(orderedSeqs.containsKey(index+""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+ break;\r
+ }\r
+ else\r
+ index++;\r
+ }\r
+\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
+ }\r
c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
\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
+ String newtitle = new String("Copied sequences");\r
+ if( title.startsWith("Copied sequences"))\r
+ newtitle = title;\r
+ else\r
+ newtitle = newtitle.concat("- from "+title);\r
+\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
}\r
else\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- alignPanel.RefreshPanels();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
}\r
\r
}catch(Exception ex){}// could be anything being pasted in here\r
{\r
this.setClosed(true);\r
}catch(Exception ex){}\r
- alignPanel.RefreshPanels();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
\r
}\r
\r
Object [] history = (Object[])redoList.remove(0);\r
SequenceI[] seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
+ viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
updateEditMenuBar();\r
- alignPanel.RefreshPanels();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
}\r
\r
\r
- public void groupsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(geditor);\r
- Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
- frame.setResizable(false);\r
- }\r
-\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
viewport.setSelectionGroup(null);\r
-\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
PaintRefresher.Refresh(null);\r
}\r
\r
PaintRefresher.Refresh(null);\r
}\r
\r
-\r
- public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.getColumnSelection().clear();\r
- repaint();\r
- }\r
-\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("delete columns");\r
int min = colSel.getMin();\r
viewport.getAlignment().trimLeft(min);\r
colSel.compensateForEdit(0,min);\r
- alignPanel.RefreshPanels();\r
+\r
+ if(viewport.getSelectionGroup()!=null)\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if(!sg.adjustForRemoveLeft(min))\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+\r
+ alignPanel.repaint();\r
}\r
}\r
\r
if (colSel.size() > 0)\r
{\r
int max = colSel.getMax();\r
- if(max>1)\r
- viewport.getAlignment().trimRight(max);\r
+ viewport.getAlignment().trimRight(max);\r
+ if(viewport.getSelectionGroup()!=null)\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if(!sg.adjustForRemoveRight(max))\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+\r
+\r
\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
}\r
{\r
addHistoryItem("delete gapped columns");\r
viewport.getAlignment().removeGaps();\r
- alignPanel.RefreshPanels();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
jSize--;\r
}\r
}\r
-\r
- alignPanel.RefreshPanels();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
}\r
\r
- public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- char thisChar = '-';\r
- char nextChar = '.';\r
- if(viewport.getGapCharacter()=='-')\r
- {\r
- thisChar = '.';\r
- nextChar = '-';\r
- }\r
- setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
- viewport.setGapCharacter(thisChar);\r
- alignPanel.RefreshPanels();\r
- }\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340,110);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ Desktop.addInternalFrame(frame, "Find", 340,110);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
\r
}\r
\r
\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- // JOptionPane op = new JOptionPane();\r
- JInternalFrame frame = new JInternalFrame();\r
- FontChooser fc = new FontChooser( alignPanel, frame );\r
- frame.setContentPane(fc);\r
- Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
+ FontChooser fc = new FontChooser( alignPanel );\r
+ }\r
+\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowFullId( fullSeqId.isSelected() );\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
+ alignPanel.repaint();\r
}\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
+ scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
+ scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
+ scaleRight.setVisible( wrapMenuItem.isSelected() );\r
+ alignPanel.repaint();\r
}\r
\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowText( viewTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
\r
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
{\r
- AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
((Alignment)viewport.alignment).featuresAdded = true;\r
}\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
+ if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+ return;\r
+ }\r
+ viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
+ alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
}\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
return;\r
\r
JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = alignPanel.getOverviewPanel();\r
- try{\r
- overview = new OverviewPanel(alignPanel, viewport);\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
frame.setContentPane(overview);\r
Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
frame.getWidth(), frame.getHeight());\r
frame.pack();\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
{ public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
{\r
alignPanel.setOverviewPanel(null);\r
};\r
});\r
- alignPanel.setOverviewPanel( overview );\r
