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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19 package jalview.gui;
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24 import java.awt.event.*;
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25 import javax.swing.*;
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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.*;
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36 * @version $Revision$
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38 public class SeqPanel
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39 extends JPanel implements MouseListener,
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40 MouseMotionListener, MouseWheelListener, SequenceListener
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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50 protected AlignViewport av;
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52 ScrollThread scrollThread = null;
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53 boolean mouseDragging = false;
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54 boolean editingSeqs = false;
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55 boolean groupEditing = false;
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57 //////////////////////////////////////////
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58 /////Everything below this is for defining the boundary of the rubberband
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59 //////////////////////////////////////////
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61 boolean changeEndSeq = false;
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62 boolean changeStartSeq = false;
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63 boolean changeEndRes = false;
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64 boolean changeStartRes = false;
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65 SequenceGroup stretchGroup = null;
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66 boolean remove = false;
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68 Point lastMousePress;
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69 boolean mouseWheelPressed = false;
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70 StringBuffer keyboardNo1;
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71 StringBuffer keyboardNo2;
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73 java.net.URL linkImageURL;
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75 StringBuffer tooltipText = new StringBuffer("<html>");
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78 EditCommand editCommand;
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80 StructureSelectionManager ssm;
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84 * Creates a new SeqPanel object.
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86 * @param avp DOCUMENT ME!
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87 * @param p DOCUMENT ME!
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89 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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91 linkImageURL = getClass().getResource("/images/link.gif");
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92 ToolTipManager.sharedInstance().registerComponent(this);
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93 ToolTipManager.sharedInstance().setInitialDelay(0);
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94 ToolTipManager.sharedInstance().setDismissDelay(10000);
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96 setBackground(Color.white);
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98 seqCanvas = new SeqCanvas(avp);
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99 setLayout(new BorderLayout());
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100 add(seqCanvas, BorderLayout.CENTER);
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104 if (!av.isDataset())
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106 addMouseMotionListener(this);
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107 addMouseListener(this);
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108 addMouseWheelListener(this);
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109 ssm = StructureSelectionManager.getStructureSelectionManager();
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110 ssm.addStructureViewerListener(this);
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114 int startWrapBlock = -1;
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115 int wrappedBlock = -1;
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116 int findRes(MouseEvent evt)
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119 int x = evt.getX();
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121 if (av.wrapAlignment)
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124 int hgap = av.charHeight;
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125 if (av.scaleAboveWrapped)
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127 hgap += av.charHeight;
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130 int cHeight = av.getAlignment().getHeight() * av.charHeight
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131 + hgap + seqCanvas.getAnnotationHeight();
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133 int y = evt.getY();
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135 x -= seqCanvas.LABEL_WEST;
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137 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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143 wrappedBlock = y / cHeight;
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144 wrappedBlock += av.getStartRes() / cwidth;
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146 res = wrappedBlock * cwidth + x / av.getCharWidth();
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151 res = (x / av.getCharWidth()) + av.getStartRes();
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154 if (av.hasHiddenColumns)
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156 res = av.getColumnSelection().adjustForHiddenColumns(res);
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163 int findSeq(MouseEvent evt)
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166 int y = evt.getY();
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168 if (av.wrapAlignment)
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170 int hgap = av.charHeight;
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171 if (av.scaleAboveWrapped)
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173 hgap += av.charHeight;
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176 int cHeight = av.getAlignment().getHeight() * av.charHeight
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177 + hgap + seqCanvas.getAnnotationHeight();
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181 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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182 av.alignment.getHeight() - 1);
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186 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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187 av.alignment.getHeight() - 1);
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193 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
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195 Vector tmp = new Vector();
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196 SequenceFeature[] features = sequence.getSequenceFeatures();
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197 if (features != null)
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199 for (int i = 0; i < features.length; i++)
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201 if (av.featuresDisplayed == null
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202 || !av.featuresDisplayed.containsKey(features[i].getType()))
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207 if ( (features[i].getBegin() <= res) &&
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208 (features[i].getEnd() >= res))
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210 tmp.addElement(features[i]);
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215 features = new SequenceFeature[tmp.size()];
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216 for (int i = 0; i < tmp.size(); i++)
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218 features[i] = (SequenceFeature) tmp.elementAt(i);
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224 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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226 Vector allFeatures = new Vector();
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228 if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null)
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230 while (index < seq.getSequenceFeatures().length)
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232 SequenceFeature sf = seq.getSequenceFeatures()[index];
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233 if (sf.getBegin() <= res &&
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234 sf.getEnd() >= res)
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236 if (av.featuresDisplayed.containsKey(sf.getType()))
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238 allFeatures.addElement(sf);
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244 return allFeatures;
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249 if (editCommand != null && editCommand.getSize() > 0)
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251 ap.alignFrame.addHistoryItem(editCommand);
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252 av.firePropertyChange("alignment", null,
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253 av.getAlignment().getSequences());
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258 editingSeqs = false;
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259 groupEditing = false;
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260 keyboardNo1 = null;
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261 keyboardNo2 = null;
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262 editCommand = null;
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265 void setCursorRow()
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267 seqCanvas.cursorY = getKeyboardNo1() - 1;
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271 void setCursorColumn()
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273 seqCanvas.cursorX = getKeyboardNo1() - 1;
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277 void setCursorRowAndColumn()
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279 if (keyboardNo2 == null)
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281 keyboardNo2 = new StringBuffer();
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285 seqCanvas.cursorX = getKeyboardNo1() - 1;
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286 seqCanvas.cursorY = getKeyboardNo2() - 1;
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291 void setCursorPosition()
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293 SequenceI sequence =
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294 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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296 seqCanvas.cursorX = sequence.findIndex(
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297 getKeyboardNo1() - 1
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302 void moveCursor(int dx, int dy)
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304 seqCanvas.cursorX += dx;
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305 seqCanvas.cursorY += dy;
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306 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
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308 int original = seqCanvas.cursorX - dx;
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309 int maxWidth = av.alignment.getWidth();
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311 while (!av.colSel.isVisible(seqCanvas.cursorX)
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312 && seqCanvas.cursorX < maxWidth
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313 && seqCanvas.cursorX > 0)
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315 seqCanvas.cursorX += dx;
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318 if (seqCanvas.cursorX >= maxWidth
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319 || !av.colSel.isVisible(seqCanvas.cursorX))
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321 seqCanvas.cursorX = original;
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328 void scrollToVisible()
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330 if (seqCanvas.cursorX < 0)
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332 seqCanvas.cursorX = 0;
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334 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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336 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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339 if (seqCanvas.cursorY < 0)
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341 seqCanvas.cursorY = 0;
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343 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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345 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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349 if (av.wrapAlignment)
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351 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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355 while (seqCanvas.cursorY < av.startSeq)
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359 while (seqCanvas.cursorY + 1 > av.endSeq)
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361 ap.scrollUp(false);
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363 if (!av.wrapAlignment)
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365 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
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367 if (!ap.scrollRight(false))
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372 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
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374 if (!ap.scrollRight(true))
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381 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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382 seqCanvas.cursorX, seqCanvas.cursorY);
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384 seqCanvas.repaint();
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387 void setSelectionAreaAtCursor(boolean topLeft)
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389 SequenceI sequence =
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390 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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392 if (av.getSelectionGroup() != null)
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394 SequenceGroup sg = av.selectionGroup;
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395 //Find the top and bottom of this group
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396 int min = av.alignment.getHeight(), max = 0;
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397 for (int i = 0; i < sg.getSize(); i++)
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399 int index = av.alignment.findIndex(sg.getSequenceAt(i));
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414 sg.setStartRes(seqCanvas.cursorX);
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415 if (sg.getEndRes() < seqCanvas.cursorX)
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417 sg.setEndRes(seqCanvas.cursorX);
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420 min = seqCanvas.cursorY;
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424 sg.setEndRes(seqCanvas.cursorX);
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425 if (sg.getStartRes() > seqCanvas.cursorX)
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427 sg.setStartRes(seqCanvas.cursorX);
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430 max = seqCanvas.cursorY + 1;
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435 // Only the user can do this
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436 av.setSelectionGroup(null);
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440 // Now add any sequences between min and max
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441 sg.getSequences(null).clear();
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442 for (int i = min; i < max; i++)
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444 sg.addSequence(av.alignment.getSequenceAt(i), false);
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449 if (av.getSelectionGroup() == null)
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451 SequenceGroup sg = new SequenceGroup();
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452 sg.setStartRes(seqCanvas.cursorX);
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453 sg.setEndRes(seqCanvas.cursorX);
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454 sg.addSequence(sequence, false);
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455 av.setSelectionGroup(sg);
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458 ap.paintAlignment(false);
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461 void insertGapAtCursor(boolean group)
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463 groupEditing = group;
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464 startseq = seqCanvas.cursorY;
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465 lastres = seqCanvas.cursorX;
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466 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
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470 void deleteGapAtCursor(boolean group)
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472 groupEditing = group;
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473 startseq = seqCanvas.cursorY;
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474 lastres = seqCanvas.cursorX + getKeyboardNo1();
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475 editSequence(false, seqCanvas.cursorX);
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479 void numberPressed(char value)
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481 if (keyboardNo1 == null)
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483 keyboardNo1 = new StringBuffer();
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486 if (keyboardNo2 != null)
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488 keyboardNo2.append(value);
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492 keyboardNo1.append(value);
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496 int getKeyboardNo1()
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498 if (keyboardNo1 == null)
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502 int value = Integer.parseInt(keyboardNo1.toString());
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503 keyboardNo1 = null;
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508 int getKeyboardNo2()
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510 if (keyboardNo2 == null)
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514 int value = Integer.parseInt(keyboardNo2.toString());
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515 keyboardNo2 = null;
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523 * @param evt DOCUMENT ME!
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525 public void mouseReleased(MouseEvent evt)
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527 mouseDragging = false;
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528 mouseWheelPressed = false;
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532 doMouseReleasedDefineMode(evt);
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538 ap.paintAlignment(true);
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544 * @param evt DOCUMENT ME!
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546 public void mousePressed(MouseEvent evt)
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548 lastMousePress = evt.getPoint();
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550 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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552 mouseWheelPressed = true;
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556 if (evt.isShiftDown() || evt.isAltDown() ||
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557 evt.isControlDown())
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559 if (evt.isAltDown() || evt.isControlDown())
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561 groupEditing = true;
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563 editingSeqs = true;
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567 doMousePressedDefineMode(evt);
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571 int seq = findSeq(evt);
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572 int res = findRes(evt);
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574 if (seq < 0 || res < 0)
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579 if ( (seq < av.getAlignment().getHeight()) &&
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580 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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594 String lastMessage;
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595 public void mouseOverSequence(SequenceI sequence, int index)
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597 String tmp = sequence.hashCode()+index+"";
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598 if (lastMessage == null || !lastMessage.equals(tmp))
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599 ssm.mouseOverSequence(sequence, index);
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605 public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
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607 if(av.alignment.findIndex(seq)>-1)
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609 SearchResults highlight = new SearchResults();
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610 highlight.addResult(seq,index,index);
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611 seqCanvas.highlightSearchResults(highlight);
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615 public void updateColours(SequenceI seq, int index)
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617 System.out.println("update the seqPanel colours");
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624 * @param evt DOCUMENT ME!
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626 public void mouseMoved(MouseEvent evt)
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630 // This is because MacOSX creates a mouseMoved
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631 // If control is down, other platforms will not.
