src/jalview/gui/AlignFrame.java

   1 /********************
   2  * 2004 Jalview Reengineered
   3  * Barton Group
   4  * Dundee University
   5  *
   6  * AM Waterhouse
   7  *******************/
   8
   9
  10
  11
  12 package jalview.gui;
  13
  14 import java.util.*;
  15
  16 import java.awt.*;
  17 import java.awt.datatransfer.*;
  18 import java.awt.event.*;
  19 import java.awt.print.*;
  20 import javax.swing.*;
  21 import javax.swing.event.*;
  22
  23 import jalview.analysis.*;
  24 import jalview.datamodel.*;
  25 import jalview.io.*;
  26 import jalview.jbgui.*;
  27 import jalview.schemes.*;
  28 import jalview.ws.*;
  29
  30
  31 public class AlignFrame extends GAlignFrame
  32 {
  33   final AlignmentPanel alignPanel;
  34   final AlignViewport viewport;
  35   public static final int NEW_WINDOW_WIDTH = 700;
  36   public static final int NEW_WINDOW_HEIGHT = 500;
  37   public String currentFileFormat = "Jalview";
  38
  39   public AlignFrame(AlignmentI al)
  40   {
  41     viewport = new AlignViewport(al);
  42
  43     alignPanel = new AlignmentPanel(this, viewport);
  44     alignPanel.annotationPanel.adjustPanelHeight();
  45     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
  46     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
  47     alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
  48
  49     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
  50
  51     addInternalFrameListener(new InternalFrameAdapter()
  52    {
  53      public void internalFrameActivated(InternalFrameEvent evt)
  54      {
  55           javax.swing.SwingUtilities.invokeLater(new Runnable()
  56           {
  57             public void run()
  58             {      alignPanel.requestFocus();    }
  59           });
  60
  61      }
  62    });
  63
  64   }
  65
  66   public void saveAlignmentMenu_actionPerformed(ActionEvent e)
  67   {
  68     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
  69         ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
  70           new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
  71           currentFileFormat);
  72
  73     chooser.setAcceptAllFileFilterUsed(false);
  74     chooser.setFileView(new JalviewFileView());
  75     chooser.setDialogTitle("Save Alignment to file");
  76     chooser.setToolTipText("Save");
  77     int value = chooser.showSaveDialog(this);
  78     if(value == JalviewFileChooser.APPROVE_OPTION)
  79     {
  80       currentFileFormat  = chooser.getSelectedFormat();
  81
  82       if (currentFileFormat.equals("Jalview"))
  83       {
  84         String shortName = title.replace('/', '_');
  85         title = title.replace('\\', '_');
  86         String choice = chooser.getSelectedFile().getPath();
  87         Jalview2XML.SaveState(this, choice, shortName);
  88         // USE Jalview2XML to save this file
  89         return;
  90       }
  91
  92       String choice =  chooser.getSelectedFile().getPath();
  93       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
  94       String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
  95       try{
  96         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
  97         out.println(output);
  98         out.close();
  99       }
 100       catch(Exception ex){}
 101     }
 102
 103   }
 104
 105   protected void outputText_actionPerformed(ActionEvent e)
 106   {
 107      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
 108      JInternalFrame frame = new JInternalFrame();
 109      cap.formatForOutput();
 110      frame.setContentPane(cap);
 111      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
 112      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
 113   }
 114
 115   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 116   {
 117     HTMLOutput htmlOutput = new HTMLOutput(viewport);
 118     htmlOutput = null;
 119   }
 120
 121   protected void createPNG_actionPerformed(ActionEvent e)
 122   {
 123     alignPanel.makePNG();
 124   }
 125
 126   protected void epsFile_actionPerformed(ActionEvent e)
 127   {
 128     alignPanel.makeEPS();
 129   }
 130
 131
 132   public void printMenuItem_actionPerformed(ActionEvent e)
 133   {
 134     //Putting in a thread avoids Swing painting problems
 135     PrintThread thread = new PrintThread();
 136     thread.start();
 137   }
 138
 139   class PrintThread extends Thread
 140   {
 141     public void run()
 142     {
 143       PrinterJob printJob = PrinterJob.getPrinterJob();
 144       PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 145       printJob.setPrintable(alignPanel, pf);
 146       if (printJob.printDialog())
 147       {
 148         try
 149         {
 150           printJob.print();
 151         }
 152         catch (Exception PrintException)
 153         {
 154           PrintException.printStackTrace();
 155         }
 156       }
 157     }
 158
 159   }
 160
 161
 162
 163
 164   public void closeMenuItem_actionPerformed(ActionEvent e)
 165   {
 166     try{
 167       this.setClosed(true);
 168     }catch(Exception ex){}
 169   }
 170
 171   Stack historyList = new Stack();
 172   Stack redoList = new Stack();
 173   private int treeCount = 0;
 174
 175   void updateEditMenuBar()
 176    {
 177      if(historyList.size()>0)
 178       {
 179         undoMenuItem.setEnabled(true);
 180         HistoryItem hi = (HistoryItem)historyList.peek();
 181         undoMenuItem.setText("Undo "+hi.getDescription());
 182       }
 183      else
 184      {
 185        undoMenuItem.setEnabled(false);
 186        undoMenuItem.setText("Undo");
 187      }
 188
 189      if(redoList.size()>0)
 190       {
 191         redoMenuItem.setEnabled(true);
 192         HistoryItem hi = (HistoryItem)redoList.peek();
 193         redoMenuItem.setText("Redo "+hi.getDescription());
 194       }
 195      else
 196      {
 197        redoMenuItem.setEnabled(false);
 198        redoMenuItem.setText("Redo");
 199      }
 200    }
 201
 202    public void addHistoryItem(HistoryItem hi)
 203    {
 204      historyList.push(hi);
 205      updateEditMenuBar();
 206    }
 207
 208    protected void undoMenuItem_actionPerformed(ActionEvent e)
 209    {
 210        HistoryItem hi = (HistoryItem)historyList.pop();
 211        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
 212        restoreHistoryItem(hi);
 213    }
 214
 215
 216    protected void redoMenuItem_actionPerformed(ActionEvent e)
 217    {
 218       HistoryItem hi = (HistoryItem)redoList.pop();
 219       restoreHistoryItem(hi);
 220       updateEditMenuBar();
 221       viewport.updateConsensus();
 222       alignPanel.repaint();
 223       alignPanel.repaint();
 224    }
 225
 226
 227    // used by undo and redo
 228    void restoreHistoryItem(HistoryItem hi)
 229    {
 230       if(hi.getType()== HistoryItem.SORT)
 231       {
 232            for(int i=0; i<hi.getSequences().size(); i++)
 233              viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
 234       }
 235       else
 236       {
 237         for (int i = 0; i < hi.getSequences().size(); i++)
 238         {
 239           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 240           if(restore.getLength()==0)
 241           {
 242             restore.setSequence(hi.getHidden().elementAt(i).toString());
 243             viewport.alignment.getSequences().insertElementAt(
 244                restore,
 245                hi.getAlignIndex(i));
 246           }
 247           else
 248             restore.setSequence(hi.getHidden().elementAt(i).toString());
 249         }
 250         if(hi.getType()==HistoryItem.PASTE)
 251         {
 252           for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
 253             viewport.alignment.deleteSequence(i);
 254         }
 255       }
 256
 257        updateEditMenuBar();
 258
 259        viewport.updateConsensus();
 260        viewport.updateConservation();
 261        alignPanel.repaint();
 262    }
 263
 264   public void moveSelectedSequences(boolean up)
 265   {
 266     SequenceGroup sg = viewport.getSelectionGroup();
 267     if (sg == null)
 268       return;
 269
 270     if (up)
 271     {
 272       for (int i = 1; i < viewport.alignment.getHeight(); i++)
 273       {
 274         SequenceI seq = viewport.alignment.getSequenceAt(i);
 275         if (!sg.sequences.contains(seq))
 276           continue;
 277
 278         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 279         if (sg.sequences.contains(temp))
 280           continue;
 281
 282         viewport.alignment.getSequences().setElementAt(temp, i);
 283         viewport.alignment.getSequences().setElementAt(seq, i - 1);
 284       }
 285     }
 286     else
 287     {
 288       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
 289       {
 290         SequenceI seq = viewport.alignment.getSequenceAt(i);
 291         if (!sg.sequences.contains(seq))
 292           continue;
 293
 294         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 295         if (sg.sequences.contains(temp))
 296           continue;
 297
 298         viewport.alignment.getSequences().setElementAt(temp, i);
 299         viewport.alignment.getSequences().setElementAt(seq, i + 1);
 300       }
 301     }
 302
 303     alignPanel.repaint();
 304   }
 305
 306
 307
 308   protected void copy_actionPerformed(ActionEvent e)
 309   {
 310      if(viewport.getSelectionGroup()==null)
 311        return;
 312
 313      SequenceGroup sg = viewport.getSelectionGroup();
 314
 315      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 316      StringBuffer buffer= new StringBuffer();
 317
 318      Hashtable orderedSeqs = new Hashtable();
 319      for(int i=0; i<sg.getSize(); i++)
 320      {
 321         SequenceI seq = sg.getSequenceAt(i);
 322         int index = viewport.alignment.findIndex(seq);
 323         orderedSeqs.put(index+"", seq);
 324      }
 325
 326      int index=0;
 327      for(int i=0; i<sg.getSize(); i++)
 328      {
 329        SequenceI seq = null;
 330        while( seq == null )
 331        {
 332          if(orderedSeqs.containsKey(index+""))
 333          {
 334            seq = (SequenceI) orderedSeqs.get(index + "");
 335            index++;
 336            break;
 337          }
 338          else
 339            index++;
 340        }
 341
 342          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
 343                         +seq.findPosition( sg.getEndRes() )+ "\t"
 344                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
 345      }
 346      c.setContents( new StringSelection( buffer.toString()) , null ) ;
 347
 348   }
 349
 350
 351   protected void pasteNew_actionPerformed(ActionEvent e)
 352   {
 353     paste(true);
 354   }
 355
 356   protected void pasteThis_actionPerformed(ActionEvent e)
 357   {
 358     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
 359     paste(false);
 360   }
 361
 362   void paste(boolean newAlignment)
 363   {
 364     try{
 365       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 366       Transferable contents = c.getContents(this);
 367       if (contents == null)
 368         return;
 369
 370       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
 371       StringTokenizer st = new StringTokenizer(str);
 372       ArrayList seqs = new ArrayList();
 373       while (st.hasMoreElements())
 374       {
 375         String name = st.nextToken();
 376         int start = Integer.parseInt(st.nextToken());
 377         int end = Integer.parseInt(st.nextToken());
 378         Sequence sequence = new Sequence(name,st.nextToken(), start, end);
 379
 380         if(!newAlignment)
 381           viewport.alignment.addSequence(sequence);
 382         else
 383           seqs.add(sequence);
 384       }
 385
 386       if(newAlignment)
 387       {
 388         SequenceI[] newSeqs = new SequenceI[seqs.size()];
 389         seqs.toArray(newSeqs);
 390         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
 391         String newtitle = new String("Copied sequences");
 392         if( title.startsWith("Copied sequences"))
 393          newtitle = title;
 394        else
 395          newtitle = newtitle.concat("- from "+title);
 396
 397         Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
 398       }
 399       else
 400       {
 401         viewport.setEndSeq(viewport.alignment.getHeight());
 402         viewport.alignment.getWidth();
 403         viewport.updateConservation();
 404         viewport.updateConsensus();
 405         alignPanel.repaint();
 406       }
 407
 408     }catch(Exception ex){}// could be anything being pasted in here
 409
 410   }
 411
 412
 413   protected void cut_actionPerformed(ActionEvent e)
 414   {
 415     copy_actionPerformed(null);
 416     delete_actionPerformed(null);
 417   }
 418
 419   protected void delete_actionPerformed(ActionEvent e)
 420   {
 421     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
 422
 423     if (viewport.getSelectionGroup() == null)
 424       return;
 425
 426      SequenceGroup sg = viewport.getSelectionGroup();
 427      for (int i=0;i < sg.sequences.size(); i++)
 428      {
 429        SequenceI seq = sg.getSequenceAt(i);
 430        int index = viewport.getAlignment().findIndex(seq);
 431        seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
 432
 433        if(seq.getSequence().length()<1)
 434           viewport.getAlignment().deleteSequence(seq);
 435       else
 436           viewport.getAlignment().getSequences().setElementAt(seq, index);
 437      }
 438
 439      viewport.setSelectionGroup(null);
 440      viewport.alignment.deleteGroup(sg);
 441      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
 442      if(viewport.getAlignment().getHeight()<1)
 443      try
 444      {
 445        this.setClosed(true);
 446      }catch(Exception ex){}
 447    viewport.updateConservation();
 448    viewport.updateConsensus();
 449      alignPanel.repaint();
 450
 451   }
 452
 453
 454   protected void deleteGroups_actionPerformed(ActionEvent e)
 455   {
 456     viewport.alignment.deleteAllGroups();
 457     viewport.setSelectionGroup(null);
 458     alignPanel.repaint();
 459   }
 460
 461
 462
 463   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 464   {
 465     SequenceGroup sg = new SequenceGroup();
 466     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 467       sg.addSequence( viewport.getAlignment().getSequenceAt(i));
 468     sg.setEndRes(viewport.alignment.getWidth());
 469     viewport.setSelectionGroup(sg);
 470     PaintRefresher.Refresh(null);
 471   }
 472
 473   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 474   {
 475     viewport.setSelectionGroup(null);
 476     viewport.getColumnSelection().clear();
 477     viewport.setSelectionGroup(null);
 478     PaintRefresher.Refresh(null);
 479   }
 480
 481   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 482   {
 483     SequenceGroup sg = viewport.getSelectionGroup();
 484     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 485       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
 486
 487     PaintRefresher.Refresh(null);
 488   }
 489
 490   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 491   {
 492     ColumnSelection colSel = viewport.getColumnSelection();
 493     if (colSel.size() > 0)
 494     {
 495       addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
 496                                      HistoryItem.HIDE));
 497       int min = colSel.getMin();
 498       viewport.getAlignment().trimLeft(min);
 499       colSel.compensateForEdit(0,min);
 500
 501       if(viewport.getSelectionGroup()!=null)
 502         viewport.getSelectionGroup().adjustForRemoveLeft(min);
 503
 504       Vector groups = viewport.alignment.getGroups();
 505       for(int i=0; i<groups.size(); i++)
 506       {
 507         SequenceGroup sg = (SequenceGroup) groups.get(i);
 508         if(!sg.adjustForRemoveLeft(min))
 509           viewport.alignment.deleteGroup(sg);
 510       }
 511
 512       alignPanel.repaint();
 513     }
 514   }
 515
 516   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
 517   {
 518     ColumnSelection colSel = viewport.getColumnSelection();
 519     if (colSel.size() > 0)
 520     {
 521       addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
 522                                      HistoryItem.HIDE));
 523
 524       int max = colSel.getMax();
 525       viewport.getAlignment().trimRight(max);
 526       if(viewport.getSelectionGroup()!=null)
 527         viewport.getSelectionGroup().adjustForRemoveRight(max);
 528
 529       Vector groups = viewport.alignment.getGroups();
 530       for(int i=0; i<groups.size(); i++)
 531       {
 532         SequenceGroup sg = (SequenceGroup) groups.get(i);
 533         if(!sg.adjustForRemoveRight(max))
 534           viewport.alignment.deleteGroup(sg);
 535       }
 536
 537
 538
 539       alignPanel.repaint();
 540     }
 541
 542   }
 543
 544   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 545   {
 546     addHistoryItem(new HistoryItem("Remove Gapped Columns",
 547                                    viewport.alignment,
 548                                    HistoryItem.HIDE));
 549
 550     viewport.getAlignment().removeGaps();
 551     viewport.updateConservation();
 552     viewport.updateConsensus();
 553     alignPanel.repaint();
 554   }
 555
 556   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 557   {
 558     addHistoryItem(new HistoryItem("Remove Gaps",
 559                                    viewport.alignment,
 560                                    HistoryItem.HIDE));
 561     SequenceI current;
 562     int jSize;
 563     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 564     {
 565       current = viewport.getAlignment().getSequenceAt(i);
 566       jSize = current.getLength();
 567       for (int j=0; j < jSize; j++)
 568         if(jalview.util.Comparison.isGap(current.getCharAt(j)))
 569         {
 570           current.deleteCharAt(j);
 571           j--;
 572           jSize--;
 573         }
 574     }
 575     viewport.updateConservation();
 576     viewport.updateConsensus();
 577     alignPanel.repaint();
 578   }
 579
 580
 581   public void padGapsMenuitem_actionPerformed(ActionEvent e)
 582     {
 583       addHistoryItem(new HistoryItem("Pad Gaps",
 584                                      viewport.alignment,
 585                                      HistoryItem.HIDE));
 586       SequenceI current;
 587       int Width = viewport.getAlignment().getWidth()-1;
 588       for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 589       {
 590         current = viewport.getAlignment().getSequenceAt(i);
 591
 592         if (current.getLength()<Width)
 593           current.insertCharAt(Width, viewport.getGapCharacter());
 594       }
 595       viewport.updateConservation();
 596       viewport.updateConsensus();
 597       alignPanel.repaint();
 598   }
 599
 600
 601   public void findMenuItem_actionPerformed(ActionEvent e)
 602   {
 603     JInternalFrame frame = new JInternalFrame();
 604     Finder finder = new Finder(viewport, alignPanel, frame);
 605     frame.setContentPane(finder);
 606     Desktop.addInternalFrame(frame, "Find", 340,110);
 607     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 608
 609   }
 610
 611
 612   public void font_actionPerformed(ActionEvent e)
 613   {
 614     FontChooser fc = new FontChooser( alignPanel );
 615   }
 616
 617   protected void fullSeqId_actionPerformed(ActionEvent e)
 618   {
 619     viewport.setShowFullId( fullSeqId.isSelected() );
 620
 621     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
 622     alignPanel.repaint();
 623   }
 624
 625   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 626   {
 627       viewport.setColourText( colourTextMenuItem.isSelected() );
 628       alignPanel.repaint();
 629   }
 630
 631   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 632   {
 633     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
 634     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
 635     scaleAbove.setVisible( wrapMenuItem.isSelected() );
 636     scaleLeft.setVisible( wrapMenuItem.isSelected() );
 637     scaleRight.setVisible( wrapMenuItem.isSelected() );
 638     alignPanel.repaint();
 639   }
 640
 641   protected void scaleAbove_actionPerformed(ActionEvent e)
 642   {
 643     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
 644     alignPanel.repaint();
 645   }
 646
 647   protected void scaleLeft_actionPerformed(ActionEvent e)
 648   {
 649     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
 650     alignPanel.repaint();
 651   }
 652
 653   protected void scaleRight_actionPerformed(ActionEvent e)
 654   {
 655     viewport.setScaleRightWrapped(scaleRight.isSelected());
 656     alignPanel.repaint();
 657   }
 658
 659
 660
 661   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 662   {
 663     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
 664     alignPanel.repaint();
 665   }
 666
 667   public void viewTextMenuItem_actionPerformed(ActionEvent e)
 668   {
 669     viewport.setShowText( viewTextMenuItem.isSelected() );
 670     alignPanel.repaint();
 671   }
 672
 673
 674   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
 675   {
 676     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
 677     alignPanel.repaint();
 678   }
 679
 680   public void sequenceFeatures_actionPerformed(ActionEvent evt)
 681   {
 682     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 683     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
 684     {
 685          SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
 686          ((Alignment)viewport.alignment).featuresAdded = true;
 687     }
 688     alignPanel.repaint();
 689   }
 690
 691   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 692   {
 693     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
 694     {
 695       annotationPanelMenuItem.setSelected(false);
 696       return;
 697     }
 698     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
 699     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
 700   }
 701
 702   public void overviewMenuItem_actionPerformed(ActionEvent e)
 703   {
 704     if (alignPanel.overviewPanel != null)
 705       return;
 706
 707     JInternalFrame frame = new JInternalFrame();
 708     OverviewPanel overview = new OverviewPanel(alignPanel);
 709      frame.setContentPane(overview);
 710     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
 711                              frame.getWidth(), frame.getHeight());
 712     frame.pack();
 713     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 714     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 715     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
 716       {
 717             alignPanel.setOverviewPanel(null);
 718       };
 719     });
 720
 721     alignPanel.setOverviewPanel( overview );
 722
 723
 724   }
 725
 726   protected void noColourmenuItem_actionPerformed(ActionEvent e)
 727   {
 728     changeColour( null );
 729   }
 730
 731
 732   public void clustalColour_actionPerformed(ActionEvent e)
 733   {
 734     abovePIDThreshold.setSelected(false);
 735     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
 736   }
 737
 738   public void zappoColour_actionPerformed(ActionEvent e)
 739   {
 740     changeColour(new ZappoColourScheme());
 741   }
 742
 743   public void taylorColour_actionPerformed(ActionEvent e)
 744   {
 745     changeColour(new TaylorColourScheme());
 746   }
 747
 748
 749   public void hydrophobicityColour_actionPerformed(ActionEvent e)
 750   {
 751     changeColour( new HydrophobicColourScheme() );
 752   }
 753
 754   public void helixColour_actionPerformed(ActionEvent e)
 755   {
 756     changeColour(new HelixColourScheme() );
 757   }
 758
 759
 760   public void strandColour_actionPerformed(ActionEvent e)
 761   {
 762     changeColour(new StrandColourScheme());
 763   }
 764
 765
 766   public void turnColour_actionPerformed(ActionEvent e)
 767   {
 768     changeColour(new TurnColourScheme());
 769   }
 770
 771
 772   public void buriedColour_actionPerformed(ActionEvent e)
 773   {
 774     changeColour(new BuriedColourScheme() );
 775   }
 776
 777   public void nucleotideColour_actionPerformed(ActionEvent e)
 778   {
 779     changeColour(new NucleotideColourScheme());
 780   }
 781
 782
 783   protected void applyToAllGroups_actionPerformed(ActionEvent e)
 784   {
 785     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
 786   }
 787
 788
 789
 790   void changeColour(ColourSchemeI cs)
 791   {
 792     int threshold = 0;
 793
 794     if ( viewport.getAbovePIDThreshold() )
 795     {
 796       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 797
 798       if (cs instanceof ResidueColourScheme)
 799         ( (ResidueColourScheme) cs).setThreshold(threshold);
 800       else if (cs instanceof ScoreColourScheme)
 801         ( (ScoreColourScheme) cs).setThreshold(threshold);
 802
 803       viewport.setGlobalColourScheme(cs);
 804     }
 805     else if (cs instanceof ResidueColourScheme)
 806       ( (ResidueColourScheme) cs).setThreshold(0);
 807     else if (cs instanceof ScoreColourScheme)
 808       ( (ScoreColourScheme) cs).setThreshold(0);
 809
 810
 811
 812     if (viewport.getConservationSelected())
 813     {
 814       ConservationColourScheme ccs = null;
 815
 816       Alignment al = (Alignment) viewport.alignment;
 817       Conservation c = new Conservation("All",
 818                                         ResidueProperties.propHash, 3,
 819                                         al.getSequences(), 0,
 820                                         al.getWidth() - 1);
 821
 822       c.calculate();
 823       c.verdict(false, viewport.ConsPercGaps);
 824
 825       ccs = new ConservationColourScheme(c, cs);
 826
 827       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 828       ccs.setConsensus( viewport.vconsensus );
 829       viewport.setGlobalColourScheme(ccs);
 830
 831       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 832
 833     }
 834     else
 835     {
 836         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 837         if (cs != null)
 838           cs.setConsensus(viewport.vconsensus);
 839         viewport.setGlobalColourScheme(cs);
 840     }
 841
 842
 843     if(viewport.getColourAppliesToAllGroups())
 844     {
 845       Vector groups = viewport.alignment.getGroups();
 846       for(int i=0; i<groups.size(); i++)
 847       {
 848         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 849
 850         if (cs instanceof ClustalxColourScheme)
 851         {
 852           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
 853         }
 854         else if(cs!=null)
 855         {
 856           try{
 857             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
 858           }catch(Exception ex){ex.printStackTrace();}
 859         }
 860
 861         if(viewport.getAbovePIDThreshold())
 862         {
 863           if (sg.cs instanceof ResidueColourScheme)
 864             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
 865           else if (sg.cs instanceof ScoreColourScheme)
 866             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 867
 868            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
 869         }
 870
 871         if( viewport.getConservationSelected() )
 872         {
 873           Conservation c = new Conservation("Group",
 874                                             ResidueProperties.propHash, 3,
 875                                             sg.sequences, 0, viewport.alignment.getWidth()-1);
 876           c.calculate();
 877           c.verdict(false, viewport.ConsPercGaps);
 878           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 879
 880           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 881           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 882           sg.cs = ccs;
 883         }
 884         else if(cs!=null)
 885         {
 886           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 887           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 888         }
 889
 890       }
 891     }
 892
 893     if(alignPanel.getOverviewPanel()!=null)
 894       alignPanel.getOverviewPanel().updateOverviewImage();
 895     alignPanel.repaint();
 896   }
 897
 898   protected void modifyPID_actionPerformed(ActionEvent e)
 899   {
 900       if(viewport.getAbovePIDThreshold())
 901       {
 902         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
 903                                    "Background");
 904         SliderPanel.showPIDSlider();
 905       }
 906   }
 907
 908   protected void modifyConservation_actionPerformed(ActionEvent e)
 909   {
 910     if(viewport.getConservationSelected())
 911     {
 912       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
 913                                         "Background");
 914       SliderPanel.showConservationSlider();
 915     }
 916   }
 917
 918
 919   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
 920   {
 921     viewport.setConservationSelected(conservationMenuItem.isSelected());
 922
 923     viewport.setAbovePIDThreshold(false);
 924     abovePIDThreshold.setSelected(false);
 925
 926    ColourSchemeI cs = viewport.getGlobalColourScheme();
 927    if(cs instanceof ConservationColourScheme )
 928      changeColour( ((ConservationColourScheme)cs).cs );
 929     else
 930       changeColour( cs );
 931
 932     modifyConservation_actionPerformed(null);
 933   }
 934
 935   public void abovePIDThreshold_actionPerformed(ActionEvent e)
 936   {
 937     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 938
 939     conservationMenuItem.setSelected(false);
 940     viewport.setConservationSelected(false);
 941
 942     ColourSchemeI cs = viewport.getGlobalColourScheme();
 943
 944     if(cs instanceof ConservationColourScheme )
 945         changeColour( ((ConservationColourScheme)cs).cs );
 946     else
 947         changeColour( cs );
 948
 949     modifyPID_actionPerformed(null);
 950   }
 951
 952
 953
 954   public void userDefinedColour_actionPerformed(ActionEvent e)
 955   {
 956     UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
 957   }
 958
 959   public void PIDColour_actionPerformed(ActionEvent e)
 960   {
 961     changeColour( new PIDColourScheme() );
 962   }
 963
 964
 965   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
 966   {
 967     changeColour(new Blosum62ColourScheme() );
 968   }
 969
 970
 971
 972   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 973   {
 974     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
 975     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
 976     alignPanel.repaint();
 977   }
 978
 979   public void sortIDMenuItem_actionPerformed(ActionEvent e)
 980   {
 981     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
 982     AlignmentSorter.sortByID( viewport.getAlignment() );
 983     alignPanel.repaint();
 984   }
 985
 986   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
 987   {
 988     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
 989     AlignmentSorter.sortByGroup(viewport.getAlignment());
 990     AlignmentSorter.sortGroups(viewport.getAlignment());
 991     alignPanel.repaint();
 992   }
 993
 994   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 995   {
 996     RedundancyPanel sp = new RedundancyPanel(alignPanel);
 997     JInternalFrame frame = new JInternalFrame();
 998     frame.setContentPane(sp);
 999     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
1000
1001   }
1002
1003   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1004   {
1005     if(viewport.getSelectionGroup().getSize()<2)
1006       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
1007     else
1008     {
1009       JInternalFrame frame = new JInternalFrame();
1010       frame.setContentPane(new PairwiseAlignPanel(viewport));
1011       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
1012     }
1013   }
1014
1015   public void PCAMenuItem_actionPerformed(ActionEvent e)
1016   {
1017
1018     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
1019        || viewport.getAlignment().getHeight()<4)
1020     {
1021       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
1022                                     +"at least 4 input sequences.",
1023                                     "Sequence selection insufficient",
1024                                     JOptionPane.WARNING_MESSAGE);
1025       return;
1026     }
1027
1028     try{
1029       PCAPanel pcaPanel = new PCAPanel(viewport, null);
1030       JInternalFrame frame = new JInternalFrame();
1031       frame.setContentPane(pcaPanel);
1032       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
1033    }catch(java.lang.OutOfMemoryError ex)
1034    {
1035      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
1036                                    "Out of memory", JOptionPane.WARNING_MESSAGE);
1037    }
1038
1039
1040   }
1041
1042   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1043   {
1044     NewTreePanel("AV", "PID", "Average distance tree using PID");
1045   }
1046
1047   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1048   {
1049     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1050   }
1051
1052
1053   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1054   {
1055     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1056   }
1057
1058   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1059   {
1060     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
1061   }
1062
1063   void NewTreePanel(String type, String pwType, String title)
1064   {
1065     //are the sequences aligned?
1066     if(!viewport.alignment.isAligned())
1067     {
1068       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
1069                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
1070       return;
1071     }
1072
1073     final TreePanel tp;
1074     if (viewport.getSelectionGroup() != null &&
1075         viewport.getSelectionGroup().getSize() > 3)
1076     {
1077       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
1078                          pwType,
1079                          0, viewport.alignment.getWidth());
1080     }
1081     else
1082     {
1083       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
1084                          type, pwType, 0, viewport.alignment.getWidth());
1085     }
1086
1087    addTreeMenuItem(tp, title);
1088
1089    Desktop.addInternalFrame(tp, title, 600, 500);
1090   }
1091
1092   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
1093     final JMenuItem item = new JMenuItem("by "+title);
1094     sort.add(item);
1095     item.addActionListener(new java.awt.event.ActionListener()
1096     {
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1100                                        HistoryItem.SORT));
1101         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
1102         AlignmentSorter.sortBy(viewport.getAlignment(), order);
1103         alignPanel.repaint();
1104       }
1105     });
1106   }
1107
1108   void addTreeMenuItem(final TreePanel treePanel, String title)
1109   {
1110     final JMenuItem item = new JMenuItem(title);
1111
1112     treeCount++;
1113
1114     if (treeCount==1)
1115       sort.add(sortByTreeMenu);
1116
1117     sortByTreeMenu.add(item);
1118     item.addActionListener(new java.awt.event.ActionListener()
1119     {
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
1123                                        HistoryItem.SORT));
1124         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1125         alignPanel.repaint();
1126       }
1127     });
1128
1129     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1130     {
1131       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
1132       {
1133         treeCount--;
1134         sortByTreeMenu.remove(item);
1135         if (treeCount==0)
1136           sort.remove(sortByTreeMenu);
1137       };
1138     });
1139
1140   }
1141
1142
1143   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1144   {
1145       // TODO:resolve which menu item was actually selected
1146       // Now, check we have enough sequences
1147         SequenceI[] msa=null;
1148         if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1149         {
