-/********************\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 java.awt.event.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import java.util.*;\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
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.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.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.getAlignment(), alignPanel.seqPanel.getColourScheme());\r
- htmlOutput = null;\r
- }\r
-\r
- public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\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
-\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
- public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\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.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
- public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete selection");\r
-\r
- for (int i=0;i < viewport.getSelection().size(); i++)\r
- viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
-\r
- viewport.getSelection().clear();\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- copySelectedMenuItem_actionPerformed(null);\r
- deleteSelectedMenuItem_actionPerformed(null);\r
- alignPanel.repaint();\r
- }\r
-\r
- public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelection().size()==0)\r
- return;\r
-\r
- SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
- for (int i=0; i < viewport.getSelection().size(); i++) {\r
- s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\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 (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || 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
- String thisChar = "-";\r
- String nextChar = ".";\r
- if(viewport.getGapCharacter().equals("-"))\r
- {\r
- thisChar = ".";\r
- nextChar = "-";\r
- }\r
- setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
- viewport.setGapCharacter(thisChar);\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.showInputDialog(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.showInputDialog(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.showInputDialog(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
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\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.showMessageDialog(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
- alignPanel.setColourScheme(null, false);\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
- conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
-\r
- public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cip);\r
- Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
- frame.setMaximizable(false);\r
- }\r
-\r
-\r
- public void abovePIDColour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\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
- alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
- }\r
-\r
-\r
-\r
- protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
- Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\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.sortGroups(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
-\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelection().size()<2)\r
- JOptionPane.showMessageDialog(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.showMessageDialog(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.showMessageDialog(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
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
- +"\nwithin the Barton Group, Dundee University."\r
- +"\nThis will be available as a web service 2005",\r
- "Web service", JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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 Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
+import java.beans.PropertyChangeEvent;
+
+public class AlignFrame extends GAlignFrame
+{
+ final AlignmentPanel alignPanel;
+ final AlignViewport viewport;
+ public static final int NEW_WINDOW_WIDTH = 700;
+ public static final int NEW_WINDOW_HEIGHT = 500;
+ public String currentFileFormat = "Jalview";
+
+ public AlignFrame(AlignmentI al)
+ {
+ viewport = new AlignViewport(al);
+
+ alignPanel = new AlignmentPanel(this, viewport);
+ alignPanel.annotationPanel.adjustPanelHeight();
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+ alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
+
+ getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameActivated(InternalFrameEvent evt)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ { alignPanel.requestFocus(); }
+ });
+
+ }
+ });
+
+ }
+
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
+ , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
+ new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+ currentFileFormat);
+
+ chooser.setAcceptAllFileFilterUsed(false);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Alignment to file");
+ chooser.setToolTipText("Save");
+ int value = chooser.showSaveDialog(this);
+ if(value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ currentFileFormat = chooser.getSelectedFormat();
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
+
+ if (currentFileFormat.equals("Jalview"))
+ {
+ String shortName = title;
+ if(shortName.indexOf(java.io.File.separatorChar)>-1)
+ shortName = shortName.substring(
+ shortName.lastIndexOf(java.io.File.separatorChar)+1);
+
+ String choice = chooser.getSelectedFile().getPath();
+ Jalview2XML.SaveState(this, choice, shortName);
+ // USE Jalview2XML to save this file
+ return;
+ }
+
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
+ try{
+ java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
+ out.println(output);
+ out.close();
+ }
+ catch(Exception ex){}
+ }
+
+ }
+
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
+ cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
+ }
+
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ new HTMLOutput(viewport);
+ }
+
+ protected void createPNG_actionPerformed(ActionEvent e)
+ {
+ alignPanel.makePNG();
+ }
+
+ protected void epsFile_actionPerformed(ActionEvent e)
+ {
+ alignPanel.makeEPS();
+ }
+
+
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread();
+ thread.start();
+ }
+
+ class PrintThread extends Thread
+ {
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ printJob.setPrintable(alignPanel, pf);
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+
+ }
+
+
+
+
+ public void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+ try{
+ this.setClosed(true);
+ }catch(Exception ex){}
+ }
+
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+ private int treeCount = 0;
+
+ void updateEditMenuBar()
+ {
+ if(historyList.size()>0)
+ {
+ undoMenuItem.setEnabled(true);
+ HistoryItem hi = (HistoryItem)historyList.peek();
+ undoMenuItem.setText("Undo "+hi.getDescription());
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ }
+
+ if(redoList.size()>0)
+ {
+ redoMenuItem.setEnabled(true);
+ HistoryItem hi = (HistoryItem)redoList.peek();
+ redoMenuItem.setText("Redo "+hi.getDescription());
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ }
+ }
+
+ public void addHistoryItem(HistoryItem hi)
+ {
+ historyList.push(hi);
+ updateEditMenuBar();
+ }
+
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem hi = (HistoryItem)historyList.pop();
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
+ restoreHistoryItem(hi);
+ }
+
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem hi = (HistoryItem)redoList.pop();
+ restoreHistoryItem(hi);
+ updateEditMenuBar();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ alignPanel.repaint();
+ }
+
+
+ // used by undo and redo
+ void restoreHistoryItem(HistoryItem hi)
+ {
+ if(hi.getType()== HistoryItem.SORT)
+ {
+ for(int i=0; i<hi.getSequences().size(); i++)
+ viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
+ }
+ else
+ {
+ for (int i = 0; i < hi.getSequences().size(); i++)
+ {
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+ if(restore.getLength()==0)
+ {
+ restore.setSequence(hi.getHidden().elementAt(i).toString());
+ viewport.alignment.getSequences().insertElementAt(
+ restore,
+ hi.getAlignIndex(i));
+ }
+ else
+ restore.setSequence(hi.getHidden().elementAt(i).toString());
+ }
+ if(hi.getType()==HistoryItem.PASTE)
+ {
+ for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
+ viewport.alignment.deleteSequence(i);
+ }
+ }
+ updateEditMenuBar();
+
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ alignPanel.repaint();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ return;
+
+ if (up)
+ {
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.sequences.contains(seq))
+ continue;
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+ if (sg.sequences.contains(temp))
+ continue;
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);
+ }
+ }
+ else
+ {
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+ if (!sg.sequences.contains(seq))
+ continue;
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+ if (sg.sequences.contains(temp))
+ continue;
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ alignPanel.repaint();
+ }
+
+
+
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getSelectionGroup()==null)
+ return;
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ StringBuffer buffer= new StringBuffer();
+
+ Hashtable orderedSeqs = new Hashtable();
+ for(int i=0; i<sg.getSize(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.alignment.findIndex(seq);
+ orderedSeqs.put(index+"", seq);
+ }
+
+ int index=0;
+ for(int i=0; i<sg.getSize(); i++)
+ {
+ SequenceI seq = null;
+ while( seq == null )
+ {
+ if(orderedSeqs.containsKey(index+""))
+ {
+ seq = (SequenceI) orderedSeqs.get(index + "");
+ index++;
+ break;
+ }
+ else
+ index++;
+ }
+
+ buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
+ +seq.findPosition( sg.getEndRes() )+ "\t"
+ +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
+ }
+ c.setContents( new StringSelection( buffer.toString()) , null ) ;
+
+ }
+
+
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ paste(true);
+ }
+
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
+ paste(false);
+ }
+
+ void paste(boolean newAlignment)
+ {
+ try{
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+ if (contents == null)
+ return;
+
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ StringTokenizer st = new StringTokenizer(str);
+ ArrayList seqs = new ArrayList();
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+ int start = Integer.parseInt(st.nextToken());
+ int end = Integer.parseInt(st.nextToken());
+ Sequence sequence = new Sequence(name,st.nextToken(), start, end);
+
+ if(!newAlignment)
+ viewport.alignment.addSequence(sequence);
+ else
+ seqs.add(sequence);
+ }
+
+ if(newAlignment)
+ {
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];
+ seqs.toArray(newSeqs);
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+ String newtitle = new String("Copied sequences");
+ if( title.startsWith("Copied sequences"))
+ newtitle = title;
+ else
+ newtitle = newtitle.concat("- from "+title);
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+ }
+ else
+ {
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ viewport.setEndSeq(viewport.alignment.getHeight());
+ viewport.alignment.getWidth();
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+ }catch(Exception ex){}// could be anything being pasted in here
+
+ }
+
+
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+ boolean seqsdeleted=false;
+
+ if (viewport.getSelectionGroup() == null)
+ return;
+
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i=0;i < sg.sequences.size(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.getAlignment().findIndex(seq);
+ seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
+
+ if(seq.getSequence().length()<1) {
+ seqsdeleted=true;
+ viewport.getAlignment().deleteSequence(seq);
+ } else {
+ viewport.getAlignment().getSequences().setElementAt(seq, index);
+ }
+ }
+
+ viewport.setSelectionGroup(null);
+ viewport.alignment.deleteGroup(sg);
+ if (seqsdeleted)
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
+ if(viewport.getAlignment().getHeight()<1)
+ try
+ {
+ this.setClosed(true);
+ }catch(Exception ex){}
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.setSelectionGroup(null);
+ alignPanel.repaint();
+ }
+
+
+
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+ sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+ sg.setEndRes(viewport.alignment.getWidth());
+ viewport.setSelectionGroup(sg);
+ PaintRefresher.Refresh(null);
+ }
+
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ PaintRefresher.Refresh(null);
+ }
+
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
+ sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
+ PaintRefresher.Refresh(null);
+ }
+
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel.size() > 0)
+ {
+ addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
+ HistoryItem.HIDE));
+ int min = colSel.getMin();
+ viewport.getAlignment().trimLeft(min);
+ colSel.compensateForEdit(0,min);
+
+ if(viewport.getSelectionGroup()!=null)
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+ if(!sg.adjustForRemoveLeft(min))
+ viewport.alignment.deleteGroup(sg);
+ }
+
+ alignPanel.repaint();
+ }
+ }
+
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel.size() > 0)
+ {
+ addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
+ HistoryItem.HIDE));
+
+ int max = colSel.getMax();
+ viewport.getAlignment().trimRight(max);
+ if(viewport.getSelectionGroup()!=null)
+ viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+ if(!sg.adjustForRemoveRight(max))
+ viewport.alignment.deleteGroup(sg);
+ }
+
+
+
+ alignPanel.repaint();
+ }
+
+ }
+
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",
+ viewport.alignment,
+ HistoryItem.HIDE));
+
+ viewport.getAlignment().removeGaps();
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Remove Gaps",
+ viewport.alignment,
+ HistoryItem.HIDE));
+ SequenceI current;
+ int jSize;
+ for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+ jSize = current.getLength();
+ for (int j=0; j < jSize; j++)
+ if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ current.deleteCharAt(j);
+ j--;
+ jSize--;
+ }
+ }
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Pad Gaps",
+ viewport.alignment,
+ HistoryItem.HIDE));
+ SequenceI current;
+ int Width = viewport.getAlignment().getWidth()-1;
+ for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+
+ if (current.getLength()<Width)
+ current.insertCharAt(Width, viewport.getGapCharacter());
+ }
+ viewport.updateConservation();
+ viewport.updateConsensus();
+ alignPanel.repaint();
+ }
+
+
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame frame = new JInternalFrame();
+ Finder finder = new Finder(viewport, alignPanel, frame);
+ frame.setContentPane(finder);
+ Desktop.addInternalFrame(frame, "Find", 340,110);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+
+ }
+
+
+ public void font_actionPerformed(ActionEvent e)
+ {
+ FontChooser fc = new FontChooser( alignPanel );
+ }
+
+ protected void fullSeqId_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowFullId( fullSeqId.isSelected() );
+
+ alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+ alignPanel.repaint();
+ }
+
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText( colourTextMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+ alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
+ scaleAbove.setVisible( wrapMenuItem.isSelected() );
+ scaleLeft.setVisible( wrapMenuItem.isSelected() );
+ scaleRight.setVisible( wrapMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.repaint();
+ }
+
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.repaint();
+ }
+
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.repaint();
+ }
+
+
+
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText( viewTextMenuItem.isSelected() );
+ alignPanel.repaint();
+ }
+
+
