src/jalview/gui/SeqPanel.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 import jalview.commands.EditCommand;\r
  23 import jalview.schemes.*;\r
  24 \r
  25 import java.awt.*;\r
  26 import java.awt.event.*;\r
  27 import javax.swing.*;\r
  28 import java.util.Vector;\r
  29 \r
  30 \r
  31 /**\r
  32  * DOCUMENT ME!\r
  33  *\r
  34  * @author $author$\r
  35  * @version $Revision$\r
  36  */\r
  37 public class SeqPanel extends JPanel implements MouseListener,\r
  38     MouseMotionListener, MouseWheelListener\r
  39 \r
  40 {\r
  41   /** DOCUMENT ME!! */\r
  42   public SeqCanvas seqCanvas;\r
  43 \r
  44   /** DOCUMENT ME!! */\r
  45   public AlignmentPanel ap;\r
  46   protected int lastres;\r
  47   protected int startseq;\r
  48   protected AlignViewport av;\r
  49 \r
  50   ScrollThread scrollThread = null;\r
  51   boolean mouseDragging = false;\r
  52   boolean editingSeqs = false;\r
  53   boolean groupEditing = false;\r
  54 \r
  55   //////////////////////////////////////////\r
  56   /////Everything below this is for defining the boundary of the rubberband\r
  57   //////////////////////////////////////////\r
  58   int oldSeq = -1;\r
  59   boolean changeEndSeq = false;\r
  60   boolean changeStartSeq = false;\r
  61   boolean changeEndRes = false;\r
  62   boolean changeStartRes = false;\r
  63   SequenceGroup stretchGroup = null;\r
  64   boolean remove = false;\r
  65 \r
  66   Point lastMousePress;\r
  67   boolean mouseWheelPressed = false;\r
  68   StringBuffer keyboardNo1;\r
  69   StringBuffer keyboardNo2;\r
  70 \r
  71   java.net.URL linkImageURL;\r
  72 \r
  73   StringBuffer tooltipText = new StringBuffer("<html>");\r
  74   String tmpString;\r
  75 \r
  76   EditCommand editCommand;\r
  77 \r
  78   /**\r
  79    * Creates a new SeqPanel object.\r
  80    *\r
  81    * @param avp DOCUMENT ME!\r
  82    * @param p DOCUMENT ME!\r
  83    */\r
  84   public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
  85   {\r
  86     linkImageURL = getClass().getResource("/images/link.gif");\r
  87     ToolTipManager.sharedInstance().registerComponent(this);\r
  88     ToolTipManager.sharedInstance().setInitialDelay(0);\r
  89     ToolTipManager.sharedInstance().setDismissDelay(10000);\r
  90     this.av = avp;\r
  91     setBackground(Color.white);\r
  92 \r
  93     seqCanvas = new SeqCanvas(avp);\r
  94     setLayout(new BorderLayout());\r
  95     add(seqCanvas, BorderLayout.CENTER);\r
  96 \r
  97     ap = p;\r
  98 \r
  99     if (!av.isDataset())\r
 100     {\r
 101       addMouseMotionListener(this);\r
 102       addMouseListener(this);\r
 103       addMouseWheelListener(this);\r
 104     }\r
 105   }\r
 106 \r
 107   int startWrapBlock = -1;\r
 108   int wrappedBlock = -1;\r
 109   int findRes(MouseEvent evt)\r
 110   {\r
 111     int res = 0;\r
 112     int x = evt.getX();\r
 113 \r
 114     if (av.wrapAlignment)\r
 115     {\r
 116 \r
 117       int hgap = av.charHeight;\r
 118       if (av.scaleAboveWrapped)\r
 119         hgap += av.charHeight;\r
 120 \r
 121       int cHeight = av.getAlignment().getHeight() * av.charHeight\r
 122           + hgap + seqCanvas.getAnnotationHeight();\r
 123 \r
 124       int y = evt.getY();\r
 125       y -= hgap;\r
 126       x -= seqCanvas.LABEL_WEST;\r
 127 \r
 128       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
 129       if (cwidth < 1)\r
 130         return 0;\r
 131 \r
 132       wrappedBlock = y / cHeight;\r
 133       wrappedBlock += av.getStartRes() / cwidth;\r
 134 \r
 135       res = wrappedBlock * cwidth + x / av.getCharWidth();\r
 136 \r
 137     }\r
 138     else\r
 139     {\r
 140       res = (x / av.getCharWidth()) + av.getStartRes();\r
 141     }\r
 142 \r
 143     if (av.hasHiddenColumns)\r
 144       res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 145 \r
 146     return res;\r
 147 \r
 148   }\r
 149 \r
 150   int findSeq(MouseEvent evt)\r
 151   {\r
 152     int seq = 0;\r
 153     int y = evt.getY();\r
 154 \r
 155     if (av.wrapAlignment)\r
 156     {\r
 157       int hgap = av.charHeight;\r
 158       if (av.scaleAboveWrapped)\r
 159         hgap += av.charHeight;\r
 160 \r
 161       int cHeight = av.getAlignment().getHeight() * av.charHeight\r
 162           + hgap + seqCanvas.getAnnotationHeight();\r
 163 \r
 164       y -= hgap;\r
 165 \r
 166       seq = Math.min( (y % cHeight) / av.getCharHeight(),\r
 167                      av.alignment.getHeight() - 1);\r
 168     }\r
 169     else\r
 170     {\r
 171       seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),\r
 172                      av.alignment.getHeight() - 1);\r
 173     }\r
 174 \r
 175     return seq;\r
 176   }\r
 177 \r
 178   SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)\r
 179   {\r
 180     Vector tmp = new Vector();\r
 181     SequenceFeature[] features = sequence.getSequenceFeatures();\r
 182     if (features != null)\r
 183     {\r
 184       for (int i = 0; i < features.length; i++)\r
 185       {\r
 186         if (av.featuresDisplayed == null\r
 187             || !av.featuresDisplayed.containsKey(features[i].getType()))\r
 188           continue;\r
 189 \r
 190         if ( (features[i].getBegin() <= res) &&\r
 191             (features[i].getEnd() >= res))\r
 192         {\r
 193           tmp.addElement(features[i]);\r
 194         }\r
 195       }\r
 196     }\r
 197 \r
 198     features = new SequenceFeature[tmp.size()];\r
 199     for(int i=0; i<tmp.size(); i++)\r
 200     {\r
 201       features[i] = (SequenceFeature)tmp.elementAt(i);\r
 202     }\r
 203 \r
 204     return features;\r
 205   }\r
 206 \r
 207    Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
 208    {\r
 209      Vector allFeatures = new Vector();\r
 210      int index = 0;\r
 211      if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)\r
 212      {\r
 213        while (index < seq.getSequenceFeatures().length)\r
 214        {\r
 215          SequenceFeature sf = seq.getSequenceFeatures()[index];\r
 216          if (sf.getBegin() <= res &&\r
 217              sf.getEnd() >= res)\r
 218          {\r
 219            if (av.featuresDisplayed.containsKey(sf.getType()))\r
 220            {\r
 221              allFeatures.addElement(sf);\r
 222            }\r
 223          }\r
 224          index++;\r
 225        }\r
 226      }\r
 227      return allFeatures;\r
 228   }\r
 229 \r
 230    void endEditing()\r
 231    {\r
 232      if (editCommand!=null && editCommand.getSize() > 0)\r
 233      {\r
 234        ap.alignFrame.addHistoryItem(editCommand);\r
 235        av.firePropertyChange("alignment", null,\r
 236                              av.getAlignment().getSequences());\r
 237      }\r
 238 \r
 239      startseq = -1;\r
 240      lastres = -1;\r
 241      editingSeqs = false;\r
 242      groupEditing = false;\r
 243      keyboardNo1 = null;\r
 244      keyboardNo2 = null;\r
 245      editCommand = null;\r
 246     }\r
 247 \r
 248     void setCursorRow()\r
 249     {\r
 250       seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;\r
 251       scrollToVisible();\r
 252     }\r
 253 \r
 254     void setCursorColumn()\r
 255     {\r
 256       seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;\r
 257       scrollToVisible();\r
 258     }\r
 259 \r
 260     void setCursorRowAndColumn()\r
 261     {\r
 262       if(keyboardNo2==null)\r
 263       {\r
 264         keyboardNo2 = new StringBuffer();\r
 265       }\r
 266       else\r
 267       {\r
 268         seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;\r
 269         seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;\r
 270         scrollToVisible();\r
 271       }\r
 272     }\r
 273 \r
 274     void setCursorPosition()\r
 275     {\r
 276       SequenceI sequence =\r
 277           (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
 278 \r
 279       seqCanvas.cursorX = sequence.findIndex(\r
 280           getKeyboardNo(keyboardNo1)-1\r
 281           );\r
 282       scrollToVisible();\r
 283     }\r
 284 \r
 285     void moveCursor(int dx, int dy)\r
 286     {\r
 287       seqCanvas.cursorX += dx;\r
 288       seqCanvas.cursorY += dy;\r
 289       if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))\r
 290       {\r
 291         int original = seqCanvas.cursorX - dx;\r
 292         int maxWidth = av.alignment.getWidth();\r
 293 \r
 294         while(!av.colSel.isVisible(seqCanvas.cursorX)\r
 295               && seqCanvas.cursorX<maxWidth\r
 296               && seqCanvas.cursorX>0)\r
 297         {\r
 298           seqCanvas.cursorX += dx;\r
 299         }\r
 300 \r
 301         if(seqCanvas.cursorX>=maxWidth\r
 302            || !av.colSel.isVisible(seqCanvas.cursorX) )\r
 303         {\r
 304           seqCanvas.cursorX = original;\r
 305         }\r
 306       }\r
 307 \r
 308       scrollToVisible();\r
 309     }\r
 310 \r
 311     void scrollToVisible()\r
 312     {\r
 313       if (seqCanvas.cursorX < 0)\r
 314         seqCanvas.cursorX = 0;\r
 315       else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)\r
 316         seqCanvas.cursorX = av.alignment.getWidth() - 1;\r
 317 \r
 318       if (seqCanvas.cursorY < 0)\r
 319         seqCanvas.cursorY = 0;\r
 320       else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)\r
 321         seqCanvas.cursorY = av.alignment.getHeight() - 1;\r
 322 \r
 323 \r
 324       endEditing();\r
 325       if(av.wrapAlignment)\r
 326       {\r
 327         ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
 328       }\r
 329       else\r
 330       {\r
 331         while (seqCanvas.cursorY < av.startSeq)\r
 332         {\r
 333           ap.scrollUp(true);\r
 334         }\r
 335         while (seqCanvas.cursorY + 1 > av.endSeq)\r
 336         {\r
 337           ap.scrollUp(false);\r
 338         }\r
 339         if (!av.wrapAlignment)\r
 340         {\r
 341           while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))\r
 342           {\r
 343             if (!ap.scrollRight(false))\r
 344               break;\r
 345           }\r
 346           while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))\r
 347           {\r
 348             if (!ap.scrollRight(true))\r
 349               break;\r
 350           }\r
 351         }\r
 352       }\r
 353       setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
 354                        seqCanvas.cursorX, seqCanvas.cursorY);\r
 355 \r
 356       seqCanvas.repaint();\r
 357     }\r
 358 \r
 359     void setSelectionAreaAtCursor(boolean topLeft)\r
 360     {\r
 361       SequenceI sequence =\r
 362           (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
 363 \r
 364       if(av.getSelectionGroup()!=null)\r
 365       {\r
 366         SequenceGroup sg = av.selectionGroup;\r
 367         //Find the top and bottom of this group\r
 368         int min = av.alignment.getHeight(), max = 0;\r
 369         for(int i=0; i<sg.getSize(false); i++)\r
 370         {\r
 371           int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
 372           if(index > max)\r
 373             max = index;\r
 374           if(index < min)\r
 375             min = index;\r
 376         }\r
 377 \r
 378         max ++;\r
 379 \r
 380         if(topLeft)\r
 381         {\r
 382           sg.setStartRes(seqCanvas.cursorX);\r
 383           if(sg.getEndRes()<seqCanvas.cursorX)\r
 384             sg.setEndRes(seqCanvas.cursorX);\r
 385 \r
 386           min = seqCanvas.cursorY;\r
 387         }\r
 388         else\r
 389         {\r
 390           sg.setEndRes(seqCanvas.cursorX);\r
 391           if(sg.getStartRes()>seqCanvas.cursorX)\r
 392             sg.setStartRes(seqCanvas.cursorX);\r
 393 \r
 394           max = seqCanvas.cursorY+1;\r
 395         }\r
 396 \r
 397         if(min>max)\r
 398         {\r
 399           // Only the user can do this\r
 400           av.setSelectionGroup(null);\r
 401         }\r
 402         else\r
 403         {\r
 404           // Now add any sequences between min and max\r
 405           sg.getSequences(false).clear();\r
 406           for (int i = min; i < max; i++)\r
 407           {\r
 408             sg.addSequence(av.alignment.getSequenceAt(i), false);\r
 409           }\r
 410         }\r
 411       }\r
 412 \r
 413       if (av.getSelectionGroup() == null)\r
 414       {\r
 415         SequenceGroup sg = new SequenceGroup();\r
 416         sg.setStartRes(seqCanvas.cursorX);\r
 417         sg.setEndRes(seqCanvas.cursorX);\r
 418         sg.addSequence(sequence, false);\r
 419         av.setSelectionGroup(sg);\r
 420       }\r
 421 \r
 422 \r
 423       ap.repaint();\r
 424     }\r
 425 \r
 426     void insertGapAtCursor(boolean group)\r
 427     {\r
 428       groupEditing = group;\r
 429       startseq = seqCanvas.cursorY;\r
 430       lastres = seqCanvas.cursorX;\r
 431       editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
 432       endEditing();\r
 433     }\r
 434 \r
 435     void deleteGapAtCursor(boolean group)\r
 436     {\r
 437       groupEditing = group;\r
 438       startseq = seqCanvas.cursorY;\r
 439       lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
 440       editSequence(false, seqCanvas.cursorX);\r
 441       endEditing();\r
 442     }\r
 443 \r
 444     void numberPressed(char value)\r
 445     {\r
 446       if(keyboardNo1==null)\r
 447         keyboardNo1 = new StringBuffer();\r
 448 \r
 449       if(keyboardNo2!=null)\r
 450         keyboardNo2.append(value);\r
 451       else\r
 452         keyboardNo1.append(value);\r
 453     }\r
 454 \r
 455     int getKeyboardNo(StringBuffer kb)\r
 456     {\r
 457       if(kb==null)\r
 458         return 1;\r
 459       else\r
 460         return Integer.parseInt(kb.toString());\r
 461     }\r
 462 \r
 463 \r
 464     /**\r
 465      * DOCUMENT ME!\r
 466      *\r
 467      * @param evt DOCUMENT ME!\r
 468      */\r
 469     public void mouseReleased(MouseEvent evt)\r
 470     {\r
 471       mouseDragging = false;\r
 472       mouseWheelPressed = false;\r
 473 \r
 474       if (!editingSeqs)\r
 475       {\r
 476          doMouseReleasedDefineMode(evt);\r
 477          return;\r
 478       }\r
 479 \r
 480        endEditing();\r
 481 \r
 482        ap.repaint();\r
 483     }\r
 484 \r
 485 \r
 486 \r
 487     /**\r
 488      * DOCUMENT ME!\r
 489      *\r
 490      * @param evt DOCUMENT ME!\r
 491      */\r
 492     public void mousePressed(MouseEvent evt)\r
 493     {\r
 494       lastMousePress = evt.getPoint();\r
 495 \r
 496       if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
 497       {\r
 498         mouseWheelPressed = true;\r
 499         return;\r
 500       }\r
 501 \r
 502       if (evt.isShiftDown() || evt.isAltDown() ||\r
 503           evt.isControlDown())\r
 504       {\r
 505         if (evt.isAltDown() || evt.isControlDown())\r
 506         {\r
 507           groupEditing = true;\r
 508         }\r
 509         editingSeqs = true;\r
 510       }\r
 511       else\r
 512       {\r
 513         doMousePressedDefineMode(evt);\r
 514         return;\r
 515       }\r
 516 \r
 517       int seq = findSeq(evt);\r
 518       int res = findRes(evt);\r
 519 \r
 520       if(seq<0 || res<0)\r
 521         return;\r
 522 \r
 523         if ((seq < av.getAlignment().getHeight()) &&\r
 524                 (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
 525         {\r
 526             startseq = seq;\r
 527             lastres = res;\r
 528         }\r
 529         else\r
 530         {\r
 531             startseq = -1;\r
 532             lastres = -1;\r
 533         }\r
 534 \r
 535         return;\r
 536     }\r
 537 \r
 538     /**\r
 539      * DOCUMENT ME!\r
 540      *\r
 541      * @param evt DOCUMENT ME!\r
 542      */\r
 543     public void mouseMoved(MouseEvent evt)\r
 544     {\r
 545       if (editingSeqs)\r
 546       {\r
 547        // This is because MacOSX creates a mouseMoved\r
 548        // If control is down, other platforms will not.\r
 549        mouseDragged(evt);\r
 550       }\r
 551 \r
 552       int res = findRes(evt);\r
 553       int seq = findSeq(evt);\r
 554 \r
 555 \r
 556       if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
 557             return;\r
 558 \r
 559       SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
 560 \r
 561       if (res > sequence.getLength())\r
 562       {\r
 563         return;\r
 564       }\r
 565 \r
 566       if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
 567       {\r
 568         seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
 569       }\r
 570 \r
 571       setStatusMessage(sequence, res, seq);\r
 572 \r
 573         // use aa to see if the mouse pointer is on a\r
 574         if (av.showSequenceFeatures)\r
 575         {\r
 576             tooltipText.setLength(6); // Cuts the buffer back to <html>\r
 577 \r
 578             SequenceFeature[] features = findFeaturesAtRes(\r
 579                 sequence.getDatasetSequence(), sequence.findPosition(res));\r
 580 \r
 581             if(features!=null)\r
 582             {\r
 583               for (int i = 0; i < features.length; i++)\r
 584               {\r
 585                   if (features[i].getType().equals("disulfide bond"))\r
 586                   {\r
 587                     if (features[i].getBegin() == sequence.findPosition(res)\r
 588                         || features[i].getEnd() == sequence.findPosition(res))\r
 589                     {\r
 590                       if (tooltipText.length() > 6)\r
 591                         tooltipText.append("<br>");\r
 592                       tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +\r
 593                                      features[i].getEnd());\r
 594                       if (features[i].links != null)\r
 595                       tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
 596                     }\r
 597                   }\r
 598                   else\r
 599                   {\r
 600                     if (tooltipText.length() > 6)\r
 601                       tooltipText.append("<br>");\r
 602 \r
 603                     tooltipText.append(features[i].getType() + " " +\r
 604                                    features[i].begin);\r
 605                     if (features[i].begin != features[i].end)\r
 606                       tooltipText.append(" " + features[i].end);\r
 607 \r
 608                     if (features[i].getDescription() != null\r
 609                         && !features[i].description.equals(features[i].getType()))\r
 610                     {\r
 611                       tmpString = features[i].getDescription();\r
 612                       int startTag=tmpString.toUpperCase().indexOf("<HTML>");\r
 613                       if(startTag>-1)\r
 614                       {\r
 615                         tmpString = tmpString.substring(startTag + 6);\r
 616                       }\r
 617                       int endTag=tmpString.toUpperCase().indexOf("</BODY>");\r
 618                       if(endTag>-1)\r
 619                       {\r
 620                         tmpString = tmpString.substring(0, endTag);\r
 621                       }\r
 622                       endTag = tmpString.toUpperCase().indexOf("</HTML>");\r
 623                       if(endTag>-1)\r
 624                       {\r
 625                         tmpString = tmpString.substring(0, endTag);\r
 626                       }\r
 627 \r
 628                       if(startTag>-1)\r
 629                       {\r
 630                         tooltipText.append("; " + tmpString);\r
 631                       }\r
 632                       else\r
 633                       {\r
 634                        if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)\r
 635                        {\r
 636                          //The description does not specify html is to\r
 637                          //be used, so we must remove < > symbols\r
 638                          tmpString = tmpString.replaceAll("<", "&lt;");\r
 639                          tmpString = tmpString.replaceAll(">", "&gt;");\r
 640 \r
 641                          tooltipText.append("; ");\r
 642                          tooltipText.append(tmpString);\r
 643 \r
 644                        }\r
 645                        else\r
 646                          tooltipText.append("; "+tmpString);\r
 647                       }\r
 648                     }\r
 649                     if (features[i].getValue("status") != null )\r
 650                     {\r
 651                       String status = features[i].getValue("status").toString();\r
 652                       if(status.length()>0)\r
 653                         tooltipText.append("; (" + features[i].getValue("status") + ")");\r
 654                     }\r
 655 \r
 656                     if (features[i].links != null)\r
 657                       tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
 658 \r
 659                   }\r
 660 \r
 661                // else if(features[i].begin==0 && features[i].end==0)\r
 662                 {\r
 663                   // seqSpecific.append(features[i].featureGroup+": "\r
 664                   //                   + features[i].getType()+" "\r
 665                    //                   +features[i].getDescription()+"<br>");\r
 666 \r
 667                 }\r
 668               }\r
 669 \r
 670               if(tooltipText.length()==6) // <html></html>\r
 671               {\r
 672 \r
 673                 setToolTipText("");\r
 674               }\r
 675               else\r
 676               {\r
 677                 tooltipText.append("</html>");\r
 678                 setToolTipText(tooltipText.toString());\r
 679               }\r
 680             }\r
 681             else\r
 682               setToolTipText("");\r
 683         }\r
 684     }\r
 685 \r
 686     void setStatusMessage(SequenceI sequence, int res, int seq)\r
 687     {\r
 688       StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
 689                                            sequence.getName());\r
 690 \r
 691       Object obj = null;\r
 692       if (av.alignment.isNucleotide())\r
 693       {\r
 694         obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
 695                                                    "");\r
 696         if (obj != null)\r
 697           text.append(" Nucleotide: ");\r
 698       }\r
 699       else\r
 700       {\r
 701         obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
 702         if (obj != null)\r
 703           text.append("  Residue: ");\r
 704       }\r
 705 \r
 706       if (obj != null)\r
 707       {\r
 708 \r
 709         if (obj != "")\r
 710         {\r
 711           text.append(obj + " (" + sequence.findPosition(res) +\r
 712                       ")");\r
 713         }\r
 714       }\r
 715       ap.alignFrame.statusBar.setText(text.toString());\r
 716 \r
 717     }\r
 718 \r
 719     /**\r
 720      * DOCUMENT ME!\r
 721      *\r
 722      * @param evt DOCUMENT ME!\r
 723      */\r
 724     public void mouseDragged(MouseEvent evt)\r
 725     {\r
 726       if (mouseWheelPressed)\r
 727       {\r
 728         int oldWidth = av.charWidth;\r
 729 \r
 730         //Which is bigger, left-right or up-down?\r
 731         if (Math.abs(evt.getY() - lastMousePress.getY())\r
 732             > Math.abs(evt.getX() - lastMousePress.getX()))\r
 733         {\r
 734           int fontSize = av.font.getSize();\r
 735 \r
 736           if (evt.getY() < lastMousePress.getY())\r
 737           {\r
 738             fontSize--;\r
 739           }\r
 740           else if (evt.getY() > lastMousePress.getY())\r
 741           {\r
 742             fontSize++;\r
 743           }\r
 744 \r
 745           if(fontSize<1)\r
 746             fontSize = 1;\r
 747 \r
 748           av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
 749           av.charWidth = oldWidth;\r
 750           ap.fontChanged();\r
 751         }\r
 752         else\r
 753         {\r
 754           if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)\r
 755           {\r
 756             av.charWidth--;\r
 757           }\r
 758           else if (evt.getX() > lastMousePress.getX())\r
 759           {\r
 760             av.charWidth++;\r
 761           }\r
 762 \r
 763           ap.repaint();\r
 764         }\r
 765 \r
 766         FontMetrics fm = getFontMetrics(av.getFont());\r
 767         av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
 768 \r
 769         lastMousePress = evt.getPoint();\r
 770 \r
 771         return;\r
 772       }\r
 773 \r
 774       if (!editingSeqs)\r
 775       {\r
 776         doMouseDraggedDefineMode(evt);\r
 777         return;\r
 778       }\r
 779 \r
 780         int res = findRes(evt);\r
 781 \r
 782         if (res < 0)\r
 783         {\r
 784             res = 0;\r
 785         }\r
 786 \r
 787         if ((lastres == -1) || (lastres == res))\r
 788         {\r
 789             return;\r
 790         }\r
 791 \r
 792         if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
 793         {\r
 794           // dragLeft, delete gap\r
 795           editSequence(false, res);\r
 796         }\r
 797         else\r
 798           editSequence(true, res);\r
 799 \r
 800         mouseDragging = true;\r
 801         if(scrollThread!=null)\r
 802           scrollThread.setEvent(evt);\r
 803 \r
 804     }\r
 805 \r
 806     synchronized void editSequence(boolean insertGap, int startres)\r
 807     {\r
 808       int fixedLeft = -1;\r
 809       int fixedRight = -1;\r
 810       boolean fixedColumns = false;\r
 811       SequenceGroup sg = av.getSelectionGroup();\r
 812 \r
 813 \r
 814         if (!groupEditing && av.hasHiddenRows)\r
 815         {\r
 816           if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
 817           {\r
 818             groupEditing = true;\r
 819           }\r
 820         }\r
 821 \r
 822         //No group, but the sequence may represent a group\r
 823         if (groupEditing\r
 824             && sg == null\r
 825             && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
 826         {\r
 827           groupEditing = false;\r
 828         }\r
 829 \r
 830         SequenceI seq = av.alignment.getSequenceAt(startseq);\r
 831         StringBuffer message = new StringBuffer();\r
 832         if (groupEditing)\r
 833         {\r
 834           message.append("Edit group:");\r
 835           if (editCommand == null)\r
 836             editCommand = new EditCommand("Edit Group");\r
 837         }\r
 838         else\r
 839          {\r
 840            message.append("Edit sequence: " + seq.getName());\r
 841            String label = seq.getName();\r
 842            if(label.length()>10)\r
 843              label = label.substring(0,10);\r
 844            if(editCommand==null)\r
 845              editCommand = new EditCommand("Edit "+label);\r
 846          }\r
 847 \r
 848        if(insertGap)\r
 849          message.append(" insert ");\r
 850        else\r
 851          message.append(" delete ");\r
 852 \r
 853        message.append(Math.abs(startres-lastres)+" gaps.");\r
 854        ap.alignFrame.statusBar.setText(message.toString());\r
 855 \r
 856 \r
 857         //Are we editing within a selection group?\r
 858         if (groupEditing\r
 859             || (sg != null && sg.getSequences(true).contains(seq)))\r
 860         {\r
 861           fixedColumns = true;\r
 862 \r
 863           //sg might be null as the user may only see 1 sequence,\r
 864           //but the sequence represents a group\r
 865           if (sg == null)\r
 866           {\r
 867             sg = new SequenceGroup(null, null, false, false, false, 0,\r
 868                                    av.alignment.getWidth()-1);\r
 869             sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
 870           }\r
 871 \r
 872           fixedLeft = sg.getStartRes();\r
 873           fixedRight = sg.getEndRes();\r
 874 \r
 875           if (   (startres < fixedLeft && lastres >= fixedLeft)\r
 876               || (startres >= fixedLeft && lastres < fixedLeft)\r
 877               || (startres > fixedRight && lastres <=fixedRight)\r
 878               || (startres <= fixedRight && lastres > fixedRight))\r
 879           {\r
 880             endEditing();\r
 881             return;\r
 882           }\r
 883 \r
 884           if (fixedLeft > startres)\r
 885           {\r
 886             fixedRight = fixedLeft - 1;\r
 887             fixedLeft = 0;\r
 888           }\r
 889           else if (fixedRight < startres)\r
 890           {\r
 891             fixedLeft = fixedRight;\r
 892             fixedRight = -1;\r
 893           }\r
 894         }\r
 895 \r
 896 \r
 897         if(av.hasHiddenColumns )\r
 898         {\r
 899             fixedColumns = true;\r
 900             int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
 901             int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
 902 \r
 903             if ( (insertGap && startres > y1 && lastres < y1)\r
 904                 || (!insertGap && startres < y2 && lastres > y2))\r
 905             {\r
 906               endEditing();\r
 907               return;\r
 908             }\r
 909 \r
 910             //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
 911             //Selection spans a hidden region\r
 912             if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
 913             {\r
 914               if(startres>=y2)\r
 915               {\r
 916                 fixedLeft = y2;\r
 917               }\r
 918               else\r
 919               {\r
 920                fixedRight = y2 - 1;\r
 921              }\r
 922             }\r
 923         }\r
 924 \r
 925 \r
 926         if (groupEditing)\r
 927         {\r
 928           Vector vseqs = sg.getSequences(true);\r
 929           int g, groupSize = vseqs.size();\r
 930           SequenceI[] groupSeqs = new SequenceI[groupSize];\r
 931           for (g = 0; g < groupSeqs.length; g++)\r
 932             groupSeqs[g] = (SequenceI) vseqs.elementAt(g);\r
 933 \r
 934           // drag to right\r
 935           if (insertGap)\r
 936           {\r
 937               //If the user has selected the whole sequence, and is dragging to\r
 938               // the right, we can still extend the alignment and selectionGroup\r
 939               if(   sg.getStartRes() == 0\r
 940                     && sg.getEndRes() == fixedRight\r
 941                     && sg.getEndRes() == av.alignment.getWidth()-1\r
 942                  )\r
 943               {\r
 944                 sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
 945                 fixedRight = sg.getEndRes();\r
 946               }\r
 947 \r
 948             // Is it valid with fixed columns??\r
 949             // Find the next gap before the end\r
 950             // of the visible region boundary\r
 951             boolean blank = false;\r
 952             for (fixedRight = fixedRight;\r
 953                  fixedRight > lastres;\r
 954                  fixedRight--)\r
 955             {\r
 956               blank = true;\r
 957 \r
 958               for (g = 0; g < groupSize; g++)\r
 959               {\r
 960                 for (int j = 0; j < startres - lastres; j++)\r
 961                 {\r
 962                   if (!jalview.util.Comparison.isGap(\r
 963                       groupSeqs[g].getCharAt(fixedRight - j)))\r
 964                   {\r
 965                     blank = false;\r
 966                     break;\r
 967                   }\r
 968                 }\r
 969               }\r
 970               if (blank)\r
 971                 break;\r
 972             }\r
 973 \r
 974             if (!blank)\r
 975             {\r
 976               if(sg.getSize(false) == av.alignment.getHeight()  )\r
 977               {\r
 978                 if((av.hasHiddenColumns\r
 979                     && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
 980                 {\r
 981                   endEditing();\r
 982                   return;\r
 983                 }\r
 984 \r
 985                 int alWidth = av.alignment.getWidth();\r
 986                 if(av.hasHiddenRows)\r
 987                 {\r
 988                   int hwidth = av.alignment.getHiddenSequences().getWidth();\r
 989                   if(hwidth>alWidth)\r
 990                     alWidth = hwidth;\r
 991                 }\r
 992                 //We can still insert gaps if the selectionGroup\r
 993                 //contains all the sequences\r
 994                 sg.setEndRes(sg.getEndRes()+startres-lastres);\r
 995                 fixedRight = alWidth+startres-lastres;\r
 996               }\r
 997               else\r
 998               {\r
 999                 endEditing();\r
1000                 return;\r
1001               }\r
1002             }\r
1003           }\r
1004 \r
1005 \r
1006           // drag to left\r
1007           else if(!insertGap)\r
1008           {\r
1009             /// Are we able to delete?\r
1010             // ie are all columns blank?\r
1011 \r
1012             for (g = 0; g < groupSize; g++)\r
1013             {\r
1014               for (int j = startres; j < lastres; j++)\r
1015               {\r
1016                 if (groupSeqs[g].getLength() <= j)\r
1017                 {\r
1018                   continue;\r
1019                 }\r
1020 \r
1021                 if (!jalview.util.Comparison.isGap(\r
1022                     groupSeqs[g].getCharAt(j)))\r
1023                 {\r
1024                   // Not a gap, block edit not valid\r
1025                   endEditing();\r
1026                   return;\r
1027                 }\r
1028               }\r
1029             }\r
1030           }\r
1031 \r
1032             if (insertGap)\r
1033             {\r
1034               // dragging to the right\r
1035               if (fixedColumns && fixedRight != -1)\r
1036               {\r
1037                 for (int j = lastres; j < startres; j++)\r
1038                 {\r
1039                     insertChar(j, groupSeqs, fixedRight);\r
1040                 }\r
1041               }\r
1042               else\r
1043               {\r
1044                 editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1045                                        groupSeqs,\r
1046                                        startres, startres-lastres,\r
1047                                        av.getGapCharacter(),\r
1048                                        true);\r
1049               }\r
1050             }\r
1051             else\r
1052             {\r
1053               // dragging to the left\r
1054               if (fixedColumns && fixedRight != -1)\r
1055               {\r
1056                 for (int j = lastres; j > startres; j--)\r
1057                 {\r
1058                   deleteChar(startres, groupSeqs, fixedRight);\r
1059                 }\r
1060               }\r
1061               else\r
1062                 editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1063                                        groupSeqs,\r
1064                                        startres, lastres - startres,\r
1065                                        av.getGapCharacter(),\r
1066                                        true);\r
1067 \r
1068             }\r
1069         }\r
1070         else /////Editing a single sequence///////////\r
1071         {\r
1072           if (insertGap)\r
1073           {\r
1074             // dragging to the right\r
1075             if (fixedColumns && fixedRight != -1)\r
1076             {\r
1077               for (int j = lastres; j < startres; j++)\r
1078               {\r
1079                 insertChar(j, new SequenceI[]{seq}, fixedRight);\r
1080               }\r
1081             }\r
1082             else\r
1083             {\r
1084               editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1085                                      new SequenceI[]\r
1086                                      {seq},\r
1087                                      lastres, startres-lastres,\r
1088                                      av.getGapCharacter(),\r
1089                                      true);\r
1090             }\r
1091           }\r
1092           else\r
1093           {\r
1094             // dragging to the left\r
1095             if (fixedColumns && fixedRight != -1)\r
1096             {\r
1097               for (int j = lastres; j > startres; j--)\r
1098               {\r
1099                 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
1100                 {\r
1101                   endEditing();\r
1102                   break;\r
1103                 }\r
1104                 deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
1105               }\r
1106             }\r
1107             else\r
1108             {\r
1109               //could be a keyboard edit trying to delete none gaps\r
1110               int max=0;\r
1111               for(int m = startres; m<lastres; m++)\r
1112               {\r
1113                 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
1114                   break;\r
1115                 max++;\r
1116               }\r
1117 \r
1118               if (max>0)\r
1119               {\r
1120                 editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1121                                        new SequenceI[]\r
1122                                        {seq},\r
1123                                        startres, max,\r
1124                                        av.getGapCharacter(),\r
1125                                        true);\r
1126               }\r
1127             }\r
1128           }\r
1129         }\r
1130 \r
1131         lastres = startres;\r
1132         seqCanvas.repaint();\r
1133     }\r
1134 \r
1135 \r
1136 \r
1137     void insertChar(int j, SequenceI [] seq, int fixedColumn)\r
1138     {\r
1139       int blankColumn = fixedColumn;\r
1140       for(int s=0; s<seq.length; s++)\r
1141       {\r
1142         //Find the next gap before the end of the visible region boundary\r
1143         //If lastCol > j, theres a boundary after the gap insertion\r
1144 \r
1145         for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
1146         {\r
1147           if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
1148           {\r
1149             //Theres a space, so break and insert the gap\r
1150             break;\r
1151           }\r
1152         }\r
1153 \r
1154         if (blankColumn <= j)\r
1155         {\r
1156           blankColumn = fixedColumn;\r
1157           endEditing();\r
1158           return;\r
1159         }\r
1160       }\r
1161 \r
1162       editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1163                              seq,\r
1164                              blankColumn, 1, av.getGapCharacter(), true);\r
1165 \r
1166       editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1167                              seq,\r
1168                              j, 1, av.getGapCharacter(),\r
1169                              true);\r
1170 \r
1171     }\r
1172 \r
1173     void deleteChar(int j, SequenceI [] seq, int fixedColumn)\r
1174     {\r
1175 \r
1176       editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1177                              seq,\r
1178                              j, 1, av.getGapCharacter(), true);\r
1179 \r
1180       editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1181                              seq,\r
1182                              fixedColumn, 1, av.getGapCharacter(), true);\r
1183     }\r
1184 \r
1185     /**\r
1186      * DOCUMENT ME!\r
1187      *\r
1188      * @param e DOCUMENT ME!\r
1189      */\r
1190     public void mouseEntered(MouseEvent e)\r
1191     {\r
1192         if(oldSeq < 0)\r
1193           oldSeq = 0;\r
1194 \r
1195         if (scrollThread != null)\r
1196         {\r
1197             scrollThread.running = false;\r
1198             scrollThread = null;\r
1199         }\r
1200     }\r
1201 \r
1202     /**\r
1203      * DOCUMENT ME!\r
1204      *\r
1205      * @param e DOCUMENT ME!\r
1206      */\r
1207     public void mouseExited(MouseEvent e)\r
1208     {\r
1209         if (av.getWrapAlignment())\r
1210         {\r
1211             return;\r
1212         }\r
1213 \r
1214         if (mouseDragging)\r
1215         {\r
1216             scrollThread = new ScrollThread();\r
1217         }\r
1218     }\r
1219 \r
1220     public void mouseClicked(MouseEvent evt)\r
1221     {\r
1222       SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
1223       if(evt.getClickCount()>1)\r
1224       {\r
1225         if (av.getSelectionGroup().getSize(false) == 1\r
1226             && av.getSelectionGroup().getEndRes()\r
1227             - av.getSelectionGroup().getStartRes() < 2)\r
1228           av.setSelectionGroup(null);\r
1229 \r
1230         SequenceFeature[] features = findFeaturesAtRes(\r
1231             sequence.getDatasetSequence(),\r
1232             sequence.findPosition( findRes(evt) )\r
1233             );\r
1234 \r
1235         if(features!=null && features.length==1)\r
1236         {\r
1237           SearchResults highlight = new SearchResults();\r
1238           highlight.addResult(sequence,\r
1239                               features[0].getBegin(),\r
1240                               features[0].getEnd());\r
1241           seqCanvas.highlightSearchResults(highlight);\r
1242         }\r
1243         if(features!=null && features.length>0)\r
1244         {\r
1245           seqCanvas.getFeatureRenderer().amendFeatures(\r
1246               new SequenceI[]\r
1247               {sequence}, features, false);\r
1248 \r
1249           seqCanvas.highlightSearchResults(null);\r
1250         }\r
1251       }\r
1252     }\r
1253 \r
1254     public void mouseWheelMoved(MouseWheelEvent e)\r
1255     {\r
1256       e.consume();\r
1257      /* if (mouseWheelPressed)\r
1258       {\r
1259         Font font = av.getFont();\r
1260         int fontSize = font.getSize();\r
1261         if (e.getWheelRotation() > 0 && fontSize < 51)\r
1262           fontSize++;\r
1263         else if (fontSize > 1)\r
1264           fontSize--;\r
1265 \r
1266 \r
1267 \r
1268         av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\r
1269 \r
1270         ap.fontChanged();\r
1271       }\r
1272       else*/\r
1273       {\r
1274         if (e.getWheelRotation() > 0)\r
1275           ap.scrollUp(false);\r
1276         else\r
1277           ap.scrollUp(true);\r
1278       }\r
1279 \r
1280     }\r
1281 \r
1282 \r
1283     /**\r
1284      * DOCUMENT ME!\r
1285      *\r
1286      * @param evt DOCUMENT ME!\r
1287      */\r
1288     public void doMousePressedDefineMode(MouseEvent evt)\r
1289     {\r
1290       int res = findRes(evt);\r
1291       int seq = findSeq(evt);\r
1292       oldSeq = seq;\r
1293 \r
1294       startWrapBlock=wrappedBlock;\r
1295 \r
1296       if(av.wrapAlignment && seq>av.alignment.getHeight())\r
1297       {\r
1298           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1299               "Cannot edit annotations in wrapped view.",\r
1300               "Wrapped view - no edit",\r
1301               JOptionPane.WARNING_MESSAGE);\r
1302           return;\r
1303       }\r
1304 \r
1305       if(seq<0 || res<0)\r
1306             return;\r
1307 \r
1308         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
1309 \r
1310         if ((sequence == null) || (res > sequence.getLength()))\r
1311         {\r
1312             return;\r
1313         }\r
1314 \r
1315         stretchGroup = av.getSelectionGroup();\r
1316 \r
1317         if (stretchGroup == null)\r
1318         {\r
1319             stretchGroup = av.alignment.findGroup(sequence);\r
1320 \r
1321             if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
1322                     (res < stretchGroup.getEndRes()))\r
1323             {\r
1324                 av.setSelectionGroup(stretchGroup);\r
1325             }\r
1326             else\r
1327             {\r
1328                 stretchGroup = null;\r
1329             }\r
1330         }\r
1331         else if (!stretchGroup.getSequences(false).contains(sequence) ||\r
1332                 (stretchGroup.getStartRes() > res) ||\r
1333                 (stretchGroup.getEndRes() < res))\r
1334         {\r
1335             stretchGroup = null;\r
1336 \r
1337             SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
1338 \r
1339             if (allGroups != null)\r
1340             {\r
1341                 for (int i = 0; i < allGroups.length; i++)\r
1342                 {\r
1343                     if ((allGroups[i].getStartRes() <= res) &&\r
1344                             (allGroups[i].getEndRes() >= res))\r
1345                     {\r
1346                         stretchGroup = allGroups[i];\r
1347                         break;\r
1348                     }\r
1349                 }\r
1350             }\r
1351 \r
1352             av.setSelectionGroup(stretchGroup);\r
1353 \r
1354         }\r
1355 \r
1356 \r
1357         if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
1358         {\r
1359           Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
1360                                                   sequence.findPosition(res));\r
1361           Vector links = new Vector();\r
1362             for (int i = 0; i < allFeatures.size(); i++)\r
1363             {\r
1364               SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
1365               if (sf.links != null)\r
1366               {\r
1367                 for (int j = 0; j < sf.links.size(); j++)\r
1368                 {\r
1369                   links.addElement(sf.links.elementAt(j));\r
1370                 }\r
1371               }\r
1372             }\r
1373 \r
1374             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
1375             pop.show(this, evt.getX(), evt.getY());\r
1376             return;\r
1377         }\r
1378 \r
1379         if (av.cursorMode)\r
1380         {\r
1381           seqCanvas.cursorX = findRes(evt);\r
1382           seqCanvas.cursorY = findSeq(evt);\r
1383           seqCanvas.repaint();\r
1384           return;\r
1385         }\r
1386 \r
1387         if (stretchGroup == null)\r
1388         {\r
1389           //Only if left mouse button do we want to change group sizes\r
1390 \r
1391           // define a new group here\r
1392           SequenceGroup sg = new SequenceGroup();\r
1393           sg.setStartRes(res);\r
1394           sg.setEndRes(res);\r
1395           sg.addSequence(sequence, false);\r
1396           av.setSelectionGroup(sg);\r
1397           stretchGroup = sg;\r
1398 \r
1399           if (av.getConservationSelected())\r
1400           {\r
1401             SliderPanel.setConservationSlider(ap,\r
1402                                               av.getGlobalColourScheme(),\r
1403                                               "Background");\r
1404           }\r
1405 \r
1406           if (av.getAbovePIDThreshold())\r
1407           {\r
1408             SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
1409                                            "Background");\r
1410           }\r
1411           if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
1412           {\r
1413             // Edit end res position of selected group\r
1414             changeEndRes = true;\r
1415           }\r
1416           else if ( (stretchGroup != null) &&\r
1417                    (stretchGroup.getStartRes() == res))\r
1418           {\r
1419             // Edit end res position of selected group\r
1420             changeStartRes = true;\r
1421           }\r
1422           stretchGroup.getWidth();\r
1423         }\r
1424 \r
1425         seqCanvas.repaint();\r
1426     }\r
1427 \r
1428     /**\r
1429      * DOCUMENT ME!\r
1430      *\r
1431      * @param evt DOCUMENT ME!\r
1432      */\r
1433     public void doMouseReleasedDefineMode(MouseEvent evt)\r
1434     {\r
1435         if (stretchGroup == null)\r
1436         {\r
1437             return;\r
1438         }\r
1439 \r
1440 \r
1441         if(stretchGroup.cs!=null)\r
1442         {\r
1443           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
1444           {\r
