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   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 300   {\r
 301     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 302     alignPanel.RefreshPanels();\r
 303   }\r
 304 \r
 305   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 306   {\r
 307     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 308     alignPanel.RefreshPanels();\r
 309   }\r
 310 \r
 311 \r
 312   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 313   {\r
 314     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 315   }\r
 316 \r
 317 \r
 318   public void clustalColour_actionPerformed(ActionEvent e)\r
 319   {\r
 320    // alignPanel.seqPanel.setColourScheme( new ClustalxColourScheme() );\r
 321   }\r
 322 \r
 323   public void zappoColour_actionPerformed(ActionEvent e)\r
 324   {\r
 325     alignPanel.seqPanel.setColourScheme( new ZappoColourScheme() );\r
 326   }\r
 327 \r
 328   public void taylorColour_actionPerformed(ActionEvent e)\r
 329   {\r
 330     alignPanel.seqPanel.setColourScheme( new TaylorColourScheme() );\r
 331   }\r
 332 \r
 333 \r
 334   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 335   {\r
 336     alignPanel.seqPanel.setColourScheme( new HydrophobicColourScheme() );\r
 337   }\r
 338 \r
 339   public void helixColour_actionPerformed(ActionEvent e)\r
 340   {\r
 341     alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );\r
 342   }\r
 343 \r
 344   public void strandColour_actionPerformed(ActionEvent e)\r
 345   {\r
 346     alignPanel.seqPanel.setColourScheme( new StrandColourScheme() );\r
 347   }\r
 348 \r
 349   public void turnColour_actionPerformed(ActionEvent e)\r
 350   {\r
 351     alignPanel.seqPanel.setColourScheme( new TurnColourScheme() );\r
 352   }\r
 353 \r
 354   public void buriedColour_actionPerformed(ActionEvent e)\r
 355   {\r
 356     alignPanel.seqPanel.setColourScheme( new BuriedColourScheme() );\r
 357   }\r
 358 \r
 359   public void conservationColour_actionPerformed(ActionEvent e)\r
 360   {\r
 361 \r
 362   }\r
 363 \r
 364   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 365  {\r
 366 \r
 367  }\r
 368 \r
 369 \r
 370   public void abovePIDColour_actionPerformed(ActionEvent e)\r
 371   {\r
 372     alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );\r
 373   }\r
 374 \r
 375 \r
 376   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 377   {\r
 378     JInternalFrame frame = new JInternalFrame();\r
 379     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );\r
 380     frame.setContentPane(chooser);\r
 381     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 382     frame.setResizable(false);\r
 383     frame.setIconifiable(false);\r
 384     frame.setMaximizable(false);\r
 385   }\r
 386 \r
 387   public void PIDColour_actionPerformed(ActionEvent e)\r
 388   {\r
 389     alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );\r
 390   }\r
 391 \r
 392   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 393   {\r
 394     alignPanel.seqPanel.setColourScheme( new Blosum62ColourScheme(viewport) );\r
 395   }\r
 396 \r
 397 \r
 398   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 399   {\r
 400     ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
 401     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 402   }\r
 403 \r
 404 \r
 405   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 406   {\r
 407     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 408     alignPanel.RefreshPanels();\r
 409   }\r
 410 \r
 411   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 412   {\r
 413     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 414     alignPanel.RefreshPanels();\r
 415   }\r
 416 \r
 417   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 418   {\r
 419     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 420     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 421     alignPanel.RefreshPanels();\r
 422   }\r
 423 \r
 424   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 425   {\r
 426     if(viewport.getCurrentTree()==null)\r
 427       return;\r
 428 \r
 429     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 430     alignPanel.RefreshPanels();\r
 431   }\r
 432 \r
 433   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 434   {\r
 435 \r
 436   }\r
 437 \r
 438   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 439   {\r
 440     if(viewport.getSelection().size()<2)\r
 441       JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 442     else\r
 443     {\r
 444       JInternalFrame frame = new JInternalFrame();\r
 445       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 446       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 447     }\r
 448   }\r
 449 \r
 450   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 451   {\r
 452     PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 453     JInternalFrame frame = new JInternalFrame();\r
 454     frame.setContentPane(pcaPanel);\r
 455     Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);\r
 456   }\r
 457 \r
 458   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 459   {\r
 460     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 461   }\r
 462 \r
 463   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 464   {\r
 465     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 466   }\r
 467 \r
 468 \r
 469   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 470   {\r
 471     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 472   }\r
 473 \r
 474   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 475   {\r
 476     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 477   }\r
 478 \r
 479   void NewTreePanel(String type, String pwType, String title)\r
 480   {\r
 481     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 482     TreePanel tp=null;\r
 483    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 484    {\r
 485      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 486                          viewport.getStartRes(), viewport.getEndRes());\r
 487    }\r
 488    else\r
 489    {\r
 490      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 491                          type, pwType, viewport.getStartRes(),\r
 492                          viewport.getEndRes());\r
 493    }\r
 494 \r
 495    frame.setContentPane(tp);\r
 496    Desktop.addInternalFrame(frame, title, 600, 500);\r
 497   }\r
 498 \r
 499 \r
 500 \r
 501   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 502   {\r
 503     JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"\r
 504                                   +"\nwithin the Barton Group, Dundee University."\r
 505                                   +"\nThis will be available as a web service 2005",\r
 506                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 507   }\r
 508 \r
 509 }\r