-/********************\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 jalview.datamodel.SequenceI;\r
-\r
-public class AlignFrame extends GAlignFrame\r
-{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public AlignFrame(AlignmentI al)\r
- {\r
- super();\r
- viewport = new AlignViewport(al,true,true,true,false);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
- fontNameMenuItem.setText(viewport.getFont().getName());\r
- fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
-\r
- AlignmentUtil.fetchSequenceFeatures(al, alignPanel);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
- chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
- 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.get(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
- 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
- ArrayList historyList = new ArrayList();\r
- ArrayList redoList = new ArrayList();\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
- 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
- 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
- viewport.setAlignment( new Alignment(seq) );\r
- updateEditMenuBar();\r
- alignPanel.RefreshPanels();\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
- updateEditMenuBar();\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
- public void groupsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(geditor);\r
- Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
- frame.setResizable(false);\r
- }\r
-\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.getSelection().clear();\r
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Selection sel = viewport.getSelection();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRubberbandGroup(null);\r
- viewport.getSelection().clear();\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Selection sel = viewport.getSelection();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
- sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
- else\r
- sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
- }\r
- PaintRefresher.Refresh(null);\r
- }\r
-\r
-\r
- public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.getColumnSelection().clear();\r
- repaint();\r
- }\r
-\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete columns");\r
- 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
- alignPanel.RefreshPanels();\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
- if(max>1)\r
- viewport.getAlignment().trimRight(max);\r
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete gapped columns");\r
- viewport.getAlignment().removeGaps();\r
- alignPanel.RefreshPanels();\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
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- char thisChar = '-';\r
- char nextChar = '.';\r
- if(viewport.getGapCharacter()=='-')\r
- {\r
- thisChar = '.';\r
- nextChar = '-';\r
- }\r
- setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
- viewport.setGapCharacter(thisChar);\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane op = new JOptionPane();\r
- JInternalFrame frame = op.createInternalFrame(this, "Find");\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setClosable(true);\r
- frame.setContentPane(finder);\r
- frame.setSize(340,110);\r
- frame.setVisible(true);\r
- }\r
-\r
-\r
-\r
- public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
-\r
-\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font",\r
- "Font selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,fonts\r
- ,fontNameMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontNameMenuItem.setText(selection);\r
- SetFont();\r
- }\r
-\r
- }\r
-\r
- public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,fontSizeMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontSizeMenuItem.setText(selection);\r
- SetFont();\r
- }\r
- }\r
-\r
- public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font style",\r
- "Font style",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"plain", "bold", "italic"}\r
- ,fontStyleMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontStyleMenuItem.setText(selection);\r
- SetFont();\r
- }\r
-\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText( colourTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- void SetFont()\r
- {\r
- int style = java.awt.Font.PLAIN;\r
- if(fontStyleMenuItem.getText().equals("bold"))\r
- style = java.awt.Font.BOLD;\r
- else if(fontStyleMenuItem.getText().equals("italic"))\r
- style = java.awt.Font.ITALIC;\r
-\r
- viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
- style,\r
- Integer.parseInt(fontSizeMenuItem.getText())));\r
- alignPanel.RefreshPanels();\r
-\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText( viewTextMenuItem.isSelected() );\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.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 = alignPanel.getOverviewPanel();\r
- try{\r
- overview = new OverviewPanel(alignPanel, viewport);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- };\r
- });\r
- alignPanel.setOverviewPanel( overview );\r
-\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
