-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-\r
-\r
-package jalview.gui;\r
-\r
-import jalview.jbgui.GAlignFrame;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\r
-import jalview.ws.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.print.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.datatransfer.*;\r
-\r
-\r
-public class AlignFrame extends GAlignFrame\r
-{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- public String currentFileFormat = "Jalview";\r
-\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
-\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
-\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
-\r
- addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameActivated(InternalFrameEvent evt)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- { alignPanel.requestFocus(); }\r
- });\r
-\r
- }\r
- });\r
-\r
- }\r
-\r
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
- , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},\r
- currentFileFormat);\r
-\r
- chooser.setAcceptAllFileFilterUsed(false);\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- currentFileFormat = chooser.getSelectedFormat();\r
-\r
- if (currentFileFormat.equals("Jalview"))\r
- {\r
- String shortName = title.replace('/', '_');\r
- title = title.replace('\\', '_');\r
- String choice = chooser.getSelectedFile().getPath();\r
- Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,\r
- choice);\r
- // USE Jalview2XML to save this file\r
- return;\r
- }\r
-\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
- out.println(output);\r
- out.close();\r
- }\r
- catch(Exception ex){}\r
- }\r
-\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
- htmlOutput = null;\r
- }\r
-\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makePNG();\r
- }\r
-\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makeEPS();\r
- }\r
-\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
- class PrintThread extends Thread\r
- {\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
- printJob.setPrintable(alignPanel, pf);\r
- 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
-\r
-\r
-\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- this.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
-\r
- void updateEditMenuBar()\r
- {\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])historyList.get(0);\r
- undoMenuItem.setText("Undo "+history[0]);\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
- Object [] history = (Object[])redoList.get(0);\r
- redoMenuItem.setText("Redo "+history[0]);\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setText("Redo");\r
- }\r
- }\r
-\r
- public void addHistoryItem(String type)\r
- {\r
- // must make sure we add new sequence objects her, not refs to the existing sequences\r
- redoList.clear();\r
-\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).getSequence());\r
- }\r
-\r
-\r
- historyList.add(0, new Object[]{type, seq} );\r
- updateEditMenuBar();\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])historyList.remove(0);\r
- // add the redo state before continuing!!\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).\r
- getSequence());\r
- }\r
- /////////\r
-\r
- redoList.add(0, new Object[] {history[0], seq});\r
-\r
- seq = (SequenceI[]) history[1];\r
- AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment( new Alignment(seq) );\r
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
- updateEditMenuBar();\r
- for(int i=0; i<old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (sg == null)\r
- return;\r
-\r
- if (up)\r
- {\r
- for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
- continue;\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
- continue;\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
- continue;\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
- continue;\r
-\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
- }\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- StringBuffer buffer= new StringBuffer();\r
-\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
- }\r
- c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
-\r
- }\r
-\r
-\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
- paste(true);\r
- }\r
-\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("Paste");\r
- paste(false);\r
- }\r
-\r
- void paste(boolean newAlignment)\r
- {\r
- try{\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
- if (contents == null)\r
- return;\r
-\r
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
-\r
- if(!newAlignment)\r
- viewport.alignment.addSequence(sequence);\r
- else\r
- seqs.add(sequence);\r
- }\r
-\r
- if(newAlignment)\r
- {\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- seqs.toArray(newSeqs);\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
- String newtitle = new String("Copied sequences");\r
- if( title.startsWith("Copied sequences"))\r
- newtitle = title;\r
- else\r
- newtitle = newtitle.concat("- from "+title);\r
-\r
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- }\r
- else\r
- {\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- }catch(Exception ex){}// could be anything being pasted in here\r
-\r
- }\r
-\r
-\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
- }\r
-\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("Delete");\r
- if (viewport.getSelectionGroup() == null)\r
- return;\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
-\r
- if(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\r
- else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setClosed(true);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
-\r
- }\r
-\r
-\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])redoList.remove(0);\r
- SequenceI[] seq = (SequenceI[]) history[1];\r
- viewport.setAlignment( new Alignment(seq) );\r
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
- sg.setEndRes(viewport.alignment.getWidth());\r
- viewport.setSelectionGroup(sg);\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
-\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0,min);\r
-\r
- if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
- }\r
-\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
- if(viewport.getSelectionGroup()!=null)\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
- if(!sg.adjustForRemoveRight(max))\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
-\r
-\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete gapped columns");\r
- viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete all gaps");\r
- SequenceI current;\r
- int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
- jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
- }\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340,110);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
-\r
- }\r
-\r
-\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- FontChooser fc = new FontChooser( alignPanel );\r
- }\r
-\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowFullId( fullSeqId.isSelected() );\r
-\r
- alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
- scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
- scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
- scaleRight.setVisible( wrapMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText( viewTextMenuItem.isSelected() );\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
- {\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
- }\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
- return;\r
- }\r
- viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- return;\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
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- };\r
- });\r
-\r
- alignPanel.setOverviewPanel( overview );\r
-\r
-\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( null );\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- abovePIDThreshold.setSelected(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new HydrophobicColourScheme() );\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme() );\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme() );\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
- }\r
-\r
-\r
-\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if ( viewport.getAbovePIDThreshold() )\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
-\r
-\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\r
-\r
- 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
- ccs = new ConservationColourScheme(c, cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
- viewport.setGlobalColourScheme(ccs);\r
-\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
-\r
- }\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
-\r
-\r
- if(viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
- }\r
- else if(cs!=null)\r
- {\r
- try{\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
- }\r
-\r
- if( viewport.getConservationSelected() )\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = ccs;\r
- }\r
- else if(cs!=null)\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- }\r
-\r
- }\r
- }\r
-\r
- if(alignPanel.getOverviewPanel()!=null)\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
- }\r
-\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getConservationSelected())\r
- {\r
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
- "Background");\r
- SliderPanel.showConservationSlider();\r
- }\r
- }\r
-\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
-\r
- modifyConservation_actionPerformed(null);\r
- }\r
-\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
-\r
- conservationMenuItem.setSelected(false);\r
- viewport.setConservationSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
-\r
- modifyPID_actionPerformed(null);\r
- }\r
-\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour( new PIDColourScheme() );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme() );\r
- }\r
-\r
-\r
-\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
- alignPanel.repaint();\r
- }\r
-\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
-\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelectionGroup().getSize()<2)\r
- JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\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
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
- +"at least 4 input sequences.",\r
- "Sequence selection insufficient",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- try{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
-\r
- }\r
-\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
- }\r
-\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- //are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
- }\r
-\r
- addTreeMenuItem(tp, title);\r
-\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- }\r
-\r
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
- {\r
- final JMenuItem item = new JMenuItem(title);\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- alignPanel.repaint();\r
- }\r
- });\r
-\r
- treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- sortByTreeMenu.remove(item);\r
- };\r
- });\r
-\r
- }\r
-\r
-\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
- "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
- +" Nucleic Acids Research, submitted, June 1994.",\r
- 450, 150);\r
-\r
- ClustalThread thread = new ClustalThread(info);\r
- thread.start();\r
- }\r
-\r
- class ClustalThread extends Thread\r
- {\r
- WebserviceInfo info;\r
- public ClustalThread(WebserviceInfo info)\r
- {this.info = info; }\r
-\r
- public void run()\r
- {\r
- info.setStatus(WebserviceInfo.STATE_RUNNING);\r
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
- Vector sv = viewport.getAlignment().getSequences();\r
- SequenceI[] seqs = new SequenceI[sv.size()];\r
-\r
- int i = 0;\r
- do\r
- {\r
- seqs[i] = (SequenceI) sv.elementAt(i);\r
- }\r
- while (++i < sv.size());\r
-\r
- SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
- if (alignment != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(alignment));\r
- Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
- NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- af.clustalColour_actionPerformed(null);\r
- af.clustalColour.setSelected(true);\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
- {\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- info.appendProgressText("Problem obtaining clustal alignment");\r
- }\r
- }\r
- }\r
-\r
- protected void jpred_actionPerformed(ActionEvent e)\r
-{\r
-\r
- if (viewport.getSelectionGroup() != null && 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
- if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
- {\r
- JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
- }\r
- else\r
- {\r
- int sz;\r
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
-\r
- JPredClient ct = new JPredClient(msa);\r
- }\r
-\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
- {\r
- JPredClient ct = new JPredClient( (SequenceI)\r
- seqs.elementAt(0));\r
- }\r
- else\r
- {\r
- SequenceI[] msa = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- JPredClient ct = new JPredClient(msa);\r
- }\r
-\r
- }\r
- }\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
-\r
- MsaWSClient ct = new jalview.ws.MsaWSClient(msa);\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1) {\r
- SequenceI[] msa = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- MsaWSClient ct = new MsaWSClient(msa);\r
- }\r
-\r
- }\r
- }\r
-\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
- // Pick the tree file\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select a newick-like tree file");\r
- chooser.setToolTipText("Load a tree file");\r
- int value = chooser.showOpenDialog(null);\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
- ShowNewickTree(fin, choice);\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "Problem reading tree file",\r
- ex.getMessage(),\r
- JOptionPane.WARNING_MESSAGE);\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public void ShowNewickTree(NewickFile nf, String title)\r
- {\r
- try{\r
- nf.parse();\r
- if (nf.getTree() != null)\r
- {\r
- TreePanel tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(),\r
- nf, "FromFile", title);\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
- }\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Softwarechang
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.util.ShiftList;
+import jalview.ws.*;
+import java.awt.dnd.*;
+import org.biojava.dasobert.eventmodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+ extends GAlignFrame implements DropTargetListener, FeatureListener
+{
+ /** DOCUMENT ME!! */
+ public static final int NEW_WINDOW_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
+ public static final int NEW_WINDOW_HEIGHT = 500;
+ AlignmentPanel alignPanel;
+ AlignViewport viewport;
+
+ // Vector viewports = new Vector();
+ // Vector alignPanels = new Vector();
+ /** DOCUMENT ME!! */
+ public String currentFileFormat = null;
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+ private int treeCount = 0;
+
+ /**
+ * new alignment window with hidden columns
+ * @param al AlignmentI
+ * @param hiddenColumns ColumnSelection or null
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
+
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+ if(viewport.vconsensus==null)
+ {
+ //Out of memory calculating consensus.
