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
 421     if (viewport.getSelectionGroup() == null)
 422       return;
 423
 424     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
 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          seqsdeleted=true;
 435          viewport.getAlignment().deleteSequence(seq);
 436         } else {
 437          viewport.getAlignment().getSequences().setElementAt(seq, index);
 438        }
 439      }
 440
 441      viewport.setSelectionGroup(null);
 442      viewport.alignment.deleteGroup(sg);
 443      if (seqsdeleted)
 444        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 445      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
 446      if(viewport.getAlignment().getHeight()<1)
 447      try
 448      {
 449        this.setClosed(true);
 450      }catch(Exception ex){}
 451    viewport.updateConservation();
 452    viewport.updateConsensus();
 453    alignPanel.repaint();
 454  }
 455
 456
 457   protected void deleteGroups_actionPerformed(ActionEvent e)
 458   {
 459     viewport.alignment.deleteAllGroups();
 460     viewport.setSelectionGroup(null);
 461     alignPanel.repaint();
 462   }
 463
 464
 465
 466   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 467   {
 468     SequenceGroup sg = new SequenceGroup();
 469     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 470       sg.addSequence( viewport.getAlignment().getSequenceAt(i));
 471     sg.setEndRes(viewport.alignment.getWidth());
 472     viewport.setSelectionGroup(sg);
 473     PaintRefresher.Refresh(null);
 474   }
 475
 476   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 477   {
 478     viewport.setSelectionGroup(null);
 479     viewport.getColumnSelection().clear();
 480     viewport.setSelectionGroup(null);
 481     PaintRefresher.Refresh(null);
 482   }
 483
 484   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 485   {
 486     SequenceGroup sg = viewport.getSelectionGroup();
 487     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
 488       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
 489
 490     PaintRefresher.Refresh(null);
 491   }
 492
 493   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 494   {
 495     ColumnSelection colSel = viewport.getColumnSelection();
 496     if (colSel.size() > 0)
 497     {
 498       addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
 499                                      HistoryItem.HIDE));
 500       int min = colSel.getMin();
 501       viewport.getAlignment().trimLeft(min);
 502       colSel.compensateForEdit(0,min);
 503
 504       if(viewport.getSelectionGroup()!=null)
 505         viewport.getSelectionGroup().adjustForRemoveLeft(min);
 506
 507       Vector groups = viewport.alignment.getGroups();
 508       for(int i=0; i<groups.size(); i++)
 509       {
 510         SequenceGroup sg = (SequenceGroup) groups.get(i);
 511         if(!sg.adjustForRemoveLeft(min))
 512           viewport.alignment.deleteGroup(sg);
 513       }
 514
 515       alignPanel.repaint();
 516     }
 517   }
 518
 519   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
 520   {
 521     ColumnSelection colSel = viewport.getColumnSelection();
 522     if (colSel.size() > 0)
 523     {
 524       addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
 525                                      HistoryItem.HIDE));
 526
 527       int max = colSel.getMax();
 528       viewport.getAlignment().trimRight(max);
 529       if(viewport.getSelectionGroup()!=null)
 530         viewport.getSelectionGroup().adjustForRemoveRight(max);
 531
 532       Vector groups = viewport.alignment.getGroups();
 533       for(int i=0; i<groups.size(); i++)
 534       {
 535         SequenceGroup sg = (SequenceGroup) groups.get(i);
 536         if(!sg.adjustForRemoveRight(max))
 537           viewport.alignment.deleteGroup(sg);
 538       }
 539
 540
 541
 542       alignPanel.repaint();
 543     }
 544
 545   }
 546
 547   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 548   {
 549     addHistoryItem(new HistoryItem("Remove Gapped Columns",
 550                                    viewport.alignment,
 551                                    HistoryItem.HIDE));
 552
 553     viewport.getAlignment().removeGaps();
 554     viewport.updateConservation();
 555     viewport.updateConsensus();
 556     alignPanel.repaint();
 557   }
 558
 559   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 560   {
 561     addHistoryItem(new HistoryItem("Remove Gaps",
 562                                    viewport.alignment,
 563                                    HistoryItem.HIDE));
 564     SequenceI current;
 565     int jSize;
 566     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 567     {
 568       current = viewport.getAlignment().getSequenceAt(i);
 569       jSize = current.getLength();
 570       for (int j=0; j < jSize; j++)
 571         if(jalview.util.Comparison.isGap(current.getCharAt(j)))
 572         {
 573           current.deleteCharAt(j);
 574           j--;
 575           jSize--;
 576         }
 577     }
 578     viewport.updateConservation();
 579     viewport.updateConsensus();
 580     alignPanel.repaint();
 581   }
 582
 583
 584   public void padGapsMenuitem_actionPerformed(ActionEvent e)
 585     {
 586       addHistoryItem(new HistoryItem("Pad Gaps",
 587                                      viewport.alignment,
 588                                      HistoryItem.HIDE));
 589       SequenceI current;
 590       int Width = viewport.getAlignment().getWidth()-1;
 591       for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
 592       {
 593         current = viewport.getAlignment().getSequenceAt(i);
 594
 595         if (current.getLength()<Width)
 596           current.insertCharAt(Width, viewport.getGapCharacter());
 597       }
 598       viewport.updateConservation();
 599       viewport.updateConsensus();
 600       alignPanel.repaint();
 601   }
 602
 603
 604   public void findMenuItem_actionPerformed(ActionEvent e)
 605   {
 606     JInternalFrame frame = new JInternalFrame();
 607     Finder finder = new Finder(viewport, alignPanel, frame);
 608     frame.setContentPane(finder);
 609     Desktop.addInternalFrame(frame, "Find", 340,110);
 610     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 611
 612   }
 613
 614
 615   public void font_actionPerformed(ActionEvent e)
 616   {
 617     FontChooser fc = new FontChooser( alignPanel );
 618   }
 619
 620   protected void fullSeqId_actionPerformed(ActionEvent e)
 621   {
 622     viewport.setShowFullId( fullSeqId.isSelected() );
 623
 624     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
 625     alignPanel.repaint();
 626   }
 627
 628   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 629   {
 630       viewport.setColourText( colourTextMenuItem.isSelected() );
 631       alignPanel.repaint();
 632   }
 633
 634   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 635   {
 636     viewport.setWrapAlignment( wrapMenuItem.isSelected() );
 637     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
 638     scaleAbove.setVisible( wrapMenuItem.isSelected() );
 639     scaleLeft.setVisible( wrapMenuItem.isSelected() );
 640     scaleRight.setVisible( wrapMenuItem.isSelected() );
 641     alignPanel.repaint();
 642   }
 643
 644   protected void scaleAbove_actionPerformed(ActionEvent e)
 645   {
 646     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
 647     alignPanel.repaint();
 648   }
 649
 650   protected void scaleLeft_actionPerformed(ActionEvent e)
 651   {
 652     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
 653     alignPanel.repaint();
 654   }
 655
 656   protected void scaleRight_actionPerformed(ActionEvent e)
 657   {
 658     viewport.setScaleRightWrapped(scaleRight.isSelected());
 659     alignPanel.repaint();
 660   }
 661
 662
 663
 664   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 665   {
 666     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
 667     alignPanel.repaint();
 668   }
 669
 670   public void viewTextMenuItem_actionPerformed(ActionEvent e)
 671   {
 672     viewport.setShowText( viewTextMenuItem.isSelected() );
 673     alignPanel.repaint();
 674   }
 675
 676
 677   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
 678   {
 679     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
 680     alignPanel.repaint();
 681   }
 682
 683   public void sequenceFeatures_actionPerformed(ActionEvent evt)
 684   {
 685     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 686     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
 687     {
 688          SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
 689          ((Alignment)viewport.alignment).featuresAdded = true;
 690     }
 691     alignPanel.repaint();
 692   }
 693
 694   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 695   {
 696     if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
 697     {
 698       annotationPanelMenuItem.setSelected(false);
 699       return;
 700     }
 701     viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
 702     alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
 703   }
 704
 705   public void overviewMenuItem_actionPerformed(ActionEvent e)
 706   {
 707     if (alignPanel.overviewPanel != null)
 708       return;
 709
 710     JInternalFrame frame = new JInternalFrame();
 711     OverviewPanel overview = new OverviewPanel(alignPanel);
 712      frame.setContentPane(overview);
 713     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
 714                              frame.getWidth(), frame.getHeight());
 715     frame.pack();
 716     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 717     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 718     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
 719       {
 720             alignPanel.setOverviewPanel(null);
 721       };
 722     });
 723
 724     alignPanel.setOverviewPanel( overview );
 725
 726
 727   }
 728
 729   protected void noColourmenuItem_actionPerformed(ActionEvent e)
 730   {
 731     changeColour( null );
 732   }
 733
 734
 735   public void clustalColour_actionPerformed(ActionEvent e)
 736   {
 737     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
 738   }
 739
 740   public void zappoColour_actionPerformed(ActionEvent e)
 741   {
 742     changeColour(new ZappoColourScheme());
 743   }
 744
 745   public void taylorColour_actionPerformed(ActionEvent e)
 746   {
 747     changeColour(new TaylorColourScheme());
 748   }
 749
 750
 751   public void hydrophobicityColour_actionPerformed(ActionEvent e)
 752   {
 753     changeColour( new HydrophobicColourScheme() );
 754   }
 755
 756   public void helixColour_actionPerformed(ActionEvent e)
 757   {
 758     changeColour(new HelixColourScheme() );
 759   }
 760
 761
 762   public void strandColour_actionPerformed(ActionEvent e)
 763   {
 764     changeColour(new StrandColourScheme());
 765   }
 766
 767
 768   public void turnColour_actionPerformed(ActionEvent e)
 769   {
 770     changeColour(new TurnColourScheme());
 771   }
 772
 773
 774   public void buriedColour_actionPerformed(ActionEvent e)
 775   {
 776     changeColour(new BuriedColourScheme() );
 777   }
 778
 779   public void nucleotideColour_actionPerformed(ActionEvent e)
 780   {
 781     changeColour(new NucleotideColourScheme());
 782   }
 783
 784
 785   protected void applyToAllGroups_actionPerformed(ActionEvent e)
 786   {
 787     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
 788   }
 789
 790
 791
 792   void changeColour(ColourSchemeI cs)
 793   {
 794     int threshold = 0;
 795
 796     if ( viewport.getAbovePIDThreshold() )
 797     {
 798       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 799
 800       if (cs instanceof ResidueColourScheme)
 801         ( (ResidueColourScheme) cs).setThreshold(threshold);
 802       else if (cs instanceof ScoreColourScheme)
 803         ( (ScoreColourScheme) cs).setThreshold(threshold);
 804
 805       viewport.setGlobalColourScheme(cs);
 806     }
 807     else if (cs instanceof ResidueColourScheme)
 808       ( (ResidueColourScheme) cs).setThreshold(0);
 809     else if (cs instanceof ScoreColourScheme)
 810       ( (ScoreColourScheme) cs).setThreshold(0);
 811
 812
 813
 814     if (viewport.getConservationSelected())
 815     {
 816       ConservationColourScheme ccs = null;
 817
 818       Alignment al = (Alignment) viewport.alignment;
 819       Conservation c = new Conservation("All",
 820                                         ResidueProperties.propHash, 3,
 821                                         al.getSequences(), 0,
 822                                         al.getWidth() - 1);
 823
 824       c.calculate();
 825       c.verdict(false, viewport.ConsPercGaps);
 826
 827       ccs = new ConservationColourScheme(c, cs);
 828
 829       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 830       ccs.setConsensus( viewport.vconsensus );
 831       viewport.setGlobalColourScheme(ccs);
 832
 833       ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 834
 835     }
 836     else
 837     {
 838         // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 839         if (cs != null)
 840           cs.setConsensus(viewport.vconsensus);
 841         viewport.setGlobalColourScheme(cs);
 842     }
 843
 844
 845     if(viewport.getColourAppliesToAllGroups())
 846     {
 847       Vector groups = viewport.alignment.getGroups();
 848       for(int i=0; i<groups.size(); i++)
 849       {
 850         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 851
 852         if(cs==null)
 853           sg.cs = null;
 854         else if (cs instanceof ClustalxColourScheme)
 855           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
 856         else if (cs instanceof UserColourScheme)
 857           sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
 858         else
 859           try{
 860             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
 861           }catch(Exception ex){}
 862
 863         if(viewport.getAbovePIDThreshold())
 864         {
 865           if (sg.cs instanceof ResidueColourScheme)
 866             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
 867           else if (sg.cs instanceof ScoreColourScheme)
 868             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
 869
 870            sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
 871         }
 872
 873         if( viewport.getConservationSelected() )
 874         {
 875           Conservation c = new Conservation("Group",
 876                                             ResidueProperties.propHash, 3,
 877                                             sg.sequences, 0, viewport.alignment.getWidth()-1);
 878           c.calculate();
 879           c.verdict(false, viewport.ConsPercGaps);
 880           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 881
 882           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 883           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 884           sg.cs = ccs;
 885         }
 886         else if(cs!=null)
 887         {
 888           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
 889           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
 890         }
 891
 892       }
 893     }
 894
 895     if(alignPanel.getOverviewPanel()!=null)
 896       alignPanel.getOverviewPanel().updateOverviewImage();
 897     alignPanel.repaint();
 898   }
 899
 900   protected void modifyPID_actionPerformed(ActionEvent e)
 901   {
 902       if(viewport.getAbovePIDThreshold())
 903       {
 904         SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
 905                                    "Background");
 906         SliderPanel.showPIDSlider();
 907       }
 908   }
 909
 910   protected void modifyConservation_actionPerformed(ActionEvent e)
 911   {
 912     if(viewport.getConservationSelected())
 913     {
 914       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
 915                                         "Background");
 916       SliderPanel.showConservationSlider();
 917     }
 918   }
 919
 920
 921   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
 922   {
 923     viewport.setConservationSelected(conservationMenuItem.isSelected());
 924
 925     viewport.setAbovePIDThreshold(false);
 926     abovePIDThreshold.setSelected(false);
 927
 928    ColourSchemeI cs = viewport.getGlobalColourScheme();
 929    if(cs instanceof ConservationColourScheme )
 930      changeColour( ((ConservationColourScheme)cs).cs );
 931     else
 932       changeColour( cs );
 933
 934     modifyConservation_actionPerformed(null);
 935   }
 936
 937   public void abovePIDThreshold_actionPerformed(ActionEvent e)
 938   {
 939     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 940
 941     conservationMenuItem.setSelected(false);
 942     viewport.setConservationSelected(false);
 943
 944     ColourSchemeI cs = viewport.getGlobalColourScheme();
 945
 946     if(cs instanceof ConservationColourScheme )
 947         changeColour( ((ConservationColourScheme)cs).cs );
 948     else
 949         changeColour( cs );
 950
 951     modifyPID_actionPerformed(null);
 952   }
 953
 954
 955
 956   public void userDefinedColour_actionPerformed(ActionEvent e)
 957   {
 958     new UserDefinedColours( alignPanel, null);
 959   }
 960
 961   public void PIDColour_actionPerformed(ActionEvent e)
 962   {
 963     changeColour( new PIDColourScheme() );
 964   }
 965
 966
 967   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
 968   {
 969     changeColour(new Blosum62ColourScheme() );
 970   }
 971
 972
 973
 974   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 975   {
 976     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
 977     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
 978     alignPanel.repaint();
 979   }
 980
 981   public void sortIDMenuItem_actionPerformed(ActionEvent e)
 982   {
 983     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
 984     AlignmentSorter.sortByID( viewport.getAlignment() );
 985     alignPanel.repaint();
 986   }
 987
 988   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
 989   {
 990     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
 991     AlignmentSorter.sortByGroup(viewport.getAlignment());
 992     AlignmentSorter.sortGroups(viewport.getAlignment());
 993     alignPanel.repaint();
 994   }
 995
 996   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 997   {
 998     RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
 999     JInternalFrame frame = new JInternalFrame();
1000     frame.setContentPane(sp);
1001     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
1002
1003   }
1004
1005   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1006   {
1007     if((viewport.getSelectionGroup()==null) ||
1008        viewport.getSelectionGroup().getSize()<2)
1009       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
1010     else
1011     {
1012       JInternalFrame frame = new JInternalFrame();
1013       frame.setContentPane(new PairwiseAlignPanel(viewport));
1014       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
1015     }
1016   }
1017
1018   public void PCAMenuItem_actionPerformed(ActionEvent e)
1019   {
1020
1021     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
1022        || viewport.getAlignment().getHeight()<4)
1023     {
1024       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
1025                                     +"at least 4 input sequences.",
1026                                     "Sequence selection insufficient",
1027                                     JOptionPane.WARNING_MESSAGE);
1028       return;
1029     }
1030
1031     try{
1032       PCAPanel pcaPanel = new PCAPanel(viewport, null);
1033       JInternalFrame frame = new JInternalFrame();
1034       frame.setContentPane(pcaPanel);
1035       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
1036    }catch(java.lang.OutOfMemoryError ex)
1037    {
1038      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
1039                                    "Out of memory", JOptionPane.WARNING_MESSAGE);
1040    }
1041
1042
1043   }
1044
1045   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1046   {
1047     NewTreePanel("AV", "PID", "Average distance tree using PID");
1048   }
1049
1050   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1051   {
1052     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
1053   }
1054
1055
1056   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1057   {
1058     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
1059   }
1060
1061   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1062   {
1063     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
1064   }
1065
1066   void NewTreePanel(String type, String pwType, String title)
1067   {
1068     //are the sequences aligned?
1069     if(!viewport.alignment.isAligned())
1070     {
1071       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
1072                                    +"Try using the Pad function in the edit menu,\n"
1073                                   +"or one of the multiple sequence alignment web services.",
1074                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
1075       return;
1076     }
1077
1078     final TreePanel tp;
1079     if (viewport.getSelectionGroup() != null &&
1080         viewport.getSelectionGroup().getSize() > 3)
1081     {
1082       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
1083                          pwType,
1084                          0, viewport.alignment.getWidth());
1085     }
1086     else
1087     {
1088       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
1089                          type, pwType, 0, viewport.alignment.getWidth());
1090     }
1091
1092    addTreeMenuItem(tp, title);
1093
1094    Desktop.addInternalFrame(tp, title, 600, 500);
1095   }
1096
1097   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
1098     final JMenuItem item = new JMenuItem("by "+title);
1099     sort.add(item);
1100     item.addActionListener(new java.awt.event.ActionListener()
1101     {
1102       public void actionPerformed(ActionEvent e)
1103       {
1104         addHistoryItem(new HistoryItem("Sort", viewport.alignment,
1105                                        HistoryItem.SORT));
1106         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
1107         AlignmentSorter.sortBy(viewport.getAlignment(), order);
1108         alignPanel.repaint();
1109       }
1110     });
1111   }
1112
1113   void addTreeMenuItem(final TreePanel treePanel, String title)
1114   {
1115     final JMenuItem item = new JMenuItem(title);
1116
1117     treeCount++;
1118
1119     if (treeCount==1)
1120       sort.add(sortByTreeMenu);
1121
1122     sortByTreeMenu.add(item);
1123     item.addActionListener(new java.awt.event.ActionListener()
1124     {
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
1128                                        HistoryItem.SORT));
1129         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
1130         alignPanel.repaint();
1131       }
1132     });
1133
1134     treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1135     {
1136       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
1137       {
1138         treeCount--;
1139         sortByTreeMenu.remove(item);
1140         if (treeCount==0)
1141           sort.remove(sortByTreeMenu);
1142       };
1143     });
1144     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
1145       public void propertyChange(PropertyChangeEvent evt)
1146       {
1147         if (evt.getPropertyName().equals("alignment")) {
1148           treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
1149           treePanel.repaint();
1150         }
1151       }
1152
1153     }
1154     );
1155   }
1156
1157
1158   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1159   {
1160       // TODO:resolve which menu item was actually selected
1161       // Now, check we have enough sequences
1162         SequenceI[] msa=null;
1163         if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1164         {
1165           // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1166           SequenceGroup seqs = viewport.getSelectionGroup();
1167           int sz;
1168           msa = new SequenceI[sz=seqs.getSize()];
1169           for (int i = 0; i < sz; i++)
1170           {
1171             msa[i] = (SequenceI) seqs.getSequenceAt(i);
1172           }
1173
1174           }
1175         else
1176         {
1177           Vector seqs = viewport.getAlignment().getSequences();
1178
1179           if (seqs.size() > 1) {
1180             msa = new SequenceI[seqs.size()];
1181             for (int i = 0; i < seqs.size(); i++)
1182             {
1183               msa[i] = (SequenceI) seqs.elementAt(i);
1184             }
1185
1186           }
1187
1188         }
1189         if (msa!=null) {
1190           jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
1191         }
1192   }
1193
1194   protected void jpred_actionPerformed(ActionEvent e)
1195 {
1196     SequenceI seq=null;