- +"\nTry reducing the font size.",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
-\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( null );\r
- changeColour();\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(\r
- new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- abovePIDThreshold.setSelected(false);\r
- changeColour();\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
- changeColour();\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
- changeColour();\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HelixColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new StrandColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new TurnColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
- changeColour();\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- void changeColour()\r
- {\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold_actionPerformed(null);\r
- else if(conservationMenuItem.isSelected())\r
- conservationMenuItem_actionPerformed(null);\r
-\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(abovePIDThreshold.isSelected())\r
- {\r
- abovePIDThreshold.setSelected(false);\r
- Desktop.hidePIDSlider();\r
- }\r
-\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
-\r
- ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
-\r
- if (ccs != null)\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
- else\r
- ccs = new ConservationColourScheme(c, oldCs);\r
-\r
-\r
- int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
-\r
- ccs.inc = threshold;\r
-\r
- if (ccs.cs instanceof ResidueColourScheme)\r
- ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
- else if (ccs.cs instanceof ScoreColourScheme)\r
- ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
-\r
- viewport.setGlobalColourScheme(ccs);\r
-\r
-\r
- }\r
- else if (oldCs instanceof ConservationColourScheme)\r
- {\r
- /// ie, if we remove ConservationColourScheme from backgroundColour\r
- oldCs = ccs.cs;\r
- viewport.setGlobalColourScheme(oldCs);\r
- Desktop.hideConservationSlider();\r
- }\r
-\r
- if(e!=null)\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
-\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
- int threshold = 0;\r
- if (oldCs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
- oldCs = ccs.cs;\r
- }\r
-\r
- if(abovePIDThreshold.isSelected())\r
- {\r
- threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
- Desktop.hideConservationSlider();\r
- }\r
- else\r
- Desktop.hidePIDSlider();\r
-\r
- if (oldCs instanceof ResidueColourScheme)\r
- ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
- else if (oldCs instanceof ScoreColourScheme)\r
- ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
-\r
- viewport.setGlobalColourScheme(oldCs);\r
- if(e!=null)\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new PIDColourScheme() );\r
- alignPanel.setColourScheme( );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- changeColour();\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.RefreshPanels();\r
- }\r
-\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
- alignPanel.RefreshPanels();\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.RefreshPanels();\r
- }\r
-\r
- public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("sort");\r
- if(viewport.getCurrentTree()==null)\r
- return;\r
-\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
- alignPanel.RefreshPanels();\r
- }\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);\r
- frame.setMaximizable(false);\r
- frame.setResizable(false);\r
-\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelection().size()<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
- if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>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
- JInternalFrame frame = new javax.swing.JInternalFrame();\r
- TreePanel tp=null;\r
- if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
- viewport.getStartRes(), viewport.getEndRes());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, viewport.getStartRes(),\r
- viewport.getEndRes());\r
- }\r
-\r
- frame.setContentPane(tp);\r
- Desktop.addInternalFrame(frame, title, 600, 500);\r
- }\r
-\r
-\r
-\r
-\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- ClustalThread ct = new ClustalThread(frame);\r
- Thread t = new Thread(ct);\r
- t.start();\r
- frame.setContentPane(ct);\r
- Desktop.addInternalFrame(frame, title, 300, 80);\r
-\r
- }\r
-\r
- class ClustalThread extends JPanel implements Runnable\r
- {\r
- Image [] image;\r
- int imageIndex = 0;\r
- boolean webServiceRunning = false;\r
- JInternalFrame frame;\r
- public ClustalThread(JInternalFrame frame)\r
- {\r
- this.frame = frame;\r
- image = new Image[9];\r
- for(int i=0; i<9; i++)\r
- {\r
- java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
- if (url != null)\r
- {\r
- image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image[i], i);\r
- try{mt.waitForID(i);}\r
- catch(Exception ex){}\r
- }\r
- }\r
- DNATwirler twirler = new DNATwirler();\r
- twirler.start();\r
- webServiceRunning = true;\r
- }\r
-\r
- class DNATwirler extends Thread\r
- {\r
- public void run()\r
- {\r
- while(webServiceRunning)\r
- {\r
- try{\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %=9;\r
- repaint();\r
- }\r
- catch(Exception ex){}\r
- }\r
- }\r
- }\r
-\r
- // JBPNote\r
- // Should check to see if the server settings are valid\r
- // Need visual-delay indication here.\r
- public void run()\r
- {\r
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
- Vector sv = viewport.getAlignment().getSequences();\r
- SequenceI[] seqs = new SequenceI[sv.size()];\r
-\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
-\r
- if (alignment != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(alignment));\r
- af.clustalColour.setSelected(true);\r
- af.clustalColour_actionPerformed(null);\r
- Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
- 700, 500); // JBPNote - is there a new window geom. property ?\r
- }\r
- else\r
- JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- webServiceRunning = false;\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
- if(image!=null)\r
- {\r
- g.drawImage(image[imageIndex],10,10,this);\r
- }\r
- g.setFont(new Font("Arial", Font.BOLD, 12));\r
- g.setColor(Color.black);\r
- g.drawString("Clustal Alignment Web Service running", 30,30);\r
- }\r
- }\r
-\r
-\r
- public void doKeyPressed(KeyEvent evt)\r
- {\r
- if(evt.isControlDown() && evt.getKeyChar()=='f')\r
- findMenuItem_actionPerformed(null);\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.dnd.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+ extends GAlignFrame implements DropTargetListener
+{
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
+ public static final int DEFAULT_HEIGHT = 500;
+ public AlignmentPanel alignPanel;
+
+ AlignViewport viewport;
+
+ Vector alignPanels = new Vector();
+
+
+ /** DOCUMENT ME!! */
+ String currentFileFormat = null;
+
+ String fileName = null;
+
+
+ /**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignFrame(AlignmentI al, int width, int height)
+ {
+ this(al, null, width, height);
+ }
+
+
+ /**
+ * new alignment window with hidden columns
+ * @param al AlignmentI
+ * @param hiddenColumns ColumnSelection or null
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height)
+ {
+ this.setSize(width, height);
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+
+ addAlignmentPanel(alignPanel, true);
+ init();
+ }
+
+ /**
+ * Make a new AlignFrame from exisiting alignmentPanels
+ * @param ap AlignmentPanel
+ * @param av AlignViewport
+ */
+ public AlignFrame(AlignmentPanel ap)
+ {
+ viewport = ap.av;
+ alignPanel = ap;
+ addAlignmentPanel(ap, false);
+ init();
+ }
+
+ void init()
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+ if (viewport.conservation == null)
+ {
+ BLOSUM62Colour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
+ }
+
+ 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);
+ }
+
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
+
+ setMenusFromViewport(viewport);
+
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+ {
+ this.overviewMenuItem_actionPerformed(null);
+ }
+
+ addKeyListener();
+
+ }
+
+ public void setFileName(String file, String format)
+ {
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
+ }
+
+ void addKeyListener()
+ {
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ if (viewport.cursorMode
+ && evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
+ {
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
+
+ switch (evt.getKeyCode())
+ {
+
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
+
+ break;
+
+ case KeyEvent.VK_DOWN:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(false);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, 1);
+ break;
+
+ case KeyEvent.VK_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(true);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, -1);
+
+ break;
+
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false,
+ alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor( -1, 0);
+
+
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true,
+ alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(1, 0);
+ break;
+
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+ }
+ break;
+
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
+ }
+
+ break;
+
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
+
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
+
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is " +
+ (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
+
+ case KeyEvent.VK_F1:
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break
+ ;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+
+ boolean hide = false;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (! (toggleCols &&
+ viewport.colSel.getSelected().size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ break;
+ }
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
+ }
+ }
+
+ public void keyReleased(KeyEvent evt)
+ {
+ switch(evt.getKeyCode())
+ {
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ break;
+ }
+ }
+ });
+ }
+
+
+ public void addAlignmentPanel(final AlignmentPanel ap,
+ boolean newPanel)
+ {
+ ap.alignFrame = this;
+
+ alignPanels.addElement(ap);
+
+ PaintRefresher.Register(ap, ap.av.getSequenceSetId());
