src/jalview/gui/SeqPanel.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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.analysis.*;\r
  22 \r
  23 import jalview.datamodel.*;\r
  24 \r
  25 import jalview.schemes.*;\r
  26 \r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 \r
  30 import java.util.*;\r
  31 \r
  32 import javax.swing.*;\r
  33 \r
  34 \r
  35 /**\r
  36  * DOCUMENT ME!\r
  37  *\r
  38  * @author $author$\r
  39  * @version $Revision$\r
  40  */\r
  41 public class SeqPanel extends JPanel\r
  42 {\r
  43     /** DOCUMENT ME!! */\r
  44     public SeqCanvas seqCanvas;\r
  45 \r
  46     /** DOCUMENT ME!! */\r
  47     public AlignmentPanel ap;\r
  48     protected int lastres;\r
  49     protected int startseq;\r
  50     int startEdit = -1;\r
  51     int endEdit = -1;\r
  52     protected AlignViewport av;\r
  53 \r
  54     // if character is inserted or deleted, we will need to recalculate the conservation\r
  55     int seqEditOccurred = -1;\r
  56     ScrollThread scrollThread = null;\r
  57     boolean mouseDragging = false;\r
  58     boolean editingSeqs = false;\r
  59     boolean groupEditing = false;\r
  60 \r
  61     //////////////////////////////////////////\r
  62     /////Everything below this is for defining the boundary of the rubberband\r
  63     //////////////////////////////////////////\r
  64     int oldSeq = -1;\r
  65     boolean changeEndSeq = false;\r
  66     boolean changeStartSeq = false;\r
  67     boolean changeEndRes = false;\r
  68     boolean changeStartRes = false;\r
  69     SequenceGroup stretchGroup = null;\r
  70     boolean remove = false;\r
  71 \r
  72     boolean mouseWheelPressed = false;\r
  73 \r
  74     /**\r
  75      * Creates a new SeqPanel object.\r
  76      *\r
  77      * @param avp DOCUMENT ME!\r
  78      * @param p DOCUMENT ME!\r
  79      */\r
  80     public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
  81     {\r
  82         ToolTipManager.sharedInstance().registerComponent(this);\r
  83         ToolTipManager.sharedInstance().setInitialDelay(0);\r
  84         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
  85         this.av = avp;\r
  86         setBackground(Color.white);\r
  87 \r
  88         seqCanvas = new SeqCanvas(avp);\r
  89         setLayout(new BorderLayout());\r
  90         add(seqCanvas, BorderLayout.CENTER);\r
  91 \r
  92         ap = p;\r
  93 \r
  94         addMouseMotionListener(new MouseMotionAdapter()\r
  95             {\r
  96                 public void mouseMoved(MouseEvent evt)\r
  97                 {\r
  98                     if (av.getWrapAlignment())\r
  99                     {\r
 100                         return;\r
 101                     }\r
 102 \r
 103                     doMouseMoved(evt);\r
 104                 }\r
 105 \r
 106                 public void mouseDragged(MouseEvent evt)\r
 107                 {\r
 108                     if (av.getWrapAlignment())\r
 109                     {\r
 110                         return;\r
 111                     }\r
 112 \r
 113                     if (editingSeqs)\r
 114                     {\r
 115                         doMouseDragged(evt);\r
 116                     }\r
 117                     else\r
 118                     {\r
 119                         doMouseDraggedDefineMode(evt);\r
 120                     }\r
 121                 }\r
 122             });\r
 123 \r
 124        addMouseWheelListener(new MouseWheelListener()\r
 125        {\r
 126          public void mouseWheelMoved(MouseWheelEvent e)\r
 127          {\r
 128 \r
 129            if (mouseWheelPressed)\r
 130            {\r
 131              Font font = av.getFont();\r
 132              int fontSize = font.getSize();\r
 133              if (e.getWheelRotation() > 0 && fontSize < 30)\r
 134                fontSize++;\r
 135              else if (fontSize > 1)\r
 136                fontSize--;\r
 137 \r
 138              av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\r
 139              ap.fontChanged();\r
 140              ap.repaint();\r
 141 \r
 142            }\r
 143            else\r
 144            {\r
 145              if (e.getWheelRotation() > 0)\r
 146                ap.scrollUp(false);\r
 147              else\r
 148                ap.scrollUp(true);\r
 149            }\r
 150 \r
 151          }\r
 152        });\r
 153 \r
 154 \r
 155         addMouseListener(new MouseAdapter()\r
 156             {\r
 157                 public void mouseReleased(MouseEvent evt)\r
 158                 {\r
 159                     mouseWheelPressed = false;\r
 160                     if (av.getWrapAlignment())\r
 161                     {\r
 162                         return;\r
 163                     }\r
 164 \r
 165                     if (editingSeqs)\r
 166                     {\r
 167                         doMouseReleased(evt);\r
 168                     }\r
 169                     else\r
 170                     {\r
 171                         doMouseReleasedDefineMode(evt);\r
 172                     }\r
 173                 }\r
 174 \r
 175                 public void mousePressed(MouseEvent evt)\r
 176                 {\r
 177                   if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
 178                   {\r
 179                     mouseWheelPressed = true;\r
 180                     return;\r
 181                   }\r
 182                     if (av.getWrapAlignment())\r
 183                     {\r
 184                         return;\r
 185                     }\r
 186 \r
 187                     if (evt.isShiftDown() || evt.isAltDown() ||\r
 188                             evt.isControlDown())\r
 189                     {\r
 190                         if (evt.isAltDown() || evt.isControlDown())\r
 191                         {\r
 192                             groupEditing = true;\r
 193                         }\r
 194 \r
 195                         editingSeqs = true;\r
 196                         doMousePressed(evt);\r
 197                     }\r
 198                     else\r
 199                     {\r
 200                         doMousePressedDefineMode(evt);\r
 201                     }\r
 202                 }\r
 203 \r
 204                 public void mouseExited(MouseEvent evt)\r
 205                 {\r
 206                     if (av.getWrapAlignment() || editingSeqs)\r
 207                     {\r
 208                         return;\r
 209                     }\r
 210 \r
 211                     doMouseExitedDefineMode(evt);\r
 212                 }\r
 213 \r
 214                 public void mouseEntered(MouseEvent evt)\r
 215                 {\r
 216                     if (av.getWrapAlignment() || editingSeqs)\r
 217                     {\r
 218                         return;\r
 219                     }\r
 220 \r
 221                     doMouseEnteredDefineMode(evt);\r
 222                 }\r
 223             });\r
 224     }\r
 225 \r
 226     /**\r
 227      * DOCUMENT ME!\r
 228      *\r
 229      * @param evt DOCUMENT ME!\r
 230      */\r
 231     public void doMouseReleased(MouseEvent evt)\r
 232     {\r
 233         if (seqEditOccurred > -1)\r
 234         {\r
 235             editOccurred(seqEditOccurred);\r
 236         }\r
 237 \r
 238         startseq = -1;\r
 239         lastres = -1;\r
 240         seqEditOccurred = -1;\r
 241         editingSeqs = false;\r
 242         groupEditing = false;\r
 243 \r
 244         ap.repaint();\r
 245     }\r
 246 \r
 247     /**\r
 248      * DOCUMENT ME!\r
 249      *\r
 250      * @param evt DOCUMENT ME!\r
 251      */\r
 252     public void doMousePressed(MouseEvent evt)\r
 253     {\r
 254         ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
 255                 av.alignment, HistoryItem.EDIT));\r
 256 \r
 257         int seq;\r
 258         int res;\r
 259 \r
 260         int x = evt.getX();\r
 261         int y = evt.getY();\r
 262 \r
 263         res = (x / av.getCharWidth()) + av.getStartRes();\r
 264         seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 265 \r
 266         if ((seq < av.getAlignment().getHeight()) &&\r
 267                 (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
 268         {\r
 269             startseq = seq;\r
 270             lastres = res;\r
 271         }\r
 272         else\r
 273         {\r
 274             startseq = -1;\r
 275             lastres = -1;\r
 276         }\r
 277 \r
 278         startEdit = lastres;\r
 279         endEdit = lastres;\r
 280 \r
 281         return;\r
 282     }\r
 283 \r
 284     /**\r
 285      * DOCUMENT ME!\r
 286      *\r
 287      * @param evt DOCUMENT ME!\r
 288      */\r
 289     public void doMouseMoved(MouseEvent evt)\r
 290     {\r
 291         int res = 0;\r
 292         int seq = 0;\r
 293         int x = evt.getX();\r
 294         int y = evt.getY();\r
 295 \r
 296         if (av.wrapAlignment)\r
 297         {\r
 298             y -= (2 * av.charHeight);\r
