2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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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 // if character is inserted or deleted, we will need to recalculate the conservation
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51 boolean seqEditOccurred = false;
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52 ScrollThread scrollThread = null;
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53 boolean mouseDragging = false;
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54 boolean editingSeqs = false;
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55 boolean groupEditing = false;
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57 //////////////////////////////////////////
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58 /////Everything below this is for defining the boundary of the rubberband
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59 //////////////////////////////////////////
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61 boolean changeEndSeq = false;
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62 boolean changeStartSeq = false;
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63 boolean changeEndRes = false;
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64 boolean changeStartRes = false;
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65 SequenceGroup stretchGroup = null;
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66 boolean remove = false;
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68 boolean mouseWheelPressed = false;
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69 StringBuffer keyboardNo1;
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70 StringBuffer keyboardNo2;
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73 * Creates a new SeqPanel object.
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75 * @param avp DOCUMENT ME!
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76 * @param p DOCUMENT ME!
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78 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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80 ToolTipManager.sharedInstance().registerComponent(this);
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81 ToolTipManager.sharedInstance().setInitialDelay(0);
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82 ToolTipManager.sharedInstance().setDismissDelay(10000);
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84 setBackground(Color.white);
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86 seqCanvas = new SeqCanvas(avp);
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87 setLayout(new BorderLayout());
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88 add(seqCanvas, BorderLayout.CENTER);
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94 addMouseMotionListener(this);
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95 addMouseListener(this);
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96 addMouseWheelListener(this);
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100 int startWrapBlock=-1;
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101 int wrappedBlock=-1;
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102 int findRes(MouseEvent evt)
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105 int x = evt.getX();
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107 if (av.wrapAlignment)
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110 int hgap = av.charHeight;
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111 if (av.scaleAboveWrapped)
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112 hgap += av.charHeight;
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114 int cHeight = av.getAlignment().getHeight() * av.charHeight
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115 + hgap + seqCanvas.getAnnotationHeight();
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117 int y = evt.getY();
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119 x -= seqCanvas.LABEL_WEST;
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122 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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124 wrappedBlock = y / cHeight;
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125 wrappedBlock += av.getStartRes() / cwidth;
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127 res = wrappedBlock * cwidth + x / av.getCharWidth();
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132 res = (x / av.getCharWidth()) + av.getStartRes();
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135 if(av.hasHiddenColumns)
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136 res = av.getColumnSelection().adjustForHiddenColumns(res);
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142 int findSeq(MouseEvent evt)
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146 int y = evt.getY();
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148 if (av.wrapAlignment)
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150 int hgap = av.charHeight;
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151 if (av.scaleAboveWrapped)
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152 hgap += av.charHeight;
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154 int cHeight = av.getAlignment().getHeight() * av.charHeight
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155 + hgap + seqCanvas.getAnnotationHeight();
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159 seq = ( (y % cHeight) / av.getCharHeight());
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163 seq = (y / av.getCharHeight()) + av.getStartSeq();
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173 seqEditOccurred = false;
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174 editingSeqs = false;
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175 groupEditing = false;
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176 keyboardNo1 = null;
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177 keyboardNo2 = null;
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180 void setCursorRow()
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182 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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186 void setCursorColumn()
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188 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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192 void setCursorRowAndColumn()
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194 if(keyboardNo2==null)
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196 keyboardNo2 = new StringBuffer();
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200 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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201 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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206 void setCursorPosition()
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208 SequenceI sequence =
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209 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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211 seqCanvas.cursorX = sequence.findIndex(
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212 getKeyboardNo(keyboardNo1)-1
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217 void moveCursor(int dx, int dy)
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219 seqCanvas.cursorX += dx;
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220 seqCanvas.cursorY += dy;
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224 void scrollToVisible()
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226 if (seqCanvas.cursorX < 0)
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227 seqCanvas.cursorX = 0;
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228 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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229 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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231 if (seqCanvas.cursorY < 0)
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232 seqCanvas.cursorY = 0;
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233 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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234 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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238 if(av.wrapAlignment)
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240 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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244 while (seqCanvas.cursorY < av.startSeq)
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248 while (seqCanvas.cursorY + 1 > av.endSeq)
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250 ap.scrollUp(false);
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252 if (!av.wrapAlignment)
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254 while (seqCanvas.cursorX < av.startRes)
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256 if (!ap.scrollRight(false))
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259 while (seqCanvas.cursorX > av.endRes)
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261 if (!ap.scrollRight(true))
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266 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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267 seqCanvas.cursorX, seqCanvas.cursorY);
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269 seqCanvas.repaint();
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272 void setSelectionAreaAtCursor(boolean topLeft)
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274 SequenceI sequence =
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275 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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277 if(av.getSelectionGroup()!=null)
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279 SequenceGroup sg = av.selectionGroup;
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280 //Find the top and bottom of this group
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281 int min = av.alignment.getHeight(), max = 0;
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282 for(int i=0; i<sg.getSize(); i++)
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284 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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295 sg.setStartRes(seqCanvas.cursorX);
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296 if(sg.getEndRes()<seqCanvas.cursorX)
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297 sg.setEndRes(seqCanvas.cursorX);
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299 min = seqCanvas.cursorY;
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303 sg.setEndRes(seqCanvas.cursorX);
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304 if(sg.getStartRes()>seqCanvas.cursorX)
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305 sg.setStartRes(seqCanvas.cursorX);
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307 max = seqCanvas.cursorY+1;
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312 // Only the user can do this
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313 av.setSelectionGroup(null);
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317 // Now add any sequences between min and max
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318 sg.sequences.clear();
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319 for (int i = min; i < max; i++)
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321 sg.addSequence(av.alignment.getSequenceAt(i), false);
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326 if (av.getSelectionGroup() == null)
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328 SequenceGroup sg = new SequenceGroup();
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329 sg.setStartRes(seqCanvas.cursorX);
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330 sg.setEndRes(seqCanvas.cursorX);
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331 sg.addSequence(sequence, false);
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332 av.setSelectionGroup(sg);
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339 void insertGapAtCursor(boolean group)
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341 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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342 av.alignment, HistoryItem.EDIT));
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343 groupEditing = group;
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344 startseq = seqCanvas.cursorY;
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345 lastres = seqCanvas.cursorX;
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346 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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350 void deleteGapAtCursor(boolean group)
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352 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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353 av.alignment, HistoryItem.EDIT));
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354 groupEditing = group;
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355 startseq = seqCanvas.cursorY;
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356 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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357 editSequence(false, seqCanvas.cursorX);
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361 void numberPressed(char value)
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363 if(keyboardNo1==null)
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364 keyboardNo1 = new StringBuffer();
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366 if(keyboardNo2!=null)
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367 keyboardNo2.append(value);
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369 keyboardNo1.append(value);
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372 int getKeyboardNo(StringBuffer kb)
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377 return Integer.parseInt(kb.toString());
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384 * @param evt DOCUMENT ME!
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386 public void mouseReleased(MouseEvent evt)
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388 mouseDragging = false;
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389 mouseWheelPressed = false;
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393 doMouseReleasedDefineMode(evt);
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408 * @param evt DOCUMENT ME!
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410 public void mousePressed(MouseEvent evt)
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412 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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414 mouseWheelPressed = true;
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418 if (evt.isShiftDown() || evt.isAltDown() ||
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419 evt.isControlDown())
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421 if (evt.isAltDown() || evt.isControlDown())
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423 groupEditing = true;
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425 editingSeqs = true;
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429 doMousePressedDefineMode(evt);
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435 int seq = findSeq(evt);
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436 int res = findRes(evt);
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441 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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442 av.alignment, HistoryItem.EDIT));
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444 if ((seq < av.getAlignment().getHeight()) &&
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445 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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462 * @param evt DOCUMENT ME!
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464 public void mouseMoved(MouseEvent evt)
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468 // This is because MacOSX creates a mouseMoved
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469 // If control is down, other platforms will not.
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473 int res = findRes(evt);
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474 int seq = findSeq(evt);
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477 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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480 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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482 if (res > sequence.getLength())
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487 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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489 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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492 setStatusMessage(sequence, res, seq);
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494 // use aa to see if the mouse pointer is on a
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495 if (av.showSequenceFeatures)
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497 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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500 StringBuffer sbuffer = new StringBuffer("<html>");
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502 for (int i = 0; i < features.length; i++)
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505 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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506 (features[i].getEnd() >= sequence.findPosition(res)))
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508 if(av.featuresDisplayed==null
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509 || !av.featuresDisplayed.containsKey(features[i].getType()))
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513 if (features[i].getType().equals("disulfide bond"))
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515 if (features[i].getBegin() == sequence.findPosition(res)
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516 || features[i].getEnd() == sequence.findPosition(res))
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518 if (sbuffer.length() > 6)
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519 sbuffer.append("<br>");
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520 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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521 features[i].getEnd());
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526 if (sbuffer.length() > 6)
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527 sbuffer.append("<br>");
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528 if(features[i].featureGroup!=null)
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529 sbuffer.append(features[i].featureGroup+";");
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531 sbuffer.append(features[i].getType());
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533 if (features[i].getDescription() != null
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534 && !features[i].description.equals(features[i].getType()))
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535 sbuffer.append("; " + features[i].getDescription());
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537 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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539 sbuffer.append("; (" + features[i].getStatus() + ")");
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546 sbuffer.append("</html>");
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547 if(sbuffer.length()==13) // <html></html>
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548 setToolTipText("");
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550 setToolTipText(sbuffer.toString());
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553 setToolTipText("");
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557 void setStatusMessage(SequenceI sequence, int res, int seq)
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559 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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560 sequence.getName());
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563 if (av.alignment.isNucleotide())
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565 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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568 text.append(" Nucleotide: ");
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572 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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574 text.append(" Residue: ");
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582 text.append(obj + " (" + sequence.findPosition(res) +
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586 ap.alignFrame.statusBar.setText(text.toString());
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593 * @param evt DOCUMENT ME!
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595 public void mouseDragged(MouseEvent evt)
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599 doMouseDraggedDefineMode(evt);
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603 int res = findRes(evt);
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610 if ((lastres == -1) || (lastres == res))
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615 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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617 // dragLeft, delete gap
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618 editSequence(false, res);
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621 editSequence(true, res);
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623 mouseDragging = true;
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624 if(scrollThread!=null)
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625 scrollThread.setEvent(evt);
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629 synchronized void editSequence(boolean insertGap, int startres)
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631 int fixedLeft = -1;
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632 int fixedRight = -1;
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633 boolean fixedColumns = false;
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634 SequenceGroup sg = av.getSelectionGroup();
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636 if(groupEditing && sg==null)
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639 if (!groupEditing && av.hasHiddenRows)
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641 //This needs to check all the sequences in a group edit,m
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642 // not just the startseq
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643 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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645 groupEditing = true;
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649 SequenceI seq = av.alignment.getSequenceAt(startseq);
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650 StringBuffer message = new StringBuffer();
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652 message.append("Edit group:");
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654 message.append("Edit sequence: "+seq.getName());
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657 message.append(" insert ");
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659 message.append(" delete ");
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661 message.append(Math.abs(startres-lastres)+" gaps.");
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662 ap.alignFrame.statusBar.setText(message.toString());
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665 //Are we editing within a selection group?
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667 || (sg != null && sg.sequences.contains(seq)))
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669 fixedColumns = true;
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671 fixedLeft = sg.getStartRes();
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672 fixedRight = sg.getEndRes();
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674 if ( (startres < fixedLeft && lastres >= fixedLeft)
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675 || (startres >= fixedLeft && lastres < fixedLeft)
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676 || (startres > fixedRight && lastres <=fixedRight)
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677 || (startres <= fixedRight && lastres > fixedRight))
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683 if (fixedLeft > startres)
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685 fixedRight = fixedLeft - 1;
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688 else if (fixedRight < startres)
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690 fixedLeft = fixedRight;
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697 if(av.hasHiddenColumns)
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699 fixedColumns = true;
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700 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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701 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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703 if( ( insertGap && startres>y1 && lastres<y1)
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704 || (!insertGap && startres<y2 && lastres>y2) )
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710 if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
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711 fixedRight = y2 -1;
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712 if(y1>fixedLeft && fixedLeft==-1)
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719 /*if (av.hasHiddenRows)
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721 //sg might be null as the user may only see 1 sequence
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724 sg = new SequenceGroup();
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725 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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728 SequenceGroup tmp = new SequenceGroup();
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730 //Do any of the sequences have hidden associates?
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731 for (int s = 0; s < sg.getSize(); s++)
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733 seq = sg.getSequenceAt(s);
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734 tmp.addSequence(seq, false);
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735 if (seq.getHiddenSequences() != null)
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737 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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738 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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745 // int blankColumn = -1;
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751 //If the user has selected the whole sequence, and is dragging to
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752 // the right, we can still extend the alignment and selectionGroup
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753 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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755 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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756 fixedRight = sg.getEndRes();
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759 // Is it valid with fixed columns??
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760 // Find the next gap before the end
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761 // of the visible region boundary
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762 boolean blank = false;
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763 for (fixedRight = fixedRight;
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764 fixedRight > lastres;
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768 for (int s = 0; s < sg.getSize(); s++)
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770 seq = sg.getSequenceAt(s);
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771 for (int j = 0; j < startres - lastres; j++)
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773 if (!jalview.util.Comparison.isGap(
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774 seq.getCharAt(fixedRight - j)))
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787 if(sg.getSize() == av.alignment.getHeight())
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789 //We can still insert gaps if the selectionGroup
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790 //contains all the sequences
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791 sg.setEndRes(sg.getEndRes()+startres-lastres);
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792 fixedRight = av.alignment.getWidth()+startres-lastres;
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804 else if(!insertGap)
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806 /// Are we able to delete?
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807 // ie are all columns blank?
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809 for (int s = 0; s < sg.getSize(); s++)
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811 seq = sg.getSequenceAt(s);
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813 for (int j = startres; j < lastres; j++)
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815 if (seq.getSequence().length() <= j)
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820 if (!jalview.util.Comparison.isGap(
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821 seq.getSequence().charAt(j)))
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823 // Not a gap, block edit not valid
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832 for (int i = 0; i < sg.getSize(); i++)
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834 seq = sg.getSequenceAt(i);
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838 // dragging to the right
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839 for (int j = lastres; j < startres; j++)
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841 if (fixedColumns && fixedRight != -1)
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843 insertChar(j, seq, fixedRight);
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846 insertChar(j, seq);
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851 // dragging to the left
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852 for (int j = lastres; j > startres; j--)
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854 if (fixedColumns && fixedRight != -1)
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856 deleteChar(startres, seq, fixedRight);
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860 deleteChar(startres, seq);
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866 else /////Editing a single sequence///////////
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870 // dragging to the right
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871 for (int j = lastres; j < startres; j++)
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873 if (fixedColumns && fixedRight != -1)
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875 if (sg.getStartRes() == 0
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876 && sg.getEndRes() + 1 == av.alignment.getWidth()
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877 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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879 //Single sequence edit, whole sequence selected,
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880 //extend the selection group
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881 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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882 fixedColumns = false;
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883 insertChar(j, seq);
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886 insertChar(j, seq, fixedRight);
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889 insertChar(j, seq);
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894 // dragging to the left
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895 for (int j = lastres; j > startres; j--)
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897 if (fixedColumns && fixedRight != -1)
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899 deleteChar(startres, seq, fixedRight);
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903 deleteChar(startres, seq);
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909 lastres = startres;
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910 seqCanvas.repaint();
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917 * @param j DOCUMENT ME!
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918 * @param seq DOCUMENT ME!
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920 void insertChar(int j, SequenceI seq)
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922 seq.insertCharAt(j, av.getGapCharacter());
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923 seqEditOccurred = true;
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926 void insertChar(int j, SequenceI seq, int fixedColumn)
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928 //Find the next gap before the end of the visible region boundary
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929 //If lastCol > j, theres a boundary after the gap insertion
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930 int blankColumn = fixedColumn;
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931 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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933 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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935 //Theres a space, so break and insert the gap
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940 if (blankColumn <= j)
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946 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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949 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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953 seq.deleteCharAt(blankColumn);
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954 seq.insertCharAt(j, av.getGapCharacter());
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955 seqEditOccurred = true;
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958 void deleteChar(int j, SequenceI seq, int fixedColumn)
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960 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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962 ap.alignFrame.statusBar.setText(
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963 "End editing: Tried removing residue " + seq.getCharAt(j));
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967 seq.deleteCharAt(j);
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968 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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969 seqEditOccurred = true;
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975 * @param j DOCUMENT ME!
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976 * @param seq DOCUMENT ME!
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978 void deleteChar(int j, SequenceI seq)
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980 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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982 ap.alignFrame.statusBar.setText(
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983 "End editing: Tried removing residue " + seq.getCharAt(j));
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987 seq.deleteCharAt(j);
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988 seqEditOccurred = true;
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989 seqCanvas.repaint();
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994 * @param e DOCUMENT ME!
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996 public void mouseEntered(MouseEvent e)
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1001 if (scrollThread != null)
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1003 scrollThread.running = false;
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1004 scrollThread = null;
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1011 * @param e DOCUMENT ME!
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1013 public void mouseExited(MouseEvent e)
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1015 if (av.getWrapAlignment())
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1020 if (mouseDragging)
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1022 scrollThread = new ScrollThread();
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1026 public void mouseClicked(MouseEvent evt)
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1029 public void mouseWheelMoved(MouseWheelEvent e)
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1032 if (mouseWheelPressed)
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1034 Font font = av.getFont();
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1035 int fontSize = font.getSize();
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1036 if (e.getWheelRotation() > 0 && fontSize < 51)
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1038 else if (fontSize > 1)
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1041 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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1046 if (e.getWheelRotation() > 0)
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1047 ap.scrollUp(false);
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1049 ap.scrollUp(true);
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1059 * @param i DOCUMENT ME!
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1061 void editOccurred()
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1063 if (!seqEditOccurred)
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1065 ap.alignFrame.historyList.pop();
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1066 ap.alignFrame.updateEditMenuBar();
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1071 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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1078 * @param evt DOCUMENT ME!
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1080 public void doMousePressedDefineMode(MouseEvent evt)
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1082 int res = findRes(evt);
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1083 int seq = findSeq(evt);
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1086 startWrapBlock=wrappedBlock;
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1088 if(av.wrapAlignment && seq>av.alignment.getHeight())
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1090 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1091 "Cannot edit annotations in wrapped view.",
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1092 "Wrapped view - no edit",
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1093 JOptionPane.WARNING_MESSAGE);
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1097 if(seq<0 || res<0)
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1100 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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1102 if ((sequence == null) || (res > sequence.getLength()))
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1107 stretchGroup = av.getSelectionGroup();
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1109 if (stretchGroup == null)
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1111 stretchGroup = av.alignment.findGroup(sequence);
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1113 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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1114 (res < stretchGroup.getEndRes()))
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1116 av.setSelectionGroup(stretchGroup);
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1120 stretchGroup = null;
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1123 else if (!stretchGroup.sequences.contains(sequence) ||
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1124 (stretchGroup.getStartRes() > res) ||
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1125 (stretchGroup.getEndRes() < res))
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1127 stretchGroup = null;
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1129 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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1131 if (allGroups != null)
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1133 for (int i = 0; i < allGroups.length; i++)
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1135 if ((allGroups[i].getStartRes() <= res) &&
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1136 (allGroups[i].getEndRes() >= res))
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1138 stretchGroup = allGroups[i];
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1139 av.setSelectionGroup(stretchGroup);
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1147 if (av.cursorMode)
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1149 seqCanvas.cursorX = findRes(evt);
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1150 seqCanvas.cursorY = findSeq(evt);
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1151 seqCanvas.repaint();
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1156 if (stretchGroup == null)
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1158 // define a new group here
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1159 SequenceGroup sg = new SequenceGroup();
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1160 sg.setStartRes(res);
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1161 sg.setEndRes(res);
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1162 sg.addSequence(sequence, false);
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1163 av.setSelectionGroup(sg);
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1164 stretchGroup = sg;
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1166 if (av.getConservationSelected())
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1168 SliderPanel.setConservationSlider(ap,
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1169 av.getGlobalColourScheme(), "Background");
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1172 if (av.getAbovePIDThreshold())
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1174 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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1178 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
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1180 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
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1181 pop.show(this, evt.getX(), evt.getY());
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1183 // edit the properties of existing group
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1186 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
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1188 // Edit end res position of selected group
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1189 changeEndRes = true;
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1191 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
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1193 // Edit end res position of selected group
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1194 changeStartRes = true;
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1197 stretchGroup.getWidth();
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1199 seqCanvas.repaint();
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1205 * @param evt DOCUMENT ME!
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1207 public void doMouseReleasedDefineMode(MouseEvent evt)
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1209 if (stretchGroup == null)
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1215 if(stretchGroup.cs!=null)
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1217 if (stretchGroup.cs instanceof ClustalxColourScheme)
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1219 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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1221 stretchGroup.getWidth());
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1224 if (stretchGroup.cs.conservationApplied())
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1226 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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1227 stretchGroup.getName());
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1228 stretchGroup.recalcConservation();
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1232 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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1233 stretchGroup.getName());
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1236 changeEndRes = false;
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1237 changeStartRes = false;
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1238 stretchGroup = null;
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1239 PaintRefresher.Refresh(av.alignment);
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1245 * @param evt DOCUMENT ME!
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1247 public void doMouseDraggedDefineMode(MouseEvent evt)
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1249 int res = findRes(evt);
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1250 int y = findSeq(evt);
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1252 if(wrappedBlock!=startWrapBlock)
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1255 if (stretchGroup == null)
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1261 if(y > av.alignment.getHeight())
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1263 y = av.alignment.getHeight() -1;
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1265 if(res> av.alignment.getWidth())
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1267 res = av.alignment.getWidth()-1;
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1270 if (stretchGroup.getEndRes() == res)
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1272 // Edit end res position of selected group
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1273 changeEndRes = true;
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1275 else if (stretchGroup.getStartRes() == res)
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1277 // Edit start res position of selected group
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1278 changeStartRes = true;
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1281 if (res < av.getStartRes())
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1283 res = av.getStartRes();
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1288 if (res > (stretchGroup.getStartRes() - 1))
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1290 stretchGroup.setEndRes(res);
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1293 else if (changeStartRes)
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1295 if (res < (stretchGroup.getEndRes() + 1))
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1297 stretchGroup.setStartRes(res);
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1301 int dragDirection = 0;
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1305 dragDirection = 1;
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1307 else if (y < oldSeq)
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1309 dragDirection = -1;
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1313 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
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1315 // This routine ensures we don't skip any sequences, as the
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1316 // selection is quite slow.
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1317 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1319 oldSeq += dragDirection;
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1324 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1326 if (stretchGroup.sequences.contains(nextSeq))
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1328 stretchGroup.deleteSequence(seq, false);
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1334 stretchGroup.addSequence(seq, false);
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1337 stretchGroup.addSequence(nextSeq, false);
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1344 mouseDragging = true;
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1346 if (scrollThread != null)
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1348 scrollThread.setEvent(evt);
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1351 seqCanvas.repaint();
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1354 void scrollCanvas(MouseEvent evt)
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1358 if(scrollThread!=null)
\r
1360 scrollThread.running = false;
\r
1361 scrollThread = null;
\r
1363 mouseDragging = false;
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1367 if (scrollThread == null)
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1368 scrollThread = new ScrollThread();
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1370 mouseDragging = true;
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1371 scrollThread.setEvent(evt);
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1377 // this class allows scrolling off the bottom of the visible alignment
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1378 class ScrollThread extends Thread
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1381 boolean running = false;
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1383 public ScrollThread()
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1388 public void setEvent(MouseEvent e)
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1393 public void stopScrolling()
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1406 if (mouseDragging && (evt.getY() < 0) &&
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1407 (av.getStartSeq() > 0))
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1409 running = ap.scrollUp(true);
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1412 if (mouseDragging && (evt.getY() >= getHeight()) &&
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1413 (av.alignment.getHeight() > av.getEndSeq()))
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1415 running = ap.scrollUp(false);
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1418 if (mouseDragging && (evt.getX() < 0))
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1420 running = ap.scrollRight(false);
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1422 else if (mouseDragging && (evt.getX() >= getWidth()))
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1424 running = ap.scrollRight(true);
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1432 catch (Exception ex)
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