+
+ int aSize = alignPanels.size();
+
+ tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+
+ if (aSize == 1 && ap.av.viewName==null)
+ {
+ this.getContentPane().add(ap, BorderLayout.CENTER);
+ }
+ else
+ {
+ if (aSize == 2)
+ {
+ setInitialTabVisible();
+ }
+
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ tabbedPane.addTab(ap.av.viewName, ap);
+
+ ap.setVisible(false);
+ }
+
+ if(newPanel)
+ {
+ if (ap.av.padGaps)
+ {
+ ap.av.alignment.padGaps();
+ }
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ }
+ }
+
+ public void setInitialTabVisible()
+ {
+ expandViews.setEnabled(true);
+ gatherViews.setEnabled(true);
+ tabbedPane.setVisible(true);
+ AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+ tabbedPane.addTab(first.av.viewName,first);
+ this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+ }
+
+
+ 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(true);
+ }
+ ;
+ });
+ }
+
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible( nucleotide );
+ conservationMenuItem.setEnabled( !nucleotide );
+ modifyConservation.setEnabled( !nucleotide );
+
+ //Remember AlignFrame always starts as protein
+ if(!nucleotide)
+ {
+ calculateMenu.remove(calculateMenu.getItemCount()-2);
+ }
+ }
+
+ /**
+ * Need to call this method when tabs are selected for multiple views,
+ * or when loading from Jalview2XML.java
+ * @param av AlignViewport
+ */
+ void setMenusFromViewport(AlignViewport av)
+ {
+ padGapsMenuitem.setSelected(av.padGaps);
+ colourTextMenuItem.setSelected(av.showColourText);
+ abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ conservationMenuItem.setSelected(av.getConservationSelected());
+ seqLimits.setSelected(av.getShowJVSuffix());
+ idRightAlign.setSelected(av.rightAlignIds);
+ renderGapsMenuItem.setSelected(av.renderGaps);
+ wrapMenuItem.setSelected(av.wrapAlignment);
+ scaleAbove.setVisible(av.wrapAlignment);
+ scaleLeft.setVisible(av.wrapAlignment);
+ scaleRight.setVisible(av.wrapAlignment);
+ annotationPanelMenuItem.setState(av.showAnnotation);
+ viewBoxesMenuItem.setSelected(av.showBoxes);
+ viewTextMenuItem.setSelected(av.showText);
+
+ setColourSelected(ColourSchemeProperty.
+ getColourName(av.getGlobalColourScheme()));
+
+ showSeqFeatures.setSelected(av.showSequenceFeatures);
+ hiddenMarkers.setState(av.showHiddenMarkers);
+ applyToAllGroups.setState(av.colourAppliesToAllGroups);
+
+ updateEditMenuBar();
+ }
+
+
+ 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 reload_actionPerformed(ActionEvent e)
+ {
+ if(fileName!=null)
+ {
+ if(currentFileFormat.equals("Jalview"))
+ {
+ JInternalFrame [] frames = Desktop.desktop.getAllFrames();
+ for(int i=0; i<frames.length; i++)
+ {
+ if (frames[i] instanceof AlignFrame
+ && frames[i] != this
+ && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+ {
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.instance.closeAssociatedWindows();
+ }
+ catch (java.beans.PropertyVetoException ex)
+ {}
+ }
+
+ }
+ Desktop.instance.closeAssociatedWindows();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:")? "URL":"File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
+
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ AlignFrame newframe =
+ loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
+
+ newframe.setBounds(bounds);
+
+ this.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+
+ public void save_actionPerformed(ActionEvent e)
+ {
+ if(fileName==null
+ || currentFileFormat==null
+ || fileName.startsWith("http")
+ )
+ {
+ saveAs_actionPerformed(null);
+ }
+ else
+ {
+ saveAlignment(fileName, currentFileFormat);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAs_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;
+ }
+
+ fileName = chooser.getSelectedFile().getPath();
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat);
+
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+
+ saveAlignment(fileName, currentFileFormat);
+ }
+ }
+
+ public boolean saveAlignment(String file, String format)
+ {
+ boolean success = true;
+
+ 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);
+ }
+
+ success = new Jalview2XML().SaveAlignment(this, file, shortName);
+
+ statusBar.setText("Successfully saved to file: "
+ +fileName+" in "
+ +format +" format.");
+
+ }
+ 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)
+ {
+ success = false;
+ }
+ else
+ {
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ statusBar.setText("Successfully saved to file: "
+ + fileName + " in "
+ + format + " format.");
+ }
+ catch (Exception ex)
+ {
+ success = false;
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ if (!success)
+ {
+ JOptionPane.showInternalMessageDialog(
+ this, "Couldn't save file: " + fileName,
+ "Error Saving File",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ return success;
+ }
+
+ /**
+ * 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();
+ cap.setForInput(null);
+ 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);
+ }
+
+
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread(alignPanel);
+ thread.start();
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+ viewport.alignment.getGroups()
+ );
+ }
+
+