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635 int res = findRes(evt);
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636 int seq = findSeq(evt);
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638 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
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643 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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645 if (res > sequence.getLength())
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651 mouseOverSequence(sequence, sequence.findPosition(res));
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653 setStatusMessage(sequence, res, seq);
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655 tooltipText.setLength(6); // Cuts the buffer back to <html>
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657 SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
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658 if (groups != null)
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660 for (int g = 0; g < groups.length; g++)
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662 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
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664 if (tooltipText.length() > 6)
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666 tooltipText.append("<br>");
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669 if (!groups[g].getName().startsWith("JTreeGroup") &&
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670 !groups[g].getName().startsWith("JGroup"))
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672 tooltipText.append(groups[g].getName());
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675 if (groups[g].getDescription() != null)
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677 tooltipText.append(": " + groups[g].getDescription());
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683 // use aa to see if the mouse pointer is on a
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684 if (av.showSequenceFeatures)
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686 SequenceFeature[] features = findFeaturesAtRes(
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687 sequence.getDatasetSequence(), sequence.findPosition(res));
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689 if (features != null)
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691 for (int i = 0; i < features.length; i++)
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693 if (features[i].getType().equals("disulfide bond"))
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695 if (features[i].getBegin() == sequence.findPosition(res)
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696 || features[i].getEnd() == sequence.findPosition(res))
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698 if (tooltipText.length() > 6)
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700 tooltipText.append("<br>");
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702 tooltipText.append("disulfide bond " + features[i].getBegin() +
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704 features[i].getEnd());
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705 if (features[i].links != null)
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707 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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713 if (tooltipText.length() > 6)
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715 tooltipText.append("<br>");
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718 tooltipText.append(features[i].getType() + " " +
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719 features[i].begin);
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720 if (features[i].begin != features[i].end)
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722 tooltipText.append(" " + features[i].end);
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725 if (features[i].getDescription() != null
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726 && !features[i].description.equals(features[i].getType()))
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728 tmpString = features[i].getDescription();
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729 int startTag = tmpString.toUpperCase().indexOf("<HTML>");
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732 tmpString = tmpString.substring(startTag + 6);
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734 int endTag = tmpString.toUpperCase().indexOf("</BODY>");
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737 tmpString = tmpString.substring(0, endTag);
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739 endTag = tmpString.toUpperCase().indexOf("</HTML>");
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742 tmpString = tmpString.substring(0, endTag);
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747 tooltipText.append("; " + tmpString);
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751 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
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753 //The description does not specify html is to
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754 //be used, so we must remove < > symbols
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755 tmpString = tmpString.replaceAll("<", "<");
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756 tmpString = tmpString.replaceAll(">", ">");
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758 tooltipText.append("; ");
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759 tooltipText.append(tmpString);
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764 tooltipText.append("; " + tmpString);
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768 if (features[i].getValue("status") != null)
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770 String status = features[i].getValue("status").toString();
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771 if (status.length() > 0)
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773 tooltipText.append("; (" + features[i].getValue("status") + ")");
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777 if (features[i].links != null)
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779 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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787 if (tooltipText.length() == 6) // <html></html>
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789 setToolTipText(null);
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793 tooltipText.append("</html>");
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794 setToolTipText(tooltipText.toString());
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797 // setToolTipText(null);
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800 void setStatusMessage(SequenceI sequence, int res, int seq)
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802 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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803 sequence.getName());
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806 if (av.alignment.isNucleotide())
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808 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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812 text.append(" Nucleotide: ");
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817 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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820 text.append(" Residue: ");
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829 text.append(obj + " (" + sequence.findPosition(res) +
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833 ap.alignFrame.statusBar.setText(text.toString());
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840 * @param evt DOCUMENT ME!
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842 public void mouseDragged(MouseEvent evt)
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844 if (mouseWheelPressed)
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846 int oldWidth = av.charWidth;
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848 //Which is bigger, left-right or up-down?
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849 if (Math.abs(evt.getY() - lastMousePress.getY())
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850 > Math.abs(evt.getX() - lastMousePress.getX()))
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852 int fontSize = av.font.getSize();
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854 if (evt.getY() < lastMousePress.getY())
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858 else if (evt.getY() > lastMousePress.getY())
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868 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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869 av.charWidth = oldWidth;
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874 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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878 else if (evt.getX() > lastMousePress.getX())
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883 ap.paintAlignment(false);
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886 FontMetrics fm = getFontMetrics(av.getFont());
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887 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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889 lastMousePress = evt.getPoint();
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896 doMouseDraggedDefineMode(evt);
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900 int res = findRes(evt);
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907 if ( (lastres == -1) || (lastres == res))
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912 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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914 // dragLeft, delete gap
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915 editSequence(false, res);
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919 editSequence(true, res);
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922 mouseDragging = true;
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923 if (scrollThread != null)
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925 scrollThread.setEvent(evt);
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931 synchronized void editSequence(boolean insertGap, int startres)
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933 int fixedLeft = -1;
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934 int fixedRight = -1;
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935 boolean fixedColumns = false;
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936 SequenceGroup sg = av.getSelectionGroup();
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938 SequenceI seq = av.alignment.getSequenceAt(startseq);
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940 //No group, but the sequence may represent a group
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941 if (!groupEditing && av.hasHiddenRows)
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943 if (av.hiddenRepSequences != null
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944 && av.hiddenRepSequences.containsKey(seq))
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946 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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947 groupEditing = true;
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951 StringBuffer message = new StringBuffer();
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954 message.append("Edit group:");
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955 if (editCommand == null)
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957 editCommand = new EditCommand("Edit Group");
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962 message.append("Edit sequence: " + seq.getName());
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963 String label = seq.getName();
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964 if (label.length() > 10)
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966 label = label.substring(0, 10);
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968 if (editCommand == null)
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970 editCommand = new EditCommand("Edit " + label);
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976 message.append(" insert ");
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980 message.append(" delete ");
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983 message.append(Math.abs(startres - lastres) + " gaps.");
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984 ap.alignFrame.statusBar.setText(message.toString());
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986 //Are we editing within a selection group?
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988 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
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990 fixedColumns = true;
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992 //sg might be null as the user may only see 1 sequence,
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993 //but the sequence represents a group
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996 if (av.hiddenRepSequences == null
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997 || !av.hiddenRepSequences.containsKey(seq))
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1002 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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1005 fixedLeft = sg.getStartRes();
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1006 fixedRight = sg.getEndRes();
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1008 if ( (startres < fixedLeft && lastres >= fixedLeft)
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1009 || (startres >= fixedLeft && lastres < fixedLeft)
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1010 || (startres > fixedRight && lastres <= fixedRight)
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1011 || (startres <= fixedRight && lastres > fixedRight))
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1017 if (fixedLeft > startres)
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1019 fixedRight = fixedLeft - 1;
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1022 else if (fixedRight < startres)
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1024 fixedLeft = fixedRight;
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1029 if (av.hasHiddenColumns)
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1031 fixedColumns = true;
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1032 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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1033 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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1035 if ( (insertGap && startres > y1 && lastres < y1)
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1036 || (!insertGap && startres < y2 && lastres > y2))
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1042 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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1043 //Selection spans a hidden region
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1044 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
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1046 if (startres >= y2)
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1052 fixedRight = y2 - 1;
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1059 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
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1060 int g, groupSize = vseqs.size();
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1061 SequenceI[] groupSeqs = new SequenceI[groupSize];
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1062 for (g = 0; g < groupSeqs.length; g++)
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1064 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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1070 //If the user has selected the whole sequence, and is dragging to
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1071 // the right, we can still extend the alignment and selectionGroup
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1072 if (sg.getStartRes() == 0
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1073 && sg.getEndRes() == fixedRight
\r
1074 && sg.getEndRes() == av.alignment.getWidth() - 1
\r
1077 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
\r
1078 fixedRight = sg.getEndRes();
\r
1081 // Is it valid with fixed columns??
\r
1082 // Find the next gap before the end
\r
1083 // of the visible region boundary
\r
1084 boolean blank = false;
\r
1085 for (fixedRight = fixedRight;
\r
1086 fixedRight > lastres;
\r
1091 for (g = 0; g < groupSize; g++)
\r
1093 for (int j = 0; j < startres - lastres; j++)
\r
1095 if (!jalview.util.Comparison.isGap(
\r
1096 groupSeqs[g].getCharAt(fixedRight - j)))
\r
1111 if (sg.getSize() == av.alignment.getHeight())
\r
1113 if ( (av.hasHiddenColumns
\r
1115 startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
1121 int alWidth = av.alignment.getWidth();
\r
1122 if (av.hasHiddenRows)
\r
1124 int hwidth = av.alignment.getHiddenSequences().getWidth();
\r
1125 if (hwidth > alWidth)
\r
1130 //We can still insert gaps if the selectionGroup
\r
1131 //contains all the sequences
\r
1132 sg.setEndRes(sg.getEndRes() + startres - lastres);
\r
1133 fixedRight = alWidth + startres - lastres;
\r
1144 else if (!insertGap)
\r
1146 /// Are we able to delete?
\r
1147 // ie are all columns blank?
\r
1149 for (g = 0; g < groupSize; g++)
\r
1151 for (int j = startres; j < lastres; j++)
\r
1153 if (groupSeqs[g].getLength() <= j)
\r
1158 if (!jalview.util.Comparison.isGap(
\r
1159 groupSeqs[g].getCharAt(j)))
\r
1161 // Not a gap, block edit not valid
\r
1171 // dragging to the right
\r
1172 if (fixedColumns && fixedRight != -1)
\r
1174 for (int j = lastres; j < startres; j++)
\r
1176 insertChar(j, groupSeqs, fixedRight);
\r
1181 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1183 startres, startres - lastres,
\r
1190 // dragging to the left
\r
1191 if (fixedColumns && fixedRight != -1)
\r
1193 for (int j = lastres; j > startres; j--)
\r
1195 deleteChar(startres, groupSeqs, fixedRight);
\r
1200 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1202 startres, lastres - startres,
\r
1209 else /////Editing a single sequence///////////
\r
1213 // dragging to the right
\r
1214 if (fixedColumns && fixedRight != -1)
\r
1216 for (int j = lastres; j < startres; j++)
\r
1218 insertChar(j, new SequenceI[]
\r
1219 {seq}, fixedRight);
\r
1224 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1227 lastres, startres - lastres,
\r
1234 // dragging to the left
\r
1235 if (fixedColumns && fixedRight != -1)
\r
1237 for (int j = lastres; j > startres; j--)
\r
1239 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1244 deleteChar(startres, new SequenceI[]
\r
1245 {seq}, fixedRight);
\r
1250 //could be a keyboard edit trying to delete none gaps
\r
1252 for (int m = startres; m < lastres; m++)
\r
1254 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1263 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1274 lastres = startres;
\r
1275 seqCanvas.repaint();
\r
1278 void insertChar(int j, SequenceI[] seq, int fixedColumn)
\r
1280 int blankColumn = fixedColumn;
\r
1281 for (int s = 0; s < seq.length; s++)
\r
1283 //Find the next gap before the end of the visible region boundary
\r
1284 //If lastCol > j, theres a boundary after the gap insertion
\r
1286 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1288 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1290 //Theres a space, so break and insert the gap
\r
1295 if (blankColumn <= j)
\r
1297 blankColumn = fixedColumn;
\r
1303 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1305 blankColumn, 1, av.alignment, true);
\r
1307 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1309 j, 1, av.alignment,
\r
1314 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
\r
1317 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1319 j, 1, av.alignment, true);
\r
1321 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1323 fixedColumn, 1, av.alignment, true);
\r
1329 * @param e DOCUMENT ME!
\r
1331 public void mouseEntered(MouseEvent e)
\r
1338 if (scrollThread != null)
\r
1340 scrollThread.running = false;
\r
1341 scrollThread = null;
\r
1348 * @param e DOCUMENT ME!
