-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-
-
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
-import java.beans.PropertyChangeEvent;
-
-public class AlignFrame extends GAlignFrame
-{
- final AlignmentPanel alignPanel;
- final AlignViewport viewport;
- public static final int NEW_WINDOW_WIDTH = 700;
- public static final int NEW_WINDOW_HEIGHT = 500;
- public String currentFileFormat = "Jalview";
-
- public AlignFrame(AlignmentI al)
- {
- viewport = new AlignViewport(al);
-
- alignPanel = new AlignmentPanel(this, viewport);
- alignPanel.annotationPanel.adjustPanelHeight();
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
- alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
-
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
-
- addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameActivated(InternalFrameEvent evt)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- { alignPanel.requestFocus(); }
- });
-
- }
- });
-
- }
-
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
- , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
- currentFileFormat);
-
- chooser.setAcceptAllFileFilterUsed(false);
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save Alignment to file");
- chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(this);
- if(value == JalviewFileChooser.APPROVE_OPTION)
- {
- currentFileFormat = chooser.getSelectedFormat();
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
-
- if (currentFileFormat.equals("Jalview"))
- {
- String shortName = title.replace('/', '_');
- title = title.replace('\\', '_');
- String choice = chooser.getSelectedFile().getPath();
- Jalview2XML.SaveState(this, choice, shortName);
- // USE Jalview2XML to save this file
- return;
- }
-
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
- try{
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
- out.println(output);
- out.close();
- }
- catch(Exception ex){}
- }
-
- }
-
- protected void outputText_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
- }
-
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
- {
- new HTMLOutput(viewport);
- }
-
- protected void createPNG_actionPerformed(ActionEvent e)
- {
- alignPanel.makePNG();
- }
-
- protected void epsFile_actionPerformed(ActionEvent e)
- {
- alignPanel.makeEPS();
- }
-
-
- public void printMenuItem_actionPerformed(ActionEvent e)
- {
- //Putting in a thread avoids Swing painting problems
- PrintThread thread = new PrintThread();
- thread.start();
- }
-
- class PrintThread extends Thread
- {
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
- printJob.setPrintable(alignPanel, pf);
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-
- }
-
-
-
-
- public void closeMenuItem_actionPerformed(ActionEvent e)
- {
- try{
- this.setClosed(true);
- }catch(Exception ex){}
- }
-
- Stack historyList = new Stack();
- Stack redoList = new Stack();
- private int treeCount = 0;
-
- void updateEditMenuBar()
- {
- if(historyList.size()>0)
- {
- undoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem)historyList.peek();
- undoMenuItem.setText("Undo "+hi.getDescription());
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
- }
-
- if(redoList.size()>0)
- {
- redoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem)redoList.peek();
- redoMenuItem.setText("Redo "+hi.getDescription());
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
- }
- }
-
- public void addHistoryItem(HistoryItem hi)
- {
- historyList.push(hi);
- updateEditMenuBar();
- }
-
- protected void undoMenuItem_actionPerformed(ActionEvent e)
- {
- HistoryItem hi = (HistoryItem)historyList.pop();
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
- restoreHistoryItem(hi);
- }
-
-
- protected void redoMenuItem_actionPerformed(ActionEvent e)
- {
- HistoryItem hi = (HistoryItem)redoList.pop();
- restoreHistoryItem(hi);
- updateEditMenuBar();
- viewport.updateConsensus();
- alignPanel.repaint();
- alignPanel.repaint();
- }
-
-
- // used by undo and redo
- void restoreHistoryItem(HistoryItem hi)
- {
- if(hi.getType()== HistoryItem.SORT)
- {
- for(int i=0; i<hi.getSequences().size(); i++)
- viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
- }
- else
- {
- for (int i = 0; i < hi.getSequences().size(); i++)
- {
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
- if(restore.getLength()==0)
- {
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- viewport.alignment.getSequences().insertElementAt(
- restore,
- hi.getAlignIndex(i));
- }
- else
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- }
- if(hi.getType()==HistoryItem.PASTE)
- {
- for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
- viewport.alignment.deleteSequence(i);
- }
- }
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- updateEditMenuBar();
-
- viewport.updateConsensus();
- viewport.updateConservation();
- alignPanel.repaint();
- }
-
- public void moveSelectedSequences(boolean up)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- return;
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
- continue;
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.sequences.contains(temp))
- continue;
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
- continue;
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.sequences.contains(temp))
- continue;
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
- alignPanel.repaint();
- }
-
-
-
- protected void copy_actionPerformed(ActionEvent e)
- {
- if(viewport.getSelectionGroup()==null)
- return;
-
- SequenceGroup sg = viewport.getSelectionGroup();
-
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- StringBuffer buffer= new StringBuffer();
-
- Hashtable orderedSeqs = new Hashtable();
- for(int i=0; i<sg.getSize(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index+"", seq);
- }
-
- int index=0;
- for(int i=0; i<sg.getSize(); i++)
- {
- SequenceI seq = null;
- while( seq == null )
- {
- if(orderedSeqs.containsKey(index+""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
- break;
- }
- else
- index++;
- }
-
- buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
- +seq.findPosition( sg.getEndRes() )+ "\t"
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
- }
- c.setContents( new StringSelection( buffer.toString()) , null ) ;
-
- }
-
-
- protected void pasteNew_actionPerformed(ActionEvent e)
- {
- paste(true);
- }
-
- protected void pasteThis_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
- paste(false);
- }
-
- void paste(boolean newAlignment)
- {
- try{
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable contents = c.getContents(this);
- if (contents == null)
- return;
-
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
- StringTokenizer st = new StringTokenizer(str);
- ArrayList seqs = new ArrayList();
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- int start = Integer.parseInt(st.nextToken());
- int end = Integer.parseInt(st.nextToken());
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);
-
- if(!newAlignment)
- viewport.alignment.addSequence(sequence);
- else
- seqs.add(sequence);
- }
-
- if(newAlignment)
- {
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- seqs.toArray(newSeqs);
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));
- String newtitle = new String("Copied sequences");
- if( title.startsWith("Copied sequences"))
- newtitle = title;
- else
- newtitle = newtitle.concat("- from "+title);
-
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
- }
- else
- {
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
- }catch(Exception ex){}// could be anything being pasted in here
-
- }
-
-
- protected void cut_actionPerformed(ActionEvent e)
- {
- copy_actionPerformed(null);
- delete_actionPerformed(null);
- }
-
- protected void delete_actionPerformed(ActionEvent e)
- {
- boolean seqsdeleted=false;
-
- if (viewport.getSelectionGroup() == null)
- return;
-
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
-
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i=0;i < sg.sequences.size(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
- seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
-
- if(seq.getSequence().length()<1) {
- seqsdeleted=true;
- viewport.getAlignment().deleteSequence(seq);
- } else {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
- }
-
- viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
- if (seqsdeleted)
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
- if(viewport.getAlignment().getHeight()<1)
- try
- {
- this.setClosed(true);
- }catch(Exception ex){}
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- protected void deleteGroups_actionPerformed(ActionEvent e)
- {
- viewport.alignment.deleteAllGroups();
- viewport.setSelectionGroup(null);
- alignPanel.repaint();
- }
-
-
-
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = new SequenceGroup();
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));
- sg.setEndRes(viewport.alignment.getWidth());
- viewport.setSelectionGroup(sg);
- PaintRefresher.Refresh(null);
- }
-
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- PaintRefresher.Refresh(null);
- }
-
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
-
- PaintRefresher.Refresh(null);
- }
-
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- if (colSel.size() > 0)
- {
- addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
- HistoryItem.HIDE));
- int min = colSel.getMin();
- viewport.getAlignment().trimLeft(min);
- colSel.compensateForEdit(0,min);
-
- if(viewport.getSelectionGroup()!=null)
- viewport.getSelectionGroup().adjustForRemoveLeft(min);
-
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.get(i);
- if(!sg.adjustForRemoveLeft(min))
- viewport.alignment.deleteGroup(sg);
- }
-
- alignPanel.repaint();
- }
- }
-
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- if (colSel.size() > 0)
- {
- addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
- HistoryItem.HIDE));
-
- int max = colSel.getMax();
- viewport.getAlignment().trimRight(max);
- if(viewport.getSelectionGroup()!=null)
- viewport.getSelectionGroup().adjustForRemoveRight(max);
-
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.get(i);
- if(!sg.adjustForRemoveRight(max))
- viewport.alignment.deleteGroup(sg);
- }
-
-
-
- alignPanel.repaint();
- }
-
- }
-
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Remove Gapped Columns",
- viewport.alignment,
- HistoryItem.HIDE));
-
- viewport.getAlignment().removeGaps();
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Remove Gaps",
- viewport.alignment,
- HistoryItem.HIDE));
- SequenceI current;
- int jSize;
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
- jSize = current.getLength();
- for (int j=0; j < jSize; j++)
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))
- {
- current.deleteCharAt(j);
- j--;
- jSize--;
- }
- }
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- public void padGapsMenuitem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Pad Gaps",
- viewport.alignment,
- HistoryItem.HIDE));
- SequenceI current;
- int Width = viewport.getAlignment().getWidth()-1;
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength()<Width)
- current.insertCharAt(Width, viewport.getGapCharacter());
- }
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
- }
-
-
- public void findMenuItem_actionPerformed(ActionEvent e)
- {
- JInternalFrame frame = new JInternalFrame();
- Finder finder = new Finder(viewport, alignPanel, frame);
- frame.setContentPane(finder);
- Desktop.addInternalFrame(frame, "Find", 340,110);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
- }
-
-
- public void font_actionPerformed(ActionEvent e)
- {
- FontChooser fc = new FontChooser( alignPanel );
- }
-
- protected void fullSeqId_actionPerformed(ActionEvent e)
- {
- viewport.setShowFullId( fullSeqId.isSelected() );
-
- alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
- alignPanel.repaint();
- }
-
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setColourText( colourTextMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
- scaleAbove.setVisible( wrapMenuItem.isSelected() );
- scaleLeft.setVisible( wrapMenuItem.isSelected() );
- scaleRight.setVisible( wrapMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- protected void scaleAbove_actionPerformed(ActionEvent e)
- {
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.repaint();
- }
-
- protected void scaleLeft_actionPerformed(ActionEvent e)
- {
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.repaint();
- }
-
- protected void scaleRight_actionPerformed(ActionEvent e)
- {
- viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.repaint();
- }
-
-
-
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
- public void viewTextMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setShowText( viewTextMenuItem.isSelected() );
- alignPanel.repaint();
- }
-
-
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.repaint();
- }
-
- public void sequenceFeatures_actionPerformed(ActionEvent evt)
- {
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
- {
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
- ((Alignment)viewport.alignment).featuresAdded = true;
- }
- alignPanel.repaint();
- }
-
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
- {
- if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
- {
- annotationPanelMenuItem.setSelected(false);
- return;
- }
- viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
- }
-
- public void overviewMenuItem_actionPerformed(ActionEvent e)
- {
- if (alignPanel.overviewPanel != null)
- return;
-
- JInternalFrame frame = new JInternalFrame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
- frame.getWidth(), frame.getHeight());
- frame.pack();
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
-
- alignPanel.setOverviewPanel( overview );
-
-
- }
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour( null );
- }
-
-
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
- }
-
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
-
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour( new HydrophobicColourScheme() );
- }
-
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme() );
- }
-
-
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
-
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
-
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme() );
- }
-
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
-
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
- }
-
-
-
- void changeColour(ColourSchemeI cs)
- {
- int threshold = 0;
-
- if ( viewport.getAbovePIDThreshold() )
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
-
- if (cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) cs).setThreshold(threshold);
- else if (cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) cs).setThreshold(threshold);
-
- viewport.setGlobalColourScheme(cs);
- }
- else if (cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) cs).setThreshold(0);
- else if (cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) cs).setThreshold(0);
-
-
-
- if (viewport.getConservationSelected())
- {
- ConservationColourScheme ccs = null;
-
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- ccs = new ConservationColourScheme(c, cs);
-
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- ccs.setConsensus( viewport.vconsensus );
- viewport.setGlobalColourScheme(ccs);
-
- ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
-
- }
- else
- {
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- if (cs != null)
- cs.setConsensus(viewport.vconsensus);
- viewport.setGlobalColourScheme(cs);
- }
-
-
- if(viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-
- if(cs==null)
- sg.cs = null;
- else if (cs instanceof ClustalxColourScheme)
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
- else if (cs instanceof UserColourScheme)
- sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
- else
- try{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }catch(Exception ex){}
-
- if(viewport.getAbovePIDThreshold())
- {
- if (sg.cs instanceof ResidueColourScheme)
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
- else if (sg.cs instanceof ScoreColourScheme)
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
-
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
- }
-
- if( viewport.getConservationSelected() )
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.sequences, 0, viewport.alignment.getWidth()-1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
- sg.cs = ccs;
- }
- else if(cs!=null)
- {
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
- }
-
- }
- }
-
- if(alignPanel.getOverviewPanel()!=null)
- alignPanel.getOverviewPanel().updateOverviewImage();
- alignPanel.repaint();
- }
-
- protected void modifyPID_actionPerformed(ActionEvent e)
- {
- if(viewport.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
- "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- protected void modifyConservation_actionPerformed(ActionEvent e)
- {
- if(viewport.getConservationSelected())
- {
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
- "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
-
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
-
- ColourSchemeI cs = viewport.getGlobalColourScheme();
- if(cs instanceof ConservationColourScheme )
- changeColour( ((ConservationColourScheme)cs).cs );
- else
- changeColour( cs );
-
- modifyConservation_actionPerformed(null);
- }
-
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- ColourSchemeI cs = viewport.getGlobalColourScheme();
-
- if(cs instanceof ConservationColourScheme )
- changeColour( ((ConservationColourScheme)cs).cs );
- else
- changeColour( cs );
-
- modifyPID_actionPerformed(null);
- }
-
-
-
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours( alignPanel, null);
- }
-
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour( new PIDColourScheme() );
- }
-
-
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme() );
- }
-
-
-
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
- alignPanel.repaint();
- }
-
- public void sortIDMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByID( viewport.getAlignment() );
- alignPanel.repaint();
- }
-
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- AlignmentSorter.sortGroups(viewport.getAlignment());
- alignPanel.repaint();
- }
-
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
- {
- RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(sp);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
-
- }
-
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
- {
- if((viewport.getSelectionGroup()==null) ||
- viewport.getSelectionGroup().getSize()<2)
- JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
- else
- {
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
- }
- }
-
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
-
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
- || viewport.getAlignment().getHeight()<4)
- {
- JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
- +"at least 4 input sequences.",
- "Sequence selection insufficient",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- try{
- PCAPanel pcaPanel = new PCAPanel(viewport, null);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(pcaPanel);
- Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
- }catch(java.lang.OutOfMemoryError ex)
- {
- JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
- "Out of memory", JOptionPane.WARNING_MESSAGE);
- }
-
-
- }
-
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
-
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- void NewTreePanel(String type, String pwType, String title)
- {
- //are the sequences aligned?
- if(!viewport.alignment.isAligned())
- {
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
- +"Try using the Pad function in the edit menu,\n"
- +"or one of the multiple sequence alignment web services.",
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- final TreePanel tp;
- if (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() > 3)
- {
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
- pwType,
- 0, viewport.alignment.getWidth());
- }
- else
- {
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
- type, pwType, 0, viewport.alignment.getWidth());
- }
-
- addTreeMenuItem(tp, title);
-
- Desktop.addInternalFrame(tp, title, 600, 500);
- }
-
- public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
- final JMenuItem item = new JMenuItem("by "+title);
- sort.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- HistoryItem.SORT));
- // TODO: JBPNote - have to map order entries to curent SequenceI pointers
- AlignmentSorter.sortBy(viewport.getAlignment(), order);
- alignPanel.repaint();
- }
- });
- }
-
- void addTreeMenuItem(final TreePanel treePanel, String title)
- {
- final JMenuItem item = new JMenuItem(title);
-
- treeCount++;
-
- if (treeCount==1)
- sort.add(sortByTreeMenu);
-
- sortByTreeMenu.add(item);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
- HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.repaint();
- }
- });
-
- treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
- {
- treeCount--;
- sortByTreeMenu.remove(item);
- if (treeCount==0)
- sort.remove(sortByTreeMenu);
- };
- });
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment")) {
- treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
- treePanel.repaint();
- }
- }
-
- }
- );
- }
-
-
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa=null;
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
-
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1) {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
-
- }
-
- }
- if (msa!=null) {
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
- }
- }
-
- protected void jpred_actionPerformed(ActionEvent e)
-{
- SequenceI seq=null;
- SequenceI[] msa=null;
-
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
- {
- seq = (SequenceI)seqs.getSequenceAt(0);
- }
- else
- {
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
- }
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() == 1 || !viewport.alignment.isAligned())
- {
- seq = (SequenceI) seqs.elementAt(0);
- }
- else
- {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
- }
- }
- if (msa!=null) {
- JPredClient ct = new JPredClient(title, msa);
- } else
- if (seq!=null) {
- JPredClient ct = new JPredClient(title, seq);
- } else {
- System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
- }
- }
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa=null;
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
- {
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz=seqs.getSize()];
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
-
-
- }
- else
- {
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1) {
- msa = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
-
- }
-
- }
- if (msa!=null) {
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
- }
- }
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a newick-like tree file");
- chooser.setToolTipText("Load a tree file");
- int value = chooser.showOpenDialog(null);
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- try
- {
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
- ShowNewickTree(fin, choice);
- }
- catch (Exception ex)
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Problem reading tree file",
- ex.getMessage(),
- JOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- }
- }
-
- public void ShowNewickTree(NewickFile nf, String title)
- {
- try{
- nf.parse();
- if (nf.getTree() != null)
- {
- TreePanel tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(),
- nf, "FromFile", title);
- Desktop.addInternalFrame(tp, title, 600, 500);
- addTreeMenuItem(tp, title);
- viewport.setCurrentTree(tp.getTree());
- }
- }catch(Exception ex){ex.printStackTrace();}
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.gui;\r
+\r
+import jalview.analysis.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.io.*;\r
+\r
+import jalview.jbgui.*;\r
+\r
+import jalview.schemes.*;\r
+\r
+import jalview.ws.*;\r
+\r
+import java.awt.*;\r
+import java.awt.datatransfer.*;\r
+import java.awt.event.*;\r
+import java.awt.print.*;\r
+\r
+import java.io.*;\r
+\r
+import java.beans.*;\r
+\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignFrame extends GAlignFrame\r
+{\r
+ /** DOCUMENT ME!! */\r
+ public static final int NEW_WINDOW_WIDTH = 700;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NEW_WINDOW_HEIGHT = 500;\r
+ final AlignmentPanel alignPanel;\r
+ final AlignViewport viewport;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String currentFileFormat = null;\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+ private int treeCount = 0;\r
+\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignFrame(AlignmentI al)\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
+ public void internalFrameActivated(InternalFrameEvent evt)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ alignPanel.requestFocus();\r
+ }\r
+ });\r
+ }\r
+ });\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void parseGroupsFile(String file)\r
+ {\r
+ try{\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq=null;\r
+ String line, text, token;\r
+ UserColourScheme ucs;\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceGroup sg;\r
+ while( (line = in.readLine())!=null)\r
+ {\r
+ st = new StringTokenizer(line, "\t");\r
+ if(st.countTokens()!=6)\r
+ {\r
+ System.out.println("Groups file "+file+" is invalid. Read help file.");\r
+ System.exit(1);\r
+ }\r
+\r
+ while(st.hasMoreElements())\r
+ {\r
+ text = st.nextToken();\r
+ token = st.nextToken();\r
+ if(!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ index = Integer.parseInt( st.nextToken() );\r
+\r
+ start=Integer.parseInt( st.nextToken() );\r
+ end = Integer.parseInt( st.nextToken() );\r
+ ucs = new UserColourScheme(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start)-1;\r
+ end = seq.findIndex(end)-1;\r
+\r
+ sg = new SequenceGroup(text,ucs,true,true,false,start,end);\r
+ sg.addSequence( seq,true);\r
+\r
+ viewport.alignment.addGroup(sg);\r
+ }\r
+ }\r
+\r
+ }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "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");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
+\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ saveAlignment(choice, currentFileFormat);\r
+ }\r
+ }\r
+\r
+ public boolean saveAlignment(String file, String format)\r
+ {\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ String shortName = title;\r
+\r
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ java.io.File.separatorChar) + 1);\r
+ }\r
+\r
+ Jalview2XML.SaveAlignment(this, file, shortName);\r
+\r
+ // USE Jalview2XML to save this file\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ String output = FormatAdapter.formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if(output==null)\r
+ return false;\r
+\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
+ out.println(output);\r
+ out.close();\r
+ return true;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600, 500);\r
+ cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().getSequences()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new HTMLOutput(viewport);\r
+ }\r
+\r
+ public void createImageMap(File file, String image)\r
+ {\r
+ alignPanel.makePNGImageMap(file, image);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
+ {\r
+ alignPanel.makePNG(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createEPS(File f)\r
+ {\r
+ alignPanel.makeEPS(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setText("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ }\r
+\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setText("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param hi DOCUMENT ME!\r
+ */\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
+ .elementAt(i),\r
+ i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+\r
+ if (restore.getLength() == 0)\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(restore,\r
+ hi.getAlignIndex(i));\r
+ }\r
+ else\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ }\r
+ }\r
+\r
+ if (hi.getType() == HistoryItem.PASTE)\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 1;\r
+ i > (hi.getSequences().size() - 1); i--)\r
+ {\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ updateEditMenuBar();\r
+\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param up DOCUMENT ME!\r
+ */\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\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
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+\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
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ buffer.append(seq.getName() + "\t" +\r
+ seq.findPosition(sg.getStartRes()) + "\t" +\r
+ seq.findPosition(sg.getEndRes()) + "\t" +\r
+ sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ c.setContents(new StringSelection(buffer.toString()), null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
+ paste(false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newAlignment DOCUMENT ME!\r
+ */\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ StringTokenizer st = new StringTokenizer(str);\r
+ ArrayList seqs = new ArrayList();\r
+\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,\r
+ end);\r
+\r
+ if (!newAlignment)\r
+ {\r
+ viewport.alignment.addSequence(sequence);\r
+ }\r
+ else\r
+ {\r
+ seqs.add(sequence);\r
+ }\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ seqs.toArray(newSeqs);\r
+\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ String newtitle = new String("Copied sequences");\r
+\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ // could be anything being pasted in here\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ boolean seqsdeleted = false;\r
+\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ seqsdeleted = true;\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
+ else\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+\r
+ if (seqsdeleted)\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setEndRes(viewport.alignment.getWidth());\r
+ viewport.setSelectionGroup(sg);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.annotationPanel.activeRes = null;\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
+\r
+ return;\r
+ }\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int min = colSel.getMin();\r
+ viewport.getAlignment().trimLeft(min);\r
+ colSel.compensateForEdit(0, min);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int max = colSel.getMax();\r
+ viewport.getAlignment().trimRight(max);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment, HistoryItem.HIDE));\r
+\r
+ viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceI current;\r
+ int jSize;\r
+\r
+ Vector seqs = null;\r
+\r
+ int start = 0;\r
+ int end = viewport.alignment.getWidth();\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequences();\r
+ }\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ current = (SequenceI) seqs.elementAt(i);\r
+ jSize = current.getLength();\r
+\r
+ int j = start;\r
+\r
+ do\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ {\r
+ current.deleteCharAt(j);\r
+ j--;\r
+ jSize--;\r
+ }\r
+\r
+ j++;\r
+ }\r
+ while (j < end);\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\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
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ FontChooser fc = new FontChooser(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+\r
+ if (viewport.showSequenceFeatures &&\r
+ !((Alignment) viewport.alignment).featuresAdded)\r
+ {\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,\r
+ alignPanel);\r
+ ((Alignment) viewport.alignment).featuresAdded = true;\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (annotationPanelMenuItem.isSelected() &&\r
+ viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+\r
+ return;\r
+ }\r
+\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ JInternalFrame frame = new JInternalFrame();\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
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ alignPanel.setOverviewPanel(null);\r
+ }\r
+ ;\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ((ResidueColourScheme) cs).setThreshold(threshold);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) cs).setThreshold(threshold);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ((ResidueColourScheme) cs).setThreshold(0);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) cs).setThreshold(0);\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ ConservationColourScheme ccs = null;\r
+\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ccs = new ConservationColourScheme(c, cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(viewport.vconsensus);\r
