-/********************
- * 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();
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(cap);
- Desktop.addInternalFrame(frame, "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;
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
-
- if (viewport.getSelectionGroup() == null)
- return;
-
- 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);
- 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().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, true, 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, true, 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 Softwarechang\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.gui;\r
+\r
+import java.beans.*;\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.datatransfer.*;\r
+import java.awt.event.*;\r
+import java.awt.print.*;\r
+import javax.swing.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
+import jalview.ws.*;\r
+import javax.swing.event.AncestorEvent;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignFrame\r
+ extends GAlignFrame implements ClipboardOwner\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
+ AlignmentPanel alignPanel;\r
+ AlignViewport viewport;\r
+\r
+ Vector viewports = new Vector();\r
+ Vector alignPanels = new Vector();\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
+ /**\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
+ viewports.add(viewport);\r
+\r
+\r
+ if(viewport.vconsensus==null)\r
+ {\r
+ //Out of memory calculating consensus.\r
+ BLOSUM62Colour.setEnabled(false);\r
+ PIDColour.setEnabled(false);\r
+ conservationMenuItem.setEnabled(false);\r
+ modifyConservation.setEnabled(false);\r
+ abovePIDThreshold.setEnabled(false);\r
+ modifyPID.setEnabled(false);\r
+ }\r
+\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+ alignPanels.add(alignPanel);\r
+\r
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
+\r
+ if(sortby.equals("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if(sortby.equals("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+\r
+ // remove(tabbedPane);\r
+ getContentPane().add(alignPanel, BorderLayout.CENTER);\r
+\r
+\r
+\r
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+ if(al.getDataset()==null)\r
+ {\r
+ al.setDataset(null);\r
+ }\r
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+ viewport.addPropertyChangeListener(new PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
+\r
+ if (Desktop.desktop != null)\r
+ {\r
+ addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
+ }\r
+\r
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
+ private void addServiceListeners()\r
+ {\r
+ final java.beans.PropertyChangeListener thisListener;\r
+ // Do this once to get current state\r
+ BuildWebServiceMenu();\r
+ Desktop.discoverer.addPropertyChangeListener(\r
+ thisListener = new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ // System.out.println("Discoverer property change.");\r
+ if (evt.getPropertyName().equals("services"))\r
+ {\r
+ // System.out.println("Rebuilding web service menu");\r
+ BuildWebServiceMenu();\r
+ }\r
+ }\r
+ });\r
+ addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ // System.out.println("deregistering discoverer listener");\r
+ Desktop.discoverer.removePropertyChangeListener(thisListener);\r
+ closeMenuItem_actionPerformed(null);\r
+ }\r
+ ;\r
+ });\r
+\r
+ }\r
+\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.setVisible( nucleotide );\r
+ sequenceFeatures.setVisible(!nucleotide );\r
+ featureSettings.setVisible( !nucleotide );\r
+ conservationMenuItem.setVisible( !nucleotide );\r
+ modifyConservation.setVisible( !nucleotide );\r
+\r
+ //Deal with separators\r
+ //Remember AlignFrame always starts as protein\r
+ if(nucleotide)\r
+ {\r
+ viewMenu.remove(viewMenu.getItemCount()-2);\r
+ }\r
+ else\r
+ {\r
+ calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+ }\r
+ }\r
+\r
+\r
+ /*\r
+ Added so Castor Mapping file can obtain Jalview Version\r
+ */\r
+ public String getVersion()\r
+ {\r
+ return jalview.bin.Cache.getProperty("VERSION");\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseGroupsFile(String file)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq = null;\r
+ String line, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = 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
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ type = st.nextToken();\r
+\r
+ if (fr.getColour(type) == null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+\r
+ // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ // sg.addSequence(seq, false);\r
+\r
+ // viewport.alignment.addGroup(sg);\r
+\r
+ }\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\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.\r
+ 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
+\r
+ if (currentFileFormat == null)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "You must select a file format before saving!",\r
+ "File format not specified",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ value = chooser.showSaveDialog(this);\r
+ return;\r
+ }\r
+\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 = new FormatAdapter().formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if (output == null)\r
+ {\r
+ return false;\r
+ }\r
+\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
+\r
+ out.print(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
+ * 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,\r
+ 500);\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().\r
+ 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
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\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
+ PaintRefresher.components.remove(viewport.alignment);\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
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\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.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\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.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
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\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
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ SequenceI[] seqs = new SequenceI[sg.getSize()];\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, startRes, endRes;\r
+ char ch;\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
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
+\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
+ startRes,\r
+ endRes);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+ }\r
+\r
+ FastaFile ff = new FastaFile();\r
+ ff.addJVSuffix( viewport.showJVSuffix );\r
+ c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\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
+ if(str.length()<1)\r
+ return;\r
+\r
+ String format = IdentifyFile.Identify(str, "Paste");\r
+ SequenceI[] sequences;\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+\r
+ Alignment alignment = new Alignment(sequences);\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
+ else\r
+ alignment.setDataset( null );\r
+\r
+\r
+ AlignFrame af = new AlignFrame(alignment);\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
+ //!newAlignment\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ Sequence newseq = new Sequence(sequences[i].getName(),\r
+ sequences[i].getSequence(), sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ viewport.alignment.addSequence(newseq);\r
+ if(sequences[i].getDatasetSequence()==null)\r
+ {\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ newseq.setDatasetSequence(ds);\r
+ viewport.alignment.getDataset().addSequence(ds);\r
+ }\r
+\r
+ }\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ // could be anything being pasted in here\r
+ }\r
+\r
+\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
+\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
+ boolean allSequences = false;\r
+ if (sg.sequences.size() == viewport.alignment.getHeight())\r
+ {\r
+ allSequences = true;\r
+ }\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 the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+ if (seq.getSequence().length() < 1)\r
+ {\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
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+\r
+\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
+\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() - 1);\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.seqPanel.seqCanvas.highlightSearchResults(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
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\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
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\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
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+ viewport.getAlignment().removeGaps();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\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
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\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
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size() > 0)\r
+ {\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\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
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
+ int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
+ do\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ {\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
+ }\r
+ }\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
+ }\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
+ if(viewport.vconsensus!=null)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\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
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = viewport.alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\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
+ alignmentChanged();\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
+ new FontChooser(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
+ }\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
+ {\r
+ new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ }\r
+\r
+ featureSettings.setEnabled(true);\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
+ 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(cs!=null)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+\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
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
+ "Background"));\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\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
+ continue;\r
+ }\r
+\r
+ 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
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
+ {\r
+ sg.cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+ else\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+ sg.cs.setConservation(c);\r
+ }\r
+ else\r
+ sg.cs.setConservation(null);\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() && viewport.globalColourScheme!=null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(),\r
+ "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() && viewport.globalColourScheme!=null)\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme,\r
+ "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
+ changeColour(viewport.getGlobalColourScheme());\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
+ changeColour(viewport.getGlobalColourScheme());\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
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ changeColour(udc);\r
+ }\r
+ }\r
+\r
+ public void updateUserColourMenu()\r
+ {\r
+\r
+ Component[] menuItems = colourMenu.getMenuComponents();\r
+ int i, iSize = menuItems.length;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (menuItems[i].getName() != null &&\r
+ menuItems[i].getName().equals("USER_DEFINED"))\r
+ {\r
+ colourMenu.remove(menuItems[i]);\r
+ iSize--;\r
+ }\r
+ }\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\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.",\r
+ "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",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ new PCAPanel(viewport);\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() <\r
+ 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",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType,\r
+ 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
+ * Maintain the Order by->Displayed Tree menu.\r
+ * Creates a new menu item for a TreePanel with an appropriate\r
+ * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added\r
+ * to remove the menu item when the treePanel is closed, and adjust\r
+ * the tree leaf to sequence mapping when the alignment is modified.\r
+ * @param treePanel Displayed tree window.\r
+ * @param title SortBy menu item title.\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.\r
+ 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
+ }\r
+\r
+ /**\r
+ * Work out whether the whole set of sequences\r
+ * or just the selected set will be submitted for multiple alignment.\r
+ *\r
+ */\r
+ private SequenceI[] gatherSequencesForAlignment()\r
+ {\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
+ return msa;\r
+ }\r
+\r
+ /**\r
+ * Decides what is submitted to a secondary structure prediction service,\r
+ * the currently selected sequence, or the currently selected alignment\r
+ * (where the first sequence in the set is the one that the prediction\r
+ * will be for).\r
+ */\r
+ SequenceI[] gatherSeqOrMsaForSecStrPrediction()\r
+ {\r
+ SequenceI seq = null;\r
+ SequenceI[] msa = null;\r
+/*\r
+ if (predictindex==-1) {\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "The alignment contains no columns or residues usable for prediction!",\r
+ "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);\r
+ this.\r
+ return;\r
+ }\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
+ if (msa != null)\r
+ {\r
+ return msa;\r
+ }\r
+ else\r
+ {\r
+ if (seq != null)\r
+ {\r
+ return new SequenceI[]\r
+ {\r
+ seq};\r
+ }\r
+ }\r
+ return null;\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.\r
+ 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",\r
+ ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ return ShowNewickTree(nf,title,600,500,4,5);\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, int w,int h,int x, int y)\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,\r
+ "FromFile",\r
+ title);\r
+\r
+ tp.setSize(w,h);\r
+\r
+ if(x>0 && y>0)\r
+ tp.setLocation(x,y);\r
+\r
+\r
+ Desktop.addInternalFrame(tp, title, w, h);\r
+ addTreeMenuItem(tp, title);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return tp;\r
+ }\r
+\r
+ class PrintThread\r
+ 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
+ /**\r
+ * Generates menu items and listener event actions for web service clients\r
+ *\r
+ */\r
+ public void BuildWebServiceMenu()\r
+ {\r
+ if ( (Discoverer.services != null)\r
+ && (Discoverer.services.size() > 0))\r
+ {\r
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");\r
+ Vector wsmenu = new Vector();\r
+ if (msaws != null)\r
+ {\r
+ // Add any Multiple Sequence Alignment Services\r
+ final JMenu msawsmenu = new JMenu("Alignment");\r
+ for (int i = 0, j = msaws.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
+ get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
+ false, true, viewport.getAlignment().getDataset());\r
+\r
+ }\r
+\r
+ });\r
+ msawsmenu.add(method);\r
+ // Deal with services that we know accept partial alignments.\r
+ if (sh.getName().indexOf("lustal") > -1)\r
+ {\r
+ // We know that ClustalWS can accept partial alignments for refinement.\r
+ final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");\r
+ methodR.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
+ true, true, viewport.getAlignment().getDataset());\r
+\r
+ }\r
+\r
+ });\r
+ msawsmenu.add(methodR);\r
+\r
+ }\r
+ }\r
+ wsmenu.add(msawsmenu);\r
+ }\r
+ if (secstrpr != null)\r
+ {\r
+ // Add any secondary structure prediction services\r
+ final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");\r
+ for (int i = 0, j = secstrpr.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)\r
+ secstrpr.get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());\r
+ if (msa==null) {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "There are no columns or residues usable for prediction!\n"\r
+ +"There must be valid residues in at least one\n"\r
+ +"of the sequences in the alignment,\n"\r
+ +"or in the currently selected region.",\r
+ "Invalid Input for Secondary Structure Prediction",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ if (msa.length == 1)\r
+ {\r
+ // Single Sequence prediction\r
+ new jalview.ws.JPredClient(sh,title, msa[0]);\r
+ }\r
+ else\r
+ {\r
+ if (msa.length > 1)\r
+ {\r
+ // Aligned Sequences prediction\r
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
+ title, msa);\r
+ }\r
+ }\r
+ }\r
+ });\r
+ secstrmenu.add(method);\r
+ }\r
+ wsmenu.add(secstrmenu);\r
+ }\r
+ this.webService.removeAll();\r
+ for (int i = 0, j = wsmenu.size(); i < j; i++)\r
+ {\r
+ webService.add( (JMenu) wsmenu.get(i));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ this.webService.removeAll();\r
+ this.webService.add(this.webServiceNoServices);\r
+ }\r
+ // TODO: add in rediscovery function\r
+ // TODO: reduce code redundancy.\r
+ // TODO: group services by location as well as function.\r
+ }\r
+\r
+ /* public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Export to Vamsas file");\r
+ chooser.setToolTipText("Export");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );\r
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
+ }\r
+ }*/\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+\r
+\r
+public void showTranslation_actionPerformed(ActionEvent e)\r
+{\r
+ int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] newSeq = new SequenceI[sSize];\r
+\r
+ int res, resSize;\r
+ StringBuffer protein;\r
+ String seq;\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ protein = new StringBuffer();\r
+ seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ resSize = seq.length();\r
+ for(res = 0; res < resSize; res+=3)\r
+ {\r
+ String codon = seq.substring(res, res+3);\r
+ codon = codon.replace('U', 'T');\r
+ String aa = ResidueProperties.codonTranslate(codon);\r
+ if(aa==null)\r
+ protein.append(viewport.getGapCharacter());\r
+ else if(aa.equals("STOP"))\r
+ protein.append("X");\r
+ else\r
+ protein.append( aa );\r
+ }\r
+ newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
+ }\r
+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+\r
+\r
+ // AlignViewport newViewport = new AlignViewport(al);\r
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ // tabbedPane.add("Protein", ap);\r
+ // viewports.add(newViewport);\r
+ // alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ // AlignViewport ds = new AlignViewport(al.getDataset());\r
+ // ds.setDataset(true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+/*public void tabSelected()\r
+ {\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+ }*/\r
+}\r
git://source.jalview.org / jalview.git / blobdiff