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