1197     SequenceI[] msa=null;
1198
1199     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
1200     {
1201       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1202       SequenceGroup seqs = viewport.getSelectionGroup();
1203       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
1204       {
1205         seq = (SequenceI)seqs.getSequenceAt(0);
1206       }
1207       else
1208       {
1209         int sz;
1210         msa = new SequenceI[sz=seqs.getSize()];
1211         for (int i = 0; i < sz; i++)
1212         {
1213           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1214         }
1215       }
1216     }
1217     else
1218     {
1219       Vector seqs = viewport.getAlignment().getSequences();
1220
1221       if (seqs.size() == 1 || !viewport.alignment.isAligned())
1222       {
1223         seq = (SequenceI) seqs.elementAt(0);
1224       }
1225       else
1226       {
1227         msa = new SequenceI[seqs.size()];
1228         for (int i = 0; i < seqs.size(); i++)
1229         {
1230           msa[i] = (SequenceI) seqs.elementAt(i);
1231         }
1232       }
1233     }
1234     if (msa!=null) {
1235       JPredClient ct = new JPredClient(title, msa);
1236     } else
1237     if (seq!=null) {
1238       JPredClient ct = new JPredClient(title, seq);
1239     } else {
1240       System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
1241     }
1242   }
1243   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
1244   {
1245     // TODO:resolve which menu item was actually selected
1246     // Now, check we have enough sequences
1247     SequenceI[] msa=null;
1248     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
1249       {
1250         // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
1251         SequenceGroup seqs = viewport.getSelectionGroup();
1252         int sz;
1253         msa = new SequenceI[sz=seqs.getSize()];
1254         for (int i = 0; i < sz; i++)
1255         {
1256           msa[i] = (SequenceI) seqs.getSequenceAt(i);
1257         }
1258
1259
1260       }
1261       else
1262       {
1263         Vector seqs = viewport.getAlignment().getSequences();
1264
1265         if (seqs.size() > 1) {
1266           msa = new SequenceI[seqs.size()];
1267           for (int i = 0; i < seqs.size(); i++)
1268           {
1269             msa[i] = (SequenceI) seqs.elementAt(i);
1270           }
1271
1272         }
1273
1274       }
1275       if (msa!=null) {
1276         MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
1277       }
1278   }
1279     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1280     // Pick the tree file
1281     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
1282         getProperty("LAST_DIRECTORY"));
1283     chooser.setFileView(new JalviewFileView());
1284     chooser.setDialogTitle("Select a newick-like tree file");
1285     chooser.setToolTipText("Load a tree file");
1286     int value = chooser.showOpenDialog(null);
1287     if (value == JalviewFileChooser.APPROVE_OPTION)
1288     {
1289       String choice = chooser.getSelectedFile().getPath();
1290       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1291       try
1292       {
1293         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
1294         ShowNewickTree(fin, choice);
1295       }
1296       catch (Exception ex)
1297       {
1298         JOptionPane.showMessageDialog(Desktop.desktop,
1299                                       "Problem reading tree file",
1300                                       ex.getMessage(),
1301                                       JOptionPane.WARNING_MESSAGE);
1302         ex.printStackTrace();
1303       }
1304     }
1305   }
1306
1307   public void ShowNewickTree(NewickFile nf, String title)
1308   {
1309     try{
1310       nf.parse();
1311       if (nf.getTree() != null)
1312       {
1313         TreePanel tp = new TreePanel(viewport,
1314                                      viewport.getAlignment().getSequences(),
1315                                      nf, "FromFile", title);
1316         Desktop.addInternalFrame(tp, title, 600, 500);
1317         addTreeMenuItem(tp, title);
1318         viewport.setCurrentTree(tp.getTree());
1319       }
1320      }catch(Exception ex){ex.printStackTrace();}
1321   }
1322
1323 }