+ 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(boolean closeAllTabs)
+ {
+ if(alignPanels!=null && alignPanels.size()<2)
+ {
+ closeAllTabs = true;
+ }
+
+ try
+ {
+ if(alignPanels!=null)
+ {
+ if (closeAllTabs)
+ {
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(ap.seqPanel, null);
+ PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(ap);
+ ap.av.alignment.destroyAlignment();
+ }
+ }
+ else
+ {
+ int index = tabbedPane.getSelectedIndex();
+
+ alignPanels.removeElement(alignPanel);
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(alignPanel);
+ alignPanel.av.alignment.destroyAlignment();
+ alignPanel = null;
+ viewport = null;
+
+ tabbedPane.removeTabAt(index);
+ tabbedPane.validate();
+
+ if(index==tabbedPane.getTabCount())
+ {
+ index --;
+ }
+
+ this.tabSelectionChanged(index);
+ }
+ }
+
+ if (closeAllTabs)
+ {
+ this.setClosed(true);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ */
+ void updateEditMenuBar()
+ {
+
+ if (viewport.historyList.size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setText("Undo " + command.getDescription());
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ }
+
+ if (viewport.redoList.size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setText("Redo " + command.getDescription());
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ }
+ }
+
+
+ public void addHistoryItem(CommandI command)
+ {
+ if(command.getSize()>0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.clear();
+ updateEditMenuBar();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ }
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ CommandI command = (CommandI)viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand();
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ updateEditMenuBar();
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment",
+ null,
+ originalSource.alignment.getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(viewport.redoList.size()<1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand();
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ updateEditMenuBar();
+
+ if(originalSource!=null)
+ {
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.firePropertyChange("alignment",
+ null,
+ originalSource.alignment.getSequences());
+ }
+ }
+
+ AlignViewport getOriginatingSource(CommandI command)
+ {
+ AlignViewport originalSource = null;
+ //For sequence removal and addition, we need to fire
+ //the property change event FROM the viewport where the
+ //original alignment was altered
+ AlignmentI al=null;
+ if (command instanceof EditCommand)
+ {
+ EditCommand editCommand = (EditCommand) command;
+ al = editCommand.getAlignment();
+ Vector comps = (Vector) PaintRefresher.components
+ .get(viewport.getSequenceSetId());
+
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+ {
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+
+ if (originalSource == null)
+ {
+ //The original view is closed, we must validate
+ //the current view against the closed view first
+ if (al != null)
+ {
+ PaintRefresher.validateSequences(al, viewport.alignment);
+ }
+
+ originalSource = viewport;
+ }
+
+ return originalSource;
+ }
+
+ /**
+ * 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(null).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+
+ if (sg.getSequences(null).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(null).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ alignPanel.paintAlignment(true);
+ }
+
+
+
+
+ synchronized void slideSequences(boolean right, int size)
+ {
+ Vector sg = new Vector();
+ if(viewport.cursorMode)
+ {
+ sg.addElement(viewport.alignment.getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if(viewport.getSelectionGroup()!=null
+ && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
+ {
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.hiddenRepSequences);
+ }
+
+ if(sg.size()<1)
+ {
+ return;
+ }
+
+ Vector invertGroup = new Vector();
+
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ {
+ if(!sg.contains(viewport.alignment.getSequenceAt(i)))
+ invertGroup.add(viewport.alignment.getSequenceAt(i));
+ }
+
+ SequenceI[] seqs1 = new SequenceI[sg.size()];
+ for (int i = 0; i < sg.size(); i++)
+ seqs1[i] = (SequenceI) sg.elementAt(i);
+
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ for (int i = 0; i < invertGroup.size(); i++)
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+ SlideSequencesCommand ssc;
+ if (right)
+ ssc = new SlideSequencesCommand("Slide Sequences",
+ seqs2, seqs1, size,
+ viewport.getGapCharacter()
+ );
+ else
+ ssc = new SlideSequencesCommand("Slide Sequences",
+ seqs1, seqs2, size,
+ viewport.getGapCharacter()
+ );
+
+ int groupAdjustment = 0;
+ if (ssc.getGapsInsertedBegin() && right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(size, 0);
+ else
+ groupAdjustment = size;
+ }
+ else if (!ssc.getGapsInsertedBegin() && !right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor( -size, 0);
+ else
+ groupAdjustment = -size;
+ }
+
+ if (groupAdjustment != 0)
+ {
+ viewport.getSelectionGroup().setStartRes(
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().setEndRes(