\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
- +"\nTry reducing the font size.",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
- }\r
+ alignPanel.setOverviewPanel( overview );\r
\r
\r
}\r
\r
void changeColour(ColourSchemeI cs)\r
{\r
+ int threshold = 0;\r
\r
- if(viewport.getColourAppliesToAllGroups())\r
+ if ( viewport.getAbovePIDThreshold() )\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
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
if (cs instanceof ResidueColourScheme)\r
( (ResidueColourScheme) cs).setThreshold(threshold);\r
( (ScoreColourScheme) cs).setThreshold(threshold);\r
\r
viewport.setGlobalColourScheme(cs);\r
-\r
}\r
- else\r
- if (cs instanceof ResidueColourScheme)\r
+ else if (cs instanceof ResidueColourScheme)\r
( (ResidueColourScheme) cs).setThreshold(0);\r
else if (cs instanceof ScoreColourScheme)\r
( (ScoreColourScheme) cs).setThreshold(0);\r
\r
\r
\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ ConservationColourScheme ccs = null;\r
\r
-if ( viewport.getConservationSelected() )\r
- {\r
- ConservationColourScheme ccs = null;\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\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
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- c.calculate();\r
- c.verdict(false, 100);\r
+ ccs = new ConservationColourScheme(c, cs);\r
\r
- ccs = new ConservationColourScheme(c, cs);\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus( viewport.vconsensus );\r
+ viewport.setGlobalColourScheme(ccs);\r
\r
- int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
- "Background");\r
+ SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
\r
- ccs.inc = threshold;\r
+ }\r
+ else\r
+ {\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ cs.setConsensus(viewport.vconsensus);\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
\r
- viewport.setGlobalColourScheme(ccs);\r
\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
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ }\r
+ else if(cs!=null)\r
+ {\r
+ try{\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ }catch(Exception ex){ex.printStackTrace();}\r
+ }\r
+\r
+ if(viewport.getAbovePIDThreshold())\r
+ {\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+\r
+ sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
+ }\r
+\r
+ if( viewport.getConservationSelected() )\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs = ccs;\r
+ }\r
+ else if(cs!=null)\r
+ {\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ if(alignPanel.getOverviewPanel()!=null)\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
}\r
- else\r
- viewport.setGlobalColourScheme( cs );\r
\r
- alignPanel.RefreshPanels();\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
+ "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
}\r
\r
\r
\r
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setSelected(false);\r
- Desktop.hidePIDSlider();\r
- if(!viewport.getConservationSelected())\r
- Desktop.hideConservationSlider();\r
\r
ColourSchemeI cs = viewport.getGlobalColourScheme();\r
if(cs instanceof ConservationColourScheme )\r
changeColour( ((ConservationColourScheme)cs).cs );\r
else\r
changeColour( cs );\r
- }\r
\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
\r
public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\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
+\r
if(cs instanceof ConservationColourScheme )\r
changeColour( ((ConservationColourScheme)cs).cs );\r
else\r
changeColour( cs );\r
\r
+ modifyPID_actionPerformed(null);\r
}\r
\r
\r
\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
+ UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new Blosum62ColourScheme(viewport) );\r
+ changeColour(new Blosum62ColourScheme() );\r
}\r
\r
\r
{\r
addHistoryItem("sort");\r
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("sort");\r
AlignmentSorter.sortByID( viewport.getAlignment() );\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
addHistoryItem("sort");\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
AlignmentSorter.sortGroups(viewport.getAlignment());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- if(viewport.getCurrentTree()==null)\r
- return;\r
-\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
- alignPanel.RefreshPanels();\r
+ alignPanel.repaint();\r
}\r
\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
JInternalFrame frame = new JInternalFrame();\r
frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
- frame.setMaximizable(false);\r
- frame.setResizable(false);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
\r
}\r
\r
return;\r
}\r
\r
- TreePanel tp=null;\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
+ final TreePanel tp;\r
+ if (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize() > 3)\r
+ {\r
+ tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+ pwType,\r
0, viewport.alignment.getWidth());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
- }\r
+ }\r
+ else\r
+ {\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ type, pwType, 0, viewport.alignment.getWidth());\r
+ }\r
+\r
+ addTreeMenuItem(tp, title);\r
\r
Desktop.addInternalFrame(tp, title, 600, 500);\r
}\r
\r
+ void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ {\r
+ final JMenuItem item = new JMenuItem(title);\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem("sort");\r
+ AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
\r
+ treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ sortByTreeMenu.remove(item);\r
+ };\r
+ });\r
+\r
+ }\r
\r
\r
public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- ClustalThread ct = new ClustalThread(frame);\r
- Thread t = new Thread(ct);\r
- t.start();\r
- frame.setContentPane(ct);\r
- Desktop.addInternalFrame(frame, title, 300, 80);\r
+ WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
+ "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
+ +" Nucleic Acids Research, submitted, June 1994.",\r
+ 450, 150);\r
\r
+ ClustalThread thread = new ClustalThread(info);\r
+ thread.start();\r
}\r
\r
- class ClustalThread extends JPanel implements Runnable\r
- {\r
- Image [] image;\r
- int imageIndex = 0;\r
- boolean webServiceRunning = false;\r
- JInternalFrame frame;\r
- public ClustalThread(JInternalFrame frame)\r
+ class ClustalThread extends Thread\r
{\r
- this.frame = frame;\r
- image = new Image[9];\r
- for(int i=0; i<9; i++)\r
+ WebserviceInfo info;\r
+ public ClustalThread(WebserviceInfo info)\r
+ {this.info = info; }\r
+\r
+ public void run()\r
{\r
- java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
- if (url != null)\r
+ info.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
+ Vector sv = viewport.getAlignment().getSequences();\r
+ SequenceI[] seqs = new SequenceI[sv.size()];\r
+\r
+ int i = 0;\r
+ do\r
+ {\r
+ seqs[i] = (SequenceI) sv.elementAt(i);\r
+ }\r
+ while (++i < sv.size());\r
+\r
+ SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+ if (alignment != null)\r
{\r
- image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image[i], i);\r
- try{mt.waitForID(i);}\r
- catch(Exception ex){}\r
+ AlignFrame af = new AlignFrame(new Alignment(alignment));\r
+ Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
+ NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+ af.clustalColour_actionPerformed(null);\r
+ af.clustalColour.setSelected(true);\r
+ info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else\r
+ {\r
+ info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ info.appendProgressText("Problem obtaining clustal alignment");\r
}\r
}\r
- DNATwirler twirler = new DNATwirler();\r
- twirler.start();\r
- webServiceRunning = true;\r
}\r
\r
- class DNATwirler extends Thread\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+{\r
+\r
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
{\r
- public void run()\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
{\r
- while(webServiceRunning)\r
+ JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
+ }\r
+ else\r
+ {\r
+ int sz;\r
+ SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
+ for (int i = 0; i < sz; i++)\r
{\r
- try{\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %=9;\r
- repaint();\r
- }\r
- catch(Exception ex){}\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
}\r
+\r
+ JPredClient ct = new JPredClient(msa);\r
}\r
+\r
}\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
\r
- // JBPNote\r
- // Should check to see if the server settings are valid\r
- // Need visual-delay indication here.\r
- public void run()\r
- {\r
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
- Vector sv = viewport.getAlignment().getSequences();\r
- SequenceI[] seqs = new SequenceI[sv.size()];\r
+ if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
+ {\r
+ JPredClient ct = new JPredClient( (SequenceI)\r
+ seqs.elementAt(0));\r
+ }\r
+ else\r
+ {\r
+ SequenceI[] msa = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
- int i = 0;\r
- do\r
- {\r
- seqs[i] = (SequenceI) sv.elementAt(i);\r
- }\r
- while (++i < sv.size());\r
+ JPredClient ct = new JPredClient(msa);\r
+ }\r
\r
- SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
+ }\r
+ }\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ int sz;\r
+ SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
\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
- else\r
- JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
- JOptionPane.WARNING_MESSAGE);\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
\r
- webServiceRunning = false;\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
+ if (seqs.size() > 1) {\r
+ SequenceI[] msa = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
- if(image!=null)\r
- {\r
- g.drawImage(image[imageIndex],10,10,this);\r
- }\r
- g.setFont(new Font("Arial", Font.BOLD, 12));\r
- g.setColor(Color.black);\r
- g.drawString("Clustal Alignment Web Service running", 30,30);\r
- }\r
+ MsaWSClient ct = new MsaWSClient(msa);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select a newick-like tree file");\r
+ chooser.setToolTipText("Load a tree file");\r
+ int value = chooser.showOpenDialog(null);\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
+ ShowNewickTree(fin, choice);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "Problem reading tree file",\r
+ ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
+\r
+ public void ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ try{\r
+ nf.parse();\r
+ if (nf.getTree() != null)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(),\r
+ nf, "FromFile", title);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+ }\r
+ }catch(Exception ex){ex.printStackTrace();}\r
+ }\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff