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            }\r
 141            else\r
 142            {\r
 143              if (e.getWheelRotation() > 0)\r
 144                ap.scrollUp(false);\r
 145              else\r
 146                ap.scrollUp(true);\r
 147            }\r
 148 \r
 149          }\r
 150        });\r
 151 \r
 152 \r
 153         addMouseListener(new MouseAdapter()\r
 154             {\r
 155                 public void mouseReleased(MouseEvent evt)\r
 156                 {\r
 157                     mouseWheelPressed = false;\r
 158                     if (av.getWrapAlignment())\r
 159                     {\r
 160                         return;\r
 161                     }\r
 162 \r
 163                     if (editingSeqs)\r
 164                     {\r
 165                         doMouseReleased(evt);\r
 166                     }\r
 167                     else\r
 168                     {\r
 169                         doMouseReleasedDefineMode(evt);\r
 170                     }\r
 171                 }\r
 172 \r
 173                 public void mousePressed(MouseEvent evt)\r
 174                 {\r
 175                   if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
 176                   {\r
 177                     mouseWheelPressed = true;\r
 178                     return;\r
 179                   }\r
 180                     if (av.getWrapAlignment())\r
 181                     {\r
 182                         return;\r
 183                     }\r
 184 \r
 185                     if (evt.isShiftDown() || evt.isAltDown() ||\r
 186                             evt.isControlDown())\r
 187                     {\r
 188                         if (evt.isAltDown() || evt.isControlDown())\r
 189                         {\r
 190                             groupEditing = true;\r
 191                         }\r
 192 \r
 193                         editingSeqs = true;\r
 194                         doMousePressed(evt);\r
 195                     }\r
 196                     else\r
 197                     {\r
 198                         doMousePressedDefineMode(evt);\r
 199                     }\r
 200                 }\r
 201 \r
 202                 public void mouseExited(MouseEvent evt)\r
 203                 {\r
 204                     if (av.getWrapAlignment() || editingSeqs)\r
 205                     {\r
 206                         return;\r
 207                     }\r
 208 \r
 209                     doMouseExitedDefineMode(evt);\r
 210                 }\r
 211 \r
 212                 public void mouseEntered(MouseEvent evt)\r
 213                 {\r
 214                     if (av.getWrapAlignment() || editingSeqs)\r
 215                     {\r
 216                         return;\r
 217                     }\r
 218 \r
 219                     doMouseEnteredDefineMode(evt);\r
 220                 }\r
 221             });\r
 222     }\r
 223 \r
 224     /**\r
 225      * DOCUMENT ME!\r
 226      *\r
 227      * @param evt DOCUMENT ME!\r
 228      */\r
 229     public void doMouseReleased(MouseEvent evt)\r
 230     {\r
 231         if (seqEditOccurred > -1)\r
 232         {\r
 233             editOccurred(seqEditOccurred);\r
 234         }\r
 235 \r
 236         startseq = -1;\r
 237         lastres = -1;\r
 238         seqEditOccurred = -1;\r
 239         editingSeqs = false;\r
 240         groupEditing = false;\r
 241 \r
 242         ap.repaint();\r
 243     }\r
 244 \r
 245     /**\r
 246      * DOCUMENT ME!\r
 247      *\r
 248      * @param evt DOCUMENT ME!\r
 249      */\r
 250     public void doMousePressed(MouseEvent evt)\r
 251     {\r
 252         ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
 253                 av.alignment, HistoryItem.EDIT));\r
 254 \r
 255         int seq;\r
 256         int res;\r
 257 \r
 258         int x = evt.getX();\r
 259         int y = evt.getY();\r
 260 \r
 261         res = (x / av.getCharWidth()) + av.getStartRes();\r
 262         seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 263 \r
 264         if ((seq < av.getAlignment().getHeight()) &&\r
 265                 (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
 266         {\r
 267             startseq = seq;\r
 268             lastres = res;\r
 269         }\r
 270         else\r
 271         {\r
 272             startseq = -1;\r
 273             lastres = -1;\r
 274         }\r
 275 \r
 276         startEdit = lastres;\r
 277         endEdit = lastres;\r
 278 \r
 279         return;\r
 280     }\r
 281 \r
 282     /**\r
 283      * DOCUMENT ME!\r
 284      *\r
 285      * @param evt DOCUMENT ME!\r
 286      */\r
 287     public void doMouseMoved(MouseEvent evt)\r
 288     {\r
 289         int res = 0;\r
 290         int seq = 0;\r
 291         int x = evt.getX();\r
 292         int y = evt.getY();\r
 293 \r
 294         if (av.wrapAlignment)\r
 295         {\r
 296             y -= (2 * av.charHeight);\r
 297 \r
 298             int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
 299 \r
 300             res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +\r
 301                 (x / av.getCharWidth()) + av.getStartRes();\r
 302 \r
 303             y %= chunkHeight;\r
 304             seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 305         }\r
 306         else\r
 307         {\r
 308             res = (x / av.getCharWidth()) + av.getStartRes();\r
 309             seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 310         }\r
 311 \r
 312         if (seq >= av.getAlignment().getHeight())\r
 313         {\r
 314             return;\r
 315         }\r
 316 \r
 317         SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
 318 \r
 319         if (res > sequence.getLength())\r
 320         {\r
 321             return;\r
 322         }\r
 323 \r
 324         Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +\r
 325                 "");\r
 326         String aa = "";\r
 327 \r
 328         if (obj != null)\r
 329         {\r
 330             aa = obj.toString();\r
 331         }\r
 332 \r
 333         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
 334                 sequence.getName());\r
 335 \r
 336         if (aa != "")\r
 337         {\r
 338             text.append("  Residue: " + aa + " (" +\r
 339                 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
 340         }\r
 341 \r
 342         ap.alignFrame.statusBar.setText(text.toString());\r
 343 \r
 344         // use aa to see if the mouse pointer is on a\r
 345         if (av.showSequenceFeatures)\r
 346         {\r
 347             Vector features = sequence.getSequenceFeatures();\r
 348             Enumeration e = features.elements();\r
 349             StringBuffer sbuffer = new StringBuffer();\r
 350 \r
 351             while (e.hasMoreElements())\r
 352             {\r
 353                 SequenceFeature sf = (SequenceFeature) e.nextElement();\r
 354 \r
 355                 if ((sf.getStart() <= sequence.findPosition(res)) &&\r
 356                         (sf.getEnd() >= sequence.findPosition(res)))\r
 357                 {\r
 358                     if (sbuffer.length() > 0)\r
 359                     {\r
 360                         sbuffer.append("; ");\r
 361                     }\r
 362 \r
 363                     sbuffer.append(sf.getType() + " " + sf.getDescription());\r
 364 \r
 365                     if (sf.getStatus().length() > 0)\r
 366                     {\r
 367                         sbuffer.append(" (" + sf.getStatus() + ")");\r
 368                     }\r
 369                 }\r
 370             }\r
 371 \r
 372             this.setToolTipText(sbuffer.toString());\r
 373         }\r
 374     }\r
 375 \r
 376     /**\r
 377      * DOCUMENT ME!\r
 378      *\r
 379      * @param evt DOCUMENT ME!\r
 380      */\r
 381     public void doMouseDragged(MouseEvent evt)\r
 382     {\r
 383         // If we're dragging we're editing\r
 384         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 385 \r
 386         if (res < 0)\r
 387         {\r
 388             res = 0;\r
 389         }\r
 390 \r
 391         if ((lastres == -1) || (lastres == res))\r
 392         {\r
 393             return;\r
 394         }\r
 395 \r
 396         boolean dragRight = true;\r
 397 \r
 398         if ((res < av.getAlignment().getWidth()) && (res < lastres))\r
 399         {\r
 400             dragRight = false;\r
 401         }\r
 402 \r
 403         if (res != lastres)\r
 404         {\r
 405             // Group editing\r
 406             if (groupEditing)\r
 407             {\r
 408                 SequenceGroup sg = av.getSelectionGroup();\r
 409 \r
 410                 if (sg == null)\r
 411                 {\r
 412                     lastres = -1;\r
 413 \r
 414                     return;\r
 415                 }\r
 416 \r
 417                 // drag to right\r
 418                 if (dragRight)\r
 419                 {\r
 420                     sg.setEndRes(sg.getEndRes() + (res - lastres));\r
 421                 }\r
 422 \r
 423                 // drag to left\r
 424                 else\r
 425                 {\r
 426                     /// Are we able to delete?\r
 427                     // ie are all columns blank?\r
 428                     boolean deleteAllowed = false;\r
 429 \r
 430                     for (int s = 0; s < sg.getSize(); s++)\r
 431                     {\r
 432                         SequenceI seq = sg.getSequenceAt(s);\r
 433 \r
 434                         for (int j = res; j < lastres; j++)\r
 435                         {\r
 436                             if (seq.getSequence().length() <= j)\r
 437                             {\r
 438                                 continue;\r
 439                             }\r
 440 \r
 441                             if (!jalview.util.Comparison.isGap(\r
 442                                         seq.getSequence().charAt(j)))\r
 443                             {\r
 444                                 // Not a gap, block edit not valid\r
 445                                 res = j + 1;\r
 446                                 deleteAllowed = false;\r
 447 \r
 448                                 continue;\r
 449                             }\r
 450 \r
 451                             deleteAllowed = true;\r
 452                         }\r
 453                     }\r
 454 \r
 455                     if (!deleteAllowed)\r
 456                     {\r
 457                         lastres = -1;\r
 458 \r
 459                         return;\r
 460                     }\r
 461 \r
 462                     sg.setEndRes(sg.getEndRes() - (lastres - res));\r
 463                 }\r
 464 \r
 465                 for (int i = 0; i < sg.getSize(); i++)\r
 466                 {\r
 467                     SequenceI s = sg.getSequenceAt(i);\r
 468                     int k = av.alignment.findIndex(s);\r
 469 \r
 470                     // drag to right\r
 471                     if (dragRight)\r
 472                     {\r
 473                         for (int j = lastres; j < res; j++)\r
 474                         {\r
 475                             insertChar(j, k);\r
 476                         }\r
 477                     }\r
 478 \r
 479                     // drag to left\r
 480                     else\r
 481                     {\r
 482                         for (int j = res; j < lastres; j++)\r
 483                         {\r
 484                             if (s.getLength() > j)\r
 485                             {\r
 486                                 deleteChar(res, k);\r
 487                             }\r
 488                         }\r
 489                     }\r
 490                 }\r
 491             }\r
 492             else /////Editing a single sequence///////////\r
 493             {\r
 494                 if ((res < av.getAlignment().getWidth()) && (res > lastres))\r
 495                 {\r
 496                     // dragging to the right\r
 497                     for (int j = lastres; j < res; j++)\r
 498                     {\r
 499                         insertChar(j, startseq);\r
 500                     }\r
 501                 }\r
 502                 else if ((res < av.getAlignment().getWidth()) &&\r
 503                         (res < lastres))\r
 504                 {\r
 505                     // dragging to the left\r
 506                     for (int j = lastres; j > res; j--)\r
 507                     {\r
 508                         if (jalview.util.Comparison.isGap(\r
 509                                     av.alignment.getSequenceAt(startseq)\r
 510                                                     .getSequence().charAt(res)))\r
 511                         {\r
 512                             deleteChar(res, startseq);\r
 513                         }\r
 514                         else\r
 515                         {\r
 516                             break;\r
 517                         }\r
 518                     }\r
 519                 }\r
 520             }\r
 521         }\r
 522 \r
 523         endEdit = res;\r
 524         lastres = res;\r
 525         seqCanvas.repaint();\r
 526     }\r
 527 \r
 528     /**\r
 529      * DOCUMENT ME!\r
 530      *\r
 531      * @param seqstart DOCUMENT ME!\r
 532      * @param seqend DOCUMENT ME!\r
 533      * @param start DOCUMENT ME!\r
 534      */\r
 535     public void drawChars(int seqstart, int seqend, int start)\r
 536     {\r
 537         seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,\r
 538             seqend, av.getStartRes(), av.getStartSeq(), 0);\r
 539         seqCanvas.repaint();\r
 540     }\r
 541 \r
 542     /**\r
 543      * DOCUMENT ME!\r
 544      *\r
 545      * @param j DOCUMENT ME!\r
 546      * @param seq DOCUMENT ME!\r
 547      */\r
 548     public void insertChar(int j, int seq)\r
 549     {\r
 550         av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
 551         seqEditOccurred = seq;\r
 552     }\r
 553 \r
 554     /**\r
 555      * DOCUMENT ME!\r
 556      *\r
 557      * @param j DOCUMENT ME!\r
 558      * @param seq DOCUMENT ME!\r
 559      */\r
 560     public void deleteChar(int j, int seq)\r
 561     {\r
 562         av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 563         seqEditOccurred = seq;\r
 564 \r
 565         av.alignment.getWidth();\r
 566         seqCanvas.repaint();\r
 567     }\r
 568 \r
 569     /**\r
 570      * DOCUMENT ME!\r
 571      *\r
 572      * @param i DOCUMENT ME!\r
 573      */\r
 574     void editOccurred(int i)\r
 575     {\r
 576       if (endEdit == startEdit)\r
 577       {\r
 578         ap.alignFrame.historyList.pop();\r
 579         ap.alignFrame.updateEditMenuBar();\r
 580       }\r
 581 \r
 582       av.updateConservation();\r
 583       av.updateConsensus();\r
 584 \r
 585       //Does the edit affect any groups?\r
 586       //////////////////////////////\r
 587       Vector groupsToUpdate = new Vector();\r
 588       SequenceGroup sg = av.getSelectionGroup();\r
 589 \r
 590       int s, g, gSize = av.alignment.getGroups().size();\r
 591       if (sg != null)\r
 592       {\r
 593         groupsToUpdate.addElement(av.getSelectionGroup());\r
 594         int sSize = sg.getSize();\r
 595         for (s = 0; s < sSize; s++)\r
 596         {\r
 597           SequenceI seq = sg.getSequenceAt(s);\r
 598 \r
 599           for (g = 0; g < gSize; g++)\r
 600           {\r
 601             SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().\r
 602                 elementAt(\r
 603                     g);\r
 604             if (sg2.sequences.contains(seq))\r
 605             {\r
 606               if (!groupsToUpdate.contains(sg2))\r
 607                 groupsToUpdate.addElement(sg2);\r
 608               continue;\r
 609             }\r
 610           }\r
 611         }\r
 612       }\r
 613       else\r
 614       {\r
 615         SequenceI seq = av.alignment.getSequenceAt(startseq);\r
 616         for (g = 0; g < gSize; g++)\r
 617         {\r
 618           SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(\r
 619               g);\r
 620           if (sg2.sequences.contains(seq))\r
 621           {\r
 622             if (!groupsToUpdate.contains(sg2))\r
 623               groupsToUpdate.addElement(sg2);\r
 624             continue;\r
 625           }\r
 626         }\r
 627       }\r
 628 \r
 629       gSize = groupsToUpdate.size();\r
 630       for (g = 0; g < gSize; g++)\r
 631       {\r
 632         ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();\r
 633       }\r
 634       ////End of updating groups\r
 635       //////////////////////////////////////////\r
 636 \r
 637         // Y O Y CLUSTALX\r
 638         ColourSchemeI cs = av.getGlobalColourScheme();\r
 639         if(cs!=null)\r
 640         {\r
 641           if (cs.conservationApplied())\r
 642           {\r
 643             Conservation c = new Conservation("All",\r
 644                                               ResidueProperties.propHash, 3,\r
 645                                               av.alignment.getSequences(),\r
 646                                               0, av.alignment.getWidth() - 1);\r
 647             c.calculate();\r
 648             c.verdict(false, av.ConsPercGaps);\r
 649 \r
 650             if (cs instanceof ClustalxColourScheme)\r
 651             {\r
 652               ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 653               cxs.resetClustalX(av.alignment.getSequences(),\r
 654                                 av.alignment.getWidth());\r
 655               cs.setConservation(c);\r
 656               av.setGlobalColourScheme(cs);\r
 657             }\r
 658             else\r
 659             {\r
 660               cs.setConservation(c);\r
 661               av.setGlobalColourScheme(cs);\r
 662             }\r
 663 \r
 664           }\r
 665 \r
 666           if (cs instanceof ClustalxColourScheme)\r
 667           {\r
 668             ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
 669                                                        av.alignment.getWidth());\r
 670             av.setGlobalColourScheme(cs);\r
 671           }\r
 672         }\r
 673     }\r
 674 \r
 675     /**\r
 676      * DOCUMENT ME!\r
 677      *\r
 678      * @param evt DOCUMENT ME!\r
 679      */\r
 680     public void doMousePressedDefineMode(MouseEvent evt)\r
 681     {\r
 682         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 683         int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
 684         oldSeq = seq;\r
 685 \r
 686         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 687 \r
 688         if ((sequence == null) || (res > sequence.getLength()))\r
 689         {\r
 690             return;\r
 691         }\r
 692 \r
 693         stretchGroup = av.getSelectionGroup();\r
 694 \r
 695         if (stretchGroup == null)\r
 696         {\r
 697             stretchGroup = av.alignment.findGroup(sequence);\r
 698 \r
 699             if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
 700                     (res < stretchGroup.getEndRes()))\r
 701             {\r
 702                 av.setSelectionGroup(stretchGroup);\r
 703             }\r
 704             else\r
 705             {\r
 706                 stretchGroup = null;\r
 707             }\r
 708         }\r
 709         else if (!stretchGroup.sequences.contains(sequence) ||\r
 710                 (stretchGroup.getStartRes() > res) ||\r
 711                 (stretchGroup.getEndRes() < res))\r
 712         {\r
 713             stretchGroup = null;\r
 714 \r
 715             SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
 716 \r
 717             if (allGroups != null)\r
 718             {\r
 719                 for (int i = 0; i < allGroups.length; i++)\r
 720                 {\r
 721                     if ((allGroups[i].getStartRes() <= res) &&\r
 722                             (allGroups[i].getEndRes() >= res))\r
 723                     {\r
 724                         stretchGroup = allGroups[i];\r
 725                         av.setSelectionGroup(stretchGroup);\r
 726 \r
 727                         break;\r
 728                     }\r
 729                 }\r
 730             }\r
 731         }\r
 732 \r
 733         if (stretchGroup == null)\r
 734         {\r
 735             // define a new group here\r
 736             SequenceGroup sg = new SequenceGroup();\r
 737             sg.setStartRes(res);\r
 738             sg.setEndRes(res);\r
 739             sg.addSequence(sequence, false);\r
 740             av.setSelectionGroup(sg);\r
 741             stretchGroup = sg;\r
 742 \r
 743             if (av.getConservationSelected())\r
 744             {\r
 745                 SliderPanel.setConservationSlider(ap,\r
 746                     av.getGlobalColourScheme(), "Background");\r
 747             }\r
 748 \r
 749             if (av.getAbovePIDThreshold())\r
 750             {\r
 751                 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
 752                     "Background");\r
 753             }\r
 754         }\r
 755         else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
 756         {\r
 757             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
 758             pop.show(this, evt.getX(), evt.getY());\r
 759 \r
 760             // edit the properties of existing group\r
 761         }\r
 762 \r
 763         if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
 764         {\r
 765             // Edit end res position of selected group\r
 766             changeEndRes = true;\r
 767         }\r
 768         else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
 769         {\r
 770             // Edit end res position of selected group\r
 771             changeStartRes = true;\r
 772         }\r
 773 \r
 774         stretchGroup.getWidth();\r
 775 \r
 776         seqCanvas.repaint();\r
 777     }\r
 778 \r
 779     /**\r
 780      * DOCUMENT ME!\r
 781      *\r
 782      * @param evt DOCUMENT ME!\r
 783      */\r
 784     public void doMouseReleasedDefineMode(MouseEvent evt)\r
 785     {\r
 786         if (mouseDragging)\r
 787         {\r
 788             stretchGroup.recalcConservation();\r
 789             mouseDragging = false;\r
 790         }\r
 791 \r
 792         if (stretchGroup == null)\r
 793         {\r
 794             return;\r
 795         }\r
 796 \r
 797         if(stretchGroup.cs!=null)\r
 798         {\r
 799           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
 800           {\r
 801             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
 802                 sequences,\r
 803                 stretchGroup.getWidth());\r
 804           }\r
 805 \r
 806           if (stretchGroup.cs.conservationApplied())\r
 807           {\r
 808             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
 809                                               stretchGroup.getName());\r
 810           }\r
 811           else\r
 812           {\r
 813             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
 814                                            stretchGroup.getName());\r
 815           }\r
 816         }\r
 817         changeEndRes = false;\r
 818         changeStartRes = false;\r
 819         stretchGroup = null;\r
 820         PaintRefresher.Refresh(av.alignment);\r
 821     }\r
 822 \r
 823     /**\r
 824      * DOCUMENT ME!\r
 825      *\r
 826      * @param evt DOCUMENT ME!\r
 827      */\r
 828     public void doMouseDraggedDefineMode(MouseEvent evt)\r
 829     {\r
 830         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 831         int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();\r
 832 \r
 833         if (stretchGroup == null)\r
 834         {\r
 835             return;\r
 836         }\r
 837 \r
 838         if (res > av.alignment.getWidth())\r
 839         {\r
 840             res = av.alignment.getWidth() - 1;\r
 841         }\r
 842 \r
 843         if (stretchGroup.getEndRes() == res)\r
 844         {\r
 845             // Edit end res position of selected group\r
 846             changeEndRes = true;\r
 847         }\r
 848         else if (stretchGroup.getStartRes() == res)\r
 849         {\r
 850             // Edit start res position of selected group\r
 851             changeStartRes = true;\r
 852         }\r
 853 \r
 854         if (res < av.getStartRes())\r
 855         {\r
 856             res = av.getStartRes();\r
 857         }\r
 858         else if (res > av.getEndRes())\r
 859         {\r
 860             res = av.getEndRes();\r
 861         }\r
 862 \r
 863         if (changeEndRes)\r
 864         {\r
 865             if (res > (stretchGroup.getStartRes() - 1))\r
 866             {\r
 867                 stretchGroup.setEndRes(res);\r
 868             }\r
 869         }\r
 870         else if (changeStartRes)\r
 871         {\r
 872             if (res < (stretchGroup.getEndRes() + 1))\r
 873             {\r
 874                 stretchGroup.setStartRes(res);\r
 875             }\r
 876         }\r
 877 \r
 878         int dragDirection = 0;\r
 879 \r
 880         if (y > oldSeq)\r
 881         {\r
 882             dragDirection = 1;\r
 883         }\r
 884         else if (y < oldSeq)\r
 885         {\r
 886             dragDirection = -1;\r
 887         }\r
 888 \r
 889         while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))\r
 890         {\r
 891             // This routine ensures we don't skip any sequences, as the\r
 892             // selection is quite slow.\r
 893             Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 894 \r
 895             oldSeq += dragDirection;\r
 896 \r
 897             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 898 \r
 899             if (stretchGroup.sequences.contains(nextSeq))\r
 900             {\r
 901                 stretchGroup.deleteSequence(seq, false);\r
 902             }\r
 903             else\r
 904             {\r
 905                 if (seq != null)\r
 906                 {\r
 907                     stretchGroup.addSequence(seq, false);\r
 908                 }\r
 909 \r
 910                 stretchGroup.addSequence(nextSeq, false);\r
 911             }\r
 912         }\r
 913 \r
 914         oldSeq = y;\r
 915         mouseDragging = true;\r
 916 \r
 917         if (scrollThread != null)\r
 918         {\r
 919             scrollThread.setEvent(evt);\r
 920         }\r
 921 \r
 922         seqCanvas.repaint();\r
 923     }\r
 924 \r
 925     /**\r
 926      * DOCUMENT ME!\r
 927      *\r
 928      * @param e DOCUMENT ME!\r
 929      */\r
 930     public void doMouseEnteredDefineMode(MouseEvent e)\r
 931     {\r
 932         if (scrollThread != null)\r
 933         {\r
 934             scrollThread.running = false;\r
 935         }\r
 936     }\r
 937 \r
 938     /**\r
 939      * DOCUMENT ME!\r
 940      *\r
 941      * @param e DOCUMENT ME!\r
 942      */\r
 943     public void doMouseExitedDefineMode(MouseEvent e)\r
 944     {\r
 945         if (av.getWrapAlignment())\r
 946         {\r
 947             return;\r
 948         }\r
 949 \r
 950         if (mouseDragging)\r
 951         {\r
 952             scrollThread = new ScrollThread();\r
 953         }\r
 954     }\r
 955 \r
 956     // this class allows scrolling off the bottom of the visible alignment\r
 957     class ScrollThread extends Thread\r
 958     {\r
 959         MouseEvent evt;\r
 960         boolean running = false;\r
 961 \r
 962         public ScrollThread()\r
 963         {\r
 964             start();\r
 965         }\r
 966 \r
 967         public void setEvent(MouseEvent e)\r
 968         {\r
 969             evt = e;\r
 970         }\r
 971 \r
 972         public void stopScrolling()\r
 973         {\r
 974             running = false;\r
 975         }\r
 976 \r
 977         public void run()\r
 978         {\r
 979             running = true;\r
 980 \r
 981             while (running)\r
 982             {\r
 983                 if (evt != null)\r
 984                 {\r
 985                     if (mouseDragging && (evt.getY() < 0) &&\r
 986                             (av.getStartSeq() > 0))\r
 987                     {\r
 988                         running = ap.scrollUp(true);\r
 989                     }\r
 990 \r
 991                     if (mouseDragging && (evt.getY() >= getHeight()) &&\r
 992                             (av.alignment.getHeight() > av.getEndSeq()))\r
 993                     {\r
 994                         running = ap.scrollUp(false);\r
 995                     }\r
 996 \r
 997                     if (mouseDragging && (evt.getX() < 0))\r
 998                     {\r
 999                         running = ap.scrollRight(true);\r
1000                     }\r
1001                     else if (mouseDragging && (evt.getX() >= getWidth()))\r
1002                     {\r
1003                         running = ap.scrollRight(false);\r
1004                     }\r
1005                 }\r
1006 \r
1007                 try\r
1008                 {\r
1009                     Thread.sleep(75);\r
1010                 }\r
1011                 catch (Exception ex)\r
1012                 {\r
1013                 }\r
1014             }\r
1015         }\r
1016     }\r
1017 }\r