+ viewport.setGlobalColourScheme(ccs);\r
+\r
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
+ "Background");\r
+ }\r
+ else\r
+ {\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+\r
+ if (viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ }\r
+ else if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
+ sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ {\r
+ ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c,\r
+ sg.cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ 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,\r
+ sg.getWidth()));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme, "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour(((ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\r
+\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
+\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour(((ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\r
+\r
+ modifyPID_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+ 100, false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ((viewport.getSelectionGroup() == null) ||\r
+ (viewport.getSelectionGroup().getSize() < 2))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "You must select at least 2 sequences.", "Invalid Selection",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (((viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() < 4) &&\r
+ (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getAlignment().getHeight() < 4))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Principal component analysis must take\n" +\r
+ "at least 4 input sequences.",\r
+ "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(pcaPanel);\r
+ Desktop.addInternalFrame(frame, "Principal component analysis",\r
+ 400, 400);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Too many sequences selected\nfor Principal Component Analysis!!",\r
+ "Out of memory", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param type DOCUMENT ME!\r
+ * @param pwType DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ */\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ final TreePanel tp;\r
+\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 3))\r
+ {\r
+ int s = 0;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ /* Decide if the selection is a column region */\r
+ while (s < sg.sequences.size())\r
+ {\r
+ if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences in selection are not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ }\r
+\r
+ title = title + " on region";\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().sequences, type, pwType,\r
+ sg.getStartRes(), sg.getEndRes());\r
+ }\r
+ else\r
+ {\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The sequences must be aligned before creating a tree.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType, 0,\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+\r
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param title DOCUMENT ME!\r
+ * @param order DOCUMENT ME!\r
+ */\r
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
+ {\r
+ final JMenuItem item = new JMenuItem("by " + title);\r
+ sort.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param treePanel DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ */\r
+ void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ {\r
+ final JMenuItem item = new JMenuItem(title);\r
+\r
+ treeCount++;\r
+\r
+ if (treeCount == 1)\r
+ {\r
+ sort.add(sortByTreeMenu);\r
+ }\r
+\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Tree Sort",\r
+ viewport.alignment, HistoryItem.SORT));\r
+ AlignmentSorter.sortByTree(viewport.getAlignment(),\r
+ treePanel.getTree());\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+\r
+ treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ treeCount--;\r
+ sortByTreeMenu.remove(item);\r
+\r
+ if (treeCount == 0)\r
+ {\r
+ sort.remove(sortByTreeMenu);\r
+ }\r
+ }\r
+ ;\r
+ });\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());\r
+ treePanel.repaint();\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (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
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, false, true);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void ClustalRealign_actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (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
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, true, true);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI seq = null;\r
+ SequenceI[] msa = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 0))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+\r
+ if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.getSequenceAt(0);\r
+ }\r
+ else\r
+ {\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if ((seqs.size() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.elementAt(0);\r
+ }\r
+ else\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ JPredClient ct = new JPredClient(title, msa);\r
+ }\r
+ else if (seq != null)\r
+ {\r
+ JPredClient ct = new JPredClient(title, seq);\r
+ }\r
+ else\r
+ {\r
+ System.err.print(\r
+ "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\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
+ SequenceI[] msa = null;\r
+\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (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
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (msa != null)\r
+ {\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
+ false, true);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select a newick-like tree file");\r
+ chooser.setToolTipText("Load a tree file");\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
+ "File");\r
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "Problem reading tree file", ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param nf DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ TreePanel tp = null;\r
+\r
+ try\r
+ {\r
+ nf.parse();\r
+\r
+ if (nf.getTree() != null)\r
+ {\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), nf, "FromFile",\r
+ title);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ addTreeMenuItem(tp, title);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return tp;\r
+ }\r
+\r
+ class PrintThread extends Thread\r
+ {\r
+ public void run()\r
+ {\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+ printJob.setPrintable(alignPanel, pf);\r
+\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff