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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30 import jalview.structure.SequenceListener;
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31 import jalview.structure.StructureSelectionManager;
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33 public class SeqPanel
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34 extends Panel implements MouseMotionListener, MouseListener, SequenceListener
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37 public SeqCanvas seqCanvas;
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38 public AlignmentPanel ap;
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40 protected int lastres;
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41 protected int startseq;
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43 protected AlignViewport av;
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45 // if character is inserted or deleted, we will need to recalculate the conservation
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46 boolean seqEditOccurred = false;
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48 ScrollThread scrollThread = null;
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49 boolean mouseDragging = false;
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50 boolean editingSeqs = false;
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51 boolean groupEditing = false;
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54 boolean changeEndSeq = false;
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55 boolean changeStartSeq = false;
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56 boolean changeEndRes = false;
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57 boolean changeStartRes = false;
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58 SequenceGroup stretchGroup = null;
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60 StringBuffer keyboardNo1;
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61 StringBuffer keyboardNo2;
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63 boolean mouseWheelPressed = false;
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64 Point lastMousePress;
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66 EditCommand editCommand;
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68 StructureSelectionManager ssm;
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71 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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75 seqCanvas = new SeqCanvas(avp);
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76 setLayout(new BorderLayout());
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81 seqCanvas.addMouseMotionListener(this);
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82 seqCanvas.addMouseListener(this);
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83 ssm = StructureSelectionManager.getStructureSelectionManager();
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84 ssm.addStructureViewerListener(this);
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86 seqCanvas.repaint();
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91 if (editCommand != null && editCommand.getSize() > 0)
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93 ap.alignFrame.addHistoryItem(editCommand);
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94 av.firePropertyChange("alignment", null,
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95 av.getAlignment().getSequences());
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100 editingSeqs = false;
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101 groupEditing = false;
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102 keyboardNo1 = null;
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103 keyboardNo2 = null;
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104 editCommand = null;
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107 void setCursorRow()
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109 seqCanvas.cursorY = getKeyboardNo1() - 1;
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113 void setCursorColumn()
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115 seqCanvas.cursorX = getKeyboardNo1() - 1;
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119 void setCursorRowAndColumn()
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121 if (keyboardNo2 == null)
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123 keyboardNo2 = new StringBuffer();
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127 seqCanvas.cursorX = getKeyboardNo1() - 1;
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128 seqCanvas.cursorY = getKeyboardNo2() - 1;
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133 void setCursorPosition()
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135 SequenceI sequence =
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136 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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138 seqCanvas.cursorX = sequence.findIndex(
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139 getKeyboardNo1() - 1
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144 void moveCursor(int dx, int dy)
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146 seqCanvas.cursorX += dx;
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147 seqCanvas.cursorY += dy;
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148 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
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150 int original = seqCanvas.cursorX - dx;
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151 int maxWidth = av.alignment.getWidth();
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153 while (!av.colSel.isVisible(seqCanvas.cursorX)
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154 && seqCanvas.cursorX < maxWidth
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155 && seqCanvas.cursorX > 0)
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157 seqCanvas.cursorX += dx;
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160 if (seqCanvas.cursorX >= maxWidth
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161 || !av.colSel.isVisible(seqCanvas.cursorX))
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163 seqCanvas.cursorX = original;
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169 void scrollToVisible()
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171 if (seqCanvas.cursorX < 0)
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173 seqCanvas.cursorX = 0;
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175 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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177 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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180 if (seqCanvas.cursorY < 0)
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182 seqCanvas.cursorY = 0;
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184 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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186 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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190 if (av.wrapAlignment)
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192 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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196 while (seqCanvas.cursorY < av.startSeq)
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200 while (seqCanvas.cursorY + 1 > av.endSeq)
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202 ap.scrollUp(false);
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204 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
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207 if (!ap.scrollRight(false))
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212 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
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214 if (!ap.scrollRight(true))
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220 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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221 seqCanvas.cursorX, seqCanvas.cursorY);
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223 seqCanvas.repaint();
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226 void setSelectionAreaAtCursor(boolean topLeft)
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228 SequenceI sequence =
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229 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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231 if (av.getSelectionGroup() != null)
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233 SequenceGroup sg = av.selectionGroup;
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234 //Find the top and bottom of this group
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235 int min = av.alignment.getHeight(), max = 0;
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236 for (int i = 0; i < sg.getSize(); i++)
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238 int index = av.alignment.findIndex(sg.getSequenceAt(i));
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253 sg.setStartRes(seqCanvas.cursorX);
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254 if (sg.getEndRes() < seqCanvas.cursorX)
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256 sg.setEndRes(seqCanvas.cursorX);
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259 min = seqCanvas.cursorY;
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263 sg.setEndRes(seqCanvas.cursorX);
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264 if (sg.getStartRes() > seqCanvas.cursorX)
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266 sg.setStartRes(seqCanvas.cursorX);
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269 max = seqCanvas.cursorY + 1;
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274 // Only the user can do this
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275 av.setSelectionGroup(null);
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279 // Now add any sequences between min and max
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280 sg.getSequences(null).removeAllElements();
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281 for (int i = min; i < max; i++)
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283 sg.addSequence(av.alignment.getSequenceAt(i), false);
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288 if (av.getSelectionGroup() == null)
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290 SequenceGroup sg = new SequenceGroup();
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291 sg.setStartRes(seqCanvas.cursorX);
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292 sg.setEndRes(seqCanvas.cursorX);
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293 sg.addSequence(sequence, false);
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294 av.setSelectionGroup(sg);
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297 ap.paintAlignment(false);
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300 void insertGapAtCursor(boolean group)
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302 groupEditing = group;
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303 startseq = seqCanvas.cursorY;
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304 lastres = seqCanvas.cursorX;
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305 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
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309 void deleteGapAtCursor(boolean group)
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311 groupEditing = group;
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312 startseq = seqCanvas.cursorY;
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313 lastres = seqCanvas.cursorX + getKeyboardNo1();
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314 editSequence(false, seqCanvas.cursorX);
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318 void numberPressed(char value)
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320 if (keyboardNo1 == null)
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322 keyboardNo1 = new StringBuffer();
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325 if (keyboardNo2 != null)
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327 keyboardNo2.append(value);
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331 keyboardNo1.append(value);
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335 int getKeyboardNo1()
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337 if (keyboardNo1 == null)
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341 int value = Integer.parseInt(keyboardNo1.toString());
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342 keyboardNo1 = null;
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347 int getKeyboardNo2()
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349 if (keyboardNo2 == null)
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353 int value = Integer.parseInt(keyboardNo2.toString());
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354 keyboardNo2 = null;
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360 void setStatusMessage(SequenceI sequence, int res, int seq)
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362 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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363 sequence.getName());
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366 if (av.alignment.isNucleotide())
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368 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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372 text.append(" Nucleotide: ");
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377 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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380 text.append(" Residue: ");
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389 text.append(obj + " (" + sequence.findPosition(res) +
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394 ap.alignFrame.statusBar.setText(text.toString());
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398 public void mousePressed(MouseEvent evt)
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400 lastMousePress = evt.getPoint();
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402 //For now, ignore the mouseWheel font resizing on Macs
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403 //As the Button2_mask always seems to be true
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404 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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405 InputEvent.BUTTON2_MASK && !av.MAC)
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407 mouseWheelPressed = true;
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411 if (evt.isShiftDown()
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412 || evt.isControlDown()
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413 || evt.isAltDown())
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415 if (evt.isControlDown() || evt.isAltDown())
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417 groupEditing = true;
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419 editingSeqs = true;
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423 doMousePressedDefineMode(evt);
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427 int seq = findSeq(evt);
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428 int res = findRes(evt);
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430 if (seq < 0 || res < 0)
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435 if ( (seq < av.getAlignment().getHeight()) &&
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436 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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450 public void mouseClicked(MouseEvent evt)
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452 SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
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453 if (evt.getClickCount() > 1)
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455 if (av.getSelectionGroup().getSize() == 1
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456 && av.getSelectionGroup().getEndRes()
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457 - av.getSelectionGroup().getStartRes() < 2)
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459 av.setSelectionGroup(null);
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462 SequenceFeature[] features = findFeaturesAtRes(
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464 sequence.findPosition(findRes(evt))
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467 if (features != null && features.length > 0)
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469 SearchResults highlight = new SearchResults();
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470 highlight.addResult(sequence,
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471 features[0].getBegin(),
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472 features[0].getEnd());
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473 seqCanvas.highlightSearchResults(highlight);
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475 if (features != null && features.length > 0)
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477 seqCanvas.getFeatureRenderer().amendFeatures(
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479 {sequence}, features, false, ap);
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481 seqCanvas.highlightSearchResults(null);
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486 public void mouseReleased(MouseEvent evt)
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488 mouseDragging = false;
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489 mouseWheelPressed = false;
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490 ap.paintAlignment(true);
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494 doMouseReleasedDefineMode(evt);
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502 int startWrapBlock = -1;
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503 int wrappedBlock = -1;
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504 int findRes(MouseEvent evt)
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507 int x = evt.getX();
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509 if (av.wrapAlignment)
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512 int hgap = av.charHeight;
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513 if (av.scaleAboveWrapped)
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515 hgap += av.charHeight;
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518 int cHeight = av.getAlignment().getHeight() * av.charHeight
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519 + hgap + seqCanvas.getAnnotationHeight();
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521 int y = evt.getY();
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523 x -= seqCanvas.LABEL_WEST;
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525 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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531 wrappedBlock = y / cHeight;
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532 wrappedBlock += av.getStartRes() / cwidth;
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534 res = wrappedBlock * cwidth + x / av.getCharWidth();
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539 res = (x / av.getCharWidth()) + av.getStartRes();
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542 if (av.hasHiddenColumns)
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544 res = av.getColumnSelection().adjustForHiddenColumns(res);
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551 int findSeq(MouseEvent evt)
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555 int y = evt.getY();
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557 if (av.wrapAlignment)
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559 int hgap = av.charHeight;
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560 if (av.scaleAboveWrapped)
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562 hgap += av.charHeight;
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565 int cHeight = av.getAlignment().getHeight() * av.charHeight
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566 + hgap + seqCanvas.getAnnotationHeight();
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570 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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571 av.alignment.getHeight() - 1);
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579 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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580 av.alignment.getHeight() - 1);
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592 public void doMousePressed(MouseEvent evt)
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595 int seq = findSeq(evt);
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596 int res = findRes(evt);
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598 if (seq < av.getAlignment().getHeight() &&
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599 res < av.getAlignment().getSequenceAt(seq).getLength())
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601 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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602 // Find the residue's position in the sequence (res is the position
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603 // in the alignment
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618 String lastMessage;
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619 public void mouseOverSequence(SequenceI sequence, int index)
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621 String tmp = sequence.hashCode()+index+"";
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622 if (lastMessage == null || !lastMessage.equals(tmp))
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623 ssm.mouseOverSequence(sequence, index);
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629 public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
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631 if(av.alignment.findIndex(seq)>-1)
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633 SearchResults highlight = new SearchResults();
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634 highlight.addResult(seq,index,index);
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635 seqCanvas.highlightSearchResults(highlight);
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639 public void updateColours(SequenceI seq, int index)
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641 System.out.println("update the seqPanel colours");
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645 public void mouseMoved(MouseEvent evt)
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647 int res = findRes(evt);
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648 int seq = findSeq(evt);
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650 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
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652 if (tooltip != null)
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654 tooltip.setTip("");
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659 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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660 if (res > sequence.getLength())
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662 if (tooltip != null)
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664 tooltip.setTip("");
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671 mouseOverSequence(sequence, sequence.findPosition(res));
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674 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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675 sequence.getName());
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678 if (av.alignment.isNucleotide())
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680 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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684 text.append(" Nucleotide: ");
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689 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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692 text.append(" Residue: ");
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700 text.append(obj + " (" + sequence.findPosition(res) + ")");
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704 ap.alignFrame.statusBar.setText(text.toString());
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706 StringBuffer tooltipText = new StringBuffer();
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707 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
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708 if (groups != null)
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710 for (int g = 0; g < groups.length; g++)
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712 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
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714 if (!groups[g].getName().startsWith("JTreeGroup") &&
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715 !groups[g].getName().startsWith("JGroup"))
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717 tooltipText.append(groups[g].getName() + " ");
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719 if (groups[g].getDescription() != null)
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721 tooltipText.append(groups[g].getDescription());
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723 tooltipText.append("\n");
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728 // use aa to see if the mouse pointer is on a
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729 SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
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730 sequence.findPosition(res));
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733 while (index < allFeatures.length)
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735 SequenceFeature sf = allFeatures[index];
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737 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
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739 if (sf.getDescription() != null)
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741 tooltipText.append(" " + sf.getDescription());
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744 if (sf.getValue("status") != null)
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746 String status = sf.getValue("status").toString();
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747 if (status.length() > 0)
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749 tooltipText.append(" (" + sf.getValue("status") + ")");
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752 tooltipText.append("\n");
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757 if (tooltip == null)
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759 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
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763 tooltip.setTip(tooltipText.toString());
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767 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
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769 Vector tmp = new Vector();
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770 SequenceFeature[] features = sequence.getSequenceFeatures();
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771 if (features != null)
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773 for (int i = 0; i < features.length; i++)
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775 if (av.featuresDisplayed == null
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776 || !av.featuresDisplayed.containsKey(features[i].getType()))
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781 if ( (features[i].getBegin() <= res) &&
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782 (features[i].getEnd() >= res))
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784 tmp.addElement(features[i]);
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789 features = new SequenceFeature[tmp.size()];
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790 tmp.copyInto(features);
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798 public void mouseDragged(MouseEvent evt)
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800 if (mouseWheelPressed)
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802 int oldWidth = av.charWidth;
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804 //Which is bigger, left-right or up-down?
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805 if (Math.abs(evt.getY() - lastMousePress.y)
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806 > Math.abs(evt.getX() - lastMousePress.x))
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808 int fontSize = av.font.getSize();
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810 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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814 else if (evt.getY() > lastMousePress.y)
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824 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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825 av.charWidth = oldWidth;
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829 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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833 else if (evt.getX() > lastMousePress.x)
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838 if (av.charWidth < 1)
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846 FontMetrics fm = getFontMetrics(av.getFont());
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847 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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849 lastMousePress = evt.getPoint();
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851 ap.paintAlignment(false);
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852 ap.annotationPanel.image = null;
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858 doMouseDraggedDefineMode(evt);
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862 int res = findRes(evt);
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869 if ( (lastres == -1) || (lastres == res))
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874 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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876 // dragLeft, delete gap
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877 editSequence(false, res);
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881 editSequence(true, res);
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884 mouseDragging = true;
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885 if (scrollThread != null)
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887 scrollThread.setEvent(evt);
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892 synchronized void editSequence(boolean insertGap, int startres)
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894 int fixedLeft = -1;
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895 int fixedRight = -1;
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896 boolean fixedColumns = false;
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897 SequenceGroup sg = av.getSelectionGroup();
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899 SequenceI seq = av.alignment.getSequenceAt(startseq);
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901 if (!groupEditing && av.hasHiddenRows)
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903 if (av.hiddenRepSequences != null
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904 && av.hiddenRepSequences.containsKey(seq))
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906 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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907 groupEditing = true;
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911 StringBuffer message = new StringBuffer();
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914 message.append("Edit group:");
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915 if (editCommand == null)
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917 editCommand = new EditCommand("Edit Group");
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922 message.append("Edit sequence: " + seq.getName());
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923 String label = seq.getName();
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924 if (label.length() > 10)
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926 label = label.substring(0, 10);
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928 if (editCommand == null)
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930 editCommand = new EditCommand("Edit " + label);
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936 message.append(" insert ");
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940 message.append(" delete ");
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943 message.append(Math.abs(startres - lastres) + " gaps.");
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944 ap.alignFrame.statusBar.setText(message.toString());
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946 //Are we editing within a selection group?
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948 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
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950 fixedColumns = true;
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952 //sg might be null as the user may only see 1 sequence,
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953 //but the sequence represents a group
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956 if (av.hiddenRepSequences == null
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957 || !av.hiddenRepSequences.containsKey(seq))
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963 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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966 fixedLeft = sg.getStartRes();
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967 fixedRight = sg.getEndRes();
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969 if ( (startres < fixedLeft && lastres >= fixedLeft)
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970 || (startres >= fixedLeft && lastres < fixedLeft)
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971 || (startres > fixedRight && lastres <= fixedRight)
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972 || (startres <= fixedRight && lastres > fixedRight))
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978 if (fixedLeft > startres)
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980 fixedRight = fixedLeft - 1;
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983 else if (fixedRight < startres)
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985 fixedLeft = fixedRight;
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990 if (av.hasHiddenColumns)
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992 fixedColumns = true;
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993 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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994 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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996 if ( (insertGap && startres > y1 && lastres < y1)
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997 || (!insertGap && startres < y2 && lastres > y2))
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1003 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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1004 //Selection spans a hidden region
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1005 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
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1007 if (startres >= y2)
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1013 fixedRight = y2 - 1;
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1020 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
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1021 int g, groupSize = vseqs.size();
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1022 SequenceI[] groupSeqs = new SequenceI[groupSize];
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1023 for (g = 0; g < groupSeqs.length; g++)
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1025 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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1031 //If the user has selected the whole sequence, and is dragging to
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1032 // the right, we can still extend the alignment and selectionGroup
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1033 if (sg.getStartRes() == 0
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1034 && sg.getEndRes() == fixedRight
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1035 && sg.getEndRes() == av.alignment.getWidth() - 1
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1038 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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1039 fixedRight = sg.getEndRes();
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1042 // Is it valid with fixed columns??
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1043 // Find the next gap before the end
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1044 // of the visible region boundary
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1045 boolean blank = false;
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1046 for (fixedRight = fixedRight;
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1047 fixedRight > lastres;
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1052 for (g = 0; g < groupSize; g++)
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1054 for (int j = 0; j < startres - lastres; j++)
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1056 if (!jalview.util.Comparison.isGap(
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1057 groupSeqs[g].getCharAt(fixedRight - j)))
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1072 if (sg.getSize() == av.alignment.getHeight())
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1074 if ( (av.hasHiddenColumns
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1076 startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
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1082 int alWidth = av.alignment.getWidth();
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1083 if (av.hasHiddenRows)
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1085 int hwidth = av.alignment.getHiddenSequences().getWidth();
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1086 if (hwidth > alWidth)
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1091 //We can still insert gaps if the selectionGroup
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1092 //contains all the sequences
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1093 sg.setEndRes(sg.getEndRes() + startres - lastres);
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1094 fixedRight = alWidth + startres - lastres;
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1105 else if (!insertGap)
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1107 /// Are we able to delete?
\r
1108 // ie are all columns blank?
\r
1110 for (g = 0; g < groupSize; g++)
\r
1112 for (int j = startres; j < lastres; j++)
\r
1114 if (groupSeqs[g].getLength() <= j)
\r
1119 if (!jalview.util.Comparison.isGap(
\r
1120 groupSeqs[g].getCharAt(j)))
\r
1122 // Not a gap, block edit not valid
\r
1132 // dragging to the right
\r
1133 if (fixedColumns && fixedRight != -1)
\r
1135 for (int j = lastres; j < startres; j++)
\r
1137 insertChar(j, groupSeqs, fixedRight);
\r
1142 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1144 startres, startres - lastres,
\r
1151 // dragging to the left
\r
1152 if (fixedColumns && fixedRight != -1)
\r
1154 for (int j = lastres; j > startres; j--)
\r
1156 deleteChar(startres, groupSeqs, fixedRight);
\r
1161 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1163 startres, lastres - startres,
\r
1170 else /////Editing a single sequence///////////
\r
1174 // dragging to the right
\r
1175 if (fixedColumns && fixedRight != -1)
\r
1177 for (int j = lastres; j < startres; j++)
\r
1179 insertChar(j, new SequenceI[]
\r
1180 {seq}, fixedRight);
\r
1185 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1188 lastres, startres - lastres,
\r
1195 // dragging to the left
\r
1196 if (fixedColumns && fixedRight != -1)
\r
1198 for (int j = lastres; j > startres; j--)
\r
1200 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1205 deleteChar(startres, new SequenceI[]
\r
1206 {seq}, fixedRight);
\r
1211 //could be a keyboard edit trying to delete none gaps
\r
1213 for (int m = startres; m < lastres; m++)
\r
1215 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1224 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1235 lastres = startres;
\r
1236 seqCanvas.repaint();
\r
1239 void insertChar(int j, SequenceI[] seq, int fixedColumn)
\r
1241 int blankColumn = fixedColumn;
\r
1242 for (int s = 0; s < seq.length; s++)
\r
1244 //Find the next gap before the end of the visible region boundary
\r
1245 //If lastCol > j, theres a boundary after the gap insertion
\r
1247 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1249 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1251 //Theres a space, so break and insert the gap
\r
1256 if (blankColumn <= j)
\r
1258 blankColumn = fixedColumn;
\r
1264 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1266 blankColumn, 1, av.alignment, true);
\r
1268 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1270 j, 1, av.alignment,
\r
1275 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
\r
1278 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1280 j, 1, av.alignment, true);
\r
1282 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1284 fixedColumn, 1, av.alignment, true);
\r
1287 //////////////////////////////////////////
\r
1288 /////Everything below this is for defining the boundary of the rubberband
\r
1289 //////////////////////////////////////////
\r
1290 public void doMousePressedDefineMode(MouseEvent evt)
\r
1292 if (scrollThread != null)
\r
1294 scrollThread.running = false;
\r
1295 scrollThread = null;
\r
1298 int res = findRes(evt);
\r
1299 int seq = findSeq(evt);
\r
1301 startWrapBlock = wrappedBlock;
\r
1308 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1310 if (sequence == null || res > sequence.getLength())
\r
1315 stretchGroup = av.getSelectionGroup();
\r
1317 if (stretchGroup == null)
\r
1319 stretchGroup = av.alignment.findGroup(sequence);
\r
1320 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1321 res < stretchGroup.getEndRes())
\r
1323 av.setSelectionGroup(stretchGroup);
\r
1327 stretchGroup = null;
\r
1331 else if (!stretchGroup.getSequences(null).contains(sequence)
\r
1332 || stretchGroup.getStartRes() > res
\r
1333 || stretchGroup.getEndRes() < res)
\r
1335 stretchGroup = null;
\r
1337 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1339 if (allGroups != null)
\r
1341 for (int i = 0; i < allGroups.length; i++)
\r
1343 if (allGroups[i].getStartRes() <= res &&
\r
1344 allGroups[i].getEndRes() >= res)
\r
1346 stretchGroup = allGroups[i];
\r
1351 av.setSelectionGroup(stretchGroup);
\r
1354 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1355 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1356 InputEvent.BUTTON3_MASK)
\r
1358 SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
\r
1359 sequence.findPosition(res));
\r
1361 Vector links = null;
\r
1362 if (allFeatures != null)
\r
1364 for (int i = 0; i < allFeatures.length; i++)
\r
1366 if (allFeatures[i].links != null)
\r
1368 links = new Vector();
\r
1369 for (int j = 0; j < allFeatures[i].links.size(); j++)
\r
1371 links.addElement(allFeatures[i].links.elementAt(j));
\r
1376 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1378 popup.show(this, evt.getX(), evt.getY());
\r
1382 if (av.cursorMode)
\r
1384 seqCanvas.cursorX = findRes(evt);
\r
1385 seqCanvas.cursorY = findSeq(evt);
\r
1386 seqCanvas.repaint();
\r
1390 //Only if left mouse button do we want to change group sizes
\r
1392 if (stretchGroup == null)
\r
1394 // define a new group here
\r
1395 SequenceGroup sg = new SequenceGroup();
\r
1396 sg.setStartRes(res);
\r
1397 sg.setEndRes(res);
\r
1398 sg.addSequence(sequence, false);
\r
1399 av.setSelectionGroup(sg);
\r
1400 stretchGroup = sg;
\r
1402 if (av.getConservationSelected())
\r
1404 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1407 if (av.getAbovePIDThreshold())
\r
1409 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1416 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1418 if (stretchGroup == null)
\r
1423 if (stretchGroup.cs != null)
\r
1425 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1427 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1428 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1429 stretchGroup.getWidth());
\r
1432 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1433 || stretchGroup.cs instanceof PIDColourScheme
\r
1434 || stretchGroup.cs.conservationApplied()
\r
1435 || stretchGroup.cs.getThreshold() > 0)
\r
1437 stretchGroup.recalcConservation();
\r
1440 if (stretchGroup.cs.conservationApplied())
\r
1442 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1443 stretchGroup.getName());
\r
1444 stretchGroup.recalcConservation();
\r
1448 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1449 stretchGroup.getName());
\r
1452 changeEndRes = false;
\r
1453 changeStartRes = false;
\r
1454 stretchGroup = null;
\r
1455 PaintRefresher.Refresh(ap, av.getSequenceSetId());
\r
1456 ap.paintAlignment(true);
\r
1459 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1461 int res = findRes(evt);
\r
1462 int y = findSeq(evt);
\r
1464 if (wrappedBlock != startWrapBlock)
\r
1469 if (stretchGroup == null)
\r
1474 mouseDragging = true;
\r
1476 if (y > av.alignment.getHeight())
\r
1478 y = av.alignment.getHeight() - 1;
\r
1481 if (res >= av.alignment.getWidth())
\r
1483 res = av.alignment.getWidth() - 1;
\r
1486 if (stretchGroup.getEndRes() == res)
\r
1488 // Edit end res position of selected group
\r
1489 changeEndRes = true;
\r
1491 else if (stretchGroup.getStartRes() == res)
\r
1493 // Edit start res position of selected group
\r
1494 changeStartRes = true;
\r
1504 if (res > (stretchGroup.getStartRes() - 1))
\r
1506 stretchGroup.setEndRes(res);
\r
1509 else if (changeStartRes)
\r
1511 if (res < (stretchGroup.getEndRes() + 1))
\r
1513 stretchGroup.setStartRes(res);
\r
1517 int dragDirection = 0;
\r
1521 dragDirection = 1;
\r
1523 else if (y < oldSeq)
\r
1525 dragDirection = -1;
\r
1528 while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1530 // This routine ensures we don't skip any sequences, as the
\r
1531 // selection is quite slow.
\r
1532 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1534 oldSeq += dragDirection;
\r
1541 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1543 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1545 stretchGroup.deleteSequence(seq, false);
\r
1551 stretchGroup.addSequence(seq, false);
\r
1554 stretchGroup.addSequence(nextSeq, false);
\r
1563 if (res > av.endRes || res < av.startRes
\r
1564 || y < av.startSeq || y > av.endSeq)
\r
1569 if (scrollThread != null)
\r
1571 scrollThread.setEvent(evt);
\r
1574 seqCanvas.repaint();
\r
1577 public void mouseEntered(MouseEvent e)
\r
1584 if (scrollThread != null)
\r
1586 scrollThread.running = false;
\r
1587 scrollThread = null;
\r
1591 public void mouseExited(MouseEvent e)
\r
1593 if (av.getWrapAlignment())
\r
1598 if (mouseDragging && scrollThread == null)
\r
1600 scrollThread = new ScrollThread();
\r
1604 void scrollCanvas(MouseEvent evt)
\r
1608 if (scrollThread != null)
\r
1610 scrollThread.running = false;
\r
1611 scrollThread = null;
\r
1613 mouseDragging = false;
\r
1617 if (scrollThread == null)
\r
1619 scrollThread = new ScrollThread();
\r
1622 mouseDragging = true;
\r
1623 scrollThread.setEvent(evt);
\r
1628 // this class allows scrolling off the bottom of the visible alignment
\r
1629 class ScrollThread
\r
1633 boolean running = false;
\r
1634 public ScrollThread()
\r
1639 public void setEvent(MouseEvent e)
\r
1644 public void stopScrolling()
\r
1658 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1660 running = ap.scrollUp(true);
\r
1663 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1664 av.alignment.getHeight() > av.getEndSeq())
\r
1666 running = ap.scrollUp(false);
\r
1669 if (mouseDragging && evt.getX() < 0)
\r
1671 running = ap.scrollRight(false);
\r
1674 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1676 running = ap.scrollRight(true);
\r
1684 catch (Exception ex)
\r