 299 \r
 300             int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
 301 \r
 302             res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +\r
 303                 (x / av.getCharWidth()) + av.getStartRes();\r
 304 \r
 305             y %= chunkHeight;\r
 306             seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 307         }\r
 308         else\r
 309         {\r
 310             res = (x / av.getCharWidth()) + av.getStartRes();\r
 311             seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 312         }\r
 313 \r
 314         if (seq >= av.getAlignment().getHeight())\r
 315         {\r
 316             return;\r
 317         }\r
 318 \r
 319         SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
 320 \r
 321         if (res > sequence.getLength())\r
 322         {\r
 323             return;\r
 324         }\r
 325 \r
 326         Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +\r
 327                 "");\r
 328         String aa = "";\r
 329 \r
 330         if (obj != null)\r
 331         {\r
 332             aa = obj.toString();\r
 333         }\r
 334 \r
 335         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
 336                 sequence.getName());\r
 337 \r
 338         if (aa != "")\r
 339         {\r
 340             text.append("  Residue: " + aa + " (" +\r
 341                 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
 342         }\r
 343 \r
 344         ap.alignFrame.statusBar.setText(text.toString());\r
 345 \r
 346         // use aa to see if the mouse pointer is on a\r
 347         if (av.showSequenceFeatures)\r
 348         {\r
 349             Vector features = sequence.getSequenceFeatures();\r
 350             Enumeration e = features.elements();\r
 351             StringBuffer sbuffer = new StringBuffer();\r
 352 \r
 353             while (e.hasMoreElements())\r
 354             {\r
 355                 SequenceFeature sf = (SequenceFeature) e.nextElement();\r
 356 \r
 357                 if ((sf.getStart() <= sequence.findPosition(res)) &&\r
 358                         (sf.getEnd() >= sequence.findPosition(res)))\r
 359                 {\r
 360                     if (sbuffer.length() > 0)\r
 361                     {\r
 362                         sbuffer.append("; ");\r
 363                     }\r
 364 \r
 365                     sbuffer.append(sf.getType() + " " + sf.getDescription());\r
 366 \r
 367                     if (sf.getStatus().length() > 0)\r
 368                     {\r
 369                         sbuffer.append(" (" + sf.getStatus() + ")");\r
 370                     }\r
 371                 }\r
 372             }\r
 373 \r
 374             this.setToolTipText(sbuffer.toString());\r
 375         }\r
 376     }\r
 377 \r
 378     /**\r
 379      * DOCUMENT ME!\r
 380      *\r
 381      * @param evt DOCUMENT ME!\r
 382      */\r
 383     public void doMouseDragged(MouseEvent evt)\r
 384     {\r
 385         // If we're dragging we're editing\r
 386         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 387 \r
 388         if (res < 0)\r
 389         {\r
 390             res = 0;\r
 391         }\r
 392 \r
 393         if ((lastres == -1) || (lastres == res))\r
 394         {\r
 395             return;\r
 396         }\r
 397 \r
 398         boolean dragRight = true;\r
 399 \r
 400         if ((res < av.getAlignment().getWidth()) && (res < lastres))\r
 401         {\r
 402             dragRight = false;\r
 403         }\r
 404 \r
 405         if (res != lastres)\r
 406         {\r
 407             // Group editing\r
 408             if (groupEditing)\r
 409             {\r
 410                 SequenceGroup sg = av.getSelectionGroup();\r
 411 \r
 412                 if (sg == null)\r
 413                 {\r
 414                     lastres = -1;\r
 415 \r
 416                     return;\r
 417                 }\r
 418 \r
 419                 // drag to right\r
 420                 if (dragRight)\r
 421                 {\r
 422                     sg.setEndRes(sg.getEndRes() + (res - lastres));\r
 423                 }\r
 424 \r
 425                 // drag to left\r
 426                 else\r
 427                 {\r
 428                     /// Are we able to delete?\r
 429                     // ie are all columns blank?\r
 430                     boolean deleteAllowed = false;\r
 431 \r
 432                     for (int s = 0; s < sg.getSize(); s++)\r
 433                     {\r
 434                         SequenceI seq = sg.getSequenceAt(s);\r
 435 \r
 436                         for (int j = res; j < lastres; j++)\r
 437                         {\r
 438                             if (seq.getSequence().length() <= j)\r
 439                             {\r
 440                                 continue;\r
 441                             }\r
 442 \r
 443                             if (!jalview.util.Comparison.isGap(\r
 444                                         seq.getSequence().charAt(j)))\r
 445                             {\r
 446                                 // Not a gap, block edit not valid\r
 447                                 res = j + 1;\r
 448                                 deleteAllowed = false;\r
 449 \r
 450                                 continue;\r
 451                             }\r
 452 \r
 453                             deleteAllowed = true;\r
 454                         }\r
 455                     }\r
 456 \r
 457                     if (!deleteAllowed)\r
 458                     {\r
 459                         lastres = -1;\r
 460 \r
 461                         return;\r
 462                     }\r
 463 \r
 464                     sg.setEndRes(sg.getEndRes() - (lastres - res));\r
 465                 }\r
 466 \r
 467                 for (int i = 0; i < sg.getSize(); i++)\r
 468                 {\r
 469                     SequenceI s = sg.getSequenceAt(i);\r
 470                     int k = av.alignment.findIndex(s);\r
 471 \r
 472                     // drag to right\r
 473                     if (dragRight)\r
 474                     {\r
 475                         for (int j = lastres; j < res; j++)\r
 476                         {\r
 477                             insertChar(j, k);\r
 478                         }\r
 479                     }\r
 480 \r
 481                     // drag to left\r
 482                     else\r
 483                     {\r
 484                         for (int j = res; j < lastres; j++)\r
 485                         {\r
 486                             if (s.getLength() > j)\r
 487                             {\r
 488                                 deleteChar(res, k);\r
 489                             }\r
 490                         }\r
 491                     }\r
 492                 }\r
 493             }\r
 494             else /////Editing a single sequence///////////\r
 495             {\r
 496                 if ((res < av.getAlignment().getWidth()) && (res > lastres))\r
 497                 {\r
 498                     // dragging to the right\r
 499                     for (int j = lastres; j < res; j++)\r
 500                     {\r
 501                         insertChar(j, startseq);\r
 502                     }\r
 503                 }\r
 504                 else if ((res < av.getAlignment().getWidth()) &&\r
 505                         (res < lastres))\r
 506                 {\r
 507                     // dragging to the left\r
 508                     for (int j = lastres; j > res; j--)\r
 509                     {\r
 510                         if (jalview.util.Comparison.isGap(\r
 511                                     av.alignment.getSequenceAt(startseq)\r
 512                                                     .getSequence().charAt(res)))\r
 513                         {\r
 514                             deleteChar(res, startseq);\r
 515                         }\r
 516                         else\r
 517                         {\r
 518                             break;\r
 519                         }\r
 520                     }\r
 521                 }\r
 522             }\r
 523         }\r
 524 \r
 525         endEdit = res;\r
 526         lastres = res;\r
 527         seqCanvas.repaint();\r
 528     }\r
 529 \r
 530     /**\r
 531      * DOCUMENT ME!\r
 532      *\r
 533      * @param seqstart DOCUMENT ME!\r
 534      * @param seqend DOCUMENT ME!\r
 535      * @param start DOCUMENT ME!\r
 536      */\r
 537     public void drawChars(int seqstart, int seqend, int start)\r
 538     {\r
 539         seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,\r
 540             seqend, av.getStartRes(), av.getStartSeq(), 0);\r
 541         seqCanvas.repaint();\r
 542     }\r
 543 \r
 544     /**\r
 545      * DOCUMENT ME!\r
 546      *\r
 547      * @param j DOCUMENT ME!\r
 548      * @param seq DOCUMENT ME!\r
 549      */\r
 550     public void insertChar(int j, int seq)\r
 551     {\r
 552         av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
 553         seqEditOccurred = seq;\r
 554     }\r
 555 \r
 556     /**\r
 557      * DOCUMENT ME!\r
 558      *\r
 559      * @param j DOCUMENT ME!\r
 560      * @param seq DOCUMENT ME!\r
 561      */\r
 562     public void deleteChar(int j, int seq)\r
 563     {\r
 564         av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 565         seqEditOccurred = seq;\r
 566 \r
 567         av.alignment.getWidth();\r
 568         seqCanvas.repaint();\r
 569     }\r
 570 \r
 571     /**\r
 572      * DOCUMENT ME!\r
 573      *\r
 574      * @param i DOCUMENT ME!\r
 575      */\r
 576     void editOccurred(int i)\r
 577     {\r
 578         if (endEdit == startEdit)\r
 579         {\r
 580             ap.alignFrame.historyList.pop();\r
 581             ap.alignFrame.updateEditMenuBar();\r
 582         }\r
 583 \r
 584         av.updateConservation();\r
 585         av.updateConsensus();\r
 586 \r
 587         // Y O Y CLUSTALX\r
 588         ColourSchemeI cs = av.getGlobalColourScheme();\r
 589 \r
 590         if (av.getSelectionGroup() != null)\r
 591         {\r
 592             av.getSelectionGroup().recalcConservation();\r
 593         }\r
 594 \r
 595         if (cs.conservationApplied())\r
 596         {\r
 597             Conservation c = new Conservation("All",\r
 598                     ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
 599                     0, av.alignment.getWidth() - 1);\r
 600             c.calculate();\r
 601             c.verdict(false, av.ConsPercGaps);\r
 602 \r
 603             if (cs instanceof ClustalxColourScheme)\r
 604             {\r
 605                 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 606                 cxs.resetClustalX(av.alignment.getSequences(),\r
 607                     av.alignment.getWidth());\r
 608                 cs.setConservation(c);\r
 609                 av.setGlobalColourScheme(cs);\r
 610             }\r
 611             else\r
 612             {\r
 613                 cs.setConservation(c);\r
 614                 av.setGlobalColourScheme(cs);\r
 615             }\r
 616         }\r
 617 \r
 618         if (cs instanceof ClustalxColourScheme)\r
 619         {\r
 620             ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
 621                 av.alignment.getWidth());\r
 622             av.setGlobalColourScheme(cs);\r
 623         }\r
 624     }\r
 625 \r
 626     /**\r
 627      * DOCUMENT ME!\r
 628      *\r
 629      * @param evt DOCUMENT ME!\r
 630      */\r
 631     public void doMousePressedDefineMode(MouseEvent evt)\r
 632     {\r
 633         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 634         int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
 635         oldSeq = seq;\r
 636 \r
 637         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 638 \r
 639         if ((sequence == null) || (res > sequence.getLength()))\r
 640         {\r
 641             return;\r
 642         }\r
 643 \r
 644         stretchGroup = av.getSelectionGroup();\r
 645 \r
 646         if (stretchGroup == null)\r
 647         {\r
 648             stretchGroup = av.alignment.findGroup(sequence);\r
 649 \r
 650             if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
 651                     (res < stretchGroup.getEndRes()))\r
 652             {\r
 653                 av.setSelectionGroup(stretchGroup);\r
 654             }\r
 655             else\r
 656             {\r
 657                 stretchGroup = null;\r
 658             }\r
 659         }\r
 660         else if (!stretchGroup.sequences.contains(sequence) ||\r
 661                 (stretchGroup.getStartRes() > res) ||\r
 662                 (stretchGroup.getEndRes() < res))\r
 663         {\r
 664             stretchGroup = null;\r
 665 \r
 666             SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
 667 \r
 668             if (allGroups != null)\r
 669             {\r
 670                 for (int i = 0; i < allGroups.length; i++)\r
 671                 {\r
 672                     if ((allGroups[i].getStartRes() <= res) &&\r
 673                             (allGroups[i].getEndRes() >= res))\r
 674                     {\r
 675                         stretchGroup = allGroups[i];\r
 676                         av.setSelectionGroup(stretchGroup);\r
 677 \r
 678                         break;\r
 679                     }\r
 680                 }\r
 681             }\r
 682         }\r
 683 \r
 684         if (stretchGroup == null)\r