\r
1350 public void mouseExited(MouseEvent e)
\r
1352 if (av.getWrapAlignment())
\r
1357 if (mouseDragging)
\r
1359 scrollThread = new ScrollThread();
\r
1363 public void mouseClicked(MouseEvent evt)
\r
1365 SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
\r
1366 if (evt.getClickCount() > 1)
\r
1368 if (av.getSelectionGroup().getSize() == 1
\r
1369 && av.getSelectionGroup().getEndRes()
\r
1370 - av.getSelectionGroup().getStartRes() < 2)
\r
1372 av.setSelectionGroup(null);
\r
1375 SequenceFeature[] features = findFeaturesAtRes(
\r
1376 sequence.getDatasetSequence(),
\r
1377 sequence.findPosition(findRes(evt))
\r
1380 if (features != null && features.length > 0)
\r
1382 SearchResults highlight = new SearchResults();
\r
1383 highlight.addResult(sequence,
\r
1384 features[0].getBegin(),
\r
1385 features[0].getEnd());
\r
1386 seqCanvas.highlightSearchResults(highlight);
\r
1388 if (features != null && features.length > 0)
\r
1390 seqCanvas.getFeatureRenderer().amendFeatures(
\r
1392 {sequence}, features, false, ap);
\r
1394 seqCanvas.highlightSearchResults(null);
\r
1399 public void mouseWheelMoved(MouseWheelEvent e)
\r
1402 if (e.getWheelRotation() > 0)
\r
1404 ap.scrollUp(false);
\r
1408 ap.scrollUp(true);
\r
1415 * @param evt DOCUMENT ME!
\r
1417 public void doMousePressedDefineMode(MouseEvent evt)
\r
1419 int res = findRes(evt);
\r
1420 int seq = findSeq(evt);
\r
1423 startWrapBlock = wrappedBlock;
\r
1425 if (av.wrapAlignment && seq > av.alignment.getHeight())
\r
1427 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1428 "Cannot edit annotations in wrapped view.",
\r
1429 "Wrapped view - no edit",
\r
1430 JOptionPane.WARNING_MESSAGE);
\r
1434 if (seq < 0 || res < 0)
\r
1439 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1441 if ( (sequence == null) || (res > sequence.getLength()))
\r
1446 stretchGroup = av.getSelectionGroup();
\r
1448 if (stretchGroup == null)
\r
1450 stretchGroup = av.alignment.findGroup(sequence);
\r
1452 if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1453 (res < stretchGroup.getEndRes()))
\r
1455 av.setSelectionGroup(stretchGroup);
\r
1459 stretchGroup = null;
\r
1462 else if (!stretchGroup.getSequences(null).contains(sequence) ||
\r
1463 (stretchGroup.getStartRes() > res) ||
\r
1464 (stretchGroup.getEndRes() < res))
\r
1466 stretchGroup = null;
\r
1468 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1470 if (allGroups != null)
\r
1472 for (int i = 0; i < allGroups.length; i++)
\r
1474 if ( (allGroups[i].getStartRes() <= res) &&
\r
1475 (allGroups[i].getEndRes() >= res))
\r
1477 stretchGroup = allGroups[i];
\r
1483 av.setSelectionGroup(stretchGroup);
\r
1487 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1489 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1490 sequence.findPosition(res));
\r
1491 Vector links = new Vector();
\r
1492 for (int i = 0; i < allFeatures.size(); i++)
\r
1494 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1495 if (sf.links != null)
\r
1497 for (int j = 0; j < sf.links.size(); j++)
\r
1499 links.addElement(sf.links.elementAt(j));
\r
1504 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1505 pop.show(this, evt.getX(), evt.getY());
\r
1509 if (av.cursorMode)
\r
1511 seqCanvas.cursorX = findRes(evt);
\r
1512 seqCanvas.cursorY = findSeq(evt);
\r
1513 seqCanvas.repaint();
\r
1517 if (stretchGroup == null)
\r
1519 //Only if left mouse button do we want to change group sizes
\r
1521 // define a new group here
\r
1522 SequenceGroup sg = new SequenceGroup();
\r
1523 sg.setStartRes(res);
\r
1524 sg.setEndRes(res);
\r
1525 sg.addSequence(sequence, false);
\r
1526 av.setSelectionGroup(sg);
\r
1527 stretchGroup = sg;
\r
1529 if (av.getConservationSelected())
\r
1531 SliderPanel.setConservationSlider(ap,
\r
1532 av.getGlobalColourScheme(),
\r
1536 if (av.getAbovePIDThreshold())
\r
1538 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1541 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1543 // Edit end res position of selected group
\r
1544 changeEndRes = true;
\r
1546 else if ( (stretchGroup != null) &&
\r
1547 (stretchGroup.getStartRes() == res))
\r
1549 // Edit end res position of selected group
\r
1550 changeStartRes = true;
\r
1552 stretchGroup.getWidth();
\r
1555 seqCanvas.repaint();
\r
1561 * @param evt DOCUMENT ME!
\r
1563 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1565 if (stretchGroup == null)
\r
1570 if (stretchGroup.cs != null)
\r
1572 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1574 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1575 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1576 stretchGroup.getWidth());
\r
1579 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1580 || stretchGroup.cs instanceof PIDColourScheme
\r
1581 || stretchGroup.cs.conservationApplied()
\r
1582 || stretchGroup.cs.getThreshold() > 0)
\r
1584 stretchGroup.recalcConservation();
\r
1587 if (stretchGroup.cs.conservationApplied())
\r
1589 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1590 stretchGroup.getName());
\r
1594 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1595 stretchGroup.getName());
\r
1598 changeEndRes = false;
\r
1599 changeStartRes = false;
\r
1600 stretchGroup = null;
\r
1602 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1603 ap.paintAlignment(true);
\r
1609 * @param evt DOCUMENT ME!
\r
1611 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1613 int res = findRes(evt);
\r
1614 int y = findSeq(evt);
\r
1616 if (wrappedBlock != startWrapBlock)
\r
1621 if (stretchGroup == null)
\r
1626 if (res >= av.alignment.getWidth())
\r
1628 res = av.alignment.getWidth() - 1;
\r
1631 if (stretchGroup.getEndRes() == res)
\r
1633 // Edit end res position of selected group
\r
1634 changeEndRes = true;
\r
1636 else if (stretchGroup.getStartRes() == res)
\r
1638 // Edit start res position of selected group
\r
1639 changeStartRes = true;
\r
1642 if (res < av.getStartRes())
\r
1644 res = av.getStartRes();
\r
1649 if (res > (stretchGroup.getStartRes() - 1))
\r
1651 stretchGroup.setEndRes(res);
\r
1654 else if (changeStartRes)
\r
1656 if (res < (stretchGroup.getEndRes() + 1))
\r
1658 stretchGroup.setStartRes(res);
\r
1662 int dragDirection = 0;
\r
1666 dragDirection = 1;
\r
1668 else if (y < oldSeq)
\r
1670 dragDirection = -1;
\r
1673 while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1675 // This routine ensures we don't skip any sequences, as the
\r
1676 // selection is quite slow.
\r
1677 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1679 oldSeq += dragDirection;
\r
1686 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1688 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1690 stretchGroup.deleteSequence(seq, false);
\r
1696 stretchGroup.addSequence(seq, false);
\r
1699 stretchGroup.addSequence(nextSeq, false);
\r
1708 mouseDragging = true;
\r
1710 if (scrollThread != null)
\r
1712 scrollThread.setEvent(evt);
\r
1715 seqCanvas.repaint();
\r
1718 void scrollCanvas(MouseEvent evt)
\r
1722 if (scrollThread != null)
\r
1724 scrollThread.running = false;
\r
1725 scrollThread = null;
\r
1727 mouseDragging = false;
\r
1731 if (scrollThread == null)
\r
1733 scrollThread = new ScrollThread();
\r
1736 mouseDragging = true;
\r
1737 scrollThread.setEvent(evt);
\r
1742 // this class allows scrolling off the bottom of the visible alignment
\r
1743 class ScrollThread
\r
1747 boolean running = false;
\r
1749 public ScrollThread()
\r
1754 public void setEvent(MouseEvent e)
\r
1759 public void stopScrolling()
\r
1772 if (mouseDragging && (evt.getY() < 0) &&
\r
1773 (av.getStartSeq() > 0))
\r
1775 running = ap.scrollUp(true);
\r
1778 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1779 (av.alignment.getHeight() > av.getEndSeq()))
\r
1781 running = ap.scrollUp(false);
\r
1784 if (mouseDragging && (evt.getX() < 0))
\r
1786 running = ap.scrollRight(false);
\r
1788 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1790 running = ap.scrollRight(true);
\r
1798 catch (Exception ex)
\r