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ }
+
+
+ boolean appendHistoryItem = false;
+ if(viewport.historyList!=null
+ && viewport.historyList.size()>0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ {
+ appendHistoryItem = ssc.appendSlideCommand(
+ (SlideSequencesCommand)viewport.historyList.peek())
+ ;
+ }
+
+ if(!appendHistoryItem)
+ addHistoryItem(ssc);
+
+ repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ System.gc();
+ 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);
+
+ StringSelection ss = new StringSelection(output);
+
+ try
+ {
+ jalview.gui.Desktop.internalCopy = true;
+ //Its really worth setting the clipboard contents
+ //to empty before setting the large StringSelection!!
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
+ }
+ catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory copying region!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ return;
+ }
+
+ 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};
+ statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+ }
+
+ /**
+ * 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)
+ {
+ 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, format;
+ try
+ {
+ str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ if (str.length() < 1)
+ {
+ return;
+ }
+
+ format = new IdentifyFile().Identify(str, "Paste");
+
+ }
+ catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory pasting sequences!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ return;
+ }
+
+ 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).
+ getSequencesArray();
+ }
+
+ 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
+ SequenceI [] newseqs = new SequenceI[sequences.length];
+ for (int i = 0; i < sequences.length; i++)
+ {
+ newseqs[i] = new Sequence(sequences[i].getName(),
+ sequences[i].getSequence(),
+ sequences[i].getStart(),
+ sequences[i].getEnd());
+
+ alignment.addSequence(newseqs[i]);
+ }
+
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand(
+ "Add sequences",
+ EditCommand.PASTE,
+ newseqs,
+ 0,
+ alignment.getWidth(),
+ alignment)
+ );
+
+
+ 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, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ 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, DEFAULT_WIDTH,
+ DEFAULT_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 evt)
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
+
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+
+ SequenceI [] cut = new SequenceI[seqs.size()];
+ for(int i=0; i<seqs.size(); i++)
+ {
+ cut[i] = (SequenceI)seqs.elementAt(i);
+ }
+
+
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences",
+ EditCommand.CUT,
+ cut,
+ sg.getStartRes(),
+ sg.getEndRes()-sg.getStartRes()+1,
+ viewport.alignment));
+
+
+ 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.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * 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);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ /**
+ * 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.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ /**
+ * 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);
+ }
+
+ alignPanel.paintAlignment(true);
+
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ trimAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ trimAlignment(false);
+ }
+
+ void trimAlignment(boolean trimLeft)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
+
+ if (colSel.size() > 0)
+ {
+ if(trimLeft)
+ {
+ column = colSel.getMin();
+ }
+ else
+ {
+ column = colSel.getMax();
+ }
+
+ SequenceI [] seqs;
+ if(viewport.getSelectionGroup()!=null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+
+ TrimRegionCommand trimRegion;
+ if(trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ viewport.setStartRes(0);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ }
+
+ statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+ addHistoryItem(trimRegion);
+
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ {
+ viewport.alignment.deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+
+ RemoveGapColCommand removeGapCols =
+ new RemoveGapColCommand("Remove Gapped Columns",
+ seqs,
+ start, end,
+ viewport.alignment);
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
+
+ //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)
+ {
+ int start = 0, end = viewport.alignment.getWidth()-1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+ seqs,
+ start, end,
+ viewport.alignment));
+
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ viewport.padGaps = padGapsMenuitem.isSelected();
+
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ new Finder();
+ }
+
+ public void newView_actionPerformed(ActionEvent e)
+ {
+ AlignmentPanel newap =
+ new Jalview2XML().copyAlignPanel(alignPanel, true);
+
+ newap.av.gatherViewsHere = false;
+
+ if (viewport.viewName == null)
+ {
+ viewport.viewName = "Original";
+ }
+
+ newap.av.historyList = viewport.historyList;
+ newap.av.redoList = viewport.redoList;
+
+ int index = Desktop.getViewCount(viewport.getSequenceSetId());
+ String newViewName = "View " +index;
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport.
+ getSequenceSetId());
+ Vector existingNames = new Vector();
+ for(int i=0; i<comps.size(); i++)
+ {
+ if(comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
+ if(!existingNames.contains(ap.av.viewName))
+ {
+ existingNames.addElement(ap.av.viewName);
+ }
+ }
+ }
+
+ while(existingNames.contains(newViewName))
+ {
+ newViewName = "View "+ (++index);
+ }
+
+ newap.av.viewName = newViewName;
+
+ addAlignmentPanel(newap, false);
+
+ if(alignPanels.size()==2)
+ {
+ viewport.gatherViewsHere = true;
+ }
+ tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ }
+
+ public void expandViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.explodeViews(this);
+ }
+
+ public void gatherViews_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.gatherViews(this);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ new FontChooser(alignPanel);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowJVSuffix(seqLimits.isSelected());
+
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+ alignPanel.paintAlignment(true);
+ }
+
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+ viewport.rightAlignIds = idRightAlign.isSelected();
+ alignPanel.paintAlignment(true);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText(colourTextMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * 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();
+ alignPanel.paintAlignment(true);
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ 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.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText(viewTextMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.paintAlignment(true);
+ }
+
+
+ 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.paintAlignment(true);
+ 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);
+ }
+
+ public void textColour_actionPerformed(ActionEvent e)
+ {
+ new TextColourChooser().chooseColour(alignPanel, null);
+ }
+
+ /**
+ * 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.hconsensus);
+ }
+
+ 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(viewport.hiddenRepSequences), 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(viewport.hiddenRepSequences), sg.getStartRes(),
+ sg.getEndRes()+1));
+ }
+ else
+ {
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+
+ if (viewport.getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(viewport.
+ hiddenRepSequences),
+ sg.getStartRes(),
+ sg.getEndRes()+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.paintAlignment(true);
+ }
+
+ /**
+ * 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)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * 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() < 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() < 4) &&
+ (viewport.getSelectionGroup().getSize() > 0)) ||
+ (viewport.getAlignment().getHeight() < 4))
+ {
+ JOptionPane.showInternalMessageDialog(this,
+ "Principal component analysis must take\n" +
+ "at least 4 input sequences.",
+ "Sequence selection insufficient",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ new PCAPanel(alignPanel);
+ }
+
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
+ {
+ viewport.firePropertyChange("alignment",
+ null,
+ viewport.getAlignment().getSequences());
+ }
+ }
+
+
+ /**
+ * 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)
+ {
+ if (viewport.getSelectionGroup().getSize() < 3)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "You need to have more than two sequences selected to build a tree!",
+ "Not enough sequences",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ int s = 0;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ while (s < sg.getSize())
+ {
+ if ( ( (SequenceI) sg.getSequences(null).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(alignPanel, 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(alignPanel, type, pwType);
+ }
+
+ title += " from ";
+
+ if(viewport.viewName!=null)
+ {
+ title+= viewport.viewName+" of ";
+ }
+
+ title += this.title;
+
+ Desktop.addInternalFrame(tp, 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)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+ viewport.alignment));
+
+ alignPanel.paintAlignment(true);
+ }
+ });
+ }
+
+ /**
+ * 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.
+ */
+ public void buildTreeMenu()
+ {
+ sortByTreeMenu.removeAll();
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport.
+ getSequenceSetId());
+ Vector treePanels = new Vector();
+ int i, iSize = comps.size();
+ for(i=0; i<iSize; i++)
+ {
+ if(comps.elementAt(i) instanceof TreePanel)
+ {
+ treePanels.add(comps.elementAt(i));
+ }
+ }
+
+ iSize = treePanels.size();
+
+ if(iSize<1)
+ {
+ sortByTreeMenu.setVisible(false);
+ return;
+ }
+
+ sortByTreeMenu.setVisible(true);
+
+ for(i=0; i<treePanels.size(); i++)
+ {
+ TreePanel tp = (TreePanel)treePanels.elementAt(i);
+ final JMenuItem item = new JMenuItem(tp.getTitle());
+ final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+
+ addHistoryItem(new OrderCommand("Tree Sort",
+ oldOrder,
+ viewport.alignment));
+
+ alignPanel.paintAlignment(true);
+ }
+ });
+
+ sortByTreeMenu.add(item);
+ }
+ }
+
+ /**
+ * 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() > 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() > 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);
+ }
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input)
+ {
+ return ShowNewickTree(nf,title, input, 600,500,4,5);
+ }
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
+ int x, int y)
+ {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
+ /**
+ * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
+ *
+ * @param nf the tree
+ * @param title tree viewer title
+ * @param input Associated alignment input data (or null)
+ * @param w width
+ * @param h height
+ * @param x position
+ * @param y position
+ * @return TreePanel handle
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input, int w, int h, int x,
+ int y)
+ {
+ TreePanel tp = null;
+
+ try
+ {
+ nf.parse();
+
+ if (nf.getTree() != null)
+ {
+ tp = new TreePanel(alignPanel,
+ "FromFile",
+ title,
+ nf, input);
+
+ tp.setSize(w,h);
+
+ if(x>0 && y>0)
+ {
+ tp.setLocation(x,y);
+ }
+
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return tp;
+ }
+
+
+ /**
+ * 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, true);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh,
+ title, true, msa, af, true);
+ }
+ }
+ }
+ });
+ 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)
+{
+ ///////////////////////////////
+ // Collect Data to be translated/transferred
+
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+ AlignmentI al = null;
+ try {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
+ viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
+ viewport.alignment.getWidth());
+ } catch (Exception ex) {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.",ex);
+ }
+ if (al==null)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+ "Translation Failed",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+}
+
+/**
+ * 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.paintAlignment(true);
+ }
+
+ 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, protocol);
+
+ 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.paintAlignment(true);
+ }
+ else
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ }
+ }
+ else
+ {
+ // (isAnnotation)
+ alignPanel.adjustAnnotationHeight();
+ }
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public void tabSelectionChanged(int index)
+ {
+ if (index > -1)
+ {
+ alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+ viewport = alignPanel.av;
+ setMenusFromViewport(viewport);
+ }
+ }
+
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
+ if(SwingUtilities.isRightMouseButton(e))
+ {
+ String reply = JOptionPane.showInternalInputDialog(this,
+ "Enter View Name",
+ "Edit View Name",
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply != null)
+ {
+ viewport.viewName = reply;
+ tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ }
+ }
+ }
+
+
+ public AlignViewport getCurrentView()
+ {
+ return viewport;
+ }
+}
+
+class PrintThread
+ extends Thread
+{
+ AlignmentPanel ap;
+ public PrintThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+ static PageFormat pf;
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ if (pf != null)
+ {
+ printJob.setPrintable(ap, pf);
+ }
+ else
+ {
+ printJob.setPrintable(ap);
+ }
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+}