 685         {\r
 686             // define a new group here\r
 687             SequenceGroup sg = new SequenceGroup();\r
 688             sg.setStartRes(res);\r
 689             sg.setEndRes(res);\r
 690             sg.addSequence(sequence, false);\r
 691             av.setSelectionGroup(sg);\r
 692             stretchGroup = sg;\r
 693 \r
 694             if (av.getConservationSelected())\r
 695             {\r
 696                 SliderPanel.setConservationSlider(ap,\r
 697                     av.getGlobalColourScheme(), "Background");\r
 698             }\r
 699 \r
 700             if (av.getAbovePIDThreshold())\r
 701             {\r
 702                 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
 703                     "Background");\r
 704             }\r
 705         }\r
 706         else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
 707         {\r
 708             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
 709             pop.show(this, evt.getX(), evt.getY());\r
 710 \r
 711             // edit the properties of existing group\r
 712         }\r
 713 \r
 714         if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
 715         {\r
 716             // Edit end res position of selected group\r
 717             changeEndRes = true;\r
 718         }\r
 719         else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
 720         {\r
 721             // Edit end res position of selected group\r
 722             changeStartRes = true;\r
 723         }\r
 724 \r
 725         stretchGroup.getWidth();\r
 726 \r
 727         seqCanvas.repaint();\r
 728     }\r
 729 \r
 730     /**\r
 731      * DOCUMENT ME!\r
 732      *\r
 733      * @param evt DOCUMENT ME!\r
 734      */\r
 735     public void doMouseReleasedDefineMode(MouseEvent evt)\r
 736     {\r
 737         if (mouseDragging)\r
 738         {\r
 739             stretchGroup.recalcConservation();\r
 740             mouseDragging = false;\r
 741         }\r
 742 \r
 743         if (stretchGroup == null)\r
 744         {\r
 745             return;\r
 746         }\r
 747 \r
 748         if(stretchGroup.cs!=null)\r
 749         {\r
 750           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
 751           {\r
 752             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
 753                 sequences,\r
 754                 stretchGroup.getWidth());\r
 755           }\r
 756 \r
 757           if (stretchGroup.cs.conservationApplied())\r
 758           {\r
 759             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
 760                                               stretchGroup.getName());\r
 761           }\r
 762           else\r
 763           {\r
 764             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
 765                                            stretchGroup.getName());\r
 766           }\r
 767         }\r
 768         changeEndRes = false;\r
 769         changeStartRes = false;\r
 770         stretchGroup = null;\r
 771         PaintRefresher.Refresh(av.alignment);\r
 772     }\r
 773 \r
 774     /**\r
 775      * DOCUMENT ME!\r
 776      *\r
 777      * @param evt DOCUMENT ME!\r
 778      */\r
 779     public void doMouseDraggedDefineMode(MouseEvent evt)\r
 780     {\r
 781         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 782         int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
 783 \r
 784         if (stretchGroup == null)\r
 785         {\r
 786             return;\r
 787         }\r
 788 \r
 789         if (res > av.alignment.getWidth())\r
 790         {\r
 791             res = av.alignment.getWidth() - 1;\r
 792         }\r
 793 \r
 794         if (stretchGroup.getEndRes() == res)\r
 795         {\r
 796             // Edit end res position of selected group\r
 797             changeEndRes = true;\r
 798         }\r
 799         else if (stretchGroup.getStartRes() == res)\r
 800         {\r
 801             // Edit start res position of selected group\r
 802             changeStartRes = true;\r
 803         }\r
 804 \r
 805         if (res < av.getStartRes())\r
 806         {\r
 807             res = av.getStartRes();\r
 808         }\r
 809         else if (res > av.getEndRes())\r
 810         {\r
 811             res = av.getEndRes();\r
 812         }\r
 813 \r
 814         if (changeEndRes)\r
 815         {\r
 816             if (res > (stretchGroup.getStartRes() - 1))\r
 817             {\r
 818                 stretchGroup.setEndRes(res);\r
 819             }\r
 820         }\r
 821         else if (changeStartRes)\r
 822         {\r
 823             if (res < (stretchGroup.getEndRes() + 1))\r
 824             {\r
 825                 stretchGroup.setStartRes(res);\r
 826             }\r
 827         }\r
 828 \r
 829         int dragDirection = 0;\r
 830 \r
 831         if (y > oldSeq)\r
 832         {\r
 833             dragDirection = 1;\r
 834         }\r
 835         else if (y < oldSeq)\r
 836         {\r
 837             dragDirection = -1;\r
 838         }\r
 839 \r
 840         while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))\r
 841         {\r
 842             // This routine ensures we don't skip any sequences, as the\r
 843             // selection is quite slow.\r
 844             Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 845 \r
 846             oldSeq += dragDirection;\r
 847 \r
 848             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 849 \r
 850             if (stretchGroup.sequences.contains(nextSeq))\r
 851             {\r
 852                 stretchGroup.deleteSequence(seq, false);\r
 853             }\r
 854             else\r
 855             {\r
 856                 if (seq != null)\r
 857                 {\r
 858                     stretchGroup.addSequence(seq, false);\r
 859                 }\r
 860 \r
 861                 stretchGroup.addSequence(nextSeq, false);\r
 862             }\r
 863         }\r
 864 \r
 865         oldSeq = y;\r
 866         mouseDragging = true;\r
 867 \r
 868         if (scrollThread != null)\r
 869         {\r
 870             scrollThread.setEvent(evt);\r
 871         }\r
 872 \r
 873         seqCanvas.repaint();\r
 874     }\r
 875 \r
 876     /**\r
 877      * DOCUMENT ME!\r
 878      *\r
 879      * @param e DOCUMENT ME!\r
 880      */\r
 881     public void doMouseEnteredDefineMode(MouseEvent e)\r
 882     {\r
 883         if (scrollThread != null)\r
 884         {\r
 885             scrollThread.running = false;\r
 886         }\r
 887     }\r
 888 \r
 889     /**\r
 890      * DOCUMENT ME!\r
 891      *\r
 892      * @param e DOCUMENT ME!\r
 893      */\r
 894     public void doMouseExitedDefineMode(MouseEvent e)\r
 895     {\r
 896         if (av.getWrapAlignment())\r
 897         {\r
 898             return;\r
 899         }\r
 900 \r
 901         if (mouseDragging)\r
 902         {\r
 903             scrollThread = new ScrollThread();\r
 904         }\r
 905     }\r
 906 \r
 907     // this class allows scrolling off the bottom of the visible alignment\r
 908     class ScrollThread extends Thread\r
 909     {\r
 910         MouseEvent evt;\r
 911         boolean running = false;\r
 912 \r
 913         public ScrollThread()\r
 914         {\r
 915             start();\r
 916         }\r
 917 \r
 918         public void setEvent(MouseEvent e)\r
 919         {\r
 920             evt = e;\r
 921         }\r
 922 \r
 923         public void stopScrolling()\r
 924         {\r
 925             running = false;\r
 926         }\r
 927 \r
 928         public void run()\r
 929         {\r
 930             running = true;\r
 931 \r
 932             while (running)\r
 933             {\r
 934                 if (evt != null)\r
 935                 {\r
 936                     if (mouseDragging && (evt.getY() < 0) &&\r
 937                             (av.getStartSeq() > 0))\r
 938                     {\r
 939                         running = ap.scrollUp(true);\r
 940                     }\r
 941 \r
 942                     if (mouseDragging && (evt.getY() >= getHeight()) &&\r
 943                             (av.alignment.getHeight() > av.getEndSeq()))\r
 944                     {\r
 945                         running = ap.scrollUp(false);\r
 946                     }\r
 947 \r
 948                     if (mouseDragging && (evt.getX() < 0))\r
 949                     {\r
 950                         running = ap.scrollRight(true);\r
 951                     }\r
 952                     else if (mouseDragging && (evt.getX() >= getWidth()))\r
 953                     {\r
 954                         running = ap.scrollRight(false);\r
 955                     }\r
 956                 }\r
 957 \r
 958                 try\r
 959                 {\r
 960                     Thread.sleep(75);\r
 961                 }\r
 962                 catch (Exception ex)\r
 963                 {\r
 964                 }\r
 965             }\r
 966         }\r
 967     }\r
 968 }\r