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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23 import jalview.schemes.*;
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26 import java.awt.event.*;
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28 import javax.swing.*;
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30 import java.util.Vector;
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37 * @version $Revision$
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39 public class SeqPanel extends JPanel implements MouseListener,
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40 MouseMotionListener, MouseWheelListener
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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50 protected AlignViewport av;
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52 // if character is inserted or deleted, we will need to recalculate the conservation
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53 boolean seqEditOccurred = false;
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54 ScrollThread scrollThread = null;
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55 boolean mouseDragging = false;
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56 boolean editingSeqs = false;
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57 boolean groupEditing = false;
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59 //////////////////////////////////////////
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60 /////Everything below this is for defining the boundary of the rubberband
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61 //////////////////////////////////////////
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63 boolean changeEndSeq = false;
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64 boolean changeStartSeq = false;
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65 boolean changeEndRes = false;
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66 boolean changeStartRes = false;
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67 SequenceGroup stretchGroup = null;
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68 boolean remove = false;
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70 Point lastMousePress;
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71 boolean mouseWheelPressed = false;
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72 StringBuffer keyboardNo1;
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73 StringBuffer keyboardNo2;
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75 java.net.URL linkImageURL;
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78 * Creates a new SeqPanel object.
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80 * @param avp DOCUMENT ME!
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81 * @param p DOCUMENT ME!
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83 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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85 linkImageURL = getClass().getResource("/images/link.gif");
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86 ToolTipManager.sharedInstance().registerComponent(this);
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87 ToolTipManager.sharedInstance().setInitialDelay(0);
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88 ToolTipManager.sharedInstance().setDismissDelay(10000);
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90 setBackground(Color.white);
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92 seqCanvas = new SeqCanvas(avp);
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93 setLayout(new BorderLayout());
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94 add(seqCanvas, BorderLayout.CENTER);
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100 addMouseMotionListener(this);
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101 addMouseListener(this);
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102 addMouseWheelListener(this);
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106 int startWrapBlock=-1;
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107 int wrappedBlock=-1;
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108 int findRes(MouseEvent evt)
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111 int x = evt.getX();
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113 if (av.wrapAlignment)
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116 int hgap = av.charHeight;
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117 if (av.scaleAboveWrapped)
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118 hgap += av.charHeight;
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120 int cHeight = av.getAlignment().getHeight() * av.charHeight
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121 + hgap + seqCanvas.getAnnotationHeight();
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123 int y = evt.getY();
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125 x -= seqCanvas.LABEL_WEST;
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128 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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130 wrappedBlock = y / cHeight;
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131 wrappedBlock += av.getStartRes() / cwidth;
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133 res = wrappedBlock * cwidth + x / av.getCharWidth();
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138 res = (x / av.getCharWidth()) + av.getStartRes();
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141 if(av.hasHiddenColumns)
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142 res = av.getColumnSelection().adjustForHiddenColumns(res);
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148 int findSeq(MouseEvent evt)
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151 int y = evt.getY();
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153 if (av.wrapAlignment)
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155 int hgap = av.charHeight;
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156 if (av.scaleAboveWrapped)
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157 hgap += av.charHeight;
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159 int cHeight = av.getAlignment().getHeight() * av.charHeight
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160 + hgap + seqCanvas.getAnnotationHeight();
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164 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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165 av.alignment.getHeight() -1);
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169 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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170 av.alignment.getHeight() -1);
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176 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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178 Vector allFeatures = new Vector();
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180 if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
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182 while (index < seq.getSequenceFeatures().length)
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184 SequenceFeature sf = seq.getSequenceFeatures()[index];
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185 if (sf.getBegin() <= res &&
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186 sf.getEnd() >= res)
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188 if (av.featuresDisplayed.containsKey(sf.getType()))
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190 allFeatures.addElement(sf);
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196 return allFeatures;
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203 seqEditOccurred = false;
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204 editingSeqs = false;
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205 groupEditing = false;
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206 keyboardNo1 = null;
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207 keyboardNo2 = null;
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210 void setCursorRow()
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212 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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216 void setCursorColumn()
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218 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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222 void setCursorRowAndColumn()
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224 if(keyboardNo2==null)
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226 keyboardNo2 = new StringBuffer();
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230 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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231 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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236 void setCursorPosition()
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238 SequenceI sequence =
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239 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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241 seqCanvas.cursorX = sequence.findIndex(
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242 getKeyboardNo(keyboardNo1)-1
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247 void moveCursor(int dx, int dy)
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249 seqCanvas.cursorX += dx;
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250 seqCanvas.cursorY += dy;
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254 void scrollToVisible()
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256 if (seqCanvas.cursorX < 0)
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257 seqCanvas.cursorX = 0;
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258 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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259 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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261 if (seqCanvas.cursorY < 0)
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262 seqCanvas.cursorY = 0;
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263 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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264 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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268 if(av.wrapAlignment)
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270 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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274 while (seqCanvas.cursorY < av.startSeq)
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278 while (seqCanvas.cursorY + 1 > av.endSeq)
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280 ap.scrollUp(false);
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282 if (!av.wrapAlignment)
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284 while (seqCanvas.cursorX < av.startRes)
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286 if (!ap.scrollRight(false))
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289 while (seqCanvas.cursorX > av.endRes)
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291 if (!ap.scrollRight(true))
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296 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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297 seqCanvas.cursorX, seqCanvas.cursorY);
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299 seqCanvas.repaint();
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302 void setSelectionAreaAtCursor(boolean topLeft)
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304 SequenceI sequence =
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305 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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307 if(av.getSelectionGroup()!=null)
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309 SequenceGroup sg = av.selectionGroup;
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310 //Find the top and bottom of this group
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311 int min = av.alignment.getHeight(), max = 0;
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312 for(int i=0; i<sg.getSize(false); i++)
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314 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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325 sg.setStartRes(seqCanvas.cursorX);
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326 if(sg.getEndRes()<seqCanvas.cursorX)
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327 sg.setEndRes(seqCanvas.cursorX);
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329 min = seqCanvas.cursorY;
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333 sg.setEndRes(seqCanvas.cursorX);
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334 if(sg.getStartRes()>seqCanvas.cursorX)
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335 sg.setStartRes(seqCanvas.cursorX);
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337 max = seqCanvas.cursorY+1;
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342 // Only the user can do this
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343 av.setSelectionGroup(null);
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347 // Now add any sequences between min and max
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348 sg.getSequences(false).clear();
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349 for (int i = min; i < max; i++)
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351 sg.addSequence(av.alignment.getSequenceAt(i), false);
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356 if (av.getSelectionGroup() == null)
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358 SequenceGroup sg = new SequenceGroup();
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359 sg.setStartRes(seqCanvas.cursorX);
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360 sg.setEndRes(seqCanvas.cursorX);
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361 sg.addSequence(sequence, false);
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362 av.setSelectionGroup(sg);
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369 void insertGapAtCursor(boolean group)
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371 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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372 av.alignment, HistoryItem.EDIT));
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373 groupEditing = group;
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374 startseq = seqCanvas.cursorY;
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375 lastres = seqCanvas.cursorX;
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376 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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380 void deleteGapAtCursor(boolean group)
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382 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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383 av.alignment, HistoryItem.EDIT));
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384 groupEditing = group;
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385 startseq = seqCanvas.cursorY;
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386 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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387 editSequence(false, seqCanvas.cursorX);
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391 void numberPressed(char value)
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393 if(keyboardNo1==null)
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394 keyboardNo1 = new StringBuffer();
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396 if(keyboardNo2!=null)
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397 keyboardNo2.append(value);
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399 keyboardNo1.append(value);
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402 int getKeyboardNo(StringBuffer kb)
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407 return Integer.parseInt(kb.toString());
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414 * @param evt DOCUMENT ME!
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416 public void mouseReleased(MouseEvent evt)
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418 mouseDragging = false;
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419 mouseWheelPressed = false;
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423 doMouseReleasedDefineMode(evt);
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437 * @param evt DOCUMENT ME!
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439 public void mousePressed(MouseEvent evt)
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441 lastMousePress = evt.getPoint();
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443 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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445 mouseWheelPressed = true;
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449 if (evt.isShiftDown() || evt.isAltDown() ||
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450 evt.isControlDown())
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452 if (evt.isAltDown() || evt.isControlDown())
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454 groupEditing = true;
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456 editingSeqs = true;
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460 doMousePressedDefineMode(evt);
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466 int seq = findSeq(evt);
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467 int res = findRes(evt);
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472 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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473 av.alignment, HistoryItem.EDIT));
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475 if ((seq < av.getAlignment().getHeight()) &&
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476 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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493 * @param evt DOCUMENT ME!
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495 public void mouseMoved(MouseEvent evt)
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499 // This is because MacOSX creates a mouseMoved
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500 // If control is down, other platforms will not.
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504 int res = findRes(evt);
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505 int seq = findSeq(evt);
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508 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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511 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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513 if (res > sequence.getLength())
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518 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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520 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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523 setStatusMessage(sequence, res, seq);
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525 // use aa to see if the mouse pointer is on a
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526 if (av.showSequenceFeatures)
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528 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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531 StringBuffer sbuffer = new StringBuffer("<html>");
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532 StringBuffer seqSpecific = new StringBuffer();
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534 for (int i = 0; i < features.length; i++)
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537 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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538 (features[i].getEnd() >= sequence.findPosition(res)))
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540 if(av.featuresDisplayed==null
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541 || !av.featuresDisplayed.containsKey(features[i].getType()))
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545 if (features[i].getType().equals("disulfide bond"))
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547 if (features[i].getBegin() == sequence.findPosition(res)
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548 || features[i].getEnd() == sequence.findPosition(res))
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550 if (sbuffer.length() > 6)
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551 sbuffer.append("<br>");
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552 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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553 features[i].getEnd());
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554 if (features[i].links != null)
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555 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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560 if (sbuffer.length() > 6)
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561 sbuffer.append("<br>");
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563 sbuffer.append(features[i].getType() + " " +
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564 features[i].begin);
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565 if (features[i].begin != features[i].end)
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566 sbuffer.append(" " + features[i].end);
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568 if (features[i].getDescription() != null
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569 && !features[i].description.equals(features[i].getType()))
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570 sbuffer.append("; " + features[i].getDescription());
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572 if (features[i].getValue("status") != null)
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574 sbuffer.append("; (" + features[i].getValue("status") + ")");
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576 if (features[i].links != null)
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577 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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581 else if(features[i].begin==0 && features[i].end==0)
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583 // seqSpecific.append(features[i].featureGroup+": "
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584 // + features[i].getType()+" "
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585 // +features[i].getDescription()+"<br>");
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590 if(seqSpecific.length()>0)
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591 seqSpecific.setLength(seqSpecific.length()-4);
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593 sbuffer.append(seqSpecific);
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594 sbuffer.append("</html>");
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595 if(sbuffer.length()==13) // <html></html>
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596 setToolTipText("");
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598 setToolTipText(sbuffer.toString());
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601 setToolTipText("");
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605 void setStatusMessage(SequenceI sequence, int res, int seq)
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607 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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608 sequence.getName());
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611 if (av.alignment.isNucleotide())
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613 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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616 text.append(" Nucleotide: ");
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620 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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622 text.append(" Residue: ");
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630 text.append(obj + " (" + sequence.findPosition(res) +
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634 ap.alignFrame.statusBar.setText(text.toString());
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641 * @param evt DOCUMENT ME!
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643 public void mouseDragged(MouseEvent evt)
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645 if (mouseWheelPressed)
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647 int oldWidth = av.charWidth;
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649 //Which is bigger, left-right or up-down?
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650 if (Math.abs(evt.getY() - lastMousePress.getY())
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651 > Math.abs(evt.getX() - lastMousePress.getX()))
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653 int fontSize = av.font.getSize();
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655 if (evt.getY() < lastMousePress.getY())
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659 else if (evt.getY() > lastMousePress.getY())
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667 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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668 av.charWidth = oldWidth;
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673 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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677 else if (evt.getX() > lastMousePress.getX())
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685 FontMetrics fm = getFontMetrics(av.getFont());
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686 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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688 lastMousePress = evt.getPoint();
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695 doMouseDraggedDefineMode(evt);
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699 int res = findRes(evt);
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706 if ((lastres == -1) || (lastres == res))
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711 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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713 // dragLeft, delete gap
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714 editSequence(false, res);
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717 editSequence(true, res);
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719 mouseDragging = true;
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720 if(scrollThread!=null)
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721 scrollThread.setEvent(evt);
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725 synchronized void editSequence(boolean insertGap, int startres)
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727 int fixedLeft = -1;
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728 int fixedRight = -1;
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729 boolean fixedColumns = false;
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730 SequenceGroup sg = av.getSelectionGroup();
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733 if (!groupEditing && av.hasHiddenRows)
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735 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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737 groupEditing = true;
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741 //No group, but the sequence may represent a group
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744 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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746 groupEditing = false;
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749 SequenceI seq = av.alignment.getSequenceAt(startseq);
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750 StringBuffer message = new StringBuffer();
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752 message.append("Edit group:");
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754 message.append("Edit sequence: "+seq.getName());
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757 message.append(" insert ");
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759 message.append(" delete ");
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761 message.append(Math.abs(startres-lastres)+" gaps.");
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762 ap.alignFrame.statusBar.setText(message.toString());
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765 //Are we editing within a selection group?
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767 || (sg != null && sg.getSequences(true).contains(seq)))
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769 fixedColumns = true;
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771 //sg might be null as the user may only see 1 sequence,
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772 //but the sequence represents a group
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775 sg = new SequenceGroup(null, null, false, false, false, 0,
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776 av.alignment.getWidth()-1);
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777 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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780 fixedLeft = sg.getStartRes();
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781 fixedRight = sg.getEndRes();
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783 if ( (startres < fixedLeft && lastres >= fixedLeft)
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784 || (startres >= fixedLeft && lastres < fixedLeft)
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785 || (startres > fixedRight && lastres <=fixedRight)
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786 || (startres <= fixedRight && lastres > fixedRight))
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792 if (fixedLeft > startres)
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794 fixedRight = fixedLeft - 1;
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797 else if (fixedRight < startres)
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799 fixedLeft = fixedRight;
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805 if(av.hasHiddenColumns )
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807 fixedColumns = true;
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808 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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809 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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811 if ( (insertGap && startres > y1 && lastres < y1)
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812 || (!insertGap && startres < y2 && lastres > y2))
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818 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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819 //Selection spans a hidden region
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820 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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828 fixedRight = y2 - 1;
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839 //If the user has selected the whole sequence, and is dragging to
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840 // the right, we can still extend the alignment and selectionGroup
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841 if( sg.getStartRes() == 0
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842 && sg.getEndRes() == fixedRight
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843 && sg.getEndRes() == av.alignment.getWidth()-1
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846 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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847 fixedRight = sg.getEndRes();
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850 // Is it valid with fixed columns??
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851 // Find the next gap before the end
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852 // of the visible region boundary
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853 boolean blank = false;
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854 for (fixedRight = fixedRight;
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855 fixedRight > lastres;
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859 for (int s = 0; s < sg.getSize(true); s++)
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861 seq = (SequenceI)sg.getSequences(true).elementAt(s);
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862 for (int j = 0; j < startres - lastres; j++)
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864 if (!jalview.util.Comparison.isGap(
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865 seq.getCharAt(fixedRight - j)))
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878 if(sg.getSize(false) == av.alignment.getHeight() )
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880 if((av.hasHiddenColumns
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881 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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887 int alWidth = av.alignment.getWidth();
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888 if(av.hasHiddenRows)
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890 int hwidth = av.alignment.getHiddenSequences().getWidth();
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894 //We can still insert gaps if the selectionGroup
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895 //contains all the sequences
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896 sg.setEndRes(sg.getEndRes()+startres-lastres);
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897 fixedRight = alWidth+startres-lastres;
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909 else if(!insertGap)
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911 /// Are we able to delete?
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912 // ie are all columns blank?
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914 for (int s = 0; s < sg.getSize(true); s++)
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916 seq = (SequenceI)sg.getSequences(true).elementAt(s);
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918 for (int j = startres; j < lastres; j++)
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920 if (seq.getSequence().length() <= j)
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925 if (!jalview.util.Comparison.isGap(
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926 seq.getSequence().charAt(j)))
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928 // Not a gap, block edit not valid
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937 for (int i = 0; i < sg.getSize(true); i++)
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939 seq = (SequenceI) sg.getSequences(true).elementAt(i);
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943 // dragging to the right
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944 for (int j = lastres; j < startres; j++)
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946 if (fixedColumns && fixedRight != -1)
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948 insertChar(j, seq, fixedRight);
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951 insertChar(j, seq);
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956 // dragging to the left
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957 for (int j = lastres; j > startres; j--)
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959 if (fixedColumns && fixedRight != -1)
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961 deleteChar(startres, seq, fixedRight);
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965 deleteChar(startres, seq);
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971 else /////Editing a single sequence///////////
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975 // dragging to the right
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976 for (int j = lastres; j < startres; j++)
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978 if (fixedColumns && fixedRight != -1)
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980 insertChar(j, seq, fixedRight);
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983 insertChar(j, seq);
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988 // dragging to the left
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989 for (int j = lastres; j > startres; j--)
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991 if (fixedColumns && fixedRight != -1)
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993 deleteChar(startres, seq, fixedRight);
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997 deleteChar(startres, seq);
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1003 lastres = startres;
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1004 seqCanvas.repaint();
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1011 * @param j DOCUMENT ME!
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1012 * @param seq DOCUMENT ME!
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1014 void insertChar(int j, SequenceI seq)
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1016 seq.insertCharAt(j, av.getGapCharacter());
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1017 seqEditOccurred = true;
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1020 void insertChar(int j, SequenceI seq, int fixedColumn)
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1022 //Find the next gap before the end of the visible region boundary
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1023 //If lastCol > j, theres a boundary after the gap insertion
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1024 int blankColumn = fixedColumn;
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1025 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1027 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1029 //Theres a space, so break and insert the gap
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1034 if (blankColumn <= j)
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1036 blankColumn = fixedColumn;
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1041 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1044 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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1048 seq.deleteCharAt(blankColumn);
\r
1049 seq.insertCharAt(j, av.getGapCharacter());
\r
1050 seqEditOccurred = true;
\r
1053 void deleteChar(int j, SequenceI seq, int fixedColumn)
\r
1055 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1057 ap.alignFrame.statusBar.setText(
\r
1058 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1062 seq.deleteCharAt(j);
\r
1063 seq.insertCharAt(fixedColumn, av.getGapCharacter());
\r
1064 seqEditOccurred = true;
\r
1070 * @param j DOCUMENT ME!
\r
1071 * @param seq DOCUMENT ME!
\r
1073 void deleteChar(int j, SequenceI seq)
\r
1075 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1077 ap.alignFrame.statusBar.setText(
\r
1078 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1082 seq.deleteCharAt(j);
\r
1083 seqEditOccurred = true;
\r
1084 seqCanvas.repaint();
\r
1089 * @param e DOCUMENT ME!
\r
1091 public void mouseEntered(MouseEvent e)
\r
1096 if (scrollThread != null)
\r
1098 scrollThread.running = false;
\r
1099 scrollThread = null;
\r
1106 * @param e DOCUMENT ME!
\r
1108 public void mouseExited(MouseEvent e)
\r
1110 if (av.getWrapAlignment())
\r
1115 if (mouseDragging)
\r
1117 scrollThread = new ScrollThread();
\r
1121 public void mouseClicked(MouseEvent evt)
\r
1124 public void mouseWheelMoved(MouseWheelEvent e)
\r
1127 /* if (mouseWheelPressed)
\r
1129 Font font = av.getFont();
\r
1130 int fontSize = font.getSize();
\r
1131 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1133 else if (fontSize > 1)
\r
1138 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1144 if (e.getWheelRotation() > 0)
\r
1145 ap.scrollUp(false);
\r
1147 ap.scrollUp(true);
\r
1157 * @param i DOCUMENT ME!
\r
1159 void editOccurred()
\r
1161 if (!seqEditOccurred)
\r
1163 ap.alignFrame.historyList.pop();
\r
1164 ap.alignFrame.updateEditMenuBar();
\r
1169 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1176 * @param evt DOCUMENT ME!
\r
1178 public void doMousePressedDefineMode(MouseEvent evt)
\r
1180 int res = findRes(evt);
\r
1181 int seq = findSeq(evt);
\r
1184 startWrapBlock=wrappedBlock;
\r
1186 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1188 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1189 "Cannot edit annotations in wrapped view.",
\r
1190 "Wrapped view - no edit",
\r
1191 JOptionPane.WARNING_MESSAGE);
\r
1195 if(seq<0 || res<0)
\r
1198 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1200 if ((sequence == null) || (res > sequence.getLength()))
\r
1205 stretchGroup = av.getSelectionGroup();
\r
1207 if (stretchGroup == null)
\r
1209 stretchGroup = av.alignment.findGroup(sequence);
\r
1211 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1212 (res < stretchGroup.getEndRes()))
\r
1214 av.setSelectionGroup(stretchGroup);
\r
1218 stretchGroup = null;
\r
1221 else if (!stretchGroup.getSequences(false).contains(sequence) ||
\r
1222 (stretchGroup.getStartRes() > res) ||
\r
1223 (stretchGroup.getEndRes() < res))
\r
1225 stretchGroup = null;
\r
1227 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1229 if (allGroups != null)
\r
1231 for (int i = 0; i < allGroups.length; i++)
\r
1233 if ((allGroups[i].getStartRes() <= res) &&
\r
1234 (allGroups[i].getEndRes() >= res))
\r
1236 stretchGroup = allGroups[i];
\r
1242 av.setSelectionGroup(stretchGroup);
\r
1247 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1249 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1250 sequence.findPosition(res));
\r
1251 Vector links = new Vector();
\r
1252 for (int i = 0; i < allFeatures.size(); i++)
\r
1254 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1255 if (sf.links != null)
\r
1257 for (int j = 0; j < sf.links.size(); j++)
\r
1259 links.addElement(sf.links.elementAt(j));
\r
1264 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1265 pop.show(this, evt.getX(), evt.getY());
\r
1269 if (av.cursorMode)
\r
1271 seqCanvas.cursorX = findRes(evt);
\r
1272 seqCanvas.cursorY = findSeq(evt);
\r
1273 seqCanvas.repaint();
\r
1277 if (stretchGroup == null)
\r
1279 //Only if left mouse button do we want to change group sizes
\r
1281 // define a new group here
\r
1282 SequenceGroup sg = new SequenceGroup();
\r
1283 sg.setStartRes(res);
\r
1284 sg.setEndRes(res);
\r
1285 sg.addSequence(sequence, false);
\r
1286 av.setSelectionGroup(sg);
\r
1287 stretchGroup = sg;
\r
1289 if (av.getConservationSelected())
\r
1291 SliderPanel.setConservationSlider(ap,
\r
1292 av.getGlobalColourScheme(),
\r
1296 if (av.getAbovePIDThreshold())
\r
1298 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1301 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1303 // Edit end res position of selected group
\r
1304 changeEndRes = true;
\r
1306 else if ( (stretchGroup != null) &&
\r
1307 (stretchGroup.getStartRes() == res))
\r
1309 // Edit end res position of selected group
\r
1310 changeStartRes = true;
\r
1312 stretchGroup.getWidth();
\r
1315 seqCanvas.repaint();
\r
1321 * @param evt DOCUMENT ME!
