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(); 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(null).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                 setToolTipText(null);\r
 673               }\r
 674               else\r
 675               {\r
 676                 tooltipText.append("</html>");\r
 677                 setToolTipText(tooltipText.toString());\r
 678               }\r
 679             }\r
 680             else\r
 681               setToolTipText(null);\r
 682         }\r
 683     }\r
 684 \r
 685     void setStatusMessage(SequenceI sequence, int res, int seq)\r
 686     {\r
 687       StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
 688                                            sequence.getName());\r
 689 \r
 690       Object obj = null;\r
 691       if (av.alignment.isNucleotide())\r
 692       {\r
 693         obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
 694                                                    "");\r
 695         if (obj != null)\r
 696           text.append(" Nucleotide: ");\r
 697       }\r
 698       else\r
 699       {\r
 700         obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
 701         if (obj != null)\r
 702           text.append("  Residue: ");\r
 703       }\r
 704 \r
 705       if (obj != null)\r
 706       {\r
 707 \r
 708         if (obj != "")\r
 709         {\r
 710           text.append(obj + " (" + sequence.findPosition(res) +\r
 711                       ")");\r
 712         }\r
 713       }\r
 714       ap.alignFrame.statusBar.setText(text.toString());\r
 715 \r
 716     }\r
 717 \r
 718     /**\r
 719      * DOCUMENT ME!\r
 720      *\r
 721      * @param evt DOCUMENT ME!\r
 722      */\r
 723     public void mouseDragged(MouseEvent evt)\r
 724     {\r
 725       if (mouseWheelPressed)\r
 726       {\r
 727         int oldWidth = av.charWidth;\r
 728 \r
 729         //Which is bigger, left-right or up-down?\r
 730         if (Math.abs(evt.getY() - lastMousePress.getY())\r
 731             > Math.abs(evt.getX() - lastMousePress.getX()))\r
 732         {\r
 733           int fontSize = av.font.getSize();\r
 734 \r
 735           if (evt.getY() < lastMousePress.getY())\r
 736           {\r
 737             fontSize--;\r
 738           }\r
 739           else if (evt.getY() > lastMousePress.getY())\r
 740           {\r
 741             fontSize++;\r
 742           }\r
 743 \r
 744           if(fontSize<1)\r
 745             fontSize = 1;\r
 746 \r
 747           av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
 748           av.charWidth = oldWidth;\r
 749           ap.fontChanged();\r
 750         }\r
 751         else\r
 752         {\r
 753           if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)\r
 754           {\r
 755             av.charWidth--;\r
 756           }\r
 757           else if (evt.getX() > lastMousePress.getX())\r
 758           {\r
 759             av.charWidth++;\r
 760           }\r
 761 \r
 762           ap.repaint();\r
 763         }\r
 764 \r
 765         FontMetrics fm = getFontMetrics(av.getFont());\r
 766         av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
 767 \r
 768         lastMousePress = evt.getPoint();\r
 769 \r
 770         return;\r
 771       }\r
 772 \r
 773       if (!editingSeqs)\r
 774       {\r
 775         doMouseDraggedDefineMode(evt);\r
 776         return;\r
 777       }\r
 778 \r
 779         int res = findRes(evt);\r
 780 \r
 781         if (res < 0)\r
 782         {\r
 783             res = 0;\r
 784         }\r
 785 \r
 786         if ((lastres == -1) || (lastres == res))\r
 787         {\r
 788             return;\r
 789         }\r
 790 \r
 791         if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
 792         {\r
 793           // dragLeft, delete gap\r
 794           editSequence(false, res);\r
 795         }\r
 796         else\r
 797           editSequence(true, res);\r
 798 \r
 799         mouseDragging = true;\r
 800         if(scrollThread!=null)\r
 801           scrollThread.setEvent(evt);\r
 802 \r
 803     }\r
 804 \r
 805     synchronized void editSequence(boolean insertGap, int startres)\r
 806     {\r
 807       int fixedLeft = -1;\r
 808       int fixedRight = -1;\r
 809       boolean fixedColumns = false;\r
 810       SequenceGroup sg = av.getSelectionGroup();\r
 811 \r
 812       SequenceI seq = av.alignment.getSequenceAt(startseq);\r
 813 \r
 814       //No group, but the sequence may represent a group\r
 815         if (!groupEditing && av.hasHiddenRows)\r
 816         {\r
 817           if (av.hiddenRepSequences!=null\r
 818               && av.hiddenRepSequences.containsKey(seq))\r
 819           {\r
 820             sg = (SequenceGroup)av.hiddenRepSequences.get(seq);\r
 821             groupEditing = true;\r
 822           }\r
 823         }\r
 824 \r
 825 \r
 826         StringBuffer message = new StringBuffer();\r
 827         if (groupEditing)\r
 828         {\r
 829           message.append("Edit group:");\r
 830           if (editCommand == null)\r
 831             editCommand = new EditCommand("Edit Group");\r
 832         }\r
 833         else\r
 834          {\r
 835            message.append("Edit sequence: " + seq.getName());\r
 836            String label = seq.getName();\r
 837            if(label.length()>10)\r
 838              label = label.substring(0,10);\r
 839            if(editCommand==null)\r
 840              editCommand = new EditCommand("Edit "+label);\r
 841          }\r
 842 \r
 843        if(insertGap)\r
 844          message.append(" insert ");\r
 845        else\r
 846          message.append(" delete ");\r
 847 \r
 848        message.append(Math.abs(startres-lastres)+" gaps.");\r
 849        ap.alignFrame.statusBar.setText(message.toString());\r
 850 \r
 851 \r
 852         //Are we editing within a selection group?\r
 853         if (groupEditing\r
 854             || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))\r
 855         {\r
 856           fixedColumns = true;\r
 857 \r
 858           //sg might be null as the user may only see 1 sequence,\r
 859           //but the sequence represents a group\r
 860           if (sg == null)\r
 861           {\r
 862             sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
 863           }\r
 864 \r
 865           fixedLeft = sg.getStartRes();\r
 866           fixedRight = sg.getEndRes();\r
 867 \r
 868           if (   (startres < fixedLeft && lastres >= fixedLeft)\r
 869               || (startres >= fixedLeft && lastres < fixedLeft)\r
 870               || (startres > fixedRight && lastres <=fixedRight)\r
 871               || (startres <= fixedRight && lastres > fixedRight))\r
 872           {\r
 873             endEditing();\r
 874             return;\r
 875           }\r
 876 \r
 877           if (fixedLeft > startres)\r
 878           {\r
 879             fixedRight = fixedLeft - 1;\r
 880             fixedLeft = 0;\r
 881           }\r
 882           else if (fixedRight < startres)\r
 883           {\r
 884             fixedLeft = fixedRight;\r
 885             fixedRight = -1;\r
 886           }\r
 887         }\r
 888 \r
 889 \r
 890         if(av.hasHiddenColumns )\r
 891         {\r
 892             fixedColumns = true;\r
 893             int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
 894             int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
 895 \r
 896             if ( (insertGap && startres > y1 && lastres < y1)\r
 897                 || (!insertGap && startres < y2 && lastres > y2))\r
 898             {\r
 899               endEditing();\r
 900               return;\r
 901             }\r
 902 \r
 903             //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
 904             //Selection spans a hidden region\r
 905             if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
 906             {\r
 907               if(startres>=y2)\r
 908               {\r
 909                 fixedLeft = y2;\r
 910               }\r
 911               else\r
 912               {\r
 913                fixedRight = y2 - 1;\r
 914              }\r
 915             }\r
 916         }\r
 917 \r
 918 \r
 919         if (groupEditing)\r
 920         {\r
 921           Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
 922           int g, groupSize = vseqs.size();\r
 923           SequenceI[] groupSeqs = new SequenceI[groupSize];\r
 924           for (g = 0; g < groupSeqs.length; g++)\r
 925             groupSeqs[g] = (SequenceI) vseqs.elementAt(g);\r
 926 \r
 927           // drag to right\r
 928           if (insertGap)\r
 929           {\r
 930               //If the user has selected the whole sequence, and is dragging to\r
 931               // the right, we can still extend the alignment and selectionGroup\r
 932               if(   sg.getStartRes() == 0\r
 933                     && sg.getEndRes() == fixedRight\r
 934                     && sg.getEndRes() == av.alignment.getWidth()-1\r
 935                  )\r
 936               {\r
 937                 sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
 938                 fixedRight = sg.getEndRes();\r
 939               }\r
 940 \r
 941             // Is it valid with fixed columns??\r
 942             // Find the next gap before the end\r
 943             // of the visible region boundary\r
 944             boolean blank = false;\r
 945             for (fixedRight = fixedRight;\r
 946                  fixedRight > lastres;\r
 947                  fixedRight--)\r
 948             {\r
 949               blank = true;\r
 950 \r
 951               for (g = 0; g < groupSize; g++)\r
 952               {\r
 953                 for (int j = 0; j < startres - lastres; j++)\r
 954                 {\r
 955                   if (!jalview.util.Comparison.isGap(\r
 956                       groupSeqs[g].getCharAt(fixedRight - j)))\r
 957                   {\r
 958                     blank = false;\r
 959                     break;\r
 960                   }\r
 961                 }\r
 962               }\r
 963               if (blank)\r
 964                 break;\r
 965             }\r
 966 \r
 967             if (!blank)\r
 968             {\r
 969               if(sg.getSize() == av.alignment.getHeight()  )\r
 970               {\r
 971                 if((av.hasHiddenColumns\r
 972                     && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
 973                 {\r
 974                   endEditing();\r
 975                   return;\r
 976                 }\r
 977 \r
 978                 int alWidth = av.alignment.getWidth();\r
 979                 if(av.hasHiddenRows)\r
 980                 {\r
 981                   int hwidth = av.alignment.getHiddenSequences().getWidth();\r
 982                   if(hwidth>alWidth)\r
 983                     alWidth = hwidth;\r
 984                 }\r
 985                 //We can still insert gaps if the selectionGroup\r
 986                 //contains all the sequences\r
 987                 sg.setEndRes(sg.getEndRes()+startres-lastres);\r
 988                 fixedRight = alWidth+startres-lastres;\r
 989               }\r
 990               else\r
 991               {\r
 992                 endEditing();\r
 993                 return;\r
 994               }\r
 995             }\r
 996           }\r
 997 \r
 998 \r
 999           // drag to left\r
1000           else if(!insertGap)\r
1001           {\r
1002             /// Are we able to delete?\r
1003             // ie are all columns blank?\r
1004 \r
1005             for (g = 0; g < groupSize; g++)\r
1006             {\r
1007               for (int j = startres; j < lastres; j++)\r
1008               {\r
1009                 if (groupSeqs[g].getLength() <= j)\r
1010                 {\r
1011                   continue;\r
1012                 }\r
1013 \r
1014                 if (!jalview.util.Comparison.isGap(\r
1015                     groupSeqs[g].getCharAt(j)))\r
1016                 {\r
1017                   // Not a gap, block edit not valid\r
1018                   endEditing();\r
1019                   return;\r
1020                 }\r
1021               }\r
1022             }\r
1023           }\r
1024 \r
1025             if (insertGap)\r
1026             {\r
1027               // dragging to the right\r
1028               if (fixedColumns && fixedRight != -1)\r
1029               {\r
1030                 for (int j = lastres; j < startres; j++)\r
1031                 {\r
1032                     insertChar(j, groupSeqs, fixedRight);\r
1033                 }\r
1034               }\r
1035               else\r
1036               {\r
1037                 editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1038                                        groupSeqs,\r
1039                                        startres, startres-lastres,\r
1040                                        av.getGapCharacter(),\r
1041                                        true);\r
1042               }\r
1043             }\r
1044             else\r
1045             {\r
1046               // dragging to the left\r
1047               if (fixedColumns && fixedRight != -1)\r
1048               {\r
1049                 for (int j = lastres; j > startres; j--)\r
1050                 {\r
1051                   deleteChar(startres, groupSeqs, fixedRight);\r
1052                 }\r
1053               }\r
1054               else\r
1055                 editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1056                                        groupSeqs,\r
1057                                        startres, lastres - startres,\r
1058                                        av.getGapCharacter(),\r
1059                                        true);\r
1060 \r
1061             }\r
1062         }\r
1063         else /////Editing a single sequence///////////\r
1064         {\r
1065           if (insertGap)\r
1066           {\r
1067             // dragging to the right\r
1068             if (fixedColumns && fixedRight != -1)\r
1069             {\r
1070               for (int j = lastres; j < startres; j++)\r
1071               {\r
1072                 insertChar(j, new SequenceI[]{seq}, fixedRight);\r
1073               }\r
1074             }\r
1075             else\r
1076             {\r
1077               editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1078                                      new SequenceI[]\r
1079                                      {seq},\r
1080                                      lastres, startres-lastres,\r
1081                                      av.getGapCharacter(),\r
1082                                      true);\r
1083             }\r
1084           }\r
1085           else\r
1086           {\r
1087             // dragging to the left\r
1088             if (fixedColumns && fixedRight != -1)\r
1089             {\r
1090               for (int j = lastres; j > startres; j--)\r
1091               {\r
1092                 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
1093                 {\r
1094                   endEditing();\r
1095                   break;\r
1096                 }\r
1097                 deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
1098               }\r
1099             }\r
1100             else\r
1101             {\r
1102               //could be a keyboard edit trying to delete none gaps\r
1103               int max=0;\r
1104               for(int m = startres; m<lastres; m++)\r
1105               {\r
1106                 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
1107                   break;\r
1108                 max++;\r
1109               }\r
1110 \r
1111               if (max>0)\r
1112               {\r
1113                 editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1114                                        new SequenceI[]\r
1115                                        {seq},\r
1116                                        startres, max,\r
1117                                        av.getGapCharacter(),\r
1118                                        true);\r
1119               }\r
1120             }\r
1121           }\r
1122         }\r
1123 \r
1124         lastres = startres;\r
1125         seqCanvas.repaint();\r
1126     }\r
1127 \r
1128 \r
1129 \r
1130     void insertChar(int j, SequenceI [] seq, int fixedColumn)\r
1131     {\r
1132       int blankColumn = fixedColumn;\r
1133       for(int s=0; s<seq.length; s++)\r
1134       {\r
1135         //Find the next gap before the end of the visible region boundary\r
1136         //If lastCol > j, theres a boundary after the gap insertion\r
1137 \r
1138         for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
1139         {\r
1140           if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
1141           {\r
1142             //Theres a space, so break and insert the gap\r
1143             break;\r
1144           }\r
1145         }\r
1146 \r
1147         if (blankColumn <= j)\r
1148         {\r
1149           blankColumn = fixedColumn;\r
1150           endEditing();\r
1151           return;\r
1152         }\r
1153       }\r
1154 \r
1155       editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1156                              seq,\r
1157                              blankColumn, 1, av.getGapCharacter(), true);\r
1158 \r
1159       editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1160                              seq,\r
1161                              j, 1, av.getGapCharacter(),\r
1162                              true);\r
1163 \r
1164     }\r
1165 \r
1166     void deleteChar(int j, SequenceI [] seq, int fixedColumn)\r
1167     {\r
1168 \r
1169       editCommand.appendEdit(EditCommand.DELETE_GAP,\r
1170                              seq,\r
1171                              j, 1, av.getGapCharacter(), true);\r
1172 \r
1173       editCommand.appendEdit(EditCommand.INSERT_GAP,\r
1174                              seq,\r
1175                              fixedColumn, 1, av.getGapCharacter(), true);\r
1176     }\r
1177 \r
1178     /**\r
1179      * DOCUMENT ME!\r
1180      *\r
1181      * @param e DOCUMENT ME!\r
1182      */\r
1183     public void mouseEntered(MouseEvent e)\r
1184     {\r
1185         if(oldSeq < 0)\r
1186           oldSeq = 0;\r
1187 \r
1188         if (scrollThread != null)\r
1189         {\r
1190             scrollThread.running = false;\r
1191             scrollThread = null;\r
1192         }\r
1193     }\r
1194 \r
1195     /**\r
1196      * DOCUMENT ME!\r
1197      *\r
1198      * @param e DOCUMENT ME!\r
1199      */\r
1200     public void mouseExited(MouseEvent e)\r
1201     {\r
1202         if (av.getWrapAlignment())\r
1203         {\r
1204             return;\r
1205         }\r
1206 \r
1207         if (mouseDragging)\r
1208         {\r
1209             scrollThread = new ScrollThread();\r
1210         }\r
1211     }\r
1212 \r
1213     public void mouseClicked(MouseEvent evt)\r
1214     {\r
1215       SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
1216       if(evt.getClickCount()>1)\r
1217       {\r
1218         if (av.getSelectionGroup().getSize() == 1\r
1219             && av.getSelectionGroup().getEndRes()\r
1220             - av.getSelectionGroup().getStartRes() < 2)\r
1221           av.setSelectionGroup(null);\r
1222 \r
1223         SequenceFeature[] features = findFeaturesAtRes(\r
1224             sequence.getDatasetSequence(),\r
1225             sequence.findPosition( findRes(evt) )\r
1226             );\r
1227 \r
1228         if(features!=null && features.length>0)\r
1229         {\r
1230           SearchResults highlight = new SearchResults();\r
1231           highlight.addResult(sequence,\r
1232                               features[0].getBegin(),\r
1233                               features[0].getEnd());\r
1234           seqCanvas.highlightSearchResults(highlight);\r
1235         }\r
1236         if(features!=null && features.length>0)\r
1237         {\r
1238           seqCanvas.getFeatureRenderer().amendFeatures(\r
1239               new SequenceI[]\r
1240               {sequence}, features, false, ap);\r
1241 \r
1242           seqCanvas.highlightSearchResults(null);\r
1243         }\r
1244       }\r
1245     }\r
1246 \r
1247     public void mouseWheelMoved(MouseWheelEvent e)\r
1248     {\r
1249       e.consume();\r
1250      /* if (mouseWheelPressed)\r
1251       {\r
1252         Font font = av.getFont();\r
1253         int fontSize = font.getSize();\r
1254         if (e.getWheelRotation() > 0 && fontSize < 51)\r
1255           fontSize++;\r
1256         else if (fontSize > 1)\r
1257           fontSize--;\r
1258 \r
1259 \r
1260 \r
1261         av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\r
1262 \r
1263         ap.fontChanged();\r
1264       }\r
1265       else*/\r
1266       {\r
1267         if (e.getWheelRotation() > 0)\r
1268           ap.scrollUp(false);\r
1269         else\r
1270           ap.scrollUp(true);\r
1271       }\r
1272 \r
1273     }\r
1274 \r
1275 \r
1276     /**\r
1277      * DOCUMENT ME!\r
1278      *\r
1279      * @param evt DOCUMENT ME!\r
1280      */\r
1281     public void doMousePressedDefineMode(MouseEvent evt)\r
1282     {\r
1283       int res = findRes(evt);\r
1284       int seq = findSeq(evt);\r
1285       oldSeq = seq;\r
1286 \r
1287       startWrapBlock=wrappedBlock;\r
1288 \r
1289       if(av.wrapAlignment && seq>av.alignment.getHeight())\r
1290       {\r
1291           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1292               "Cannot edit annotations in wrapped view.",\r
1293               "Wrapped view - no edit",\r
1294               JOptionPane.WARNING_MESSAGE);\r
1295           return;\r
1296       }\r
1297 \r
1298       if(seq<0 || res<0)\r
1299             return;\r
1300 \r
1301         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
1302 \r
1303         if ((sequence == null) || (res > sequence.getLength()))\r
1304         {\r
1305             return;\r
1306         }\r
1307 \r
1308         stretchGroup = av.getSelectionGroup();\r
1309 \r
1310         if (stretchGroup == null)\r
1311         {\r
1312             stretchGroup = av.alignment.findGroup(sequence);\r
1313 \r
1314             if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
1315                     (res < stretchGroup.getEndRes()))\r
1316             {\r
1317                 av.setSelectionGroup(stretchGroup);\r
1318             }\r
1319             else\r
1320             {\r
1321                 stretchGroup = null;\r
1322             }\r
1323         }\r
1324         else if (!stretchGroup.getSequences(null).contains(sequence) ||\r
1325                 (stretchGroup.getStartRes() > res) ||\r
1326                 (stretchGroup.getEndRes() < res))\r
1327         {\r
1328             stretchGroup = null;\r
1329 \r
1330             SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
1331 \r
1332             if (allGroups != null)\r
1333             {\r
1334                 for (int i = 0; i < allGroups.length; i++)\r
1335                 {\r
1336                     if ((allGroups[i].getStartRes() <= res) &&\r
1337                             (allGroups[i].getEndRes() >= res))\r
1338                     {\r
1339                         stretchGroup = allGroups[i];\r
1340                         break;\r
1341                     }\r
1342                 }\r
1343             }\r
1344 \r
1345             av.setSelectionGroup(stretchGroup);\r
1346 \r
1347         }\r
1348 \r
1349 \r
1350         if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
1351         {\r
1352           Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
1353                                                   sequence.findPosition(res));\r
1354           Vector links = new Vector();\r
1355             for (int i = 0; i < allFeatures.size(); i++)\r
1356             {\r
1357               SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
1358               if (sf.links != null)\r
1359               {\r
1360                 for (int j = 0; j < sf.links.size(); j++)\r
1361                 {\r
1362                   links.addElement(sf.links.elementAt(j));\r
1363                 }\r
1364               }\r
1365             }\r
1366 \r
1367             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
1368             pop.show(this, evt.getX(), evt.getY());\r
1369             return;\r
1370         }\r
1371 \r
1372         if (av.cursorMode)\r
1373         {\r
1374           seqCanvas.cursorX = findRes(evt);\r
1375           seqCanvas.cursorY = findSeq(evt);\r
1376           seqCanvas.repaint();\r
1377           return;\r
1378         }\r
1379 \r
1380         if (stretchGroup == null)\r
1381         {\r
1382           //Only if left mouse button do we want to change group sizes\r
1383 \r
1384           // define a new group here\r
1385           SequenceGroup sg = new SequenceGroup();\r
1386           sg.setStartRes(res);\r
1387           sg.setEndRes(res);\r
1388           sg.addSequence(sequence, false);\r
1389           av.setSelectionGroup(sg);\r
1390           stretchGroup = sg;\r
1391 \r
1392           if (av.getConservationSelected())\r
1393           {\r
1394             SliderPanel.setConservationSlider(ap,\r
1395                                               av.getGlobalColourScheme(),\r
1396                                               "Background");\r
1397           }\r
1398 \r
1399           if (av.getAbovePIDThreshold())\r
1400           {\r
1401             SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
1402                                            "Background");\r
1403           }\r
1404           if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
1405           {\r
1406             // Edit end res position of selected group\r
1407             changeEndRes = true;\r
1408           }\r
1409           else if ( (stretchGroup != null) &&\r
1410                    (stretchGroup.getStartRes() == res))\r
1411           {\r
1412             // Edit end res position of selected group\r
1413             changeStartRes = true;\r
1414           }\r
1415           stretchGroup.getWidth();\r
1416         }\r
1417 \r
1418         seqCanvas.repaint();\r
1419     }\r
1420 \r
1421     /**\r
1422      * DOCUMENT ME!\r
1423      *\r
1424      * @param evt DOCUMENT ME!\r
1425      */\r
1426     public void doMouseReleasedDefineMode(MouseEvent evt)\r
1427     {\r
1428         if (stretchGroup == null)\r
1429         {\r
1430             return;\r
1431         }\r
1432 \r
1433 \r
1434         if(stretchGroup.cs!=null)\r
1435         {\r
1436           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
1437           {\r
1438             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
1439                 stretchGroup.getSequences(av.hiddenRepSequences),\r
1440                 stretchGroup.getWidth());\r
1441           }\r
1442 \r
1443           if (stretchGroup.cs instanceof Blosum62ColourScheme\r
1444               || stretchGroup.cs instanceof PIDColourScheme\r
1445               || stretchGroup.cs.conservationApplied()\r
1446               || stretchGroup.cs.getThreshold()>0)\r
1447             stretchGroup.recalcConservation();\r
1448 \r
1449           if (stretchGroup.cs.conservationApplied())\r
1450           {\r
1451             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
1452                                               stretchGroup.getName());\r
1453           }\r
1454           else\r
1455           {\r
1456             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
1457                                            stretchGroup.getName());\r
1458           }\r
1459         }\r
1460         changeEndRes = false;\r
1461         changeStartRes = false;\r
1462         stretchGroup = null;\r
1463 \r
1464         PaintRefresher.Refresh(this, av.getSequenceSetId());\r
1465     }\r
1466 \r
1467     /**\r
1468      * DOCUMENT ME!\r
1469      *\r
1470      * @param evt DOCUMENT ME!\r
1471      */\r
1472     public void doMouseDraggedDefineMode(MouseEvent evt)\r
1473     {\r
1474       int res = findRes(evt);\r
1475       int y = findSeq(evt);\r
1476 \r
1477       if(wrappedBlock!=startWrapBlock)\r
1478         return;\r
1479 \r
1480        if (stretchGroup == null)\r
1481        {\r
1482             return;\r
1483        }\r
1484 \r
1485         if(res>= av.alignment.getWidth())\r
1486         {\r
1487           res = av.alignment.getWidth()-1;\r
1488         }\r
1489 \r
1490         if (stretchGroup.getEndRes() == res)\r
1491         {\r
1492             // Edit end res position of selected group\r
1493             changeEndRes = true;\r
1494         }\r
1495         else if (stretchGroup.getStartRes() == res)\r
1496         {\r
1497             // Edit start res position of selected group\r
1498             changeStartRes = true;\r
1499         }\r
1500 \r
1501         if (res < av.getStartRes())\r
1502         {\r
1503             res = av.getStartRes();\r
1504         }\r
1505 \r
1506         if (changeEndRes)\r
1507         {\r
1508             if (res > (stretchGroup.getStartRes() - 1))\r
1509             {\r
1510                 stretchGroup.setEndRes(res);\r
1511             }\r
1512         }\r
1513         else if (changeStartRes)\r
1514         {\r
1515             if (res < (stretchGroup.getEndRes() + 1))\r
1516             {\r
1517                 stretchGroup.setStartRes(res);\r
1518             }\r
1519         }\r
1520 \r
1521         int dragDirection = 0;\r
1522 \r
1523         if (y > oldSeq)\r
1524         {\r
1525             dragDirection = 1;\r
1526         }\r
1527         else if (y < oldSeq)\r
1528         {\r
1529             dragDirection = -1;\r
1530         }\r
1531 \r
1532 \r
1533         while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
1534         {\r
1535             // This routine ensures we don't skip any sequences, as the\r
1536             // selection is quite slow.\r
1537             Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
1538 \r
1539             oldSeq += dragDirection;\r
1540 \r
1541             if(oldSeq<0)\r
1542               break;\r
1543 \r
1544             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
1545 \r
1546             if (stretchGroup.getSequences(null).contains(nextSeq))\r
1547             {\r
1548                 stretchGroup.deleteSequence(seq, false);\r
1549             }\r
1550             else\r
1551             {\r
1552                 if (seq != null)\r
1553                 {\r
1554                     stretchGroup.addSequence(seq, false);\r
1555                 }\r
1556 \r
1557                 stretchGroup.addSequence(nextSeq, false);\r
1558             }\r
1559         }\r
1560 \r
1561         if(oldSeq < 0)\r
1562           oldSeq = -1;\r
1563 \r
1564         mouseDragging = true;\r
1565 \r
1566         if (scrollThread != null)\r
1567         {\r
1568             scrollThread.setEvent(evt);\r
1569         }\r
1570 \r
1571         seqCanvas.repaint();\r
1572     }\r
1573 \r
1574     void scrollCanvas(MouseEvent evt)\r
1575     {\r
1576       if(evt==null)\r
1577       {\r
1578         if(scrollThread!=null)\r
1579         {\r
1580           scrollThread.running = false;\r
1581           scrollThread = null;\r
1582         }\r
1583         mouseDragging = false;\r
1584       }\r
1585       else\r
1586       {\r
1587         if (scrollThread == null)\r
1588           scrollThread = new ScrollThread();\r
1589 \r
1590         mouseDragging = true;\r
1591         scrollThread.setEvent(evt);\r
1592       }\r
1593 \r
1594     }\r
1595 \r
1596 \r
1597     // this class allows scrolling off the bottom of the visible alignment\r
1598     class ScrollThread extends Thread\r
1599     {\r
1600         MouseEvent evt;\r
1601         boolean running = false;\r
1602 \r
1603         public ScrollThread()\r
1604         {\r
1605             start();\r
1606         }\r
1607 \r
1608         public void setEvent(MouseEvent e)\r
1609         {\r
1610             evt = e;\r
1611         }\r
1612 \r
1613         public void stopScrolling()\r
1614         {\r
1615             running = false;\r
1616         }\r
1617 \r
1618         public void run()\r
1619         {\r
1620             running = true;\r
1621 \r
1622             while (running)\r
1623             {\r
1624                 if (evt != null)\r
1625                 {\r
1626                     if (mouseDragging && (evt.getY() < 0) &&\r
1627                             (av.getStartSeq() > 0))\r
1628                     {\r
1629                         running = ap.scrollUp(true);\r
1630                     }\r
1631 \r
1632                     if (mouseDragging && (evt.getY() >= getHeight()) &&\r
1633                             (av.alignment.getHeight() > av.getEndSeq()))\r
1634                     {\r
1635                         running = ap.scrollUp(false);\r
1636                     }\r
1637 \r
1638                     if (mouseDragging && (evt.getX() < 0))\r
1639                     {\r
1640                         running = ap.scrollRight(false);\r
1641                     }\r
1642                     else if (mouseDragging && (evt.getX() >= getWidth()))\r
1643                     {\r
1644                         running = ap.scrollRight(true);\r
1645                     }\r
1646                 }\r
1647 \r
1648                 try\r
1649                 {\r
1650                     Thread.sleep(20);\r
1651                 }\r
1652                 catch (Exception ex)\r
1653                 {\r
1654                 }\r
1655             }\r
1656         }\r
1657     }\r
1658 }\r