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+ if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
+ {
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
+ ((Alignment)viewport.alignment).featuresAdded = true;
+ }
+ alignPanel.repaint();
+ }
+
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+ {
+ annotationPanelMenuItem.setSelected(false);
+ return;
+ }
+ viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+ alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
+ }
+
+ public void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (alignPanel.overviewPanel != null)
+ return;
+
+ JInternalFrame frame = new JInternalFrame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.setContentPane(overview);
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ frame.getWidth(), frame.getHeight());
+ frame.pack();
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
+
+ alignPanel.setOverviewPanel( overview );
+
+
+ }
+
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ changeColour( null );
+ }
+
+
+ public void clustalColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+
+
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ changeColour( new HydrophobicColourScheme() );
+ }
+
+ public void helixColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HelixColourScheme() );
+ }
+
+
+ public void strandColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new StrandColourScheme());
+ }
+
+
+ public void turnColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TurnColourScheme());
+ }
+
+
+ public void buriedColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new BuriedColourScheme() );
+ }
+
+ public void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+
+
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+
+
+ void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if ( viewport.getAbovePIDThreshold() )
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+
+ if (cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) cs).setThreshold(threshold);
+ else if (cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) cs).setThreshold(threshold);
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else if (cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) cs).setThreshold(0);
+ else if (cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) cs).setThreshold(0);
+
+
+
+ if (viewport.getConservationSelected())
+ {
+ ConservationColourScheme ccs = null;
+
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ ccs = new ConservationColourScheme(c, cs);
+
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ ccs.setConsensus( viewport.vconsensus );
+ viewport.setGlobalColourScheme(ccs);
+
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+
+ }
+ else
+ {
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ if (cs != null)
+ cs.setConsensus(viewport.vconsensus);
+ viewport.setGlobalColourScheme(cs);
+ }
+
+
+ if(viewport.getColourAppliesToAllGroups())
+ {
+ Vector groups = viewport.alignment.getGroups();
+ for(int i=0; i<groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+ if(cs==null)
+ sg.cs = null;
+ else if (cs instanceof ClustalxColourScheme)
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+ else if (cs instanceof UserColourScheme)
+ sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
+ else
+ try{
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ }catch(Exception ex){}
+
+ if(viewport.getAbovePIDThreshold())
+ {
+ if (sg.cs instanceof ResidueColourScheme)
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+ else if (sg.cs instanceof ScoreColourScheme)
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+
+ sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+ }
+
+ if( viewport.getConservationSelected() )
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.sequences, 0, viewport.alignment.getWidth()-1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+ sg.cs = ccs;
+ }
+ else if(cs!=null)
+ {
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+ }
+
+ }
+ }
+
+ if(alignPanel.getOverviewPanel()!=null)
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ alignPanel.repaint();
+ }
+
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+ "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
+ "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setSelected(false);
+
+ ColourSchemeI cs = viewport.getGlobalColourScheme();
+ if(cs instanceof ConservationColourScheme )
+ changeColour( ((ConservationColourScheme)cs).cs );
+ else
+ changeColour( cs );
+
+ modifyConservation_actionPerformed(null);
+ }
+
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+ conservationMenuItem.setSelected(false);
+ viewport.setConservationSelected(false);
+
+ ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+ if(cs instanceof ConservationColourScheme )
+ changeColour( ((ConservationColourScheme)cs).cs );
+ else
+ changeColour( cs );
+
+ modifyPID_actionPerformed(null);
+ }
+
+
+
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ new UserDefinedColours( alignPanel, null);
+ }
+
+ public void PIDColour_actionPerformed(ActionEvent e)
+ {
+ changeColour( new PIDColourScheme() );
+ }
+
+
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new Blosum62ColourScheme() );
+ }
+
+
+
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
+ alignPanel.repaint();