\r
1323 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1325 if (stretchGroup == null)
\r
1331 if(stretchGroup.cs!=null)
\r
1333 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1335 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1336 stretchGroup.getSequences(true),
\r
1337 stretchGroup.getWidth());
\r
1340 if (stretchGroup.cs.conservationApplied())
\r
1342 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1343 stretchGroup.getName());
\r
1344 stretchGroup.recalcConservation();
\r
1348 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1349 stretchGroup.getName());
\r
1352 changeEndRes = false;
\r
1353 changeStartRes = false;
\r
1354 stretchGroup = null;
\r
1355 PaintRefresher.Refresh(av.alignment);
\r
1361 * @param evt DOCUMENT ME!
\r
1363 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1365 int res = findRes(evt);
\r
1366 int y = findSeq(evt);
\r
1368 if(wrappedBlock!=startWrapBlock)
\r
1371 if (stretchGroup == null)
\r
1376 if(res> av.alignment.getWidth())
\r
1378 res = av.alignment.getWidth()-1;
\r
1381 if (stretchGroup.getEndRes() == res)
\r
1383 // Edit end res position of selected group
\r
1384 changeEndRes = true;
\r
1386 else if (stretchGroup.getStartRes() == res)
\r
1388 // Edit start res position of selected group
\r
1389 changeStartRes = true;
\r
1392 if (res < av.getStartRes())
\r
1394 res = av.getStartRes();
\r
1399 if (res > (stretchGroup.getStartRes() - 1))
\r
1401 stretchGroup.setEndRes(res);
\r
1404 else if (changeStartRes)
\r
1406 if (res < (stretchGroup.getEndRes() + 1))
\r
1408 stretchGroup.setStartRes(res);
\r
1412 int dragDirection = 0;
\r
1416 dragDirection = 1;
\r
1418 else if (y < oldSeq)
\r
1420 dragDirection = -1;
\r
1424 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1426 // This routine ensures we don't skip any sequences, as the
\r
1427 // selection is quite slow.
\r
1428 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1430 oldSeq += dragDirection;
\r
1435 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1437 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1439 stretchGroup.deleteSequence(seq, false);
\r
1445 stretchGroup.addSequence(seq, false);
\r
1448 stretchGroup.addSequence(nextSeq, false);
\r
1455 mouseDragging = true;
\r
1457 if (scrollThread != null)
\r
1459 scrollThread.setEvent(evt);
\r
1462 seqCanvas.repaint();
\r
1465 void scrollCanvas(MouseEvent evt)
\r
1469 if(scrollThread!=null)
\r
1471 scrollThread.running = false;
\r
1472 scrollThread = null;
\r
1474 mouseDragging = false;
\r
1478 if (scrollThread == null)
\r
1479 scrollThread = new ScrollThread();
\r
1481 mouseDragging = true;
\r
1482 scrollThread.setEvent(evt);
\r
1488 // this class allows scrolling off the bottom of the visible alignment
\r
1489 class ScrollThread extends Thread
\r
1492 boolean running = false;
\r
1494 public ScrollThread()
\r
1499 public void setEvent(MouseEvent e)
\r
1504 public void stopScrolling()
\r
1517 if (mouseDragging && (evt.getY() < 0) &&
\r
1518 (av.getStartSeq() > 0))
\r
1520 running = ap.scrollUp(true);
\r
1523 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1524 (av.alignment.getHeight() > av.getEndSeq()))
\r
1526 running = ap.scrollUp(false);
\r
1529 if (mouseDragging && (evt.getX() < 0))
\r
1531 running = ap.scrollRight(false);
\r
1533 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1535 running = ap.scrollRight(true);
\r
1543 catch (Exception ex)
\r