2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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21 import jalview.datamodel.*;
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22 import jalview.commands.EditCommand;
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23 import jalview.schemes.*;
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26 import java.awt.event.*;
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27 import javax.swing.*;
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28 import java.util.Vector;
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35 * @version $Revision$
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37 public class SeqPanel extends JPanel implements MouseListener,
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38 MouseMotionListener, MouseWheelListener
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41 /** DOCUMENT ME!! */
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42 public SeqCanvas seqCanvas;
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44 /** DOCUMENT ME!! */
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45 public AlignmentPanel ap;
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46 protected int lastres;
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47 protected int startseq;
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48 protected AlignViewport av;
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50 ScrollThread scrollThread = null;
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51 boolean mouseDragging = false;
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52 boolean editingSeqs = false;
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53 boolean groupEditing = false;
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55 //////////////////////////////////////////
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56 /////Everything below this is for defining the boundary of the rubberband
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57 //////////////////////////////////////////
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59 boolean changeEndSeq = false;
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60 boolean changeStartSeq = false;
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61 boolean changeEndRes = false;
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62 boolean changeStartRes = false;
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63 SequenceGroup stretchGroup = null;
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64 boolean remove = false;
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66 Point lastMousePress;
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67 boolean mouseWheelPressed = false;
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68 StringBuffer keyboardNo1;
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69 StringBuffer keyboardNo2;
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71 java.net.URL linkImageURL;
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73 StringBuffer tooltipText = new StringBuffer("<html>");
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76 EditCommand editCommand;
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79 * Creates a new SeqPanel object.
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81 * @param avp DOCUMENT ME!
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82 * @param p DOCUMENT ME!
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84 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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86 linkImageURL = getClass().getResource("/images/link.gif");
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87 ToolTipManager.sharedInstance().registerComponent(this);
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88 ToolTipManager.sharedInstance().setInitialDelay(0);
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89 ToolTipManager.sharedInstance().setDismissDelay(10000);
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91 setBackground(Color.white);
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93 seqCanvas = new SeqCanvas(avp);
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94 setLayout(new BorderLayout());
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95 add(seqCanvas, BorderLayout.CENTER);
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99 if (!av.isDataset())
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101 addMouseMotionListener(this);
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102 addMouseListener(this);
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103 addMouseWheelListener(this);
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107 int startWrapBlock = -1;
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108 int wrappedBlock = -1;
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109 int findRes(MouseEvent evt)
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112 int x = evt.getX();
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114 if (av.wrapAlignment)
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117 int hgap = av.charHeight;
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118 if (av.scaleAboveWrapped)
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119 hgap += av.charHeight;
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121 int cHeight = av.getAlignment().getHeight() * av.charHeight
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122 + hgap + seqCanvas.getAnnotationHeight();
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124 int y = evt.getY();
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126 x -= seqCanvas.LABEL_WEST;
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128 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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132 wrappedBlock = y / cHeight;
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133 wrappedBlock += av.getStartRes() / cwidth;
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135 res = wrappedBlock * cwidth + x / av.getCharWidth();
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140 res = (x / av.getCharWidth()) + av.getStartRes();
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143 if (av.hasHiddenColumns)
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144 res = av.getColumnSelection().adjustForHiddenColumns(res);
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150 int findSeq(MouseEvent evt)
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153 int y = evt.getY();
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155 if (av.wrapAlignment)
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157 int hgap = av.charHeight;
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158 if (av.scaleAboveWrapped)
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159 hgap += av.charHeight;
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161 int cHeight = av.getAlignment().getHeight() * av.charHeight
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162 + hgap + seqCanvas.getAnnotationHeight();
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166 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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167 av.alignment.getHeight() - 1);
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171 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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172 av.alignment.getHeight() - 1);
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178 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
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180 Vector tmp = new Vector();
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181 SequenceFeature[] features = sequence.getSequenceFeatures();
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182 if (features != null)
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184 for (int i = 0; i < features.length; i++)
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186 if (av.featuresDisplayed == null
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187 || !av.featuresDisplayed.containsKey(features[i].getType()))
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190 if ( (features[i].getBegin() <= res) &&
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191 (features[i].getEnd() >= res))
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193 tmp.addElement(features[i]);
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198 features = new SequenceFeature[tmp.size()];
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199 for(int i=0; i<tmp.size(); i++)
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201 features[i] = (SequenceFeature)tmp.elementAt(i);
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207 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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209 Vector allFeatures = new Vector();
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211 if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
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213 while (index < seq.getSequenceFeatures().length)
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215 SequenceFeature sf = seq.getSequenceFeatures()[index];
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216 if (sf.getBegin() <= res &&
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217 sf.getEnd() >= res)
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219 if (av.featuresDisplayed.containsKey(sf.getType()))
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221 allFeatures.addElement(sf);
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227 return allFeatures;
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232 if (editCommand!=null && editCommand.getSize() > 0)
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234 ap.alignFrame.addHistoryItem(editCommand);
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235 av.firePropertyChange("alignment", null,
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236 av.getAlignment().getSequences());
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241 editingSeqs = false;
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242 groupEditing = false;
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243 keyboardNo1 = null;
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244 keyboardNo2 = null;
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245 editCommand = null;
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248 void setCursorRow()
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250 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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254 void setCursorColumn()
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256 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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260 void setCursorRowAndColumn()
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262 if(keyboardNo2==null)
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264 keyboardNo2 = new StringBuffer();
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268 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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269 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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274 void setCursorPosition()
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276 SequenceI sequence =
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277 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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279 seqCanvas.cursorX = sequence.findIndex(
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280 getKeyboardNo(keyboardNo1)-1
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285 void moveCursor(int dx, int dy)
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287 seqCanvas.cursorX += dx;
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288 seqCanvas.cursorY += dy;
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292 void scrollToVisible()
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294 if (seqCanvas.cursorX < 0)
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295 seqCanvas.cursorX = 0;
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296 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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297 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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299 if (seqCanvas.cursorY < 0)
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300 seqCanvas.cursorY = 0;
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301 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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302 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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306 if(av.wrapAlignment)
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308 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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312 while (seqCanvas.cursorY < av.startSeq)
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316 while (seqCanvas.cursorY + 1 > av.endSeq)
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318 ap.scrollUp(false);
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320 if (!av.wrapAlignment)
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322 while (seqCanvas.cursorX < av.startRes)
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324 if (!ap.scrollRight(false))
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327 while (seqCanvas.cursorX > av.endRes)
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329 if (!ap.scrollRight(true))
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334 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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335 seqCanvas.cursorX, seqCanvas.cursorY);
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337 seqCanvas.repaint();
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340 void setSelectionAreaAtCursor(boolean topLeft)
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342 SequenceI sequence =
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343 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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345 if(av.getSelectionGroup()!=null)
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347 SequenceGroup sg = av.selectionGroup;
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348 //Find the top and bottom of this group
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349 int min = av.alignment.getHeight(), max = 0;
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350 for(int i=0; i<sg.getSize(false); i++)
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352 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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363 sg.setStartRes(seqCanvas.cursorX);
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364 if(sg.getEndRes()<seqCanvas.cursorX)
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365 sg.setEndRes(seqCanvas.cursorX);
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367 min = seqCanvas.cursorY;
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371 sg.setEndRes(seqCanvas.cursorX);
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372 if(sg.getStartRes()>seqCanvas.cursorX)
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373 sg.setStartRes(seqCanvas.cursorX);
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375 max = seqCanvas.cursorY+1;
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380 // Only the user can do this
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381 av.setSelectionGroup(null);
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385 // Now add any sequences between min and max
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386 sg.getSequences(false).clear();
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387 for (int i = min; i < max; i++)
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389 sg.addSequence(av.alignment.getSequenceAt(i), false);
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394 if (av.getSelectionGroup() == null)
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396 SequenceGroup sg = new SequenceGroup();
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397 sg.setStartRes(seqCanvas.cursorX);
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398 sg.setEndRes(seqCanvas.cursorX);
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399 sg.addSequence(sequence, false);
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400 av.setSelectionGroup(sg);
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407 void insertGapAtCursor(boolean group)
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409 groupEditing = group;
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410 startseq = seqCanvas.cursorY;
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411 lastres = seqCanvas.cursorX;
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412 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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416 void deleteGapAtCursor(boolean group)
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418 groupEditing = group;
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419 startseq = seqCanvas.cursorY;
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420 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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421 editSequence(false, seqCanvas.cursorX);
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425 void numberPressed(char value)
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427 if(keyboardNo1==null)
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428 keyboardNo1 = new StringBuffer();
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430 if(keyboardNo2!=null)
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431 keyboardNo2.append(value);
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433 keyboardNo1.append(value);
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436 int getKeyboardNo(StringBuffer kb)
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441 return Integer.parseInt(kb.toString());
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448 * @param evt DOCUMENT ME!
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450 public void mouseReleased(MouseEvent evt)
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452 mouseDragging = false;
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453 mouseWheelPressed = false;
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457 doMouseReleasedDefineMode(evt);
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471 * @param evt DOCUMENT ME!
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473 public void mousePressed(MouseEvent evt)
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475 lastMousePress = evt.getPoint();
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477 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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479 mouseWheelPressed = true;
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483 if (evt.isShiftDown() || evt.isAltDown() ||
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484 evt.isControlDown())
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486 if (evt.isAltDown() || evt.isControlDown())
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488 groupEditing = true;
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490 editingSeqs = true;
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494 doMousePressedDefineMode(evt);
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498 int seq = findSeq(evt);
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499 int res = findRes(evt);
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504 if ((seq < av.getAlignment().getHeight()) &&
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505 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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522 * @param evt DOCUMENT ME!
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524 public void mouseMoved(MouseEvent evt)
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528 // This is because MacOSX creates a mouseMoved
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529 // If control is down, other platforms will not.
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533 int res = findRes(evt);
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534 int seq = findSeq(evt);
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537 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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540 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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542 if (res > sequence.getLength())
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547 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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549 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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552 setStatusMessage(sequence, res, seq);
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554 // use aa to see if the mouse pointer is on a
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555 if (av.showSequenceFeatures)
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557 tooltipText.setLength(6); // Cuts the buffer back to <html>
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559 SequenceFeature[] features = findFeaturesAtRes(
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560 sequence.getDatasetSequence(), sequence.findPosition(res));
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564 for (int i = 0; i < features.length; i++)
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566 if (features[i].getType().equals("disulfide bond"))
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568 if (features[i].getBegin() == sequence.findPosition(res)
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569 || features[i].getEnd() == sequence.findPosition(res))
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571 if (tooltipText.length() > 6)
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572 tooltipText.append("<br>");
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573 tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +
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574 features[i].getEnd());
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575 if (features[i].links != null)
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576 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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581 if (tooltipText.length() > 6)
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582 tooltipText.append("<br>");
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584 tooltipText.append(features[i].getType() + " " +
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585 features[i].begin);
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586 if (features[i].begin != features[i].end)
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587 tooltipText.append(" " + features[i].end);
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589 if (features[i].getDescription() != null
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590 && !features[i].description.equals(features[i].getType()))
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592 tmpString = features[i].getDescription();
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593 int startTag=tmpString.toUpperCase().indexOf("<HTML>");
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596 tmpString = tmpString.substring(startTag + 6);
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598 int endTag=tmpString.toUpperCase().indexOf("</BODY>");
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601 tmpString = tmpString.substring(0, endTag);
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603 endTag = tmpString.toUpperCase().indexOf("</HTML>");
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606 tmpString = tmpString.substring(0, endTag);
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611 tooltipText.append("; " + tmpString);
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615 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
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617 //The description does not specify html is to
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618 //be used, so we must remove < > symbols
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619 tmpString = tmpString.replaceAll("<", "<");
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620 tmpString = tmpString.replaceAll(">", ">");
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622 tooltipText.append("; ");
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623 tooltipText.append(tmpString);
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627 tooltipText.append("; "+tmpString);
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630 if (features[i].getValue("status") != null )
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632 String status = features[i].getValue("status").toString();
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633 if(status.length()>0)
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634 tooltipText.append("; (" + features[i].getValue("status") + ")");
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637 if (features[i].links != null)
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638 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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642 // else if(features[i].begin==0 && features[i].end==0)
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644 // seqSpecific.append(features[i].featureGroup+": "
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645 // + features[i].getType()+" "
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646 // +features[i].getDescription()+"<br>");
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651 if(tooltipText.length()==6) // <html></html>
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654 setToolTipText("");
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658 tooltipText.append("</html>");
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659 setToolTipText(tooltipText.toString());
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663 setToolTipText("");
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667 void setStatusMessage(SequenceI sequence, int res, int seq)
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669 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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670 sequence.getName());
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673 if (av.alignment.isNucleotide())
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675 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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678 text.append(" Nucleotide: ");
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682 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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684 text.append(" Residue: ");
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692 text.append(obj + " (" + sequence.findPosition(res) +
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696 ap.alignFrame.statusBar.setText(text.toString());
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703 * @param evt DOCUMENT ME!
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705 public void mouseDragged(MouseEvent evt)
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707 if (mouseWheelPressed)
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709 int oldWidth = av.charWidth;
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711 //Which is bigger, left-right or up-down?
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712 if (Math.abs(evt.getY() - lastMousePress.getY())
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713 > Math.abs(evt.getX() - lastMousePress.getX()))
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715 int fontSize = av.font.getSize();
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717 if (evt.getY() < lastMousePress.getY())
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721 else if (evt.getY() > lastMousePress.getY())
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729 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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730 av.charWidth = oldWidth;
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735 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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739 else if (evt.getX() > lastMousePress.getX())
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747 FontMetrics fm = getFontMetrics(av.getFont());
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748 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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750 lastMousePress = evt.getPoint();
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757 doMouseDraggedDefineMode(evt);
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761 int res = findRes(evt);
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768 if ((lastres == -1) || (lastres == res))
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773 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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775 // dragLeft, delete gap
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776 editSequence(false, res);
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779 editSequence(true, res);
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781 mouseDragging = true;
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782 if(scrollThread!=null)
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783 scrollThread.setEvent(evt);
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787 synchronized void editSequence(boolean insertGap, int startres)
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789 int fixedLeft = -1;
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790 int fixedRight = -1;
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791 boolean fixedColumns = false;
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792 SequenceGroup sg = av.getSelectionGroup();
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795 if (!groupEditing && av.hasHiddenRows)
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797 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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799 groupEditing = true;
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803 //No group, but the sequence may represent a group
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806 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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808 groupEditing = false;
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811 SequenceI seq = av.alignment.getSequenceAt(startseq);
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812 StringBuffer message = new StringBuffer();
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815 message.append("Edit group:");
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816 if (editCommand == null)
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817 editCommand = new EditCommand("Edit Group");
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821 message.append("Edit sequence: " + seq.getName());
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822 String label = seq.getName();
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823 if(label.length()>10)
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824 label = label.substring(0,10);
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825 if(editCommand==null)
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826 editCommand = new EditCommand("Edit "+label);
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830 message.append(" insert ");
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832 message.append(" delete ");
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834 message.append(Math.abs(startres-lastres)+" gaps.");
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835 ap.alignFrame.statusBar.setText(message.toString());
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838 //Are we editing within a selection group?
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840 || (sg != null && sg.getSequences(true).contains(seq)))
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842 fixedColumns = true;
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844 //sg might be null as the user may only see 1 sequence,
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845 //but the sequence represents a group
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848 sg = new SequenceGroup(null, null, false, false, false, 0,
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849 av.alignment.getWidth()-1);
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850 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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853 fixedLeft = sg.getStartRes();
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854 fixedRight = sg.getEndRes();
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856 if ( (startres < fixedLeft && lastres >= fixedLeft)
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857 || (startres >= fixedLeft && lastres < fixedLeft)
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858 || (startres > fixedRight && lastres <=fixedRight)
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859 || (startres <= fixedRight && lastres > fixedRight))
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865 if (fixedLeft > startres)
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867 fixedRight = fixedLeft - 1;
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870 else if (fixedRight < startres)
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872 fixedLeft = fixedRight;
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878 if(av.hasHiddenColumns )
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880 fixedColumns = true;
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881 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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882 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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884 if ( (insertGap && startres > y1 && lastres < y1)
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885 || (!insertGap && startres < y2 && lastres > y2))
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891 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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892 //Selection spans a hidden region
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893 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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901 fixedRight = y2 - 1;
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909 Vector vseqs = sg.getSequences(true);
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910 int g, groupSize = vseqs.size();
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911 SequenceI[] groupSeqs = new SequenceI[groupSize];
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912 for (g = 0; g < groupSeqs.length; g++)
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913 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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918 //If the user has selected the whole sequence, and is dragging to
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919 // the right, we can still extend the alignment and selectionGroup
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920 if( sg.getStartRes() == 0
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921 && sg.getEndRes() == fixedRight
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922 && sg.getEndRes() == av.alignment.getWidth()-1
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925 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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926 fixedRight = sg.getEndRes();
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929 // Is it valid with fixed columns??
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930 // Find the next gap before the end
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931 // of the visible region boundary
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932 boolean blank = false;
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933 for (fixedRight = fixedRight;
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934 fixedRight > lastres;
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939 for (g = 0; g < groupSize; g++)
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941 for (int j = 0; j < startres - lastres; j++)
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943 if (!jalview.util.Comparison.isGap(
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944 groupSeqs[g].getCharAt(fixedRight - j)))
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957 if(sg.getSize(false) == av.alignment.getHeight() )
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959 if((av.hasHiddenColumns
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960 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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966 int alWidth = av.alignment.getWidth();
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967 if(av.hasHiddenRows)
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969 int hwidth = av.alignment.getHiddenSequences().getWidth();
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973 //We can still insert gaps if the selectionGroup
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974 //contains all the sequences
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975 sg.setEndRes(sg.getEndRes()+startres-lastres);
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976 fixedRight = alWidth+startres-lastres;
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988 else if(!insertGap)
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990 /// Are we able to delete?
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991 // ie are all columns blank?
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993 for (g = 0; g < groupSize; g++)
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995 for (int j = startres; j < lastres; j++)
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997 if (groupSeqs[g].getLength() <= j)
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1002 if (!jalview.util.Comparison.isGap(
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1003 groupSeqs[g].getCharAt(j)))
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1005 // Not a gap, block edit not valid
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1015 // dragging to the right
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1016 if (fixedColumns && fixedRight != -1)
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1018 for (int j = lastres; j < startres; j++)
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1020 insertChar(j, groupSeqs, fixedRight);
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1025 editCommand.appendEdit(EditCommand.INSERT_GAP,
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1027 startres, startres-lastres,
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1028 av.getGapCharacter(),
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1034 // dragging to the left
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1035 if (fixedColumns && fixedRight != -1)
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1037 for (int j = lastres; j > startres; j--)
\r
1039 deleteChar(startres, groupSeqs, fixedRight);
\r
1043 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1045 startres, lastres - startres,
\r
1046 av.getGapCharacter(),
\r
1051 else /////Editing a single sequence///////////
\r
1055 // dragging to the right
\r
1056 if (fixedColumns && fixedRight != -1)
\r
1058 for (int j = lastres; j < startres; j++)
\r
1060 insertChar(j, new SequenceI[]{seq}, fixedRight);
\r
1065 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1068 lastres, startres-lastres,
\r
1069 av.getGapCharacter(),
\r
1075 // dragging to the left
\r
1076 if (fixedColumns && fixedRight != -1)
\r
1078 for (int j = lastres; j > startres; j--)
\r
1080 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1085 deleteChar(startres, new SequenceI[]{seq}, fixedRight);
\r
1090 //could be a keyboard edit trying to delete none gaps
\r
1092 for(int m = startres; m<lastres; m++)
\r
1094 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1101 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1105 av.getGapCharacter(),
\r
1112 lastres = startres;
\r
1113 seqCanvas.repaint();
\r
1118 void insertChar(int j, SequenceI [] seq, int fixedColumn)
\r
1120 int blankColumn = fixedColumn;
\r
1121 for(int s=0; s<seq.length; s++)
\r
1123 //Find the next gap before the end of the visible region boundary
\r
1124 //If lastCol > j, theres a boundary after the gap insertion
\r
1126 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1128 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1130 //Theres a space, so break and insert the gap
\r
1135 if (blankColumn <= j)
\r
1137 blankColumn = fixedColumn;
\r
1143 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1145 blankColumn, 1, av.getGapCharacter(), true);
\r
1147 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1149 j, 1, av.getGapCharacter(),
\r
1154 void deleteChar(int j, SequenceI [] seq, int fixedColumn)
\r
1157 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1159 j, 1, av.getGapCharacter(), true);
\r
1161 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1163 fixedColumn, 1, av.getGapCharacter(), true);
\r
1169 * @param e DOCUMENT ME!
\r
1171 public void mouseEntered(MouseEvent e)
\r
1176 if (scrollThread != null)
\r
1178 scrollThread.running = false;
\r
1179 scrollThread = null;
\r
1186 * @param e DOCUMENT ME!
\r
1188 public void mouseExited(MouseEvent e)
\r
1190 if (av.getWrapAlignment())
\r
1195 if (mouseDragging)
\r
1197 scrollThread = new ScrollThread();
\r
1201 public void mouseClicked(MouseEvent evt)
\r
1203 SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
\r
1204 if(evt.getClickCount()>1)
\r
1206 if (av.getSelectionGroup().getSize(false) == 1
\r
1207 && av.getSelectionGroup().getEndRes()
\r
1208 - av.getSelectionGroup().getStartRes() < 2)
\r
1209 av.setSelectionGroup(null);
\r
1211 SequenceFeature[] features = findFeaturesAtRes(
\r
1212 sequence.getDatasetSequence(),
\r
1213 sequence.findPosition( findRes(evt) )
\r
1216 if(features!=null && features.length==1)
\r
1218 SearchResults highlight = new SearchResults();
\r
1219 highlight.addResult(sequence,
\r
1220 features[0].getBegin(),
\r
1221 features[0].getEnd());
\r
1222 seqCanvas.highlightSearchResults(highlight);
\r
1224 if(features!=null)
\r
1226 seqCanvas.getFeatureRenderer().amendFeatures(
\r
1228 {sequence}, features, false);
\r
1230 seqCanvas.highlightSearchResults(null);
\r
1235 public void mouseWheelMoved(MouseWheelEvent e)
\r
1238 /* if (mouseWheelPressed)
\r
1240 Font font = av.getFont();
\r
1241 int fontSize = font.getSize();
\r
1242 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1244 else if (fontSize > 1)
\r
1249 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1255 if (e.getWheelRotation() > 0)
\r
1256 ap.scrollUp(false);
\r
1258 ap.scrollUp(true);
\r
1267 * @param evt DOCUMENT ME!
\r
1269 public void doMousePressedDefineMode(MouseEvent evt)
\r
1271 int res = findRes(evt);
\r
1272 int seq = findSeq(evt);
\r
1275 startWrapBlock=wrappedBlock;
\r
1277 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1279 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1280 "Cannot edit annotations in wrapped view.",
\r
1281 "Wrapped view - no edit",
\r
1282 JOptionPane.WARNING_MESSAGE);
\r
1286 if(seq<0 || res<0)
\r
1289 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1291 if ((sequence == null) || (res > sequence.getLength()))
\r
1296 stretchGroup = av.getSelectionGroup();
\r
1298 if (stretchGroup == null)
\r
1300 stretchGroup = av.alignment.findGroup(sequence);
\r
1302 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1303 (res < stretchGroup.getEndRes()))
\r
1305 av.setSelectionGroup(stretchGroup);
\r
1309 stretchGroup = null;
\r
1312 else if (!stretchGroup.getSequences(false).contains(sequence) ||
\r
1313 (stretchGroup.getStartRes() > res) ||
\r
1314 (stretchGroup.getEndRes() < res))
\r
1316 stretchGroup = null;
\r
1318 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1320 if (allGroups != null)
\r
1322 for (int i = 0; i < allGroups.length; i++)
\r
1324 if ((allGroups[i].getStartRes() <= res) &&
\r
1325 (allGroups[i].getEndRes() >= res))
\r
1327 stretchGroup = allGroups[i];
\r
1333 av.setSelectionGroup(stretchGroup);
\r
1338 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1340 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1341 sequence.findPosition(res));
\r
1342 Vector links = new Vector();
\r
1343 for (int i = 0; i < allFeatures.size(); i++)
\r
1345 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1346 if (sf.links != null)
\r
1348 for (int j = 0; j < sf.links.size(); j++)
\r
1350 links.addElement(sf.links.elementAt(j));
\r
1355 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1356 pop.show(this, evt.getX(), evt.getY());
\r
1360 if (av.cursorMode)
\r
1362 seqCanvas.cursorX = findRes(evt);
\r
1363 seqCanvas.cursorY = findSeq(evt);
\r
1364 seqCanvas.repaint();
\r
1368 if (stretchGroup == null)
\r
1370 //Only if left mouse button do we want to change group sizes
\r
1372 // define a new group here
\r
1373 SequenceGroup sg = new SequenceGroup();
\r
1374 sg.setStartRes(res);
\r
1375 sg.setEndRes(res);
\r
1376 sg.addSequence(sequence, false);
\r
1377 av.setSelectionGroup(sg);
\r
1378 stretchGroup = sg;
\r
1380 if (av.getConservationSelected())
\r
1382 SliderPanel.setConservationSlider(ap,
\r
1383 av.getGlobalColourScheme(),
\r
1387 if (av.getAbovePIDThreshold())
\r
1389 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1392 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1394 // Edit end res position of selected group
\r
1395 changeEndRes = true;
\r
1397 else if ( (stretchGroup != null) &&
\r
1398 (stretchGroup.getStartRes() == res))
\r
1400 // Edit end res position of selected group
\r
1401 changeStartRes = true;
\r
1403 stretchGroup.getWidth();
\r
1406 seqCanvas.repaint();
\r
1412 * @param evt DOCUMENT ME!
\r
1414 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1416 if (stretchGroup == null)
\r
1422 if(stretchGroup.cs!=null)
\r
1424 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1426 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1427 stretchGroup.getSequences(true),
\r
1428 stretchGroup.getWidth());
\r
1431 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1432 || stretchGroup.cs instanceof PIDColourScheme
\r
1433 || stretchGroup.cs.conservationApplied())
\r
1434 stretchGroup.recalcConservation();
\r
1436 if (stretchGroup.cs.conservationApplied())
\r
1438 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1439 stretchGroup.getName());
\r
1443 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1444 stretchGroup.getName());
\r
1447 changeEndRes = false;
\r
1448 changeStartRes = false;
\r
1449 stretchGroup = null;
\r
1451 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1457 * @param evt DOCUMENT ME!
\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
1467 if (stretchGroup == null)
\r
1472 if(res>= av.alignment.getWidth())
\r
1474 res = av.alignment.getWidth()-1;
\r
1477 if (stretchGroup.getEndRes() == res)
\r
1479 // Edit end res position of selected group
\r
1480 changeEndRes = true;
\r
1482 else if (stretchGroup.getStartRes() == res)
\r
1484 // Edit start res position of selected group
\r
1485 changeStartRes = true;
\r
1488 if (res < av.getStartRes())
\r
1490 res = av.getStartRes();
\r
1495 if (res > (stretchGroup.getStartRes() - 1))
\r
1497 stretchGroup.setEndRes(res);
\r
1500 else if (changeStartRes)
\r
1502 if (res < (stretchGroup.getEndRes() + 1))
\r
1504 stretchGroup.setStartRes(res);
\r
1508 int dragDirection = 0;
\r
1512 dragDirection = 1;
\r
1514 else if (y < oldSeq)
\r
1516 dragDirection = -1;
\r
1520 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1522 // This routine ensures we don't skip any sequences, as the
\r
1523 // selection is quite slow.
\r
1524 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1526 oldSeq += dragDirection;
\r
1531 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1533 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1535 stretchGroup.deleteSequence(seq, false);
\r
1541 stretchGroup.addSequence(seq, false);
\r
1544 stretchGroup.addSequence(nextSeq, false);
\r
1551 mouseDragging = true;
\r
1553 if (scrollThread != null)
\r
1555 scrollThread.setEvent(evt);
\r
1558 seqCanvas.repaint();
\r
1561 void scrollCanvas(MouseEvent evt)
\r
1565 if(scrollThread!=null)
\r
1567 scrollThread.running = false;
\r
1568 scrollThread = null;
\r
1570 mouseDragging = false;
\r
1574 if (scrollThread == null)
\r
1575 scrollThread = new ScrollThread();
\r
1577 mouseDragging = true;
\r
1578 scrollThread.setEvent(evt);
\r
1584 // this class allows scrolling off the bottom of the visible alignment
\r
1585 class ScrollThread extends Thread
\r
1588 boolean running = false;
\r
1590 public ScrollThread()
\r
1595 public void setEvent(MouseEvent e)
\r
1600 public void stopScrolling()
\r
1613 if (mouseDragging && (evt.getY() < 0) &&
\r
1614 (av.getStartSeq() > 0))
\r
1616 running = ap.scrollUp(true);
\r
1619 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1620 (av.alignment.getHeight() > av.getEndSeq()))
\r
1622 running = ap.scrollUp(false);
\r
1625 if (mouseDragging && (evt.getX() < 0))
\r
1627 running = ap.scrollRight(false);
\r
1629 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1631 running = ap.scrollRight(true);
\r
1639 catch (Exception ex)
\r