+ BLOSUM62Colour.setEnabled(false);
+ PIDColour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ abovePIDThreshold.setEnabled(false);
+ modifyPID.setEnabled(false);
+ }
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+ if(sortby.equals("Id"))
+ sortIDMenuItem_actionPerformed(null);
+ else if(sortby.equals("Pairwise Identity"))
+ sortPairwiseMenuItem_actionPerformed(null);
+
+ // remove(tabbedPane);
+ getContentPane().add(alignPanel, BorderLayout.CENTER);
+
+
+
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+ ///Dataset tab
+ /////////////////////////
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);
+ // tabbedPane.add("Dataset", dap);
+ // viewports.add(ds);
+ // alignPanels.add(dap);
+ /////////////////////////
+
+
+ viewport.addPropertyChangeListener(new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ alignmentChanged();
+ }
+ }
+ });
+
+
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(al.isNucleotide());
+ }
+
+
+ if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+ {
+ wrapMenuItem.setSelected(true);
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ }
+
+
+ /**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignFrame(AlignmentI al)
+ {
+ this(al, null);
+ }
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
+ }
+
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */
+ private void addServiceListeners()
+ {
+ final java.beans.PropertyChangeListener thisListener;
+ // Do this once to get current state
+ BuildWebServiceMenu();
+ Desktop.discoverer.addPropertyChangeListener(
+ thisListener = new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // System.out.println("Discoverer property change.");
+ if (evt.getPropertyName().equals("services"))
+ {
+ // System.out.println("Rebuilding web service menu");
+ BuildWebServiceMenu();
+ }
+ }
+ });
+ addInternalFrameListener(new javax.swing.event.
+ InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ Desktop.discoverer.removePropertyChangeListener(thisListener);
+ closeMenuItem_actionPerformed(null);
+ }
+ ;
+ });
+ }
+
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible( nucleotide );
+ //sequenceFeatures.setVisible(!nucleotide );
+ //featureSettings.setVisible( !nucleotide );
+ conservationMenuItem.setVisible( !nucleotide );
+ modifyConservation.setVisible( !nucleotide );
+
+ //Remember AlignFrame always starts as protein
+ if(!nucleotide)
+ {
+ calculateMenu.remove(calculateMenu.getItemCount()-2);
+ }
+ }
+
+ public void comeBackLater(FeatureEvent evt)
+ {}
+
+ public void newFeatures(FeatureEvent evt)
+ {
+ if (evt.getFeatures().length > 0)
+ {
+ alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+ alignPanel.repaint();
+ }
+ }
+
+ Hashtable progressBars;
+ public void setProgressBar(String message, long id)
+ {
+ if(progressBars == null)
+ progressBars = new Hashtable();
+
+ JPanel progressPanel;
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if(progressBars.get( new Long(id) )!=null)
+ {
+ progressPanel = (JPanel)progressBars.get( new Long(id) );
+ statusPanel.remove(progressPanel);
+ progressBars.remove( progressPanel );
+ progressPanel = null;
+ if(message!=null)
+ statusBar.setText(message);
+
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(new Long(id), progressPanel);
+ }
+
+ validate();
+ }
+
+
+ /*
+ Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
+ {
+ return jalview.bin.Cache.getProperty("VERSION");
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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,
+ 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();
+
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified",
+ JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat);
+
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+ saveAlignment(choice, currentFileFormat);
+ }
+ }
+
+ public boolean saveAlignment(String file, String format)
+ {
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ String shortName = title;
+
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName.lastIndexOf(
+ java.io.File.separatorChar) + 1);
+ }
+
+ new Jalview2XML().SaveAlignment(this, file, shortName);
+
+ // USE Jalview2XML to save this file
+ return true;
+ }
+ else
+ {
+
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to save only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ format,
+ viewport.alignment.getSequencesArray(),
+ omitHidden);
+
+ if (output == null)
+ {
+ return false;
+ }
+
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ return true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ String [] omitHidden = null;
+
+ if(viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ +"\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600,
+ 500);
+
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ viewport.alignment.getSequencesArray(),
+ omitHidden));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ new HTMLOutput(viewport,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ public void createImageMap(File file, String image)
+ {
+ alignPanel.makePNGImageMap(file, image);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createPNG(File f)
+ {
+ alignPanel.makePNG(f);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createEPS(File f)
+ {
+ alignPanel.makeEPS(f);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread();
+ thread.start();
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.alignment.getAlignmentAnnotation()
+ );
+ }
+
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Jalview Annotations or Features File");
+ chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ PaintRefresher.components.remove(viewport.alignment);
+ this.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ 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");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param hi DOCUMENT ME!
+ */
+ public void addHistoryItem(HistoryItem hi)
+ {
+ historyList.push(hi);
+ redoList.clear();
+ updateEditMenuBar();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem nh,hi = (HistoryItem) historyList.pop();
+ redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
+ HistoryItem.HIDE));
+ if (hi.alColumnChanges!=null)
+ nh.alColumnChanges = hi.alColumnChanges.getInverse();
+ restoreHistoryItem(hi);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem nh,hi = (HistoryItem) redoList.pop();
+ historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
+ HistoryItem.HIDE));
+ if (hi.alColumnChanges!=null)
+ nh.alColumnChanges=hi.alColumnChanges.getInverse();
+ restoreHistoryItem(hi);
+ updateEditMenuBar();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ // used by undo and redo
+ void restoreHistoryItem(HistoryItem hi)
+ {
+
+ hi.restore(viewport.getColumnSelection());
+
+ updateEditMenuBar();
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param up DOCUMENT ME!
+ */
+ 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.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+
+ if (sg.getSequences(false).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.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+ if (sg.getSequences(false).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ alignPanel.repaint();
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ omitHidden = viewport.getViewAsString(true);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ "Fasta",
+ seqs,
+ omitHidden);
+
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
+
+ Vector hiddenColumns = null;
+ if(viewport.hasHiddenColumns)
+ {
+ hiddenColumns =new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[])
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+
+ hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+ region[1]-hiddenOffset});
+ }
+ }
+
+ Desktop.jalviewClipboard = new Object[]{ seqs,
+ viewport.alignment.getDataset(),
+ hiddenColumns};
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ paste(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+ HistoryItem.PASTE));
+ paste(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newAlignment DOCUMENT ME!
+ */
+ 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);
+ if(str.length()<1)
+ return;
+
+ String format = new IdentifyFile().Identify(str, "Paste");
+ SequenceI[] sequences;
+
+
+ if(Desktop.jalviewClipboard!=null)
+ {
+ // The clipboard was filled from within Jalview, we must use the sequences
+ // And dataset from the copied alignment
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+ }
+ else
+ {
+ sequences = new FormatAdapter().readFile(str, "Paste", format);
+ }
+
+ AlignmentI alignment = null;
+
+ if (newAlignment)
+ {
+ alignment = new Alignment(sequences);
+
+ if(Desktop.jalviewClipboard!=null)
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
+ else
+ alignment.setDataset( null );
+
+ }
+ else
+ {
+ alignment = viewport.getAlignment();
+
+ //!newAlignment
+ for (int i = 0; i < sequences.length; i++)
+ {
+ Sequence newseq = new Sequence(sequences[i].getName(),
+ sequences[i].getSequence(), sequences[i].getStart(),
+ sequences[i].getEnd());
+
+ alignment.addSequence(newseq);
+ }
+
+
+ viewport.setEndSeq(alignment.getHeight());
+ alignment.getWidth();
+ viewport.firePropertyChange("alignment", null, alignment.getSequences());
+ }
+
+
+
+
+
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ AlignmentAnnotation newAnnot =
+ new AlignmentAnnotation(
+ sequences[i].getAnnotation()[a].label,
+ sequences[i].getAnnotation()[a].description,
+ sequences[i].getAnnotation()[a].annotations,
+ sequences[i].getAnnotation()[a].graphMin,
+ sequences[i].getAnnotation()[a].graphMax,
+ sequences[i].getAnnotation()[a].graph);
+
+ sequences[i].getAnnotation()[a] = newAnnot;
+ newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+ sequenceMapping;
+ newAnnot.sequenceRef = sequences[i];
+ newAnnot.adjustForAlignment();
+ alignment.addAnnotation(newAnnot);
+ alignment.setAnnotationIndex(newAnnot, a);
+ }
+
+ alignPanel.annotationPanel.adjustPanelHeight();
+ }
+ }
+
+ if(newAlignment)
+ {
+ AlignFrame af = new AlignFrame(alignment);
+ String newtitle = new String("Copied sequences");
+
+ if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
+ {
+ Vector hc = (Vector)Desktop.jalviewClipboard[2];
+ for(int i=0; i<hc.size(); i++)
+ {
+ int [] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+ }
+
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: "+ex);
+ // could be anything being pasted in here
+ }
+
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+
+
+ //Jalview no longer allows deletion of residues.
+ //Check here whether any residues are in selection area
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+ {
+ for (int i = 0; i < sg.sequences.size(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int j = sg.getStartRes();
+ do
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, "Cannot delete residues from alignment!\n"
+ + "Try hiding columns instead.",
+ "Deletion of residues not permitted",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ j++;
+ }while(j<=sg.getEndRes());
+ }
+ }*/
+
+
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+ HistoryItem.HIDE));
+
+
+ for (int i = 0; i < sg.getSize(false); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.getAlignment().findIndex(seq);
+
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize(false) == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+ if (seq.getSequence().length() < 1)
+ {
+ viewport.getAlignment().deleteSequence(seq);
+ }
+ else
+ {
+ viewport.getAlignment().getSequences().setElementAt(seq, index);
+ }
+ }
+
+ viewport.setSelectionGroup(null);
+ viewport.alignment.deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+
+
+
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ this.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.setSelectionGroup(null);
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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), false);
+ }
+
+ sg.setEndRes(viewport.alignment.getWidth() - 1);
+ viewport.setSelectionGroup(sg);
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(viewport.cursorMode)
+ {
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
+ }
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+ alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.repaint();
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (sg == null)
+ {
+ selectAllSequenceMenuItem_actionPerformed(null);
+
+ return;
+ }
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();
+ i++)
+ {
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+
+ if (colSel.size() > 0)
+ {
+ HistoryItem edit;
+ addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
+ HistoryItem.HIDE));
+
+ int min = colSel.getMin();
+ viewport.getAlignment().trimLeft(min);
+ colSel.compensateForEdit(0, min);
+ edit.addShift(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);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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);
+ // TODO: delete hidden column entries in colSel to right of max
+ // TODO: record hidden columns in history for undo.
+ 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);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem edit;
+ addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
+ viewport.alignment, HistoryItem.HIDE));
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ ShiftList shifts;
+ viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ edit.alColumnChanges=shifts.getInverse();
+ if (viewport.hasHiddenColumns)
+ viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
+ // TODO: columnSelection.compensateforedits should be called (and passed to history item)
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+ HistoryItem.HIDE));
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+
+ SequenceI current;
+ int jSize;
+
+ Vector seqs = null;
+
+ int start = 0;
+ int end = viewport.alignment.getWidth();
+
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSequences(true) != null
+ && viewport.getSelectionGroup().getSize(true) > 0)
+ {
+ seqs = viewport.getSelectionGroup().getSequences(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes()+1;
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequences();
+ }
+ /* Commented out regions below are partial implementation of todo above.
+ * divide start,end into visible chunks, and for each:
+ int diff=end-start+1;
+ int diffmax=0;
+ int dr[] = new int[seqs.size()];
+ */
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ current = (SequenceI) seqs.elementAt(i);
+ //dr[i]=
+ current.removeGaps(start, end);
+ /*if (d<diff) // can only shift
+ diff=d;
+ if (diffmax<d)
+ diffmax=d;
+ */
+ }
+ /* // after the end of each chunk -
+ * if (diff>0) {
+ // record shift for history.
+ editgaps.addShift(start, diff);
+ if (viewport.hasHiddenColumns && diffmax>diff) {
+ // pad sequence
+ StringBuffer gaps=new StringBuffer(diffmax);
+ for (int i=0,j=diffmax-diff; i<j; i++)
+ gaps.append(viewport.getGapCharacter());
+ for (int i=0, j=seqs.size(); i<j; i++) {
+ current = (SequenceI) seqs.elementAt(i);
+ if (dr[i]-diff>0) {
+ String sq = current.getSequence();
+ current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
+ }
+ }
+ }
+ }*/
+
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ public void alignmentChanged()
+ {
+ if(viewport.padGaps)
+ viewport.getAlignment().padGaps();
+
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
+ {
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ }
+
+ resetAllColourSchemes();
+ if(alignPanel.overviewPanel!=null)
+ alignPanel.overviewPanel.updateOverviewImage();
+
+ viewport.alignment.adjustSequenceAnnotations();
+
+ if(alignPanel.overviewPanel!=null)
+ alignPanel.overviewPanel.updateOverviewImage();
+ // JBPNote: could push a vamsas document update here.
