src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import java.awt.event.*;\r
  20 import java.awt.*;\r
  21 import javax.swing.*;\r
  22 \r
  23 public class AlignFrame extends GAlignFrame\r
  24 {\r
  25   AlignmentPanel alignPanel;\r
  26   AlignViewport viewport;\r
  27   public AlignFrame(AlignmentI al)\r
  28   {\r
  29     super();\r
  30     viewport = new AlignViewport(al,true,true,true,false);\r
  31     alignPanel = new AlignmentPanel(this, viewport);\r
  32     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  33     fontNameMenuItem.setText(viewport.getFont().getName());\r
  34     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  35   }\r
  36 \r
  37   protected void saveAs_actionPerformed(ActionEvent e)\r
  38   {\r
  39     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  40     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  41     chooser.setToolTipText("Save");\r
  42     int value = chooser.showSaveDialog(this);\r
  43     if(value == JFileChooser.APPROVE_OPTION)\r
  44     {\r
  45       String choice =  chooser.getSelectedFile().getPath();\r
  46       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  47       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  48       try{\r
  49         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  50         out.println(output);\r
  51         out.close();\r
  52       }\r
  53       catch(Exception ex){}\r
  54     }\r
  55 \r
  56   }\r
  57 \r
  58   protected void outputText_actionPerformed(ActionEvent e)\r
  59   {\r
  60      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  61      JInternalFrame frame = new JInternalFrame();\r
  62      cap.formatForOutput();\r
  63      frame.setContentPane(cap);\r
  64      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  65      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  66   }\r
  67 \r
  68   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  69   {\r
  70     HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());\r
  71     htmlOutput = null;\r
  72   }\r
  73 \r
  74   public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
  75   {\r
  76 \r
  77   }\r
  78 \r
  79   public void closeMenuItem_actionPerformed(ActionEvent e)\r
  80   {\r
  81     try{\r
  82       this.setClosed(true);\r
  83     }catch(Exception ex){}\r
  84   }\r
  85 \r
  86   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
  87   {\r
  88 \r
  89   }\r
  90 \r
  91   public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
  92   {\r
  93 \r
  94   }\r
  95 \r
  96   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
  97   {\r
  98     Selection sel = viewport.getSelection();\r
  99     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 100       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 101     PaintRefresher.Refresh(null);\r
 102   }\r
 103 \r
 104   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 105   {\r
 106     viewport.getSelection().clear();\r
 107     PaintRefresher.Refresh(null);\r
 108   }\r
 109 \r
 110   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 111   {\r
 112     Selection sel = viewport.getSelection();\r
 113     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 114     {\r
 115       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 116         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 117       else\r
 118         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 119     }\r
 120     PaintRefresher.Refresh(null);\r
 121   }\r
 122 \r
 123   public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 124   {\r
 125     for (int i=0;i < viewport.getSelection().size(); i++)\r
 126             viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
 127 \r
 128     viewport.getSelection().clear();\r
 129     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
 130     alignPanel.RefreshPanels();\r
 131   }\r
 132 \r
 133   public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 134   {\r
 135     copySelectedMenuItem_actionPerformed(null);\r
 136     deleteSelectedMenuItem_actionPerformed(null);\r
 137     alignPanel.repaint();\r
 138   }\r
 139 \r
 140   public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 141   {\r
 142     if(viewport.getSelection().size()==0)\r
 143       return;\r
 144 \r
 145    SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
 146    for (int i=0; i < viewport.getSelection().size(); i++) {\r
 147      s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
 148     }\r
 149     AlignFrame af = new AlignFrame(new Alignment(s));\r
 150 \r
 151     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
 152     if(newHeight>500)\r
 153       newHeight=500;\r
 154     Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
 155   }\r
 156 \r
 157   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 158   {\r
 159     viewport.getColumnSelection().clear();\r
 160     repaint();\r
 161   }\r
 162 \r
 163   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 164   {\r
 165     ColumnSelection colSel = viewport.getColumnSelection();\r
 166     if (colSel.size() > 0)\r
 167     {\r
 168       int min = colSel.getMin();\r
 169       viewport.getAlignment().trimLeft(min);\r
 170       colSel.compensateForEdit(0,min);\r
 171       alignPanel.RefreshPanels();\r
 172     }\r
 173   }\r
 174 \r
 175   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 176   {\r
 177     ColumnSelection colSel = viewport.getColumnSelection();\r
 178     if (colSel.size() > 0)\r
 179     {\r
 180       int max = colSel.getMax();\r
 181       if(max>1)\r
 182         viewport.getAlignment().trimRight(max);\r
 183 \r
 184       alignPanel.RefreshPanels();\r
 185     }\r
 186 \r
 187   }\r
 188 \r
 189   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 190   {\r
 191     viewport.getAlignment().removeGaps();\r
 192     alignPanel.RefreshPanels();\r
 193   }\r
 194 \r
 195   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 196   {\r
 197     SequenceI current;\r
 198     int jSize;\r
 199     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 200     {\r
 201       current = viewport.getAlignment().getSequenceAt(i);\r
 202       jSize = current.getLength();\r
 203       for (int j=0; j < jSize; j++)\r
 204         if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
 205         {\r
 206           current.deleteCharAt(j);\r
 207           j--;\r
 208           jSize--;\r
 209         }\r
 210     }\r
 211 \r
 212     alignPanel.RefreshPanels();\r
 213   }\r
 214 \r
 215   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 216   {\r
 217     String thisChar = "-";\r
 218     String nextChar = ".";\r
 219     if(viewport.getGapCharacter().equals("-"))\r
 220     {\r
 221       thisChar = ".";\r
 222       nextChar = "-";\r
 223     }\r
 224     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 225     viewport.setGapCharacter(thisChar);\r
 226   }\r
 227 \r
 228 \r
 229   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 230   {\r
 231     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 232 \r
 233 \r
 234     String selection = JOptionPane.showInputDialog(this,\r
 235                                 "Select font",\r
 236                                 "Font selection",\r
 237                                 JOptionPane.QUESTION_MESSAGE,\r
 238                                 null,fonts\r
 239                                 ,fontNameMenuItem.getText()).toString();\r
 240     if(selection!=null)\r
 241     {\r
 242        fontNameMenuItem.setText(selection);\r
 243        SetFont();\r
 244      }\r
 245 \r
 246   }\r
 247 \r
 248   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 249   {\r
 250     String selection = JOptionPane.showInputDialog(this,\r
 251                                 "Select font size",\r
 252                                 "Font size",\r
 253                                 JOptionPane.QUESTION_MESSAGE,\r
 254                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 255                                 ,fontSizeMenuItem.getText()).toString();\r
 256     if(selection!=null)\r
 257      {\r
 258        fontSizeMenuItem.setText(selection);\r
 259        SetFont();\r
 260      }\r
 261   }\r
 262 \r
 263   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 264   {\r
 265     String selection = JOptionPane.showInputDialog(this,\r
 266                                 "Select font style",\r
 267                                 "Font style",\r
 268                                 JOptionPane.QUESTION_MESSAGE,\r
 269                                 null, new String[]{"plain", "bold", "italic"}\r
 270                                 ,fontStyleMenuItem.getText()).toString();\r
 271     if(selection!=null)\r
 272     {\r
 273       fontStyleMenuItem.setText(selection);\r
 274       SetFont();\r
 275     }\r
 276 \r
 277   }\r
 278 \r
 279   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 280   {\r
 281     viewport.setColourText( colourTextMenuItem.isSelected() );\r
 282     alignPanel.RefreshPanels();\r
 283   }\r
 284 \r
 285   void SetFont()\r
 286   {\r
 287       int style = java.awt.Font.PLAIN;\r
 288       if(fontStyleMenuItem.getText().equals("bold"))\r
 289         style = java.awt.Font.BOLD;\r
 290       else if(fontStyleMenuItem.getText().equals("italic"))\r
 291         style = java.awt.Font.ITALIC;\r
 292 \r
 293       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 294                                            style,\r
 295                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 296       alignPanel.RefreshPanels();\r
 297 \r
 298   }\r
 299 \r
 300   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 301   {\r
 302     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 303     alignPanel.RefreshPanels();\r
 304   }\r
 305 \r
 306   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 307   {\r
 308     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 309     alignPanel.RefreshPanels();\r
 310   }\r
 311 \r
 312 \r
 313   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 314   {\r
 315     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 316   }\r
 317 \r
 318   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 319   {\r
 320 \r
 321     JInternalFrame frame = new JInternalFrame();\r
 322     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 323    try{\r
 324      overview = new OverviewPanel(alignPanel, viewport);\r
 325      frame.setContentPane(overview);\r
 326     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 327                              frame.getWidth(), frame.getHeight());\r
 328     frame.pack();\r
 329     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 330     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 331       {\r
 332             alignPanel.setOverviewPanel(null);\r
 333       };\r
 334     });\r
 335     alignPanel.setOverviewPanel( overview );\r
 336 \r
 337   }catch(java.lang.OutOfMemoryError ex)\r
 338    {\r
 339      JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",\r
 340                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 341    }\r
 342 \r
 343 \r
 344   }\r
 345 \r
 346 \r
 347   public void clustalColour_actionPerformed(ActionEvent e)\r
 348   {\r
 349    // alignPanel.setColourScheme( new ClustalxColourScheme() );\r
 350   }\r
 351 \r
 352   public void zappoColour_actionPerformed(ActionEvent e)\r
 353   {\r
 354     alignPanel.setColourScheme( new ZappoColourScheme() );\r
 355   }\r
 356 \r
 357   public void taylorColour_actionPerformed(ActionEvent e)\r
 358   {\r
 359     alignPanel.setColourScheme( new TaylorColourScheme() );\r
 360   }\r
 361 \r
 362 \r
 363   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 364   {\r
 365     alignPanel.setColourScheme( new HydrophobicColourScheme() );\r
 366   }\r
 367 \r
 368   public void helixColour_actionPerformed(ActionEvent e)\r
 369   {\r
 370     alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );\r
 371   }\r
 372 \r
 373   public void strandColour_actionPerformed(ActionEvent e)\r
 374   {\r
 375     alignPanel.setColourScheme( new StrandColourScheme() );\r
 376   }\r
 377 \r
 378   public void turnColour_actionPerformed(ActionEvent e)\r
 379   {\r
 380     alignPanel.setColourScheme( new TurnColourScheme() );\r
 381   }\r
 382 \r
 383   public void buriedColour_actionPerformed(ActionEvent e)\r
 384   {\r
 385     alignPanel.setColourScheme( new BuriedColourScheme() );\r
 386   }\r
 387 \r
 388   public void conservationColour_actionPerformed(ActionEvent e)\r
 389   {\r
 390 \r
 391   }\r
 392 \r
 393   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 394  {\r
 395 \r
 396  }\r
 397 \r
 398 \r
 399   public void abovePIDColour_actionPerformed(ActionEvent e)\r
 400   {\r
 401     alignPanel.setColourScheme( new PIDColourScheme() );\r
 402   }\r
 403 \r
 404 \r
 405   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 406   {\r
 407     JInternalFrame frame = new JInternalFrame();\r
 408     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\r
 409     frame.setContentPane(chooser);\r
 410     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 411     frame.setResizable(false);\r
 412     frame.setIconifiable(false);\r
 413     frame.setMaximizable(false);\r
 414   }\r
 415 \r
 416   public void PIDColour_actionPerformed(ActionEvent e)\r
 417   {\r
 418     alignPanel.setColourScheme( new PIDColourScheme() );\r
 419   }\r
 420 \r
 421   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 422   {\r
 423     alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );\r
 424   }\r
 425 \r
 426 \r
 427   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 428   {\r
 429     ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
 430     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 431   }\r
 432 \r
 433 \r
 434   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 435   {\r
 436     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 437     alignPanel.RefreshPanels();\r
 438   }\r
 439 \r
 440   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 441   {\r
 442     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 443     alignPanel.RefreshPanels();\r
 444   }\r
 445 \r
 446   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 447   {\r
 448     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 449     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 450     alignPanel.RefreshPanels();\r
 451   }\r
 452 \r
 453   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 454   {\r
 455     if(viewport.getCurrentTree()==null)\r
 456       return;\r
 457 \r
 458     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 459     alignPanel.RefreshPanels();\r
 460   }\r
 461 \r
 462   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 463   {\r
 464 \r
 465   }\r
 466 \r
 467   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 468   {\r
 469     if(viewport.getSelection().size()<2)\r
 470       JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 471     else\r
 472     {\r
 473       JInternalFrame frame = new JInternalFrame();\r
 474       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 475       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 476     }\r
 477   }\r
 478 \r
 479   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 480   {\r
 481     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 482        || viewport.getAlignment().getHeight()<4)\r
 483     {\r
 484       JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"\r
 485                                     +"at least 4 input sequences.",\r
 486                                     "Sequence selection insufficient",\r
 487                                     JOptionPane.WARNING_MESSAGE);\r
 488       return;\r
 489     }\r
 490 \r
 491     PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 492     JInternalFrame frame = new JInternalFrame();\r
 493     frame.setContentPane(pcaPanel);\r
 494     Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);\r
 495   }\r
 496 \r
 497   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 498   {\r
 499     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 500   }\r
 501 \r
 502   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 503   {\r
 504     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 505   }\r
 506 \r
 507 \r
 508   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 509   {\r
 510     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 511   }\r
 512 \r
 513   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 514   {\r
 515     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 516   }\r
 517 \r
 518   void NewTreePanel(String type, String pwType, String title)\r
 519   {\r
 520     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 521     TreePanel tp=null;\r
 522    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 523    {\r
 524      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 525                          viewport.getStartRes(), viewport.getEndRes());\r
 526    }\r
 527    else\r
 528    {\r
 529      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 530                          type, pwType, viewport.getStartRes(),\r
 531                          viewport.getEndRes());\r
 532    }\r
 533 \r
 534    frame.setContentPane(tp);\r
 535    Desktop.addInternalFrame(frame, title, 600, 500);\r
 536   }\r
 537 \r
 538 \r
 539 \r
 540   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 541   {\r
 542     JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
 543                                   +"\nwithin the Barton Group, Dundee University."\r
 544                                   +"\nThis will be available as a web service 2005",\r
 545                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 546   }\r
 547 \r
 548 }\r