1150           // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1151           SequenceGroup seqs = viewport.getSelectionGroup();
1152           int sz;
1153           msa = new SequenceI[sz=seqs.getSize()];
1154           for (int i = 0; i < sz; i++)
1155           {
1156             msa[i] = (SequenceI) seqs.getSequenceAt(i);
1157           }
1158
1159           }
1160         else
1161         {
1162           Vector seqs = viewport.getAlignment().getSequences();
1163
1164           if (seqs.size() > 1) {
1165             msa = new SequenceI[seqs.size()];
1166             for (int i = 0; i < seqs.size(); i++)
1167             {
1168               msa[i] = (SequenceI) seqs.elementAt(i);
1169             }
1170
1171           }
1172
1173         }
1174         if (msa!=null) {
1175           jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
1176         }
1177   }
1178
1179   protected void jpred_actionPerformed(ActionEvent e)
1180 {
1181
1182     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
1183     {
1184       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1185       SequenceGroup seqs = viewport.getSelectionGroup();
1186       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
1187       {
1188         JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
1189       }
1190       else
1191       {
1192         int sz;
1193         SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
1194         for (int i = 0; i < sz; i++)
1195         {
1196           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1197         }
1198
1199         JPredClient ct = new JPredClient(title, msa);
1200       }
1201
1202     }
1203     else
1204     {
1205       Vector seqs = viewport.getAlignment().getSequences();
1206
1207       if (seqs.size() == 1 || !viewport.alignment.isAligned())
1208       {
1209         JPredClient ct = new JPredClient( (SequenceI)
1210                                          seqs.elementAt(0));
1211       }
1212       else
1213       {
1214         SequenceI[] msa = new SequenceI[seqs.size()];
1215         for (int i = 0; i < seqs.size(); i++)
1216         {
1217           msa[i] = (SequenceI) seqs.elementAt(i);
1218         }
1219
1220         JPredClient ct = new JPredClient(title, msa);
1221       }
1222
1223     }
1224   }
1225   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
1226   {
1227     // TODO:resolve which menu item was actually selected
1228     // Now, check we have enough sequences
1229     SequenceI[] msa=null;
1230     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1231       {
1232         // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1233         SequenceGroup seqs = viewport.getSelectionGroup();
1234         int sz;
1235         msa = new SequenceI[sz=seqs.getSize()];
1236         for (int i = 0; i < sz; i++)
1237         {
1238           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1239         }
1240
1241
1242       }
1243       else
1244       {
1245         Vector seqs = viewport.getAlignment().getSequences();
1246
1247         if (seqs.size() > 1) {
1248           msa = new SequenceI[seqs.size()];
1249           for (int i = 0; i < seqs.size(); i++)
1250           {
1251             msa[i] = (SequenceI) seqs.elementAt(i);
1252           }
1253
1254         }
1255
1256       }
1257       if (msa!=null) {
1258         MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
1259       }
1260   }
1261     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1262     // Pick the tree file
1263     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
1264         getProperty("LAST_DIRECTORY"));
1265     chooser.setFileView(new JalviewFileView());
1266     chooser.setDialogTitle("Select a newick-like tree file");
1267     chooser.setToolTipText("Load a tree file");
1268     int value = chooser.showOpenDialog(null);
1269     if (value == JalviewFileChooser.APPROVE_OPTION)
1270     {
1271       String choice = chooser.getSelectedFile().getPath();
1272       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1273       try
1274       {
1275         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
1276         ShowNewickTree(fin, choice);
1277       }
1278       catch (Exception ex)
1279       {
1280         JOptionPane.showMessageDialog(Desktop.desktop,
1281                                       "Problem reading tree file",
1282                                       ex.getMessage(),
1283                                       JOptionPane.WARNING_MESSAGE);
1284         ex.printStackTrace();
1285       }
1286     }
1287   }
1288
1289   public void ShowNewickTree(NewickFile nf, String title)
1290   {
1291     try{
1292       nf.parse();
1293       if (nf.getTree() != null)
1294       {
1295         TreePanel tp = new TreePanel(viewport,
1296                                      viewport.getAlignment().getSequences(),
1297                                      nf, "FromFile", title);
1298         Desktop.addInternalFrame(tp, title, 600, 500);
1299         addTreeMenuItem(tp, title);
1300         viewport.setCurrentTree(tp.getTree());
1301       }
1302      }catch(Exception ex){ex.printStackTrace();}
1303   }
1304
1305 }