+ }
+
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
+ AlignmentSorter.sortByID( viewport.getAlignment() );
+ alignPanel.repaint();
+ }
+
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
+ // AlignmentSorter.sortByGroup(viewport.getAlignment());
+ AlignmentSorter.sortGroups(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(sp);
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
+
+ }
+
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if((viewport.getSelectionGroup()==null) ||
+ viewport.getSelectionGroup().getSize()<2)
+ JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+ else
+ {
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(new PairwiseAlignPanel(viewport));
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ }
+ }
+
+ public void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
+ || viewport.getAlignment().getHeight()<4)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
+ +"at least 4 input sequences.",
+ "Sequence selection insufficient",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ try{
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(pcaPanel);
+ Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
+ }catch(java.lang.OutOfMemoryError ex)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
+ "Out of memory", JOptionPane.WARNING_MESSAGE);
+ }
+
+
+ }
+
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ String ltitle;
+ final TreePanel tp;
+ if (viewport.getSelectionGroup() != null &&
+ viewport.getSelectionGroup().getSize() > 3)
+ {
+ int s=0;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ while (s<sg.sequences.size()) {
+ if (((SequenceI) sg.sequences.elementAt(s++)).getLength()<sg.getEndRes()) {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The selected region to create a tree may\nonly contain residues or gaps.\n"
+ +"Try using the Pad function in the edit menu,\n"
+ +"or one of the multiple sequence alignment web services.",
+ "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ }
+ title=title+" on region";
+ tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+ pwType,
+ sg.getStartRes(), sg.getEndRes());
+ }
+ 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;
+ }
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+ type, pwType, 0, viewport.alignment.getWidth());
+ }
+
+ addTreeMenuItem(tp, title);
+ viewport.setCurrentTree(tp.getTree());
+
+ Desktop.addInternalFrame(tp, title+" from "+this.title, 600, 500);
+ }
+
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
+ final JMenuItem item = new JMenuItem("by "+title);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ HistoryItem.SORT));
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+ alignPanel.repaint();
+ }
+ });
+ }
+
+ void addTreeMenuItem(final TreePanel treePanel, String title)
+ {
+ final JMenuItem item = new JMenuItem(title);
+
+ treeCount++;
+
+ if (treeCount==1)
+ sort.add(sortByTreeMenu);
+
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
+ HistoryItem.SORT));
+ AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+ alignPanel.repaint();
+ }
+ });
+
+ treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+ {
+ treeCount--;
+ sortByTreeMenu.remove(item);
+ if (treeCount==0)
+ sort.remove(sortByTreeMenu);
+ };
+ });
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment")) {
+ treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
+ treePanel.repaint();
+ }
+ }
+
+ }
+ );
+ }
+
+
+ public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
+ }
+ }
+ public void ClustalRealign_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
+ }
+ }
+
+
+ protected void jpred_actionPerformed(ActionEvent e)
+{
+ SequenceI seq=null;
+ SequenceI[] msa=null;
+
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+ {
+ seq = (SequenceI)seqs.getSequenceAt(0);
+ }
+ else
+ {
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+ }
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() == 1 || !viewport.alignment.isAligned())
+ {
+ seq = (SequenceI) seqs.elementAt(0);
+ }
+ else
+ {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+ }
+ }
+ if (msa!=null) {
+ JPredClient ct = new JPredClient(title, msa);
+ } else
+ if (seq!=null) {
+ JPredClient ct = new JPredClient(title, seq);
+ } else {
+ System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
+ }
+ }
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
+ }
+ }
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select a newick-like tree file");
+ chooser.setToolTipText("Load a tree file");
+ int value = chooser.showOpenDialog(null);
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ try
+ {
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
+ ShowNewickTree(fin, choice);
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Problem reading tree file",
+ ex.getMessage(),
+ JOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ public void ShowNewickTree(NewickFile nf, String title)
+ {
+ try{
+ nf.parse();
+ if (nf.getTree() != null)
+ {
+ TreePanel tp = new TreePanel(viewport,
+ viewport.getAlignment().getSequences(),
+ nf, "FromFile", title);
+ Desktop.addInternalFrame(tp, title, 600, 500);
+ addTreeMenuItem(tp, title);
+ viewport.setCurrentTree(tp.getTree());
+ }
+ }catch(Exception ex){ex.printStackTrace();}
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff