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.datamodel.*;\r
  22 \r
  23 import jalview.schemes.*;\r
  24 \r
  25 import java.awt.*;\r
  26 import java.awt.event.*;\r
  27 \r
  28 import java.util.*;\r
  29 \r
  30 import javax.swing.*;\r
  31 \r
  32 \r
  33 /**\r
  34  * DOCUMENT ME!\r
  35  *\r
  36  * @author $author$\r
  37  * @version $Revision$\r
  38  */\r
  39 public class SeqPanel extends JPanel\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     int startEdit = -1;\r
  49     int endEdit = -1;\r
  50     protected AlignViewport av;\r
  51 \r
  52     // if character is inserted or deleted, we will need to recalculate the conservation\r
  53     int seqEditOccurred = -1;\r
  54     ScrollThread scrollThread = null;\r
  55     boolean mouseDragging = false;\r
  56     boolean editingSeqs = false;\r
  57     boolean groupEditing = false;\r
  58 \r
  59     //////////////////////////////////////////\r
  60     /////Everything below this is for defining the boundary of the rubberband\r
  61     //////////////////////////////////////////\r
  62     int oldSeq = -1;\r
  63     boolean changeEndSeq = false;\r
  64     boolean changeStartSeq = false;\r
  65     boolean changeEndRes = false;\r
  66     boolean changeStartRes = false;\r
  67     SequenceGroup stretchGroup = null;\r
  68     boolean remove = false;\r
  69 \r
  70     boolean mouseWheelPressed = false;\r
  71 \r
  72     /**\r
  73      * Creates a new SeqPanel object.\r
  74      *\r
  75      * @param avp DOCUMENT ME!\r
  76      * @param p DOCUMENT ME!\r
  77      */\r
  78     public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
  79     {\r
  80         ToolTipManager.sharedInstance().registerComponent(this);\r
  81         ToolTipManager.sharedInstance().setInitialDelay(0);\r
  82         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
  83         this.av = avp;\r
  84         setBackground(Color.white);\r
  85 \r
  86         seqCanvas = new SeqCanvas(avp);\r
  87         setLayout(new BorderLayout());\r
  88         add(seqCanvas, BorderLayout.CENTER);\r
  89 \r
  90         ap = p;\r
  91 \r
  92 \r
  93         addMouseMotionListener(new MouseMotionAdapter()\r
  94             {\r
  95                 public void mouseMoved(MouseEvent evt)\r
  96                 {\r
  97                     doMouseMoved(evt);\r
  98                     if (editingSeqs)\r
  99                     {\r
 100                       // This is because MacOSX creates a mouseMoved\r
 101                       // If control is down\r
 102                       if(!av.isDataset())\r
 103                         doMouseDragged(evt);\r
 104                     }\r
 105                 }\r
 106 \r
 107                 public void mouseDragged(MouseEvent evt)\r
 108                 {\r
 109                     if (editingSeqs)\r
 110                     {\r
 111                       if(!av.isDataset())\r
 112                         doMouseDragged(evt);\r
 113                     }\r
 114                     else\r
 115                     {\r
 116                       if(!av.isDataset())\r
 117                         doMouseDraggedDefineMode(evt);\r
 118                     }\r
 119                 }\r
 120             });\r
 121 \r
 122        addMouseWheelListener(new MouseWheelListener()\r
 123        {\r
 124          public void mouseWheelMoved(MouseWheelEvent e)\r
 125          {\r
 126 \r
 127            if (mouseWheelPressed)\r
 128            {\r
 129              Font font = av.getFont();\r
 130              int fontSize = font.getSize();\r
 131              if (e.getWheelRotation() > 0 && fontSize < 51)\r
 132                fontSize++;\r
 133              else if (fontSize > 1)\r
 134                fontSize--;\r
 135 \r
 136              av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\r
 137              ap.fontChanged();\r
 138            }\r
 139            else\r
 140            {\r
 141              if (e.getWheelRotation() > 0)\r
 142                ap.scrollUp(false);\r
 143              else\r
 144                ap.scrollUp(true);\r
 145            }\r
 146 \r
 147          }\r
 148        });\r
 149 \r
 150 \r
 151        if(!av.isDataset())\r
 152        {\r
 153          addMouseListener(new MouseAdapter()\r
 154          {\r
 155            public void mouseReleased(MouseEvent evt)\r
 156            {\r
 157              mouseWheelPressed = false;\r
 158 \r
 159              if (editingSeqs)\r
 160              {\r
 161                doMouseReleased(evt);\r
 162              }\r
 163              else\r
 164              {\r
 165                doMouseReleasedDefineMode(evt);\r
 166              }\r
 167            }\r
 168 \r
 169            public void mousePressed(MouseEvent evt)\r
 170            {\r
 171              if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
 172              {\r
 173                mouseWheelPressed = true;\r
 174                return;\r
 175              }\r
 176 \r
 177              if (evt.isShiftDown() || evt.isAltDown() ||\r
 178                  evt.isControlDown())\r
 179              {\r
 180                if (evt.isAltDown() || evt.isControlDown())\r
 181                {\r
 182                  groupEditing = true;\r
 183 \r
 184                }\r
 185 \r
 186                editingSeqs = true;\r
 187                doMousePressed(evt);\r
 188              }\r
 189              else\r
 190              {\r
 191                doMousePressedDefineMode(evt);\r
 192              }\r
 193            }\r
 194 \r
 195            public void mouseExited(MouseEvent evt)\r
 196            {\r
 197              if (editingSeqs)\r
 198              {\r
 199                return;\r
 200              }\r
 201 \r
 202              doMouseExitedDefineMode(evt);\r
 203            }\r
 204 \r
 205            public void mouseEntered(MouseEvent evt)\r
 206            {\r
 207              if (editingSeqs)\r
 208              {\r
 209                return;\r
 210              }\r
 211 \r
 212              doMouseEnteredDefineMode(evt);\r
 213            }\r
 214          });\r
 215        }\r
 216     }\r
 217 \r
 218     int startWrapBlock=-1;\r
 219     int wrappedBlock=-1;\r
 220     int findRes(MouseEvent evt)\r
 221    {\r
 222      int res = 0;\r
 223      int x = evt.getX();\r
 224 \r
 225     if (av.wrapAlignment)\r
 226     {\r
 227 \r
 228       int hgap = av.charHeight;\r
 229       if (av.scaleAboveWrapped)\r
 230         hgap += av.charHeight;\r
 231 \r
 232       int cHeight = av.getAlignment().getHeight() * av.charHeight\r
 233           + hgap + seqCanvas.getAnnotationHeight();\r
 234 \r
 235         int y = evt.getY();\r
 236         y -= hgap;\r
 237         x -= seqCanvas.LABEL_WEST;\r
 238 \r
 239 \r
 240         int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
 241 \r
 242         wrappedBlock = y / cHeight;\r
 243         wrappedBlock += av.getStartRes() / cwidth;\r
 244 \r
 245         res = wrappedBlock * cwidth + x / av.getCharWidth();\r
 246 \r
 247     }\r
 248     else\r
 249     {\r
 250         res = (x / av.getCharWidth()) + av.getStartRes();\r
 251     }\r
 252 \r
 253     if(av.hasHiddenColumns)\r
 254           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 255 \r
 256     return res;\r
 257 \r
 258    }\r
 259 \r
 260    int findSeq(MouseEvent evt)\r
 261    {\r
 262 \r
 263      int seq = 0;\r
 264      int y = evt.getY();\r
 265 \r
 266      if (av.wrapAlignment)\r
 267      {\r
 268        int hgap = av.charHeight;\r
 269        if (av.scaleAboveWrapped)\r
 270          hgap += av.charHeight;\r
 271 \r
 272        int cHeight = av.getAlignment().getHeight() * av.charHeight\r
 273            + hgap + seqCanvas.getAnnotationHeight();\r
 274 \r
 275          y -= hgap;\r
 276 \r
 277        seq = ( (y % cHeight) / av.getCharHeight());\r
 278      }\r
 279      else\r
 280      {\r
 281        seq = (y / av.getCharHeight()) + av.getStartSeq();\r
 282      }\r
 283 \r
 284      return seq;\r
 285    }\r
 286 \r
 287 \r
 288     /**\r
 289      * DOCUMENT ME!\r
 290      *\r
 291      * @param evt DOCUMENT ME!\r
 292      */\r
 293     public void doMouseReleased(MouseEvent evt)\r
 294     {\r
 295         if (seqEditOccurred > -1)\r
 296         {\r
 297             editOccurred(seqEditOccurred);\r
 298         }\r
 299 \r
 300         startseq = -1;\r
 301         lastres = -1;\r
 302         seqEditOccurred = -1;\r
 303         editingSeqs = false;\r
 304         groupEditing = false;\r
 305 \r
 306         ap.repaint();\r
 307     }\r
 308 \r
 309     /**\r
 310      * DOCUMENT ME!\r
 311      *\r
 312      * @param evt DOCUMENT ME!\r
 313      */\r
 314     public void doMousePressed(MouseEvent evt)\r
 315     {\r
 316       ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
 317                                                    av.alignment, HistoryItem.EDIT));\r
 318 \r
 319       int seq = findSeq(evt);\r
 320       int res = findRes(evt);\r
 321 \r
 322       if(seq<0 || res<0)\r
 323         return;\r
 324 \r
 325         if ((seq < av.getAlignment().getHeight()) &&\r
 326                 (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
 327         {\r
 328             startseq = seq;\r
 329             lastres = res;\r
 330         }\r
 331         else\r
 332         {\r
 333             startseq = -1;\r
 334             lastres = -1;\r
 335         }\r
 336 \r
 337         startEdit = lastres;\r
 338         endEdit = lastres;\r
 339 \r
 340         return;\r
 341     }\r
 342 \r
 343     /**\r
 344      * DOCUMENT ME!\r
 345      *\r
 346      * @param evt DOCUMENT ME!\r
 347      */\r
 348     public void doMouseMoved(MouseEvent evt)\r
 349     {\r
 350       int res = findRes(evt);\r
 351       int seq = findSeq(evt);\r
 352 \r
 353       if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
 354             return;\r
 355 \r
 356       SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
 357 \r
 358       if (res > sequence.getLength())\r
 359       {\r
 360         return;\r
 361       }\r
 362 \r
 363       if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
 364       {\r
 365         seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
 366       }\r
 367 \r
 368 \r
 369         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
 370                 sequence.getName());\r
 371 \r
 372         Object obj = null;\r
 373         if (av.alignment.isNucleotide())\r
 374         {\r
 375           obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
 376               "");\r
 377           if(obj!=null)\r
 378             text.append(" Nucleotide: ");\r
 379         }\r
 380         else\r
 381         {\r
 382           obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
 383           if(obj!=null)\r
 384             text.append("  Residue: ");\r
 385         }\r
 386 \r
 387         if (obj != null)\r
 388         {\r
 389 \r
 390           if (obj != "")\r
 391           {\r
 392             text.append( obj + " (" +\r
 393                         av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
 394           }\r
 395         }\r
 396 \r
 397         ap.alignFrame.statusBar.setText(text.toString());\r
 398 \r
 399         // use aa to see if the mouse pointer is on a\r
 400         if (av.showSequenceFeatures)\r
 401         {\r
 402             SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();\r
 403             if(features!=null)\r
 404             {\r
 405               StringBuffer sbuffer = new StringBuffer("<html>");\r
 406 \r
 407               for (int i = 0; i < features.length; i++)\r
 408               {\r
 409 \r
 410                 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&\r
 411                     (features[i].getEnd() >= sequence.findPosition(res)))\r
 412                 {\r
 413                   if(!av.featuresDisplayed.containsKey(features[i].getType()))\r
 414                   continue;\r
 415 \r
 416 \r
 417                   if (features[i].getType().equals("disulfide bond"))\r
 418                   {\r
 419                     if (features[i].getBegin() == sequence.findPosition(res)\r
 420                         || features[i].getEnd() == sequence.findPosition(res))\r
 421                     {\r
 422                       if (sbuffer.length() > 6)\r
 423                         sbuffer.append("<br>");\r
 424                       sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
 425                                      features[i].getEnd());\r
 426                     }\r
 427                   }\r
 428                   else\r
 429                   {\r
 430                     if (sbuffer.length() > 6)\r
 431                       sbuffer.append("<br>");\r
 432                     if(features[i].featureGroup!=null)\r
 433                       sbuffer.append(features[i].featureGroup+";");\r
 434 \r
 435                     sbuffer.append(features[i].getType());\r
 436 \r
 437                     if (features[i].getDescription() != null\r
 438                         && !features[i].description.equals(features[i].getType()))\r
 439                       sbuffer.append("; " + features[i].getDescription());\r
 440 \r
 441                     if (features[i].getStatus() != null && features[i].getStatus().length()>0)\r
 442                     {\r
 443                       sbuffer.append("; (" + features[i].getStatus() + ")");\r
 444                     }\r
 445                   }\r
 446                 }\r
 447 \r
 448               }\r
 449 \r
 450               sbuffer.append("</html>");\r
 451               if(sbuffer.length()==13) // <html></html>\r
 452                 setToolTipText("");\r
 453               else\r
 454                setToolTipText(sbuffer.toString());\r
 455             }\r
 456             else\r
 457               setToolTipText("");\r
 458         }\r
 459     }\r
 460 \r
 461     /**\r
 462      * DOCUMENT ME!\r
 463      *\r
 464      * @param evt DOCUMENT ME!\r
 465      */\r
 466     public void doMouseDragged(MouseEvent evt)\r
 467     {\r
 468         // If we're dragging we're editing\r
 469         int res = findRes(evt);\r
 470 \r
 471         if (res < 0)\r
 472         {\r
 473             res = 0;\r
 474         }\r
 475 \r
 476         if ((lastres == -1) || (lastres == res))\r
 477         {\r
 478             return;\r
 479         }\r
 480 \r
 481         boolean dragRight = true;\r
 482 \r
 483         if ((res < av.getAlignment().getWidth()) && (res < lastres))\r
 484         {\r
 485             dragRight = false;\r
 486         }\r
 487 \r
 488         if (res != lastres)\r
 489         {\r
 490             // Group editing\r
 491             if (groupEditing)\r
 492             {\r
 493                 SequenceGroup sg = av.getSelectionGroup();\r
 494 \r
 495                 if (sg == null)\r
 496                 {\r
 497                     lastres = -1;\r
 498 \r
 499                     return;\r
 500                 }\r
 501 \r
 502                 // drag to right\r
 503                 if (dragRight)\r
 504                 {\r
 505                     sg.setEndRes(sg.getEndRes() + (res - lastres));\r
 506                 }\r
 507 \r
 508                 // drag to left\r
 509                 else\r
 510                 {\r
 511                     /// Are we able to delete?\r
 512                     // ie are all columns blank?\r
 513                     boolean deleteAllowed = false;\r
 514 \r
 515                     for (int s = 0; s < sg.getSize(); s++)\r
 516                     {\r
 517                         SequenceI seq = sg.getSequenceAt(s);\r
 518 \r
 519                         for (int j = res; j < lastres; j++)\r
 520                         {\r
 521                             if (seq.getSequence().length() <= j)\r
 522                             {\r
 523                                 continue;\r
 524                             }\r
 525 \r
 526                             if (!jalview.util.Comparison.isGap(\r
 527                                         seq.getSequence().charAt(j)))\r
 528                             {\r
 529                                 // Not a gap, block edit not valid\r
 530                                 res = j + 1;\r
 531                                 deleteAllowed = false;\r
 532 \r
 533                                 continue;\r
 534                             }\r
 535 \r
 536                             deleteAllowed = true;\r
 537                         }\r
 538                     }\r
 539 \r
 540                     if (!deleteAllowed)\r
 541                     {\r
 542                         lastres = -1;\r
 543 \r
 544                         return;\r
 545                     }\r
 546 \r
 547                     sg.setEndRes(sg.getEndRes() - (lastres - res));\r
 548                 }\r
 549 \r
 550                 for (int i = 0; i < sg.getSize(); i++)\r
 551                 {\r
 552                     SequenceI s = sg.getSequenceAt(i);\r
 553                     int k = av.alignment.findIndex(s);\r
 554 \r
 555                     // drag to right\r
 556                     if (dragRight)\r
 557                     {\r
 558                         for (int j = lastres; j < res; j++)\r
 559                         {\r
 560                             insertChar(j, k);\r
 561                         }\r
 562                     }\r
 563 \r
 564                     // drag to left\r
 565                     else\r
 566                     {\r
 567                         for (int j = res; j < lastres; j++)\r
 568                         {\r
 569                             if (s.getLength() > j)\r
 570                             {\r
 571                                 deleteChar(res, k);\r
 572                             }\r
 573                         }\r
 574                     }\r
 575                 }\r
 576             }\r
 577             else /////Editing a single sequence///////////\r
 578             {\r
 579                 if ((res < av.getAlignment().getWidth()) && (res > lastres))\r
 580                 {\r
 581                     // dragging to the right\r
 582                     for (int j = lastres; j < res; j++)\r
 583                     {\r
 584                         insertChar(j, startseq);\r
 585                     }\r
 586                 }\r
 587                 else if ((res < av.getAlignment().getWidth()) &&\r
 588                         (res < lastres))\r
 589                 {\r
 590                     // dragging to the left\r
 591                     for (int j = lastres; j > res; j--)\r
 592                     {\r
 593                         if (jalview.util.Comparison.isGap(\r
 594                                     av.alignment.getSequenceAt(startseq)\r
 595                                                     .getSequence().charAt(res)))\r
 596                         {\r
 597                             deleteChar(res, startseq);\r
 598                         }\r
 599                         else\r
 600                         {\r
 601                             break;\r
 602                         }\r
 603                     }\r
 604                 }\r
 605             }\r
 606         }\r
 607 \r
 608         endEdit = res;\r
 609         lastres = res;\r
 610         seqCanvas.repaint();\r
 611     }\r
 612 \r
 613 \r
 614     /**\r
 615      * DOCUMENT ME!\r
 616      *\r
 617      * @param j DOCUMENT ME!\r
 618      * @param seq DOCUMENT ME!\r
 619      */\r
 620     public void insertChar(int j, int seq)\r
 621     {\r
 622         av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
 623         seqEditOccurred = seq;\r
 624     }\r
 625 \r
 626     /**\r
 627      * DOCUMENT ME!\r
 628      *\r
 629      * @param j DOCUMENT ME!\r
 630      * @param seq DOCUMENT ME!\r
 631      */\r
 632     public void deleteChar(int j, int seq)\r
 633     {\r
 634         av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
 635         seqEditOccurred = seq;\r
 636 \r
 637         av.alignment.getWidth();\r
 638         seqCanvas.repaint();\r
 639     }\r
 640 \r
 641     /**\r
 642      * DOCUMENT ME!\r
 643      *\r
 644      * @param i DOCUMENT ME!\r
 645      */\r
 646     void editOccurred(int i)\r
 647     {\r
 648       if (endEdit == startEdit)\r
 649       {\r
 650         ap.alignFrame.historyList.pop();\r
 651         ap.alignFrame.updateEditMenuBar();\r
 652       }\r
 653 \r
 654       av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
 655 \r
 656     }\r
 657 \r
 658     /**\r
 659      * DOCUMENT ME!\r
 660      *\r
 661      * @param evt DOCUMENT ME!\r
 662      */\r
 663     public void doMousePressedDefineMode(MouseEvent evt)\r
 664     {\r
 665       int res = findRes(evt);\r
 666       int seq = findSeq(evt);\r
 667       oldSeq = seq;\r
 668 \r
 669       startWrapBlock=wrappedBlock;\r
 670 \r
 671       if(av.wrapAlignment && seq>av.alignment.getHeight())\r
 672       {\r
 673           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 674               "Cannot edit annotations in wrapped view.",\r
 675               "Wrapped view - no edit",\r
 676               JOptionPane.WARNING_MESSAGE);\r
 677         return;\r
 678       }\r
 679 \r
 680       if(seq<0 || res<0)\r
 681             return;\r
 682 \r
 683 \r
 684         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 685 \r
 686         if ((sequence == null) || (res > sequence.getLength()))\r
 687         {\r
 688             return;\r
 689         }\r
 690 \r
 691         stretchGroup = av.getSelectionGroup();\r
 692 \r
 693         if (stretchGroup == null)\r
 694         {\r
 695             stretchGroup = av.alignment.findGroup(sequence);\r
 696 \r
 697             if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
 698                     (res < stretchGroup.getEndRes()))\r
 699             {\r
 700                 av.setSelectionGroup(stretchGroup);\r
 701             }\r
 702             else\r
 703             {\r
 704                 stretchGroup = null;\r
 705             }\r
 706         }\r
 707         else if (!stretchGroup.sequences.contains(sequence) ||\r
 708                 (stretchGroup.getStartRes() > res) ||\r
 709                 (stretchGroup.getEndRes() < res))\r
 710         {\r
 711             stretchGroup = null;\r
 712 \r
 713             SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
 714 \r
 715             if (allGroups != null)\r
 716             {\r
 717                 for (int i = 0; i < allGroups.length; i++)\r
 718                 {\r
 719                     if ((allGroups[i].getStartRes() <= res) &&\r
 720                             (allGroups[i].getEndRes() >= res))\r
 721                     {\r
 722                         stretchGroup = allGroups[i];\r
 723                         av.setSelectionGroup(stretchGroup);\r
 724 \r
 725                         break;\r
 726                     }\r
 727                 }\r
 728             }\r
 729         }\r
 730 \r
 731         if (stretchGroup == null)\r
 732         {\r
 733             // define a new group here\r
 734             SequenceGroup sg = new SequenceGroup();\r
 735             sg.setStartRes(res);\r
 736             sg.setEndRes(res);\r
 737             sg.addSequence(sequence, false);\r
 738             av.setSelectionGroup(sg);\r
 739             stretchGroup = sg;\r
 740 \r
 741             if (av.getConservationSelected())\r
 742             {\r
 743                 SliderPanel.setConservationSlider(ap,\r
 744                     av.getGlobalColourScheme(), "Background");\r
 745             }\r
 746 \r
 747             if (av.getAbovePIDThreshold())\r
 748             {\r
 749                 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
 750                     "Background");\r
 751             }\r
 752         }\r
 753         else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
 754         {\r
 755             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
 756             pop.show(this, evt.getX(), evt.getY());\r
 757 \r
 758             // edit the properties of existing group\r
 759         }\r
 760 \r
 761         if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
 762         {\r
 763             // Edit end res position of selected group\r
 764             changeEndRes = true;\r
 765         }\r
 766         else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
 767         {\r
 768             // Edit end res position of selected group\r
 769             changeStartRes = true;\r
 770         }\r
 771 \r
 772         stretchGroup.getWidth();\r
 773 \r
 774         seqCanvas.repaint();\r
 775     }\r
 776 \r
 777     /**\r
 778      * DOCUMENT ME!\r
 779      *\r
 780      * @param evt DOCUMENT ME!\r
 781      */\r
 782     public void doMouseReleasedDefineMode(MouseEvent evt)\r
 783     {\r
 784         if (mouseDragging)\r
 785         {\r
 786             stretchGroup.recalcConservation();\r
 787             mouseDragging = false;\r
 788         }\r
 789 \r
 790         if (stretchGroup == null)\r
 791         {\r
 792             return;\r
 793         }\r
 794 \r
 795         if(stretchGroup.cs!=null)\r
 796         {\r
 797           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
 798           {\r
 799             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
 800                 sequences,\r
 801                 stretchGroup.getWidth());\r
 802           }\r
 803 \r
 804           if (stretchGroup.cs.conservationApplied())\r
 805           {\r
 806             SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
 807                                               stretchGroup.getName());\r
 808           }\r
 809           else\r
 810           {\r
 811             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
 812                                            stretchGroup.getName());\r
 813           }\r
 814         }\r
 815         changeEndRes = false;\r
 816         changeStartRes = false;\r
 817         stretchGroup = null;\r
 818         PaintRefresher.Refresh(av.alignment);\r
 819     }\r
 820 \r
 821     /**\r
 822      * DOCUMENT ME!\r
 823      *\r
 824      * @param evt DOCUMENT ME!\r
 825      */\r
 826     public void doMouseDraggedDefineMode(MouseEvent evt)\r
 827     {\r
 828       int res = findRes(evt);\r
 829       int y = findSeq(evt);\r
 830 \r
 831       if(wrappedBlock!=startWrapBlock)\r
 832         return;\r
 833 \r
 834       if (stretchGroup == null)\r
 835       {\r
 836             return;\r
 837         }\r
 838 \r
 839         if (res > av.alignment.getWidth())\r
 840         {\r
 841             res = av.alignment.getWidth() - 1;\r
 842         }\r
 843 \r
 844         if (stretchGroup.getEndRes() == res)\r
 845         {\r
 846             // Edit end res position of selected group\r
 847             changeEndRes = true;\r
 848         }\r
 849         else if (stretchGroup.getStartRes() == res)\r
 850         {\r
 851             // Edit start res position of selected group\r
 852             changeStartRes = true;\r
 853         }\r
 854 \r
 855         if (res < av.getStartRes())\r
 856         {\r
 857             res = av.getStartRes();\r
 858         }\r
 859         else if (res > av.getEndRes() && !av.getWrapAlignment())\r
 860         {\r
 861             res = av.getEndRes();\r
 862         }\r
 863 \r
 864         if (changeEndRes)\r
 865         {\r
 866             if (res > (stretchGroup.getStartRes() - 1))\r
 867             {\r
 868                 stretchGroup.setEndRes(res);\r
 869             }\r
 870         }\r
 871         else if (changeStartRes)\r
 872         {\r
 873             if (res < (stretchGroup.getEndRes() + 1))\r
 874             {\r
 875                 stretchGroup.setStartRes(res);\r
 876             }\r
 877         }\r
 878 \r
 879         int dragDirection = 0;\r
 880 \r
 881         if (y > oldSeq)\r
 882         {\r
 883             dragDirection = 1;\r
 884         }\r
 885         else if (y < oldSeq)\r
 886         {\r
 887             dragDirection = -1;\r
 888         }\r
 889 \r
 890         while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))\r
 891         {\r
 892             // This routine ensures we don't skip any sequences, as the\r
 893             // selection is quite slow.\r
 894             Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 895 \r
 896             oldSeq += dragDirection;\r
 897 \r
 898             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 899 \r
 900             if (stretchGroup.sequences.contains(nextSeq))\r
 901             {\r
 902                 stretchGroup.deleteSequence(seq, false);\r
 903             }\r
 904             else\r
 905             {\r
 906                 if (seq != null)\r
 907                 {\r
 908                     stretchGroup.addSequence(seq, false);\r
 909                 }\r
 910 \r
 911                 stretchGroup.addSequence(nextSeq, false);\r
 912             }\r
 913         }\r
 914 \r
 915         oldSeq = y;\r
 916         mouseDragging = true;\r
 917 \r
 918         if (scrollThread != null)\r
 919         {\r
 920             scrollThread.setEvent(evt);\r
 921         }\r
 922 \r
 923         seqCanvas.repaint();\r
 924     }\r
 925 \r
 926     /**\r
 927      * DOCUMENT ME!\r
 928      *\r
 929      * @param e DOCUMENT ME!\r
 930      */\r
 931     public void doMouseEnteredDefineMode(MouseEvent e)\r
 932     {\r
 933         if (scrollThread != null)\r
 934         {\r
 935             scrollThread.running = false;\r
 936         }\r
 937     }\r
 938 \r
 939     /**\r
 940      * DOCUMENT ME!\r
 941      *\r
 942      * @param e DOCUMENT ME!\r
 943      */\r
 944     public void doMouseExitedDefineMode(MouseEvent e)\r
 945     {\r
 946         if (av.getWrapAlignment())\r
 947         {\r
 948             return;\r
 949         }\r
 950 \r
 951         if (mouseDragging)\r
 952         {\r
 953             scrollThread = new ScrollThread();\r
 954         }\r
 955     }\r
 956 \r
 957     // this class allows scrolling off the bottom of the visible alignment\r
 958     class ScrollThread extends Thread\r
 959     {\r
 960         MouseEvent evt;\r
 961         boolean running = false;\r
 962 \r
 963         public ScrollThread()\r
 964         {\r
 965             start();\r
 966         }\r
 967 \r
 968         public void setEvent(MouseEvent e)\r
 969         {\r
 970             evt = e;\r
 971         }\r
 972 \r
 973         public void stopScrolling()\r
 974         {\r
 975             running = false;\r
 976         }\r
 977 \r
 978         public void run()\r
 979         {\r
 980             running = true;\r
 981 \r
 982             while (running)\r
 983             {\r
 984                 if (evt != null)\r
 985                 {\r
 986                     if (mouseDragging && (evt.getY() < 0) &&\r
 987                             (av.getStartSeq() > 0))\r
 988                     {\r
 989                         running = ap.scrollUp(true);\r
 990                     }\r
 991 \r
 992                     if (mouseDragging && (evt.getY() >= getHeight()) &&\r
 993                             (av.alignment.getHeight() > av.getEndSeq()))\r
 994                     {\r
 995                         running = ap.scrollUp(false);\r
 996                     }\r
 997 \r
 998                     if (mouseDragging && (evt.getX() < 0))\r
 999                     {\r
1000                         running = ap.scrollRight(true);\r
1001                     }\r
1002                     else if (mouseDragging && (evt.getX() >= getWidth()))\r
1003                     {\r
1004                         running = ap.scrollRight(false);\r
1005                     }\r
1006                 }\r
1007 \r
1008                 try\r
1009                 {\r
1010                     Thread.sleep(20);\r
1011                 }\r
1012                 catch (Exception ex)\r
1013                 {\r
1014                 }\r
1015             }\r
1016         }\r
1017     }\r
1018 }\r