2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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25 import java.awt.event.*;
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27 import jalview.commands.*;
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28 import jalview.datamodel.*;
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29 import jalview.schemes.*;
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31 public class SeqPanel
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32 extends Panel implements MouseMotionListener, MouseListener
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35 public SeqCanvas seqCanvas;
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36 public AlignmentPanel ap;
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38 protected int lastres;
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39 protected int startseq;
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41 protected AlignViewport av;
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43 // if character is inserted or deleted, we will need to recalculate the conservation
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44 boolean seqEditOccurred = false;
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46 ScrollThread scrollThread = null;
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47 boolean mouseDragging = false;
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48 boolean editingSeqs = false;
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49 boolean groupEditing = false;
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52 boolean changeEndSeq = false;
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53 boolean changeStartSeq = false;
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54 boolean changeEndRes = false;
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55 boolean changeStartRes = false;
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56 SequenceGroup stretchGroup = null;
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58 StringBuffer keyboardNo1;
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59 StringBuffer keyboardNo2;
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61 boolean mouseWheelPressed = false;
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62 Point lastMousePress;
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64 EditCommand editCommand;
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66 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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70 seqCanvas = new SeqCanvas(avp);
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71 setLayout(new BorderLayout());
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76 seqCanvas.addMouseMotionListener(this);
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77 seqCanvas.addMouseListener(this);
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79 seqCanvas.repaint();
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84 if (editCommand != null && editCommand.getSize() > 0)
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86 ap.alignFrame.addHistoryItem(editCommand);
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87 av.firePropertyChange("alignment", null,
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88 av.getAlignment().getSequences());
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93 editingSeqs = false;
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94 groupEditing = false;
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100 void setCursorRow()
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102 seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1;
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106 void setCursorColumn()
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108 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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112 void setCursorRowAndColumn()
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114 if (keyboardNo2 == null)
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116 keyboardNo2 = new StringBuffer();
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120 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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121 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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126 void setCursorPosition()
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128 SequenceI sequence =
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129 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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131 seqCanvas.cursorX = sequence.findIndex(
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132 getKeyboardNo(keyboardNo1) - 1
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137 void moveCursor(int dx, int dy)
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139 seqCanvas.cursorX += dx;
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140 seqCanvas.cursorY += dy;
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141 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
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143 int original = seqCanvas.cursorX - dx;
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144 int maxWidth = av.alignment.getWidth();
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146 while (!av.colSel.isVisible(seqCanvas.cursorX)
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147 && seqCanvas.cursorX < maxWidth
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148 && seqCanvas.cursorX > 0)
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150 seqCanvas.cursorX += dx;
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153 if (seqCanvas.cursorX >= maxWidth
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154 || !av.colSel.isVisible(seqCanvas.cursorX))
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156 seqCanvas.cursorX = original;
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162 void scrollToVisible()
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164 if (seqCanvas.cursorX < 0)
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166 seqCanvas.cursorX = 0;
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168 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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170 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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173 if (seqCanvas.cursorY < 0)
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175 seqCanvas.cursorY = 0;
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177 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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179 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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183 if (av.wrapAlignment)
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185 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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189 while (seqCanvas.cursorY < av.startSeq)
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193 while (seqCanvas.cursorY + 1 > av.endSeq)
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195 ap.scrollUp(false);
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197 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
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200 if (!ap.scrollRight(false))
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205 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
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207 if (!ap.scrollRight(true))
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213 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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214 seqCanvas.cursorX, seqCanvas.cursorY);
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216 seqCanvas.repaint();
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219 void setSelectionAreaAtCursor(boolean topLeft)
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221 SequenceI sequence =
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222 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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224 if (av.getSelectionGroup() != null)
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226 SequenceGroup sg = av.selectionGroup;
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227 //Find the top and bottom of this group
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228 int min = av.alignment.getHeight(), max = 0;
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229 for (int i = 0; i < sg.getSize(); i++)
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231 int index = av.alignment.findIndex(sg.getSequenceAt(i));
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246 sg.setStartRes(seqCanvas.cursorX);
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247 if (sg.getEndRes() < seqCanvas.cursorX)
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249 sg.setEndRes(seqCanvas.cursorX);
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252 min = seqCanvas.cursorY;
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256 sg.setEndRes(seqCanvas.cursorX);
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257 if (sg.getStartRes() > seqCanvas.cursorX)
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259 sg.setStartRes(seqCanvas.cursorX);
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262 max = seqCanvas.cursorY + 1;
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267 // Only the user can do this
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268 av.setSelectionGroup(null);
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272 // Now add any sequences between min and max
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273 sg.getSequences(null).removeAllElements();
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274 for (int i = min; i < max; i++)
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276 sg.addSequence(av.alignment.getSequenceAt(i), false);
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281 if (av.getSelectionGroup() == null)
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283 SequenceGroup sg = new SequenceGroup();
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284 sg.setStartRes(seqCanvas.cursorX);
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285 sg.setEndRes(seqCanvas.cursorX);
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286 sg.addSequence(sequence, false);
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287 av.setSelectionGroup(sg);
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293 void insertGapAtCursor(boolean group)
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295 groupEditing = group;
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296 startseq = seqCanvas.cursorY;
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297 lastres = seqCanvas.cursorX;
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298 editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1));
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302 void deleteGapAtCursor(boolean group)
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304 groupEditing = group;
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305 startseq = seqCanvas.cursorY;
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306 lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1);
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307 editSequence(false, seqCanvas.cursorX);
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311 void numberPressed(char value)
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313 if (keyboardNo1 == null)
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315 keyboardNo1 = new StringBuffer();
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318 if (keyboardNo2 != null)
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320 keyboardNo2.append(value);
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324 keyboardNo1.append(value);
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328 int getKeyboardNo(StringBuffer kb)
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336 return Integer.parseInt(kb.toString());
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340 void setStatusMessage(SequenceI sequence, int res, int seq)
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342 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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343 sequence.getName());
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346 if (av.alignment.isNucleotide())
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348 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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352 text.append(" Nucleotide: ");
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357 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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360 text.append(" Residue: ");
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369 text.append(obj + " (" + sequence.findPosition(res) +
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374 ap.alignFrame.statusBar.setText(text.toString());
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378 public void mousePressed(MouseEvent evt)
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380 lastMousePress = evt.getPoint();
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382 //For now, ignore the mouseWheel font resizing on Macs
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383 //As the Button2_mask always seems to be true
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384 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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385 InputEvent.BUTTON2_MASK && !av.MAC)
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387 mouseWheelPressed = true;
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391 if (evt.isShiftDown()
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392 || evt.isControlDown()
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393 || evt.isAltDown())
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395 if (evt.isControlDown() || evt.isAltDown())
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397 groupEditing = true;
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399 editingSeqs = true;
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403 doMousePressedDefineMode(evt);
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407 int seq = findSeq(evt);
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408 int res = findRes(evt);
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410 if (seq < 0 || res < 0)
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415 if ( (seq < av.getAlignment().getHeight()) &&
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416 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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430 public void mouseClicked(MouseEvent evt)
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433 public void mouseReleased(MouseEvent evt)
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435 mouseDragging = false;
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436 mouseWheelPressed = false;
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440 doMouseReleasedDefineMode(evt);
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448 int startWrapBlock = -1;
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449 int wrappedBlock = -1;
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450 int findRes(MouseEvent evt)
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453 int x = evt.getX();
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455 if (av.wrapAlignment)
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458 int hgap = av.charHeight;
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459 if (av.scaleAboveWrapped)
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461 hgap += av.charHeight;
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464 int cHeight = av.getAlignment().getHeight() * av.charHeight
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465 + hgap + seqCanvas.getAnnotationHeight();
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467 int y = evt.getY();
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469 x -= seqCanvas.LABEL_WEST;
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471 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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477 wrappedBlock = y / cHeight;
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478 wrappedBlock += av.getStartRes() / cwidth;
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480 res = wrappedBlock * cwidth + x / av.getCharWidth();
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485 res = (x / av.getCharWidth()) + av.getStartRes();
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488 if (av.hasHiddenColumns)
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490 res = av.getColumnSelection().adjustForHiddenColumns(res);
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497 int findSeq(MouseEvent evt)
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501 int y = evt.getY();
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503 if (av.wrapAlignment)
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505 int hgap = av.charHeight;
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506 if (av.scaleAboveWrapped)
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508 hgap += av.charHeight;
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511 int cHeight = av.getAlignment().getHeight() * av.charHeight
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512 + hgap + seqCanvas.getAnnotationHeight();
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516 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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517 av.alignment.getHeight() - 1);
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525 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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526 av.alignment.getHeight() - 1);
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536 public void doMousePressed(MouseEvent evt)
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539 int seq = findSeq(evt);
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540 int res = findRes(evt);
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542 if (seq < av.getAlignment().getHeight() &&
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543 res < av.getAlignment().getSequenceAt(seq).getLength())
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545 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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546 // Find the residue's position in the sequence (res is the position
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547 // in the alignment
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561 public void mouseMoved(MouseEvent evt)
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563 int res = findRes(evt);
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564 int seq = findSeq(evt);
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566 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
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568 if (tooltip != null)
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570 tooltip.setTip("");
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575 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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576 if (res > sequence.getLength())
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578 if (tooltip != null)
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580 tooltip.setTip("");
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585 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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586 sequence.getName());
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589 if (av.alignment.isNucleotide())
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591 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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595 text.append(" Nucleotide: ");
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600 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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603 text.append(" Residue: ");
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611 text.append(obj + " (" + sequence.findPosition(res) + ")");
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615 if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence)
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617 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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620 ap.alignFrame.statusBar.setText(text.toString());
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622 StringBuffer tooltipText = new StringBuffer();
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623 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
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624 if (groups != null)
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626 for (int g = 0; g < groups.length; g++)
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628 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
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630 if (!groups[g].getName().startsWith("JTreeGroup") &&
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631 !groups[g].getName().startsWith("JGroup"))
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633 tooltipText.append(groups[g].getName() + " ");
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635 if (groups[g].getDescription() != null)
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637 tooltipText.append(groups[g].getDescription());
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639 tooltipText.append("\n");
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644 // use aa to see if the mouse pointer is on a
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645 if (av.showSequenceFeatures
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646 && sequence.getSequenceFeatures() != null
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647 && av.featuresDisplayed != null)
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650 Vector allFeatures = getAllFeaturesAtRes(sequence,
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651 sequence.findPosition(res));
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654 while (index < allFeatures.size())
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656 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
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658 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
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660 if (sf.getDescription() != null)
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662 tooltipText.append(" " + sf.getDescription());
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665 if (sf.getValue("status") != null)
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667 String status = sf.getValue("status").toString();
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668 if (status.length() > 0)
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670 tooltipText.append(" (" + sf.getValue("status") + ")");
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673 tooltipText.append("\n");
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679 if (tooltip == null)
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681 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
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685 tooltip.setTip(tooltipText.toString());
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689 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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691 Vector allFeatures = new Vector();
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693 if (seq.getSequenceFeatures() != null)
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695 while (index < seq.getSequenceFeatures().length)
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697 SequenceFeature sf = seq.getSequenceFeatures()[index];
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698 if (sf.getBegin() <= res &&
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699 sf.getEnd() >= res)
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701 if (av.featuresDisplayed.containsKey(sf.getType()))
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703 allFeatures.addElement(sf);
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709 return allFeatures;
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714 public void mouseDragged(MouseEvent evt)
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716 if (mouseWheelPressed)
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718 int oldWidth = av.charWidth;
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720 //Which is bigger, left-right or up-down?
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721 if (Math.abs(evt.getY() - lastMousePress.y)
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722 > Math.abs(evt.getX() - lastMousePress.x))
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724 int fontSize = av.font.getSize();
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726 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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730 else if (evt.getY() > lastMousePress.y)
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740 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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741 av.charWidth = oldWidth;
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745 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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749 else if (evt.getX() > lastMousePress.x)
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754 if (av.charWidth < 1)
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762 FontMetrics fm = getFontMetrics(av.getFont());
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763 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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765 lastMousePress = evt.getPoint();
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768 ap.annotationPanel.image = null;
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774 doMouseDraggedDefineMode(evt);
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778 int res = findRes(evt);
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785 if ( (lastres == -1) || (lastres == res))
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790 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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792 // dragLeft, delete gap
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793 editSequence(false, res);
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797 editSequence(true, res);
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800 mouseDragging = true;
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801 if (scrollThread != null)
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803 scrollThread.setEvent(evt);
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808 synchronized void editSequence(boolean insertGap, int startres)
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810 int fixedLeft = -1;
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811 int fixedRight = -1;
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812 boolean fixedColumns = false;
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813 SequenceGroup sg = av.getSelectionGroup();
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815 SequenceI seq = av.alignment.getSequenceAt(startseq);
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817 if (!groupEditing && av.hasHiddenRows)
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819 if (av.hiddenRepSequences != null
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820 && av.hiddenRepSequences.containsKey(seq))
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822 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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823 groupEditing = true;
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827 StringBuffer message = new StringBuffer();
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830 message.append("Edit group:");
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831 if (editCommand == null)
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833 editCommand = new EditCommand("Edit Group");
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838 message.append("Edit sequence: " + seq.getName());
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839 String label = seq.getName();
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840 if (label.length() > 10)
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842 label = label.substring(0, 10);
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844 if (editCommand == null)
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846 editCommand = new EditCommand("Edit " + label);
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852 message.append(" insert ");
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856 message.append(" delete ");
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859 message.append(Math.abs(startres - lastres) + " gaps.");
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860 ap.alignFrame.statusBar.setText(message.toString());
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862 //Are we editing within a selection group?
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864 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
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866 fixedColumns = true;
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868 //sg might be null as the user may only see 1 sequence,
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869 //but the sequence represents a group
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872 if (av.hiddenRepSequences == null
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873 || !av.hiddenRepSequences.containsKey(seq))
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879 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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882 fixedLeft = sg.getStartRes();
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883 fixedRight = sg.getEndRes();
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885 if ( (startres < fixedLeft && lastres >= fixedLeft)
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886 || (startres >= fixedLeft && lastres < fixedLeft)
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887 || (startres > fixedRight && lastres <= fixedRight)
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888 || (startres <= fixedRight && lastres > fixedRight))
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894 if (fixedLeft > startres)
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896 fixedRight = fixedLeft - 1;
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899 else if (fixedRight < startres)
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901 fixedLeft = fixedRight;
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906 if (av.hasHiddenColumns)
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908 fixedColumns = true;
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909 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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910 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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912 if ( (insertGap && startres > y1 && lastres < y1)
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913 || (!insertGap && startres < y2 && lastres > y2))
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919 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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920 //Selection spans a hidden region
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921 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
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923 if (startres >= y2)
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929 fixedRight = y2 - 1;
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936 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
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937 int g, groupSize = vseqs.size();
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938 SequenceI[] groupSeqs = new SequenceI[groupSize];
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939 for (g = 0; g < groupSeqs.length; g++)
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941 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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947 //If the user has selected the whole sequence, and is dragging to
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948 // the right, we can still extend the alignment and selectionGroup
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949 if (sg.getStartRes() == 0
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950 && sg.getEndRes() == fixedRight
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951 && sg.getEndRes() == av.alignment.getWidth() - 1
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954 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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955 fixedRight = sg.getEndRes();
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958 // Is it valid with fixed columns??
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959 // Find the next gap before the end
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960 // of the visible region boundary
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961 boolean blank = false;
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962 for (fixedRight = fixedRight;
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963 fixedRight > lastres;
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968 for (g = 0; g < groupSize; g++)
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970 for (int j = 0; j < startres - lastres; j++)
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972 if (!jalview.util.Comparison.isGap(
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973 groupSeqs[g].getCharAt(fixedRight - j)))
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988 if (sg.getSize() == av.alignment.getHeight())
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990 if ( (av.hasHiddenColumns
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992 startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
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998 int alWidth = av.alignment.getWidth();
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999 if (av.hasHiddenRows)
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1001 int hwidth = av.alignment.getHiddenSequences().getWidth();
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1002 if (hwidth > alWidth)
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1007 //We can still insert gaps if the selectionGroup
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1008 //contains all the sequences
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1009 sg.setEndRes(sg.getEndRes() + startres - lastres);
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1010 fixedRight = alWidth + startres - lastres;
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1021 else if (!insertGap)
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1023 /// Are we able to delete?
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1024 // ie are all columns blank?
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1026 for (g = 0; g < groupSize; g++)
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1028 for (int j = startres; j < lastres; j++)
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1030 if (groupSeqs[g].getLength() <= j)
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1035 if (!jalview.util.Comparison.isGap(
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1036 groupSeqs[g].getCharAt(j)))
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1038 // Not a gap, block edit not valid
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1048 // dragging to the right
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1049 if (fixedColumns && fixedRight != -1)
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1051 for (int j = lastres; j < startres; j++)
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1053 insertChar(j, groupSeqs, fixedRight);
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1058 editCommand.appendEdit(EditCommand.INSERT_GAP,
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1060 startres, startres - lastres,
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1067 // dragging to the left
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1068 if (fixedColumns && fixedRight != -1)
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1070 for (int j = lastres; j > startres; j--)
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1072 deleteChar(startres, groupSeqs, fixedRight);
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1077 editCommand.appendEdit(EditCommand.DELETE_GAP,
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1079 startres, lastres - startres,
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1086 else /////Editing a single sequence///////////
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1090 // dragging to the right
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1091 if (fixedColumns && fixedRight != -1)
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1093 for (int j = lastres; j < startres; j++)
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1095 insertChar(j, new SequenceI[]
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1096 {seq}, fixedRight);
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1101 editCommand.appendEdit(EditCommand.INSERT_GAP,
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1104 lastres, startres - lastres,
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1111 // dragging to the left
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1112 if (fixedColumns && fixedRight != -1)
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1114 for (int j = lastres; j > startres; j--)
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1116 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
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1121 deleteChar(startres, new SequenceI[]
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1122 {seq}, fixedRight);
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1127 //could be a keyboard edit trying to delete none gaps
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1129 for (int m = startres; m < lastres; m++)
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1131 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
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1140 editCommand.appendEdit(EditCommand.DELETE_GAP,
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1151 lastres = startres;
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1152 seqCanvas.repaint();
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1155 void insertChar(int j, SequenceI[] seq, int fixedColumn)
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1157 int blankColumn = fixedColumn;
\r
1158 for (int s = 0; s < seq.length; s++)
\r
1160 //Find the next gap before the end of the visible region boundary
\r
1161 //If lastCol > j, theres a boundary after the gap insertion
\r
1163 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1165 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1167 //Theres a space, so break and insert the gap
\r
1172 if (blankColumn <= j)
\r
1174 blankColumn = fixedColumn;
\r
1180 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1182 blankColumn, 1, av.alignment, true);
\r
1184 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1186 j, 1, av.alignment,
\r
1191 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
\r
1194 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1196 j, 1, av.alignment, true);
\r
1198 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1200 fixedColumn, 1, av.alignment, true);
\r
1203 //////////////////////////////////////////
\r
1204 /////Everything below this is for defining the boundary of the rubberband
\r
1205 //////////////////////////////////////////
\r
1206 public void doMousePressedDefineMode(MouseEvent evt)
\r
1208 if (scrollThread != null)
\r
1210 scrollThread.running = false;
\r
1211 scrollThread = null;
\r
1214 int res = findRes(evt);
\r
1215 int seq = findSeq(evt);
\r
1217 startWrapBlock = wrappedBlock;
\r
1224 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1226 if (sequence == null || res > sequence.getLength())
\r
1231 stretchGroup = av.getSelectionGroup();
\r
1233 if (stretchGroup == null)
\r
1235 stretchGroup = av.alignment.findGroup(sequence);
\r
1236 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1237 res < stretchGroup.getEndRes())
\r
1239 av.setSelectionGroup(stretchGroup);
\r
1243 stretchGroup = null;
\r
1247 else if (!stretchGroup.getSequences(null).contains(sequence)
\r
1248 || stretchGroup.getStartRes() > res
\r
1249 || stretchGroup.getEndRes() < res)
\r
1251 stretchGroup = null;
\r
1253 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1255 if (allGroups != null)
\r
1257 for (int i = 0; i < allGroups.length; i++)
\r
1259 if (allGroups[i].getStartRes() <= res &&
\r
1260 allGroups[i].getEndRes() >= res)
\r
1262 stretchGroup = allGroups[i];
\r
1267 av.setSelectionGroup(stretchGroup);
\r
1270 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1271 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1272 InputEvent.BUTTON3_MASK)
\r
1274 Vector allFeatures = getAllFeaturesAtRes(sequence,
\r
1275 sequence.findPosition(res));
\r
1277 Vector links = null;
\r
1278 if (allFeatures != null)
\r
1280 for (int i = 0; i < allFeatures.size(); i++)
\r
1282 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1283 if (sf.links != null)
\r
1285 links = new Vector();
\r
1286 for (int j = 0; j < sf.links.size(); j++)
\r
1288 links.addElement(sf.links.elementAt(j));
\r
1293 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1295 popup.show(this, evt.getX(), evt.getY());
\r
1300 if (av.cursorMode)
\r
1302 seqCanvas.cursorX = findRes(evt);
\r
1303 seqCanvas.cursorY = findSeq(evt);
\r
1304 seqCanvas.repaint();
\r
1308 //Only if left mouse button do we want to change group sizes
\r
1310 if (stretchGroup == null)
\r
1312 // define a new group here
\r
1313 SequenceGroup sg = new SequenceGroup();
\r
1314 sg.setStartRes(res);
\r
1315 sg.setEndRes(res);
\r
1316 sg.addSequence(sequence, false);
\r
1317 av.setSelectionGroup(sg);
\r
1318 stretchGroup = sg;
\r
1320 if (av.getConservationSelected())
\r
1322 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1325 if (av.getAbovePIDThreshold())
\r
1327 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1334 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1336 if (stretchGroup == null)
\r
1341 if (stretchGroup.cs != null)
\r
1343 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1345 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1346 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1347 stretchGroup.getWidth());
\r
1350 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1351 || stretchGroup.cs instanceof PIDColourScheme
\r
1352 || stretchGroup.cs.conservationApplied()
\r
1353 || stretchGroup.cs.getThreshold() > 0)
\r
1355 stretchGroup.recalcConservation();
\r
1358 if (stretchGroup.cs.conservationApplied())
\r
1360 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1361 stretchGroup.getName());
\r
1362 stretchGroup.recalcConservation();
\r
1366 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1367 stretchGroup.getName());
\r
1370 changeEndRes = false;
\r
1371 changeStartRes = false;
\r
1372 stretchGroup = null;
\r
1373 PaintRefresher.Refresh(ap, av.getSequenceSetId());
\r
1377 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1379 int res = findRes(evt);
\r
1380 int y = findSeq(evt);
\r
1382 if (wrappedBlock != startWrapBlock)
\r
1387 if (stretchGroup == null)
\r
1392 mouseDragging = true;
\r
1394 if (y > av.alignment.getHeight())
\r
1396 y = av.alignment.getHeight() - 1;
\r
1399 if (res >= av.alignment.getWidth())
\r
1401 res = av.alignment.getWidth() - 1;
\r
1404 if (stretchGroup.getEndRes() == res)
\r
1406 // Edit end res position of selected group
\r
1407 changeEndRes = true;
\r
1409 else if (stretchGroup.getStartRes() == res)
\r
1411 // Edit start res position of selected group
\r
1412 changeStartRes = true;
\r
1422 if (res > (stretchGroup.getStartRes() - 1))
\r
1424 stretchGroup.setEndRes(res);
\r
1427 else if (changeStartRes)
\r
1429 if (res < (stretchGroup.getEndRes() + 1))
\r
1431 stretchGroup.setStartRes(res);
\r
1435 int dragDirection = 0;
\r
1439 dragDirection = 1;
\r
1441 else if (y < oldSeq)
\r
1443 dragDirection = -1;
\r
1446 while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1448 // This routine ensures we don't skip any sequences, as the
\r
1449 // selection is quite slow.
\r
1450 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1452 oldSeq += dragDirection;
\r
1459 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1461 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1463 stretchGroup.deleteSequence(seq, false);
\r
1469 stretchGroup.addSequence(seq, false);
\r
1472 stretchGroup.addSequence(nextSeq, false);
\r
1481 if (res > av.endRes || res < av.startRes
\r
1482 || y < av.startSeq || y > av.endSeq)
\r
1487 if (scrollThread != null)
\r
1489 scrollThread.setEvent(evt);
\r
1492 seqCanvas.repaint();
\r
1495 public void mouseEntered(MouseEvent e)
\r
1502 if (scrollThread != null)
\r
1504 scrollThread.running = false;
\r
1505 scrollThread = null;
\r
1509 public void mouseExited(MouseEvent e)
\r
1511 if (av.getWrapAlignment())
\r
1516 if (mouseDragging && scrollThread == null)
\r
1518 scrollThread = new ScrollThread();
\r
1522 void scrollCanvas(MouseEvent evt)
\r
1526 if (scrollThread != null)
\r
1528 scrollThread.running = false;
\r
1529 scrollThread = null;
\r
1531 mouseDragging = false;
\r
1535 if (scrollThread == null)
\r
1537 scrollThread = new ScrollThread();
\r
1540 mouseDragging = true;
\r
1541 scrollThread.setEvent(evt);
\r
1546 // this class allows scrolling off the bottom of the visible alignment
\r
1547 class ScrollThread
\r
1551 boolean running = false;
\r
1552 public ScrollThread()
\r
1557 public void setEvent(MouseEvent e)
\r
1562 public void stopScrolling()
\r
1576 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1578 running = ap.scrollUp(true);
\r
1581 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1582 av.alignment.getHeight() > av.getEndSeq())
\r
1584 running = ap.scrollUp(false);
\r
1587 if (mouseDragging && evt.getX() < 0)
\r
1589 running = ap.scrollRight(false);
\r
1592 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1594 running = ap.scrollRight(true);
\r
1602 catch (Exception ex)
\r