+ alignPanel.repaint();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = viewport.globalColourScheme;
+ if(cs!=null)
+ {
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+ resetClustalX(viewport.alignment.getSequences(),
+ viewport.alignment.getWidth());
+ }
+
+ cs.setConsensus(viewport.vconsensus);
+ if (cs.conservationApplied())
+ {
+ 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);
+
+ cs.setConservation(c);
+ }
+ }
+
+ int s, sSize = viewport.alignment.getGroups().size();
+ for(s=0; s<sSize; s++)
+ {
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme)sg.cs).resetClustalX(
+ sg.getSequences(true), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
+ HistoryItem.HIDE));
+
+ viewport.padGaps = padGapsMenuitem.isSelected();
+
+ // if (viewport.padGaps)
+ alignmentChanged();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame frame = new JInternalFrame();
+ Finder finder = new Finder(viewport, alignPanel, frame);
+ frame.setContentPane(finder);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ new FontChooser(alignPanel);
+ }
+
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+ viewport.antiAlias = smoothFont.isSelected();
+ alignPanel.annotationPanel.image = null;
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowJVSuffix(seqLimits.isSelected());
+
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText(colourTextMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ scaleAbove.setVisible(wrapMenuItem.isSelected());
+ scaleLeft.setVisible(wrapMenuItem.isSelected());
+ scaleRight.setVisible(wrapMenuItem.isSelected());
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenSeqs();
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ repaint();
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+ viewport.hideAllSelectedSeqs();
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.repaint();
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText(viewTextMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+
+ public FeatureSettings featureSettings;
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+ if(featureSettings !=null )
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
+ featureSettings = new FeatureSettings(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+ alignPanel.repaint();
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ changeColour(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void clustalColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ClustalxColourScheme(
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void zappoColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void taylorColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HydrophobicColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void helixColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HelixColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void strandColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new StrandColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void turnColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TurnColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void buriedColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new BuriedColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ */
+ public void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if(cs!=null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
+
+ cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else
+ {
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+
+ 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);
+
+ cs.setConservation(c);
+
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+ "Background"));
+ }
+ else
+ {
+ cs.setConservation(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;
+ continue;
+ }
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(true), 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()
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(true), 0,
+ sg.getWidth()));
+ }
+ else
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
+
+ if (viewport.getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(true), 0,
+ viewport.alignment.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ sg.cs.setConservation(c);
+ }
+ else
+ sg.cs.setConservation(null);
+ }
+ }
+
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(),
+ "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.globalColourScheme,
+ "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyConservation_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+ conservationMenuItem.setSelected(false);
+ viewport.setConservationSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(alignPanel, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ changeColour(udc);
+ }
+ }
+
+ public void updateUserColourMenu()
+ {
+
+ Component[] menuItems = colourMenu.getMenuComponents();
+ int i, iSize = menuItems.length;
+ for (i = 0; i < iSize; i++)
+ {
+ if (menuItems[i].getName() != null &&
+ menuItems[i].getName().equals("USER_DEFINED"))
+ {
+ colourMenu.remove(menuItems[i]);
+ iSize--;
+ }
+ }
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void PIDColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PIDColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new Blosum62ColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+ HistoryItem.SORT));
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+ HistoryItem.SORT));
+
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ new RedundancyPanel(alignPanel, this);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ( (viewport.getSelectionGroup() == null) ||
+ (viewport.getSelectionGroup().getSize(false) < 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);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ( ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) < 4) &&
+ (viewport.getSelectionGroup().getSize(false) > 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;
+ }
+
+ new PCAPanel(viewport);
+ }
+
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
+ {
+ alignmentChanged();
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param pwType DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ TreePanel tp;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 3))
+ {
+ int s = 0;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ while (s < sg.getSize(false))
+ {
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+ sg.getEndRes())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The selected region to create a tree may\nonly contain residues or gaps.\n" +
+ "Try using the Pad function in the edit menu,\n" +
+ "or one of the multiple sequence alignment web services.",
+ "Sequences in selection are not aligned",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ }
+
+ title = title + " on region";
+ tp = new TreePanel(viewport, type, pwType);
+ }
+ else
+ {
+ //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;
+ }
+
+ if(viewport.alignment.getHeight()<2)
+ return;
+
+ tp = new TreePanel(viewport, type, pwType);
+ }
+
+ addTreeMenuItem(tp, title);
+
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title DOCUMENT ME!
+ * @param order DOCUMENT ME!
+ */
+ 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();
+ }
+ });
+ }
+
+ /**
+ * Maintain the Order by->Displayed Tree menu.
+ * Creates a new menu item for a TreePanel with an appropriate
+ * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
+ * to remove the menu item when the treePanel is closed, and adjust
+ * the tree leaf to sequence mapping when the alignment is modified.
+ * @param treePanel Displayed tree window.
+ * @param title SortBy menu item title.
+ */
+ 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);
+ }
+ }
+ ;
+ });
+ }
+
+ /**
+ * Work out whether the whole set of sequences
+ * or just the selected set will be submitted for multiple alignment.
+ *
+ */
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+ {
+ // Now, check we have enough sequences
+ AlignmentView msa = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 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(false)];
+
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ } */
+ msa = viewport.getAlignmentView(true);
+ }
+ 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);
+ }
+ }*/
+ msa = viewport.getAlignmentView(false);
+ }
+ return msa;
+ }
+
+ /**
+ * Decides what is submitted to a secondary structure prediction service,
+ * the currently selected sequence, or the currently selected alignment
+ * (where the first sequence in the set is the one that the prediction
+ * will be for).
+ */
+ AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ {
+ AlignmentView seqs = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 0))
+ {
+ seqs = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ seqs = viewport.getAlignmentView(false);
+ }
+ // limit sequences - JBPNote in future - could spawn multiple prediction jobs
+ // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.alignment.isAligned())
+ {
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+ }
+ return seqs;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ 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");
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Problem reading tree file",
+ ex.getMessage(),
+ JOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ }
+ }
+
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title)
+ {
+ return ShowNewickTree(nf,title,600,500,4,5);
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nf DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
+ {
+ TreePanel tp = null;
+
+ try
+ {
+ nf.parse();
+
+ if (nf.getTree() != null)
+ {
+ tp = new TreePanel(viewport,
+ "FromFile",
+ title,
+ nf);
+
+ tp.setSize(w,h);
+
+ if(x>0 && y>0)
+ tp.setLocation(x,y);
+
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ addTreeMenuItem(tp, title);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return tp;
+ }
+
+ 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();
+ }
+ }
+ }
+ }
+
+ /**
+ * Generates menu items and listener event actions for web service clients
+ *
+ */
+ public void BuildWebServiceMenu()
+ {
+ if ( (Discoverer.services != null)
+ && (Discoverer.services.size() > 0))
+ {
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector wsmenu = new Vector();
+ final AlignFrame af = this;
+ if (msaws != null)
+ {
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
+ get(i);
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ false, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ msawsmenu.add(method);
+ // Deal with services that we know accept partial alignments.
+ if (sh.getName().indexOf("lustal") > -1)
+ {
+ // We know that ClustalWS can accept partial alignments for refinement.
+ final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+ methodR.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ true, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ msawsmenu.add(methodR);
+
+ }
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
+ secstrpr.get(i);
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
+ if (msa.getSequences().length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh, title, false, msa, af);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh,
+ title, true, msa, af);
+ }
+ }
+ }
+ });
+ secstrmenu.add(method);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ this.webService.removeAll();
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add( (JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ this.webService.removeAll();
+ this.webService.add(this.webServiceNoServices);
+ }
+ // TODO: add in rediscovery function
+ // TODO: reduce code redundancy.
+ // TODO: group services by location as well as function.
