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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289 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
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291 int original = seqCanvas.cursorX - dx;
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292 int maxWidth = av.alignment.getWidth();
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294 while(!av.colSel.isVisible(seqCanvas.cursorX)
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295 && seqCanvas.cursorX<maxWidth
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296 && seqCanvas.cursorX>0)
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298 seqCanvas.cursorX += dx;
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301 if(seqCanvas.cursorX>=maxWidth
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302 || !av.colSel.isVisible(seqCanvas.cursorX) )
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304 seqCanvas.cursorX = original;
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311 void scrollToVisible()
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313 if (seqCanvas.cursorX < 0)
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314 seqCanvas.cursorX = 0;
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315 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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316 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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318 if (seqCanvas.cursorY < 0)
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319 seqCanvas.cursorY = 0;
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320 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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321 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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325 if(av.wrapAlignment)
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327 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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331 while (seqCanvas.cursorY < av.startSeq)
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335 while (seqCanvas.cursorY + 1 > av.endSeq)
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337 ap.scrollUp(false);
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339 if (!av.wrapAlignment)
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341 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
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343 if (!ap.scrollRight(false))
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346 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
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348 if (!ap.scrollRight(true))
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353 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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354 seqCanvas.cursorX, seqCanvas.cursorY);
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356 seqCanvas.repaint();
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359 void setSelectionAreaAtCursor(boolean topLeft)
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361 SequenceI sequence =
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362 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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364 if(av.getSelectionGroup()!=null)
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366 SequenceGroup sg = av.selectionGroup;
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367 //Find the top and bottom of this group
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368 int min = av.alignment.getHeight(), max = 0;
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369 for(int i=0; i<sg.getSize(); i++)
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371 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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382 sg.setStartRes(seqCanvas.cursorX);
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383 if(sg.getEndRes()<seqCanvas.cursorX)
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384 sg.setEndRes(seqCanvas.cursorX);
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386 min = seqCanvas.cursorY;
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390 sg.setEndRes(seqCanvas.cursorX);
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391 if(sg.getStartRes()>seqCanvas.cursorX)
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392 sg.setStartRes(seqCanvas.cursorX);
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394 max = seqCanvas.cursorY+1;
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399 // Only the user can do this
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400 av.setSelectionGroup(null);
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404 // Now add any sequences between min and max
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405 sg.getSequences(null).clear();
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406 for (int i = min; i < max; i++)
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408 sg.addSequence(av.alignment.getSequenceAt(i), false);
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413 if (av.getSelectionGroup() == null)
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415 SequenceGroup sg = new SequenceGroup();
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416 sg.setStartRes(seqCanvas.cursorX);
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417 sg.setEndRes(seqCanvas.cursorX);
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418 sg.addSequence(sequence, false);
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419 av.setSelectionGroup(sg);
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426 void insertGapAtCursor(boolean group)
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428 groupEditing = group;
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429 startseq = seqCanvas.cursorY;
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430 lastres = seqCanvas.cursorX;
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431 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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435 void deleteGapAtCursor(boolean group)
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437 groupEditing = group;
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438 startseq = seqCanvas.cursorY;
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439 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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440 editSequence(false, seqCanvas.cursorX);
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444 void numberPressed(char value)
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446 if(keyboardNo1==null)
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447 keyboardNo1 = new StringBuffer();
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449 if(keyboardNo2!=null)
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450 keyboardNo2.append(value);
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452 keyboardNo1.append(value);
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455 int getKeyboardNo(StringBuffer kb)
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460 return Integer.parseInt(kb.toString());
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467 * @param evt DOCUMENT ME!
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469 public void mouseReleased(MouseEvent evt)
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471 mouseDragging = false;
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472 mouseWheelPressed = false;
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476 doMouseReleasedDefineMode(evt);
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490 * @param evt DOCUMENT ME!
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492 public void mousePressed(MouseEvent evt)
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494 lastMousePress = evt.getPoint();
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496 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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498 mouseWheelPressed = true;
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502 if (evt.isShiftDown() || evt.isAltDown() ||
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503 evt.isControlDown())
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505 if (evt.isAltDown() || evt.isControlDown())
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507 groupEditing = true;
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509 editingSeqs = true;
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513 doMousePressedDefineMode(evt);
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517 int seq = findSeq(evt);
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518 int res = findRes(evt);
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523 if ((seq < av.getAlignment().getHeight()) &&
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524 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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541 * @param evt DOCUMENT ME!
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543 public void mouseMoved(MouseEvent evt)
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547 // This is because MacOSX creates a mouseMoved
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548 // If control is down, other platforms will not.
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552 int res = findRes(evt);
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553 int seq = findSeq(evt);
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556 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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559 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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561 if (res > sequence.getLength())
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566 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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568 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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571 setStatusMessage(sequence, res, seq);
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575 tooltipText.setLength(6); // Cuts the buffer back to <html>
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577 SequenceGroup [] groups = av.alignment.findAllGroups(sequence);
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580 for(int g=0; g<groups.length; g++)
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582 if(groups[g].getStartRes()<=res && groups[g].getEndRes()>=res)
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584 if (tooltipText.length() > 6)
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585 tooltipText.append("<br>");
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587 if (!groups[g].getName().startsWith("JTreeGroup") &&
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588 !groups[g].getName().startsWith("JGroup"))
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589 tooltipText.append(groups[g].getName());
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591 if(groups[g].getDescription()!=null)
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592 tooltipText.append(": "+groups[g].getDescription());
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598 // use aa to see if the mouse pointer is on a
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599 if (av.showSequenceFeatures)
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601 SequenceFeature[] features = findFeaturesAtRes(
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602 sequence.getDatasetSequence(), sequence.findPosition(res));
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604 if (features != null)
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606 for (int i = 0; i < features.length; i++)
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608 if (features[i].getType().equals("disulfide bond"))
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610 if (features[i].getBegin() == sequence.findPosition(res)
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611 || features[i].getEnd() == sequence.findPosition(res))
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613 if (tooltipText.length() > 6)
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614 tooltipText.append("<br>");
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615 tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +
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616 features[i].getEnd());
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617 if (features[i].links != null)
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618 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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623 if (tooltipText.length() > 6)
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624 tooltipText.append("<br>");
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626 tooltipText.append(features[i].getType() + " " +
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627 features[i].begin);
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628 if (features[i].begin != features[i].end)
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629 tooltipText.append(" " + features[i].end);
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631 if (features[i].getDescription() != null
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632 && !features[i].description.equals(features[i].getType()))
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634 tmpString = features[i].getDescription();
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635 int startTag = tmpString.toUpperCase().indexOf("<HTML>");
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638 tmpString = tmpString.substring(startTag + 6);
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640 int endTag = tmpString.toUpperCase().indexOf("</BODY>");
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643 tmpString = tmpString.substring(0, endTag);
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645 endTag = tmpString.toUpperCase().indexOf("</HTML>");
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648 tmpString = tmpString.substring(0, endTag);
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653 tooltipText.append("; " + tmpString);
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657 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
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659 //The description does not specify html is to
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660 //be used, so we must remove < > symbols
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661 tmpString = tmpString.replaceAll("<", "<");
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662 tmpString = tmpString.replaceAll(">", ">");
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664 tooltipText.append("; ");
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665 tooltipText.append(tmpString);
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669 tooltipText.append("; " + tmpString);
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672 if (features[i].getValue("status") != null)
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674 String status = features[i].getValue("status").toString();
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675 if (status.length() > 0)
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676 tooltipText.append("; (" + features[i].getValue("status") + ")");
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679 if (features[i].links != null)
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680 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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687 if (tooltipText.length() == 6) // <html></html>
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689 setToolTipText(null);
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693 tooltipText.append("</html>");
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694 setToolTipText(tooltipText.toString());
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697 // setToolTipText(null);
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700 void setStatusMessage(SequenceI sequence, int res, int seq)
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702 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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703 sequence.getName());
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706 if (av.alignment.isNucleotide())
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708 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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711 text.append(" Nucleotide: ");
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715 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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717 text.append(" Residue: ");
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725 text.append(obj + " (" + sequence.findPosition(res) +
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729 ap.alignFrame.statusBar.setText(text.toString());
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736 * @param evt DOCUMENT ME!
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738 public void mouseDragged(MouseEvent evt)
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740 if (mouseWheelPressed)
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742 int oldWidth = av.charWidth;
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744 //Which is bigger, left-right or up-down?
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745 if (Math.abs(evt.getY() - lastMousePress.getY())
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746 > Math.abs(evt.getX() - lastMousePress.getX()))
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748 int fontSize = av.font.getSize();
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750 if (evt.getY() < lastMousePress.getY())
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754 else if (evt.getY() > lastMousePress.getY())
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762 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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763 av.charWidth = oldWidth;
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768 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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772 else if (evt.getX() > lastMousePress.getX())
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780 FontMetrics fm = getFontMetrics(av.getFont());
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781 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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783 lastMousePress = evt.getPoint();
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790 doMouseDraggedDefineMode(evt);
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794 int res = findRes(evt);
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801 if ((lastres == -1) || (lastres == res))
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806 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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808 // dragLeft, delete gap
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809 editSequence(false, res);
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812 editSequence(true, res);
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814 mouseDragging = true;
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815 if(scrollThread!=null)
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816 scrollThread.setEvent(evt);
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820 synchronized void editSequence(boolean insertGap, int startres)
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822 int fixedLeft = -1;
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823 int fixedRight = -1;
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824 boolean fixedColumns = false;
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825 SequenceGroup sg = av.getSelectionGroup();
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827 SequenceI seq = av.alignment.getSequenceAt(startseq);
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829 //No group, but the sequence may represent a group
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830 if (!groupEditing && av.hasHiddenRows)
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832 if (av.hiddenRepSequences!=null
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833 && av.hiddenRepSequences.containsKey(seq))
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835 sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
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836 groupEditing = true;
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841 StringBuffer message = new StringBuffer();
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844 message.append("Edit group:");
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845 if (editCommand == null)
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846 editCommand = new EditCommand("Edit Group");
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850 message.append("Edit sequence: " + seq.getName());
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851 String label = seq.getName();
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852 if(label.length()>10)
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853 label = label.substring(0,10);
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854 if(editCommand==null)
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855 editCommand = new EditCommand("Edit "+label);
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859 message.append(" insert ");
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861 message.append(" delete ");
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863 message.append(Math.abs(startres-lastres)+" gaps.");
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864 ap.alignFrame.statusBar.setText(message.toString());
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867 //Are we editing within a selection group?
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869 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
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871 fixedColumns = true;
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873 //sg might be null as the user may only see 1 sequence,
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874 //but the sequence represents a group
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877 if(av.hiddenRepSequences==null
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878 || !av.hiddenRepSequences.containsKey(seq))
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883 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
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886 fixedLeft = sg.getStartRes();
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887 fixedRight = sg.getEndRes();
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889 if ( (startres < fixedLeft && lastres >= fixedLeft)
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890 || (startres >= fixedLeft && lastres < fixedLeft)
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891 || (startres > fixedRight && lastres <=fixedRight)
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892 || (startres <= fixedRight && lastres > fixedRight))
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898 if (fixedLeft > startres)
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900 fixedRight = fixedLeft - 1;
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903 else if (fixedRight < startres)
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905 fixedLeft = fixedRight;
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911 if(av.hasHiddenColumns )
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913 fixedColumns = true;
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914 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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915 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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917 if ( (insertGap && startres > y1 && lastres < y1)
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918 || (!insertGap && startres < y2 && lastres > y2))
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924 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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925 //Selection spans a hidden region
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926 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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934 fixedRight = y2 - 1;
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942 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
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943 int g, groupSize = vseqs.size();
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944 SequenceI[] groupSeqs = new SequenceI[groupSize];
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945 for (g = 0; g < groupSeqs.length; g++)
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946 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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951 //If the user has selected the whole sequence, and is dragging to
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952 // the right, we can still extend the alignment and selectionGroup
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953 if( sg.getStartRes() == 0
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954 && sg.getEndRes() == fixedRight
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955 && sg.getEndRes() == av.alignment.getWidth()-1
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958 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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959 fixedRight = sg.getEndRes();
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962 // Is it valid with fixed columns??
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963 // Find the next gap before the end
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964 // of the visible region boundary
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965 boolean blank = false;
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966 for (fixedRight = fixedRight;
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967 fixedRight > lastres;
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972 for (g = 0; g < groupSize; g++)
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974 for (int j = 0; j < startres - lastres; j++)
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976 if (!jalview.util.Comparison.isGap(
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977 groupSeqs[g].getCharAt(fixedRight - j)))
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990 if(sg.getSize() == av.alignment.getHeight() )
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992 if((av.hasHiddenColumns
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993 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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999 int alWidth = av.alignment.getWidth();
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1000 if(av.hasHiddenRows)
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1002 int hwidth = av.alignment.getHiddenSequences().getWidth();
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1003 if(hwidth>alWidth)
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1006 //We can still insert gaps if the selectionGroup
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1007 //contains all the sequences
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1008 sg.setEndRes(sg.getEndRes()+startres-lastres);
\r
1009 fixedRight = alWidth+startres-lastres;
\r
1021 else if(!insertGap)
\r
1023 /// Are we able to delete?
\r
1024 // ie are all columns blank?
\r
1026 for (g = 0; g < groupSize; g++)
\r
1028 for (int j = startres; j < lastres; j++)
\r
1030 if (groupSeqs[g].getLength() <= j)
\r
1035 if (!jalview.util.Comparison.isGap(
\r
1036 groupSeqs[g].getCharAt(j)))
\r
1038 // Not a gap, block edit not valid
\r
1048 // dragging to the right
\r
1049 if (fixedColumns && fixedRight != -1)
\r
1051 for (int j = lastres; j < startres; j++)
\r
1053 insertChar(j, groupSeqs, fixedRight);
\r
1058 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1060 startres, startres-lastres,
\r
1067 // dragging to the left
\r
1068 if (fixedColumns && fixedRight != -1)
\r
1070 for (int j = lastres; j > startres; j--)
\r
1072 deleteChar(startres, groupSeqs, fixedRight);
\r
1076 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1078 startres, lastres - startres,
\r
1084 else /////Editing a single sequence///////////
\r
1088 // dragging to the right
\r
1089 if (fixedColumns && fixedRight != -1)
\r
1091 for (int j = lastres; j < startres; j++)
\r
1093 insertChar(j, new SequenceI[]{seq}, fixedRight);
\r
1098 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1101 lastres, startres-lastres,
\r
1108 // dragging to the left
\r
1109 if (fixedColumns && fixedRight != -1)
\r
1111 for (int j = lastres; j > startres; j--)
\r
1113 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1118 deleteChar(startres, new SequenceI[]{seq}, fixedRight);
\r
1123 //could be a keyboard edit trying to delete none gaps
\r
1125 for(int m = startres; m<lastres; m++)
\r
1127 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1134 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1145 lastres = startres;
\r
1146 seqCanvas.repaint();
\r
1151 void insertChar(int j, SequenceI [] seq, int fixedColumn)
\r
1153 int blankColumn = fixedColumn;
\r
1154 for(int s=0; s<seq.length; s++)
\r
1156 //Find the next gap before the end of the visible region boundary
\r
1157 //If lastCol > j, theres a boundary after the gap insertion
\r
1159 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1161 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1163 //Theres a space, so break and insert the gap
\r
1168 if (blankColumn <= j)
\r
1170 blankColumn = fixedColumn;
\r
1176 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1178 blankColumn, 1, av.alignment, true);
\r
1180 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1182 j, 1, av.alignment,
\r
1187 void deleteChar(int j, SequenceI [] seq, int fixedColumn)
\r
1190 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1192 j, 1, av.alignment, true);
\r
1194 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1196 fixedColumn, 1, av.alignment, true);
\r
1202 * @param e DOCUMENT ME!
\r
1204 public void mouseEntered(MouseEvent e)
\r
1209 if (scrollThread != null)
\r
1211 scrollThread.running = false;
\r
1212 scrollThread = null;
\r
1219 * @param e DOCUMENT ME!
\r
1221 public void mouseExited(MouseEvent e)
\r
1223 if (av.getWrapAlignment())
\r
1228 if (mouseDragging)
\r
1230 scrollThread = new ScrollThread();
\r
1234 public void mouseClicked(MouseEvent evt)
\r
1236 SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
\r
1237 if(evt.getClickCount()>1)
\r
1239 if (av.getSelectionGroup().getSize() == 1
\r
1240 && av.getSelectionGroup().getEndRes()
\r
1241 - av.getSelectionGroup().getStartRes() < 2)
\r
1242 av.setSelectionGroup(null);
\r
1244 SequenceFeature[] features = findFeaturesAtRes(
\r
1245 sequence.getDatasetSequence(),
\r
1246 sequence.findPosition( findRes(evt) )
\r
1249 if(features!=null && features.length>0)
\r
1251 SearchResults highlight = new SearchResults();
\r
1252 highlight.addResult(sequence,
\r
1253 features[0].getBegin(),
\r
1254 features[0].getEnd());
\r
1255 seqCanvas.highlightSearchResults(highlight);
\r
1257 if(features!=null && features.length>0)
\r
1259 seqCanvas.getFeatureRenderer().amendFeatures(
\r
1261 {sequence}, features, false, ap);
\r
1263 seqCanvas.highlightSearchResults(null);
\r
1268 public void mouseWheelMoved(MouseWheelEvent e)
\r
1271 /* if (mouseWheelPressed)
\r
1273 Font font = av.getFont();
\r
1274 int fontSize = font.getSize();
\r
1275 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1277 else if (fontSize > 1)
\r
1282 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1288 if (e.getWheelRotation() > 0)
\r
1289 ap.scrollUp(false);
\r
1291 ap.scrollUp(true);
\r
1300 * @param evt DOCUMENT ME!
\r
1302 public void doMousePressedDefineMode(MouseEvent evt)
\r
1304 int res = findRes(evt);
\r
1305 int seq = findSeq(evt);
\r
1308 startWrapBlock=wrappedBlock;
\r
1310 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1312 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1313 "Cannot edit annotations in wrapped view.",
\r
1314 "Wrapped view - no edit",
\r
1315 JOptionPane.WARNING_MESSAGE);
\r
1319 if(seq<0 || res<0)
\r
1322 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1324 if ((sequence == null) || (res > sequence.getLength()))
\r
1329 stretchGroup = av.getSelectionGroup();
\r
1331 if (stretchGroup == null)
\r
1333 stretchGroup = av.alignment.findGroup(sequence);
\r
1335 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1336 (res < stretchGroup.getEndRes()))
\r
1338 av.setSelectionGroup(stretchGroup);
\r
1342 stretchGroup = null;
\r
1345 else if (!stretchGroup.getSequences(null).contains(sequence) ||
\r
1346 (stretchGroup.getStartRes() > res) ||
\r
1347 (stretchGroup.getEndRes() < res))
\r
1349 stretchGroup = null;
\r
1351 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1353 if (allGroups != null)
\r
1355 for (int i = 0; i < allGroups.length; i++)
\r
1357 if ((allGroups[i].getStartRes() <= res) &&
\r
1358 (allGroups[i].getEndRes() >= res))
\r
1360 stretchGroup = allGroups[i];
\r
1366 av.setSelectionGroup(stretchGroup);
\r
1371 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1373 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1374 sequence.findPosition(res));
\r
1375 Vector links = new Vector();
\r
1376 for (int i = 0; i < allFeatures.size(); i++)
\r
1378 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1379 if (sf.links != null)
\r
1381 for (int j = 0; j < sf.links.size(); j++)
\r
1383 links.addElement(sf.links.elementAt(j));
\r
1388 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1389 pop.show(this, evt.getX(), evt.getY());
\r
1393 if (av.cursorMode)
\r
1395 seqCanvas.cursorX = findRes(evt);
\r
1396 seqCanvas.cursorY = findSeq(evt);
\r
1397 seqCanvas.repaint();
\r
1401 if (stretchGroup == null)
\r
1403 //Only if left mouse button do we want to change group sizes
\r
1405 // define a new group here
\r
1406 SequenceGroup sg = new SequenceGroup();
\r
1407 sg.setStartRes(res);
\r
1408 sg.setEndRes(res);
\r
1409 sg.addSequence(sequence, false);
\r
1410 av.setSelectionGroup(sg);
\r
1411 stretchGroup = sg;
\r
1413 if (av.getConservationSelected())
\r
1415 SliderPanel.setConservationSlider(ap,
\r
1416 av.getGlobalColourScheme(),
\r
1420 if (av.getAbovePIDThreshold())
\r
1422 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1425 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1427 // Edit end res position of selected group
\r
1428 changeEndRes = true;
\r
1430 else if ( (stretchGroup != null) &&
\r
1431 (stretchGroup.getStartRes() == res))
\r
1433 // Edit end res position of selected group
\r
1434 changeStartRes = true;
\r
1436 stretchGroup.getWidth();
\r
1439 seqCanvas.repaint();
\r
1445 * @param evt DOCUMENT ME!
\r
1447 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1449 if (stretchGroup == null)
\r
1455 if(stretchGroup.cs!=null)
\r
1457 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1459 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1460 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1461 stretchGroup.getWidth());
\r
1464 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1465 || stretchGroup.cs instanceof PIDColourScheme
\r
1466 || stretchGroup.cs.conservationApplied()
\r
1467 || stretchGroup.cs.getThreshold()>0)
\r
1468 stretchGroup.recalcConservation();
\r
1470 if (stretchGroup.cs.conservationApplied())
\r
1472 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1473 stretchGroup.getName());
\r
1477 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1478 stretchGroup.getName());
\r
1481 changeEndRes = false;
\r
1482 changeStartRes = false;
\r
1483 stretchGroup = null;
\r
1485 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1491 * @param evt DOCUMENT ME!
\r
1493 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1495 int res = findRes(evt);
\r
1496 int y = findSeq(evt);
\r
1498 if(wrappedBlock!=startWrapBlock)
\r
1501 if (stretchGroup == null)
\r
1506 if(res>= av.alignment.getWidth())
\r
1508 res = av.alignment.getWidth()-1;
\r
1511 if (stretchGroup.getEndRes() == res)
\r
1513 // Edit end res position of selected group
\r
1514 changeEndRes = true;
\r
1516 else if (stretchGroup.getStartRes() == res)
\r
1518 // Edit start res position of selected group
\r
1519 changeStartRes = true;
\r
1522 if (res < av.getStartRes())
\r
1524 res = av.getStartRes();
\r
1529 if (res > (stretchGroup.getStartRes() - 1))
\r
1531 stretchGroup.setEndRes(res);
\r
1534 else if (changeStartRes)
\r
1536 if (res < (stretchGroup.getEndRes() + 1))
\r
1538 stretchGroup.setStartRes(res);
\r
1542 int dragDirection = 0;
\r
1546 dragDirection = 1;
\r
1548 else if (y < oldSeq)
\r
1550 dragDirection = -1;
\r
1554 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1556 // This routine ensures we don't skip any sequences, as the
\r
1557 // selection is quite slow.
\r
1558 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1560 oldSeq += dragDirection;
\r
1565 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1567 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1569 stretchGroup.deleteSequence(seq, false);
\r
1575 stretchGroup.addSequence(seq, false);
\r
1578 stretchGroup.addSequence(nextSeq, false);
\r
1585 mouseDragging = true;
\r
1587 if (scrollThread != null)
\r
1589 scrollThread.setEvent(evt);
\r
1592 seqCanvas.repaint();
\r
1595 void scrollCanvas(MouseEvent evt)
\r
1599 if(scrollThread!=null)
\r
1601 scrollThread.running = false;
\r
1602 scrollThread = null;
\r
1604 mouseDragging = false;
\r
1608 if (scrollThread == null)
\r
1609 scrollThread = new ScrollThread();
\r
1611 mouseDragging = true;
\r
1612 scrollThread.setEvent(evt);
\r
1618 // this class allows scrolling off the bottom of the visible alignment
\r
1619 class ScrollThread extends Thread
\r
1622 boolean running = false;
\r
1624 public ScrollThread()
\r
1629 public void setEvent(MouseEvent e)
\r
1634 public void stopScrolling()
\r
1647 if (mouseDragging && (evt.getY() < 0) &&
\r
1648 (av.getStartSeq() > 0))
\r
1650 running = ap.scrollUp(true);
\r
1653 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1654 (av.alignment.getHeight() > av.getEndSeq()))
\r
1656 running = ap.scrollUp(false);
\r
1659 if (mouseDragging && (evt.getX() < 0))
\r
1661 running = ap.scrollRight(false);
\r
1663 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1665 running = ap.scrollRight(true);
\r
1673 catch (Exception ex)
\r