1445             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
1446                 stretchGroup.getSequences(true),\r
1447                 stretchGroup.getWidth());\r
1448           }\r
1449 \r
1450           if (stretchGroup.cs instanceof Blosum62ColourScheme\r
1451               || stretchGroup.cs instanceof PIDColourScheme\r
1452               || stretchGroup.cs.conservationApplied()\r
1453               || stretchGroup.cs.getThreshold()>0)\r
1454             stretchGroup.recalcConservation();\r
1455 \r
1456           if (stretchGroup.cs.conservationApplied())\r
1457           {\r
1458             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
1459                                               stretchGroup.getName());\r
1460           }\r
1461           else\r
1462           {\r
1463             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
1464                                            stretchGroup.getName());\r
1465           }\r
1466         }\r
1467         changeEndRes = false;\r
1468         changeStartRes = false;\r
1469         stretchGroup = null;\r
1470 \r
1471         PaintRefresher.Refresh(this, av.getSequenceSetId());\r
1472     }\r
1473 \r
1474     /**\r
1475      * DOCUMENT ME!\r
1476      *\r
1477      * @param evt DOCUMENT ME!\r
1478      */\r
1479     public void doMouseDraggedDefineMode(MouseEvent evt)\r
1480     {\r
1481       int res = findRes(evt);\r
1482       int y = findSeq(evt);\r
1483 \r
1484       if(wrappedBlock!=startWrapBlock)\r
1485         return;\r
1486 \r
1487        if (stretchGroup == null)\r
1488        {\r
1489             return;\r
1490        }\r
1491 \r
1492         if(res>= av.alignment.getWidth())\r
1493         {\r
1494           res = av.alignment.getWidth()-1;\r
1495         }\r
1496 \r
1497         if (stretchGroup.getEndRes() == res)\r
1498         {\r
1499             // Edit end res position of selected group\r
1500             changeEndRes = true;\r
1501         }\r
1502         else if (stretchGroup.getStartRes() == res)\r
1503         {\r
1504             // Edit start res position of selected group\r
1505             changeStartRes = true;\r
1506         }\r
1507 \r
1508         if (res < av.getStartRes())\r
1509         {\r
1510             res = av.getStartRes();\r
1511         }\r
1512 \r
1513         if (changeEndRes)\r
1514         {\r
1515             if (res > (stretchGroup.getStartRes() - 1))\r
1516             {\r
1517                 stretchGroup.setEndRes(res);\r
1518             }\r
1519         }\r
1520         else if (changeStartRes)\r
1521         {\r
1522             if (res < (stretchGroup.getEndRes() + 1))\r
1523             {\r
1524                 stretchGroup.setStartRes(res);\r
1525             }\r
1526         }\r
1527 \r
1528         int dragDirection = 0;\r
1529 \r
1530         if (y > oldSeq)\r
1531         {\r
1532             dragDirection = 1;\r
1533         }\r
1534         else if (y < oldSeq)\r
1535         {\r
1536             dragDirection = -1;\r
1537         }\r
1538 \r
1539 \r
1540         while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
1541         {\r
1542             // This routine ensures we don't skip any sequences, as the\r
1543             // selection is quite slow.\r
1544             Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
1545 \r
1546             oldSeq += dragDirection;\r
1547 \r
1548             if(oldSeq<0)\r
1549               break;\r
1550 \r
1551             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
1552 \r
1553             if (stretchGroup.getSequences(false).contains(nextSeq))\r
1554             {\r
1555                 stretchGroup.deleteSequence(seq, false);\r
1556             }\r
1557             else\r
1558             {\r
1559                 if (seq != null)\r
1560                 {\r
1561                     stretchGroup.addSequence(seq, false);\r
1562                 }\r
1563 \r
1564                 stretchGroup.addSequence(nextSeq, false);\r
1565             }\r
1566         }\r
1567 \r
1568         if(oldSeq < 0)\r
1569           oldSeq = -1;\r
1570 \r
1571         mouseDragging = true;\r
1572 \r
1573         if (scrollThread != null)\r
1574         {\r
1575             scrollThread.setEvent(evt);\r
1576         }\r
1577 \r
1578         seqCanvas.repaint();\r
1579     }\r
1580 \r
1581     void scrollCanvas(MouseEvent evt)\r
1582     {\r
1583       if(evt==null)\r
1584       {\r
1585         if(scrollThread!=null)\r
1586         {\r
1587           scrollThread.running = false;\r
1588           scrollThread = null;\r
1589         }\r
1590         mouseDragging = false;\r
1591       }\r
1592       else\r
1593       {\r
1594         if (scrollThread == null)\r
1595           scrollThread = new ScrollThread();\r
1596 \r
1597         mouseDragging = true;\r
1598         scrollThread.setEvent(evt);\r
1599       }\r
1600 \r
1601     }\r
1602 \r
1603 \r
1604     // this class allows scrolling off the bottom of the visible alignment\r
1605     class ScrollThread extends Thread\r
1606     {\r
1607         MouseEvent evt;\r
1608         boolean running = false;\r
1609 \r
1610         public ScrollThread()\r
1611         {\r
1612             start();\r
1613         }\r
1614 \r
1615         public void setEvent(MouseEvent e)\r
1616         {\r
1617             evt = e;\r
1618         }\r
1619 \r
1620         public void stopScrolling()\r
1621         {\r
1622             running = false;\r
1623         }\r
1624 \r
1625         public void run()\r
1626         {\r
1627             running = true;\r
1628 \r
1629             while (running)\r
1630             {\r
1631                 if (evt != null)\r
1632                 {\r
1633                     if (mouseDragging && (evt.getY() < 0) &&\r
1634                             (av.getStartSeq() > 0))\r
1635                     {\r
1636                         running = ap.scrollUp(true);\r
1637                     }\r
1638 \r
1639                     if (mouseDragging && (evt.getY() >= getHeight()) &&\r
1640                             (av.alignment.getHeight() > av.getEndSeq()))\r
1641                     {\r
1642                         running = ap.scrollUp(false);\r
1643                     }\r
1644 \r
1645                     if (mouseDragging && (evt.getX() < 0))\r
1646                     {\r
1647                         running = ap.scrollRight(false);\r
1648                     }\r
1649                     else if (mouseDragging && (evt.getX() >= getWidth()))\r
1650                     {\r
1651                         running = ap.scrollRight(true);\r
1652                     }\r
1653                 }\r
1654 \r
1655                 try\r
1656                 {\r
1657                     Thread.sleep(20);\r
1658                 }\r
1659                 catch (Exception ex)\r
1660                 {\r
1661                 }\r
1662             }\r
1663         }\r
1664     }\r
1665 }\r