+ }
+
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Export to Vamsas file");
+ chooser.setToolTipText("Export");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+ }
+ }*/
+
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+
+ int s, sSize = selection.length;
+ SequenceI [] newSeq = new SequenceI[sSize];
+
+ int res, resSize;
+ StringBuffer protein;
+ String seq;
+ for(s=0; s<sSize; s++)
+ {
+ protein = new StringBuffer();
+ seq = AlignSeq.extractGaps("-. ", seqstring[s]);
+ resSize = seq.length();
+ resSize -= resSize%3;
+
+ for(res = 0; res < resSize; res+=3)
+ {
+ String codon = seq.substring(res, res+3);
+ codon = codon.replace('U', 'T');
+ String aa = ResidueProperties.codonTranslate(codon);
+ if(aa==null)
+ protein.append(viewport.getGapCharacter());
+ else if(aa.equals("STOP"))
+ protein.append("X");
+ else
+ protein.append( aa );
+ }
+ newSeq[s] = new Sequence(selection[s].getName(),
+ protein.toString());
+ }
+
+
+ AlignmentI al = new Alignment(newSeq);
+ al.setDataset(null);
+
+
+ ////////////////////////////////
+ // Copy annotations across
+ jalview.datamodel.AlignmentAnnotation[] annotations
+ = viewport.alignment.getAlignmentAnnotation();
+ int a, aSize;
+ if(annotations!=null)
+ {
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].label.equals("Quality") ||
+ annotations[i].label.equals("Conservation") ||
+ annotations[i].label.equals("Consensus"))
+ {
+ continue;
+ }
+
+ aSize = viewport.alignment.getWidth() / 3;
+ jalview.datamodel.Annotation[] anots =
+ new jalview.datamodel.Annotation[aSize];
+
+ for (a = 0; a < viewport.alignment.getWidth(); a++)
+ {
+ if (annotations[i].annotations[a] == null
+ || annotations[i].annotations[a] == null)
+ continue;
+
+ anots[a / 3] = new Annotation(
+ annotations[i].annotations[a].displayCharacter,
+ annotations[i].annotations[a].description,
+ annotations[i].annotations[a].secondaryStructure,
+ annotations[i].annotations[a].value,
+ annotations[i].annotations[a].colour);
+ }
+
+ jalview.datamodel.AlignmentAnnotation aa
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+ annotations[i].description, anots);
+ al.addAnnotation(aa);
+ }
+ }
+
+ AlignFrame af = new AlignFrame(al);
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+
+ // AlignViewport newViewport = new AlignViewport(al);
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
+ // tabbedPane.add("Protein", ap);
+ // viewports.add(newViewport);
+ // alignPanels.add(ap);
+
+ ///Dataset tab
+ /////////////////////////
+
+ // AlignViewport ds = new AlignViewport(al.getDataset());
+ // ds.setDataset(true);
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);
+ // tabbedPane.add("Dataset", dap);
+ // viewports.add(ds);
+ // alignPanels.add(dap);
+ /////////////////////////
+
+
+}
+
+/*public void tabSelected()
+ {
+ int index = tabbedPane.getSelectedIndex();
+ viewport = (AlignViewport)viewports.elementAt(index);
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
+ }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseFeaturesFile(String file, String type)
+{
+ boolean featuresFile = false;
+ try{
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
+ alignPanel.seqPanel.seqCanvas.
+ getFeatureRenderer().featureColours,
+ false);
+ }
+ catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if(featuresFile)
+ {
+ viewport.showSequenceFeatures = true;
+ showSeqFeatures.setSelected(true);
+ alignPanel.repaint();
+ }
+
+ return featuresFile;
+}
+
+public void dragEnter(DropTargetDragEvent evt)
+{}
+
+public void dragExit(DropTargetEvent evt)
+{}
+
+public void dragOver(DropTargetDragEvent evt)
+{}
+
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
+
+public void drop(DropTargetDropEvent evt)
+{
+ Transferable t = evt.getTransferable();
+ java.util.List files = null;
+
+ try
+ {
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ //Works on Windows and MacOSX
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ }
+ else if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ // This is used by Unix drag system
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ String data = (String) t.getTransferData(uriListFlavor);
+ files = new java.util.ArrayList(1);
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data,
+ "\r\n");
+ st.hasMoreTokens(); )
+ {
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+
+ java.net.URI uri = new java.net.URI(s);
+ java.io.File file = new java.io.File(uri);
+ files.add(file);
+ }
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (files != null)
+ {
+ try
+ {
+
+ for (int i = 0; i < files.size(); i++)
+ {
+ loadJalviewDataFile(files.get(i).toString());
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+}
+
+ // This method will attempt to load a "dropped" file first by testing
+ // whether its and Annotation file, then features file. If both are
+ // false then the user may have dropped an alignment file onto this
+ // AlignFrame
+ public void loadJalviewDataFile(String file)
+ {
+ try{
+ String protocol = "File";
+
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
+ alignment, file);
+
+ if (!isAnnotation)
+ {
+ boolean isGroupsFile = parseFeaturesFile(file,protocol);
+ if (!isGroupsFile)
+ {
+ String format = new IdentifyFile().Identify(file, protocol);
+
+ if(format.equalsIgnoreCase("JnetFile"))
+ {
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(),
+ 0, false);
+ alignPanel.adjustAnnotationHeight();
+ alignPanel.repaint();
+ }
+ else
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ }
+ else
+ {
+ // (isAnnotation)
+ alignPanel.adjustAnnotationHeight();
+ }
+
+ }catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+}