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 import java.beans.PropertyChangeEvent;
  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       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
  82
  83       if (currentFileFormat.equals("Jalview"))
  84       {
  85         String shortName = title.replace('/', '_');
  86         title = title.replace('\\', '_');
  87         String choice = chooser.getSelectedFile().getPath();
  88         Jalview2XML.SaveState(this, choice, shortName);
  89         // USE Jalview2XML to save this file
  90         return;
  91       }
  92
  93       String choice =  chooser.getSelectedFile().getPath();
  94       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
  95       String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
  96       try{
  97         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
  98         out.println(output);
  99         out.close();
 100       }
 101       catch(Exception ex){}
 102     }
 103
 104   }
 105
 106   protected void outputText_actionPerformed(ActionEvent e)
 107   {
 108      CutAndPasteTransfer cap = new CutAndPasteTransfer();
 109      Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
 110      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
 111   }
 112
 113   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 114   {
 115     new HTMLOutput(viewport);
 116   }
 117
 118   protected void createPNG_actionPerformed(ActionEvent e)
 119   {
 120     alignPanel.makePNG();
 121   }
 122
 123   protected void epsFile_actionPerformed(ActionEvent e)
 124   {
 125     alignPanel.makeEPS();
 126   }
 127
 128
 129   public void printMenuItem_actionPerformed(ActionEvent e)
 130   {
 131     //Putting in a thread avoids Swing painting problems
 132     PrintThread thread = new PrintThread();
 133     thread.start();
 134   }
 135
 136   class PrintThread extends Thread
 137   {
 138     public void run()
 139     {
 140       PrinterJob printJob = PrinterJob.getPrinterJob();
 141       PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 142       printJob.setPrintable(alignPanel, pf);
 143       if (printJob.printDialog())
 144       {
 145         try
 146         {
 147           printJob.print();
 148         }
 149         catch (Exception PrintException)
 150         {
 151           PrintException.printStackTrace();
 152         }
 153       }
 154     }
 155
 156   }
 157
 158
 159
 160
 161   public void closeMenuItem_actionPerformed(ActionEvent e)
 162   {
 163     try{
 164       this.setClosed(true);
 165     }catch(Exception ex){}
 166   }
 167
 168   Stack historyList = new Stack();
 169   Stack redoList = new Stack();
 170   private int treeCount = 0;
 171
 172   void updateEditMenuBar()
 173    {
 174      if(historyList.size()>0)
 175       {
 176         undoMenuItem.setEnabled(true);
 177         HistoryItem hi = (HistoryItem)historyList.peek();
 178         undoMenuItem.setText("Undo "+hi.getDescription());
 179       }
 180      else
 181      {
 182        undoMenuItem.setEnabled(false);
 183        undoMenuItem.setText("Undo");
 184      }
 185
 186      if(redoList.size()>0)
 187       {
 188         redoMenuItem.setEnabled(true);
 189         HistoryItem hi = (HistoryItem)redoList.peek();
 190         redoMenuItem.setText("Redo "+hi.getDescription());
 191       }
 192      else
 193      {
 194        redoMenuItem.setEnabled(false);
 195        redoMenuItem.setText("Redo");
 196      }
 197    }
 198
 199    public void addHistoryItem(HistoryItem hi)
 200    {
 201      historyList.push(hi);
 202      updateEditMenuBar();
 203    }
 204
 205    protected void undoMenuItem_actionPerformed(ActionEvent e)
 206    {
 207        HistoryItem hi = (HistoryItem)historyList.pop();
 208        redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
 209        restoreHistoryItem(hi);
 210    }
 211
 212
 213    protected void redoMenuItem_actionPerformed(ActionEvent e)
 214    {
 215       HistoryItem hi = (HistoryItem)redoList.pop();
 216       restoreHistoryItem(hi);
 217       updateEditMenuBar();
 218       viewport.updateConsensus();
 219       alignPanel.repaint();
 220       alignPanel.repaint();
 221    }
 222
 223
 224    // used by undo and redo
 225    void restoreHistoryItem(HistoryItem hi)
 226    {
 227       if(hi.getType()== HistoryItem.SORT)
 228       {
 229            for(int i=0; i<hi.getSequences().size(); i++)
 230              viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
 231       }
 232       else
 233       {
 234         for (int i = 0; i < hi.getSequences().size(); i++)
 235         {
 236           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 237           if(restore.getLength()==0)
 238           {
 239             restore.setSequence(hi.getHidden().elementAt(i).toString());
 240             viewport.alignment.getSequences().insertElementAt(
 241                restore,
 242                hi.getAlignIndex(i));
 243           }
 244           else
 245             restore.setSequence(hi.getHidden().elementAt(i).toString());
 246         }
 247         if(hi.getType()==HistoryItem.PASTE)
 248         {
 249           for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
 250             viewport.alignment.deleteSequence(i);
 251         }
 252       }
 253       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 254       updateEditMenuBar();
 255
 256       viewport.updateConsensus();
 257       viewport.updateConservation();
 258       alignPanel.repaint();
 259   }
 260
 261   public void moveSelectedSequences(boolean up)
 262   {
 263     SequenceGroup sg = viewport.getSelectionGroup();
 264     if (sg == null)
 265       return;
 266
 267     if (up)
 268     {
 269       for (int i = 1; i < viewport.alignment.getHeight(); i++)
 270       {
 271         SequenceI seq = viewport.alignment.getSequenceAt(i);
 272         if (!sg.sequences.contains(seq))
 273           continue;
 274
 275         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 276         if (sg.sequences.contains(temp))
 277           continue;
 278
 279         viewport.alignment.getSequences().setElementAt(temp, i);
 280         viewport.alignment.getSequences().setElementAt(seq, i - 1);
 281       }
 282     }
 283     else
 284     {
 285       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
 286       {
 287         SequenceI seq = viewport.alignment.getSequenceAt(i);
 288         if (!sg.sequences.contains(seq))
 289           continue;
 290
 291         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 292         if (sg.sequences.contains(temp))
 293           continue;
 294
 295         viewport.alignment.getSequences().setElementAt(temp, i);
 296         viewport.alignment.getSequences().setElementAt(seq, i + 1);
 297       }
 298     }
 299
 300     alignPanel.repaint();
 301   }
 302
 303
 304
 305   protected void copy_actionPerformed(ActionEvent e)
 306   {
 307      if(viewport.getSelectionGroup()==null)
 308        return;
 309
 310      SequenceGroup sg = viewport.getSelectionGroup();
 311
 312      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 313      StringBuffer buffer= new StringBuffer();
 314
 315      Hashtable orderedSeqs = new Hashtable();
 316      for(int i=0; i<sg.getSize(); i++)
 317      {
 318         SequenceI seq = sg.getSequenceAt(i);
 319         int index = viewport.alignment.findIndex(seq);
 320         orderedSeqs.put(index+"", seq);
 321      }
 322
 323      int index=0;
 324      for(int i=0; i<sg.getSize(); i++)
 325      {
 326        SequenceI seq = null;
 327        while( seq == null )
 328        {
 329          if(orderedSeqs.containsKey(index+""))
 330          {
 331            seq = (SequenceI) orderedSeqs.get(index + "");
 332            index++;
 333            break;
 334          }
 335          else
 336            index++;
 337        }
 338
 339          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
 340                         +seq.findPosition( sg.getEndRes() )+ "\t"
 341                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
 342      }
 343      c.setContents( new StringSelection( buffer.toString()) , null ) ;
 344
 345   }
 346
 347
 348   protected void pasteNew_actionPerformed(ActionEvent e)
 349   {
 350     paste(true);
 351   }
 352
 353   protected void pasteThis_actionPerformed(ActionEvent e)
 354   {
 355     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
 356     paste(false);
 357   }
 358
 359   void paste(boolean newAlignment)
 360   {
 361     try{
 362       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 363       Transferable contents = c.getContents(this);
 364       if (contents == null)
 365         return;
 366
 367       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
 368       StringTokenizer st = new StringTokenizer(str);
 369       ArrayList seqs = new ArrayList();
 370       while (st.hasMoreElements())
 371       {
 372         String name = st.nextToken();
 373         int start = Integer.parseInt(st.nextToken());
 374         int end = Integer.parseInt(st.nextToken());
 375         Sequence sequence = new Sequence(name,st.nextToken(), start, end);
 376
 377         if(!newAlignment)
 378           viewport.alignment.addSequence(sequence);
 379         else
 380           seqs.add(sequence);
 381       }
 382
 383       if(newAlignment)
 384       {
 385         SequenceI[] newSeqs = new SequenceI[seqs.size()];
 386         seqs.toArray(newSeqs);
 387         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
 388         String newtitle = new String("Copied sequences");
 389         if( title.startsWith("Copied sequences"))
 390          newtitle = title;
 391        else
 392          newtitle = newtitle.concat("- from "+title);
 393
 394         Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
 395       }
 396       else
 397       {
 398         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 399         viewport.setEndSeq(viewport.alignment.getHeight());
 400         viewport.alignment.getWidth();
 401         viewport.updateConservation();
 402         viewport.updateConsensus();
 403         alignPanel.repaint();
 404       }
 405
 406     }catch(Exception ex){}// could be anything being pasted in here
 407
 408   }
 409
 410
 411   protected void cut_actionPerformed(ActionEvent e)
 412   {
 413     copy_actionPerformed(null);
 414     delete_actionPerformed(null);
 415   }
 416
 417   protected void delete_actionPerformed(ActionEvent e)
 418   {
 419     boolean seqsdeleted=false;
 420     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
 421
 422     if (viewport.getSelectionGroup() == null)
 423       return;
 424
 425      SequenceGroup sg = viewport.getSelectionGroup();
 426      for (int i=0;i < sg.sequences.size(); i++)
 427      {
 428        SequenceI seq = sg.getSequenceAt(i);
 429        int index = viewport.getAlignment().findIndex(seq);
 430        seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
 431
 432        if(seq.getSequence().length()<1) {
 433          seqsdeleted=true;
 434          viewport.getAlignment().deleteSequence(seq);
 435         } else {
 436          viewport.getAlignment().getSequences().setElementAt(seq, index);
 437        }
 438      }
 439
 440      viewport.setSelectionGroup(null);
 441      viewport.alignment.deleteGroup(sg);
 442      if (seqsdeleted)
 443        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 444      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
 445      if(viewport.getAlignment().getHeight()<1)
 446      try
 447      {
 448        this.setClosed(true);
 449      }catch(Exception ex){}
 450    viewport.updateConservation();
 451    viewport.updateConsensus();
 452    alignPanel.repaint();
 453  }
 454
 455
 456   protected void deleteGroups_actionPerformed(ActionEvent e)
 457   {
 458     viewport.alignment.deleteAllGroups();
 459     viewport.setSelectionGroup(null);
 460     alignPanel.repaint();
 461   }
 462
 463
 464
 465   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 466   {
 467     SequenceGroup sg = new SequenceGroup();
 468     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 469       sg.addSequence( viewport.getAlignment().getSequenceAt(i));
 470     sg.setEndRes(viewport.alignment.getWidth());
 471     viewport.setSelectionGroup(sg);
 472     PaintRefresher.Refresh(null);
 473   }
 474
 475   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 476   {
 477     viewport.setSelectionGroup(null);
 478     viewport.getColumnSelection().clear();
 479     viewport.setSelectionGroup(null);
 480     PaintRefresher.Refresh(null);
 481   }
 482
 483   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 484   {
 485     SequenceGroup sg = viewport.getSelectionGroup();
 486     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 487       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
 488
 489     PaintRefresher.Refresh(null);
 490   }
 491
 492   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 493   {
 494     ColumnSelection colSel = viewport.getColumnSelection();
 495     if (colSel.size() > 0)
 496     {
 497       addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
 498                                      HistoryItem.HIDE));
 499       int min = colSel.getMin();
 500       viewport.getAlignment().trimLeft(min);
 501       colSel.compensateForEdit(0,min);
 502
 503       if(viewport.getSelectionGroup()!=null)
 504         viewport.getSelectionGroup().adjustForRemoveLeft(min);
 505
 506       Vector groups = viewport.alignment.getGroups();
 507       for(int i=0; i<groups.size(); i++)
 508       {
 509         SequenceGroup sg = (SequenceGroup) groups.get(i);
 510         if(!sg.adjustForRemoveLeft(min))
 511           viewport.alignment.deleteGroup(sg);
 512       }
 513
 514       alignPanel.repaint();
 515     }
 516   }
 517
 518   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
 519   {
 520     ColumnSelection colSel = viewport.getColumnSelection();
 521     if (colSel.size() > 0)
 522     {
 523       addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
 524                                      HistoryItem.HIDE));
 525
 526       int max = colSel.getMax();
 527       viewport.getAlignment().trimRight(max);
 528       if(viewport.getSelectionGroup()!=null)
 529         viewport.getSelectionGroup().adjustForRemoveRight(max);
 530
 531       Vector groups = viewport.alignment.getGroups();
 532       for(int i=0; i<groups.size(); i++)
 533       {
 534         SequenceGroup sg = (SequenceGroup) groups.get(i);
 535         if(!sg.adjustForRemoveRight(max))
 536           viewport.alignment.deleteGroup(sg);
 537       }
 538
 539
 540
 541       alignPanel.repaint();
 542     }
 543
 544   }
 545
 546   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 547   {
 548     addHistoryItem(new HistoryItem("Remove Gapped Columns",
 549                                    viewport.alignment,
 550                                    HistoryItem.HIDE));
 551
 552     viewport.getAlignment().removeGaps();
 553     viewport.updateConservation();
 554     viewport.updateConsensus();
 555     alignPanel.repaint();
 556   }
 557
 558   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 559   {
 560     addHistoryItem(new HistoryItem("Remove Gaps",
 561                                    viewport.alignment,
 562                                    HistoryItem.HIDE));
 563     SequenceI current;
 564     int jSize;
 565     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 566     {
 567       current = viewport.getAlignment().getSequenceAt(i);
 568       jSize = current.getLength();
 569       for (int j=0; j < jSize; j++)
 570         if(jalview.util.Comparison.isGap(current.getCharAt(j)))
 571         {
 572           current.deleteCharAt(j);
 573           j--;
 574           jSize--;
 575         }
 576     }
 577     viewport.updateConservation();
 578     viewport.updateConsensus();
 579     alignPanel.repaint();
 580   }
 581
 582
 583   public void padGapsMenuitem_actionPerformed(ActionEvent e)
 584     {
 585       addHistoryItem(new HistoryItem("Pad Gaps",
 586                                      viewport.alignment,
 587                                      HistoryItem.HIDE));
 588       SequenceI current;
 589       int Width = viewport.getAlignment().getWidth()-1;
 590       for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 591       {
 592         current = viewport.getAlignment().getSequenceAt(i);
 593
 594         if (current.getLength()<Width)
 595           current.insertCharAt(Width, viewport.getGapCharacter());
 596       }
 597       viewport.updateConservation();
 598       viewport.updateConsensus();
 599       alignPanel.repaint();
 600   }
 601
 602
 603   public void findMenuItem_actionPerformed(ActionEvent e)
 604   {
 605     JInternalFrame frame = new JInternalFrame();
 606     Finder finder = new Finder(viewport, alignPanel, frame);
 607     frame.setContentPane(finder);
 608     Desktop.addInternalFrame(frame, "Find", 340,110);
 609     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 610
 611   }
 612
 613
 614   public void font_actionPerformed(ActionEvent e)
 615   {
 616     FontChooser fc = new FontChooser( alignPanel );
 617   }
 618
 619   protected void fullSeqId_actionPerformed(ActionEvent e)
 620   {
 621     viewport.setShowFullId( fullSeqId.isSelected() );
 622
 623     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
 624     alignPanel.repaint();
 625   }
 626
 627   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 628   {
 629       viewport.setColourText( colourTextMenuItem.isSelected() );
 630       alignPanel.repaint();
 631   }
 632
 633   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 634   {
 635     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
 636     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
 637     scaleAbove.setVisible( wrapMenuItem.isSelected() );
 638     scaleLeft.setVisible( wrapMenuItem.isSelected() );
 639     scaleRight.setVisible( wrapMenuItem.isSelected() );
 640     alignPanel.repaint();
 641   }
 642
 643   protected void scaleAbove_actionPerformed(ActionEvent e)
 644   {
 645     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
 646     alignPanel.repaint();
 647   }
 648
 649   protected void scaleLeft_actionPerformed(ActionEvent e)
 650   {
 651     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
 652     alignPanel.repaint();
 653   }
 654
 655   protected void scaleRight_actionPerformed(ActionEvent e)
 656   {
 657     viewport.setScaleRightWrapped(scaleRight.isSelected());
 658     alignPanel.repaint();
 659   }
 660
 661
 662
 663   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 664   {
 665     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
 666     alignPanel.repaint();
 667   }
 668
 669   public void viewTextMenuItem_actionPerformed(ActionEvent e)
 670   {
 671     viewport.setShowText( viewTextMenuItem.isSelected() );
 672     alignPanel.repaint();
 673   }
 674
 675
 676   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
 677   {
 678     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
 679     alignPanel.repaint();
 680   }
 681
 682   public void sequenceFeatures_actionPerformed(ActionEvent evt)
 683   {
 684     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 685     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
 686     {
 687          SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
 688          ((Alignment)viewport.alignment).featuresAdded = true;
 689     }
 690     alignPanel.repaint();
 691   }
 692
 693   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 694   {
 695     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
 696     {
 697       annotationPanelMenuItem.setSelected(false);
 698       return;
 699     }
 700     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
 701     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
 702   }
 703
 704   public void overviewMenuItem_actionPerformed(ActionEvent e)
 705   {
 706     if (alignPanel.overviewPanel != null)
 707       return;
 708
 709     JInternalFrame frame = new JInternalFrame();
 710     OverviewPanel overview = new OverviewPanel(alignPanel);
 711      frame.setContentPane(overview);
 712     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
 713                              frame.getWidth(), frame.getHeight());
 714     frame.pack();
 715     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 716     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 717     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
 718       {
 719             alignPanel.setOverviewPanel(null);
 720       };
 721     });
 722
 723     alignPanel.setOverviewPanel( overview );
 724
 725
 726   }
 727
 728   protected void noColourmenuItem_actionPerformed(ActionEvent e)
 729   {
 730     changeColour( null );
 731   }
 732
 733
 734   public void clustalColour_actionPerformed(ActionEvent e)
 735   {
 736     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
 737   }
 738
 739   public void zappoColour_actionPerformed(ActionEvent e)
 740   {
 741     changeColour(new ZappoColourScheme());
 742   }
 743
 744   public void taylorColour_actionPerformed(ActionEvent e)
 745   {
 746     changeColour(new TaylorColourScheme());
 747   }
 748
 749
 750   public void hydrophobicityColour_actionPerformed(ActionEvent e)
 751   {
 752     changeColour( new HydrophobicColourScheme() );
 753   }
 754
 755   public void helixColour_actionPerformed(ActionEvent e)
 756   {
 757     changeColour(new HelixColourScheme() );
 758   }
 759
 760
 761   public void strandColour_actionPerformed(ActionEvent e)
 762   {
 763     changeColour(new StrandColourScheme());
 764   }
 765
 766
 767   public void turnColour_actionPerformed(ActionEvent e)
 768   {
 769     changeColour(new TurnColourScheme());
 770   }
 771
 772
 773   public void buriedColour_actionPerformed(ActionEvent e)
 774   {
 775     changeColour(new BuriedColourScheme() );
 776   }
 777
 778   public void nucleotideColour_actionPerformed(ActionEvent e)
 779   {
 780     changeColour(new NucleotideColourScheme());
 781   }
 782
 783
 784   protected void applyToAllGroups_actionPerformed(ActionEvent e)
 785   {
 786     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
 787   }
 788
 789
 790
 791   void changeColour(ColourSchemeI cs)
 792   {
 793     int threshold = 0;
 794
 795     if ( viewport.getAbovePIDThreshold() )
 796     {
 797       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 798
 799       if (cs instanceof ResidueColourScheme)
 800         ( (ResidueColourScheme) cs).setThreshold(threshold);
 801       else if (cs instanceof ScoreColourScheme)
 802         ( (ScoreColourScheme) cs).setThreshold(threshold);
 803
 804       viewport.setGlobalColourScheme(cs);
 805     }
 806     else if (cs instanceof ResidueColourScheme)
 807       ( (ResidueColourScheme) cs).setThreshold(0);
 808     else if (cs instanceof ScoreColourScheme)
 809       ( (ScoreColourScheme) cs).setThreshold(0);
 810
 811
 812
 813     if (viewport.getConservationSelected())
 814     {
 815       ConservationColourScheme ccs = null;
 816
 817       Alignment al = (Alignment) viewport.alignment;
 818       Conservation c = new Conservation("All",
 819                                         ResidueProperties.propHash, 3,
 820                                         al.getSequences(), 0,
 821                                         al.getWidth() - 1);
 822
 823       c.calculate();
 824       c.verdict(false, viewport.ConsPercGaps);
 825
 826       ccs = new ConservationColourScheme(c, cs);
 827
 828       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 829       ccs.setConsensus( viewport.vconsensus );
 830       viewport.setGlobalColourScheme(ccs);
 831
 832       ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 833
 834     }
 835     else
 836     {
 837         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 838         if (cs != null)
 839           cs.setConsensus(viewport.vconsensus);
 840         viewport.setGlobalColourScheme(cs);
 841     }
 842
 843
 844     if(viewport.getColourAppliesToAllGroups())
 845     {
 846       Vector groups = viewport.alignment.getGroups();
 847       for(int i=0; i<groups.size(); i++)
 848       {
 849         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 850
 851         if(cs==null)
 852           sg.cs = null;
 853         else if (cs instanceof ClustalxColourScheme)
 854           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
 855         else if (cs instanceof UserColourScheme)
 856           sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
 857         else
 858           try{
 859             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
 860           }catch(Exception ex){}
 861
 862         if(viewport.getAbovePIDThreshold())
 863         {
 864           if (sg.cs instanceof ResidueColourScheme)
 865             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
 866           else if (sg.cs instanceof ScoreColourScheme)
 867             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 868
 869            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
 870         }
 871
 872         if( viewport.getConservationSelected() )
 873         {
 874           Conservation c = new Conservation("Group",
 875                                             ResidueProperties.propHash, 3,
 876                                             sg.sequences, 0, viewport.alignment.getWidth()-1);
 877           c.calculate();
 878           c.verdict(false, viewport.ConsPercGaps);
 879           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 880
 881           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 882           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 883           sg.cs = ccs;
 884         }
 885         else if(cs!=null)
 886         {
 887           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 888           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 889         }
 890
 891       }
 892     }
 893
 894     if(alignPanel.getOverviewPanel()!=null)
 895       alignPanel.getOverviewPanel().updateOverviewImage();
 896     alignPanel.repaint();
 897   }
 898
 899   protected void modifyPID_actionPerformed(ActionEvent e)
 900   {
 901       if(viewport.getAbovePIDThreshold())
 902       {
 903         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
 904                                    "Background");
 905         SliderPanel.showPIDSlider();
 906       }
 907   }
 908
 909   protected void modifyConservation_actionPerformed(ActionEvent e)
 910   {
 911     if(viewport.getConservationSelected())
 912     {
 913       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
 914                                         "Background");
 915       SliderPanel.showConservationSlider();
 916     }
 917   }
 918
 919
 920   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
 921   {
 922     viewport.setConservationSelected(conservationMenuItem.isSelected());
 923
 924     viewport.setAbovePIDThreshold(false);
 925     abovePIDThreshold.setSelected(false);
 926
 927    ColourSchemeI cs = viewport.getGlobalColourScheme();
 928    if(cs instanceof ConservationColourScheme )
 929      changeColour( ((ConservationColourScheme)cs).cs );
 930     else
 931       changeColour( cs );
 932
 933     modifyConservation_actionPerformed(null);
 934   }
 935
 936   public void abovePIDThreshold_actionPerformed(ActionEvent e)
 937   {
 938     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 939
 940     conservationMenuItem.setSelected(false);
 941     viewport.setConservationSelected(false);
 942
 943     ColourSchemeI cs = viewport.getGlobalColourScheme();
 944
 945     if(cs instanceof ConservationColourScheme )
 946         changeColour( ((ConservationColourScheme)cs).cs );
 947     else
 948         changeColour( cs );
 949
 950     modifyPID_actionPerformed(null);
 951   }
 952
 953
 954
 955   public void userDefinedColour_actionPerformed(ActionEvent e)
 956   {
 957     new UserDefinedColours( alignPanel, null);
 958   }
 959
 960   public void PIDColour_actionPerformed(ActionEvent e)
 961   {
 962     changeColour( new PIDColourScheme() );
 963   }
 964
 965
 966   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
 967   {
 968     changeColour(new Blosum62ColourScheme() );
 969   }
 970
 971
 972
 973   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 974   {
 975     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
 976     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
 977     alignPanel.repaint();
 978   }
 979
 980   public void sortIDMenuItem_actionPerformed(ActionEvent e)
 981   {
 982     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
 983     AlignmentSorter.sortByID( viewport.getAlignment() );
 984     alignPanel.repaint();
 985   }
 986
 987   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
 988   {
 989     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
 990     AlignmentSorter.sortByGroup(viewport.getAlignment());
 991     AlignmentSorter.sortGroups(viewport.getAlignment());
 992     alignPanel.repaint();
 993   }
 994
 995   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 996   {
 997     RedundancyPanel sp = new RedundancyPanel(alignPanel);
 998     JInternalFrame frame = new JInternalFrame();
 999     frame.setContentPane(sp);
1000     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
1001
1002   }
1003
1004   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1005   {
1006     if(viewport.getSelectionGroup().getSize()<2)
1007       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
1008     else
1009     {
1010       JInternalFrame frame = new JInternalFrame();
1011       frame.setContentPane(new PairwiseAlignPanel(viewport));
1012       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
1013     }
1014   }
1015
1016   public void PCAMenuItem_actionPerformed(ActionEvent e)
1017   {
1018
1019     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
1020        || viewport.getAlignment().getHeight()<4)
1021     {
1022       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
1023                                     +"at least 4 input sequences.",
1024                                     "Sequence selection insufficient",
1025                                     JOptionPane.WARNING_MESSAGE);
1026       return;
1027     }
1028
1029     try{
1030       PCAPanel pcaPanel = new PCAPanel(viewport, null);
1031       JInternalFrame frame = new JInternalFrame();
1032       frame.setContentPane(pcaPanel);
1033       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
1034    }catch(java.lang.OutOfMemoryError ex)
1035    {
1036      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
1037                                    "Out of memory", JOptionPane.WARNING_MESSAGE);
1038    }
1039
1040
1041   }
1042
1043   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1044   {
1045     NewTreePanel("AV", "PID", "Average distance tree using PID");
1046   }
1047
1048   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1049   {
1050     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1051   }
1052
1053
1054   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1055   {
1056     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1057   }
1058
1059   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1060   {
1061     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
1062   }
1063
1064   void NewTreePanel(String type, String pwType, String title)
1065   {
1066     //are the sequences aligned?
1067     if(!viewport.alignment.isAligned())
1068     {
1069       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
1070                                    +"Try using the Pad function in the edit menu,\n"
1071                                   +"or one of the multiple sequence alignment web services.",
1072                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
1073       return;
1074     }
1075
1076     final TreePanel tp;
1077     if (viewport.getSelectionGroup() != null &&
1078         viewport.getSelectionGroup().getSize() > 3)
1079     {
1080       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
1081                          pwType,
1082                          0, viewport.alignment.getWidth());
1083     }
1084     else
1085     {
1086       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
1087                          type, pwType, 0, viewport.alignment.getWidth());
1088     }
1089
1090    addTreeMenuItem(tp, title);
1091
1092    Desktop.addInternalFrame(tp, title, 600, 500);
1093   }
1094
1095   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
1096     final JMenuItem item = new JMenuItem("by "+title);
1097     sort.add(item);
1098     item.addActionListener(new java.awt.event.ActionListener()
1099     {
1100       public void actionPerformed(ActionEvent e)
1101       {
1102         addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1103                                        HistoryItem.SORT));
1104         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
1105         AlignmentSorter.sortBy(viewport.getAlignment(), order);
1106         alignPanel.repaint();
1107       }
1108     });
1109   }
1110
1111   void addTreeMenuItem(final TreePanel treePanel, String title)
1112   {
1113     final JMenuItem item = new JMenuItem(title);
1114
1115     treeCount++;
1116
1117     if (treeCount==1)
1118       sort.add(sortByTreeMenu);
1119
1120     sortByTreeMenu.add(item);
1121     item.addActionListener(new java.awt.event.ActionListener()
1122     {
1123       public void actionPerformed(ActionEvent e)
1124       {
1125         addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
1126                                        HistoryItem.SORT));
1127         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1128         alignPanel.repaint();
1129       }
1130     });
1131
1132     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1133     {
1134       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
1135       {
1136         treeCount--;
1137         sortByTreeMenu.remove(item);
1138         if (treeCount==0)
1139           sort.remove(sortByTreeMenu);
1140       };
1141     });
1142     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
1143       public void propertyChange(PropertyChangeEvent evt)
1144       {
1145         if (evt.getPropertyName().equals("alignment")) {
1146           treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
1147           treePanel.repaint();
1148         }
1149       }
1150
1151     }
1152     );
1153   }
1154
1155
1156   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1157   {
1158       // TODO:resolve which menu item was actually selected
1159       // Now, check we have enough sequences
1160         SequenceI[] msa=null;
1161         if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1162         {
1163           // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1164           SequenceGroup seqs = viewport.getSelectionGroup();
1165           int sz;
1166           msa = new SequenceI[sz=seqs.getSize()];
1167           for (int i = 0; i < sz; i++)
1168           {
1169             msa[i] = (SequenceI) seqs.getSequenceAt(i);
1170           }
1171
1172           }
1173         else
1174         {
1175           Vector seqs = viewport.getAlignment().getSequences();
1176
1177           if (seqs.size() > 1) {
1178             msa = new SequenceI[seqs.size()];
1179             for (int i = 0; i < seqs.size(); i++)
1180             {
1181               msa[i] = (SequenceI) seqs.elementAt(i);
1182             }
1183
1184           }
1185
1186         }
1187         if (msa!=null) {
1188           jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
1189         }
1190   }
1191
1192   protected void jpred_actionPerformed(ActionEvent e)
1193 {
1194     SequenceI seq=null;
1195     SequenceI[] msa=null;
1196
1197     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
1198     {
1199       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1200       SequenceGroup seqs = viewport.getSelectionGroup();
1201       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
1202       {
1203         seq = (SequenceI)seqs.getSequenceAt(0);
1204       }
1205       else
1206       {
1207         int sz;
1208         msa = new SequenceI[sz=seqs.getSize()];
1209         for (int i = 0; i < sz; i++)
1210         {
1211           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1212         }
1213       }
1214     }
1215     else
1216     {
1217       Vector seqs = viewport.getAlignment().getSequences();
1218
1219       if (seqs.size() == 1 || !viewport.alignment.isAligned())
1220       {
1221         seq = (SequenceI) seqs.elementAt(0);
1222       }
1223       else
1224       {
1225         msa = new SequenceI[seqs.size()];
1226         for (int i = 0; i < seqs.size(); i++)
1227         {
1228           msa[i] = (SequenceI) seqs.elementAt(i);
1229         }
1230       }
1231     }
1232     if (msa!=null) {
1233       JPredClient ct = new JPredClient(title, msa);
1234     } else
1235     if (seq!=null) {
1236       JPredClient ct = new JPredClient(title, seq);
1237     } else {
1238       System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
1239     }
1240   }
1241   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
1242   {
1243     // TODO:resolve which menu item was actually selected
1244     // Now, check we have enough sequences
1245     SequenceI[] msa=null;
1246     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1247       {
1248         // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1249         SequenceGroup seqs = viewport.getSelectionGroup();
1250         int sz;
1251         msa = new SequenceI[sz=seqs.getSize()];
1252         for (int i = 0; i < sz; i++)
1253         {
1254           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1255         }
1256
1257
1258       }
1259       else
1260       {
1261         Vector seqs = viewport.getAlignment().getSequences();
1262
1263         if (seqs.size() > 1) {
1264           msa = new SequenceI[seqs.size()];
1265           for (int i = 0; i < seqs.size(); i++)
1266           {
1267             msa[i] = (SequenceI) seqs.elementAt(i);
1268           }
1269
1270         }
1271
1272       }
1273       if (msa!=null) {
1274         MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
1275       }
1276   }
1277     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1278     // Pick the tree file
1279     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
1280         getProperty("LAST_DIRECTORY"));
1281     chooser.setFileView(new JalviewFileView());
1282     chooser.setDialogTitle("Select a newick-like tree file");
1283     chooser.setToolTipText("Load a tree file");
1284     int value = chooser.showOpenDialog(null);
1285     if (value == JalviewFileChooser.APPROVE_OPTION)
1286     {
1287       String choice = chooser.getSelectedFile().getPath();
1288       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1289       try
1290       {
1291         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
1292         ShowNewickTree(fin, choice);
1293       }
1294       catch (Exception ex)
1295       {
1296         JOptionPane.showMessageDialog(Desktop.desktop,
1297                                       "Problem reading tree file",
1298                                       ex.getMessage(),
1299                                       JOptionPane.WARNING_MESSAGE);
1300         ex.printStackTrace();
1301       }
1302     }
1303   }
1304
1305   public void ShowNewickTree(NewickFile nf, String title)
1306   {
1307     try{
1308       nf.parse();
1309       if (nf.getTree() != null)
1310       {
1311         TreePanel tp = new TreePanel(viewport,
1312                                      viewport.getAlignment().getSequences(),
1313                                      nf, "FromFile", title);
1314         Desktop.addInternalFrame(tp, title, 600, 500);
1315         addTreeMenuItem(tp, title);
1316         viewport.setCurrentTree(tp.getTree());
1317       }
1318      }catch(Exception ex){ex.printStackTrace();}
1319   }
1320
1321 }