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 Point lastMousePress;
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69 boolean mouseWheelPressed = false;
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70 StringBuffer keyboardNo1;
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71 StringBuffer keyboardNo2;
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74 * Creates a new SeqPanel object.
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76 * @param avp DOCUMENT ME!
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77 * @param p DOCUMENT ME!
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79 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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81 ToolTipManager.sharedInstance().registerComponent(this);
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82 ToolTipManager.sharedInstance().setInitialDelay(0);
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83 ToolTipManager.sharedInstance().setDismissDelay(10000);
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85 setBackground(Color.white);
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87 seqCanvas = new SeqCanvas(avp);
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88 setLayout(new BorderLayout());
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89 add(seqCanvas, BorderLayout.CENTER);
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95 addMouseMotionListener(this);
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96 addMouseListener(this);
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97 addMouseWheelListener(this);
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101 int startWrapBlock=-1;
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102 int wrappedBlock=-1;
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103 int findRes(MouseEvent evt)
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106 int x = evt.getX();
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108 if (av.wrapAlignment)
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111 int hgap = av.charHeight;
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112 if (av.scaleAboveWrapped)
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113 hgap += av.charHeight;
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115 int cHeight = av.getAlignment().getHeight() * av.charHeight
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116 + hgap + seqCanvas.getAnnotationHeight();
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118 int y = evt.getY();
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120 x -= seqCanvas.LABEL_WEST;
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123 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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125 wrappedBlock = y / cHeight;
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126 wrappedBlock += av.getStartRes() / cwidth;
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128 res = wrappedBlock * cwidth + x / av.getCharWidth();
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133 res = (x / av.getCharWidth()) + av.getStartRes();
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136 if(av.hasHiddenColumns)
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137 res = av.getColumnSelection().adjustForHiddenColumns(res);
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143 int findSeq(MouseEvent evt)
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147 int y = evt.getY();
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149 if (av.wrapAlignment)
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151 int hgap = av.charHeight;
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152 if (av.scaleAboveWrapped)
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153 hgap += av.charHeight;
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155 int cHeight = av.getAlignment().getHeight() * av.charHeight
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156 + hgap + seqCanvas.getAnnotationHeight();
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160 seq = ( (y % cHeight) / av.getCharHeight());
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164 seq = (y / av.getCharHeight()) + av.getStartSeq();
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174 seqEditOccurred = false;
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175 editingSeqs = false;
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176 groupEditing = false;
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177 keyboardNo1 = null;
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178 keyboardNo2 = null;
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181 void setCursorRow()
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183 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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187 void setCursorColumn()
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189 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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193 void setCursorRowAndColumn()
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195 if(keyboardNo2==null)
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197 keyboardNo2 = new StringBuffer();
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201 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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202 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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207 void setCursorPosition()
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209 SequenceI sequence =
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210 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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212 seqCanvas.cursorX = sequence.findIndex(
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213 getKeyboardNo(keyboardNo1)-1
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218 void moveCursor(int dx, int dy)
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220 seqCanvas.cursorX += dx;
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221 seqCanvas.cursorY += dy;
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225 void scrollToVisible()
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227 if (seqCanvas.cursorX < 0)
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228 seqCanvas.cursorX = 0;
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229 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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230 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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232 if (seqCanvas.cursorY < 0)
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233 seqCanvas.cursorY = 0;
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234 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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235 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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239 if(av.wrapAlignment)
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241 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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245 while (seqCanvas.cursorY < av.startSeq)
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249 while (seqCanvas.cursorY + 1 > av.endSeq)
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251 ap.scrollUp(false);
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253 if (!av.wrapAlignment)
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255 while (seqCanvas.cursorX < av.startRes)
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257 if (!ap.scrollRight(false))
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260 while (seqCanvas.cursorX > av.endRes)
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262 if (!ap.scrollRight(true))
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267 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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268 seqCanvas.cursorX, seqCanvas.cursorY);
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270 seqCanvas.repaint();
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273 void setSelectionAreaAtCursor(boolean topLeft)
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275 SequenceI sequence =
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276 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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278 if(av.getSelectionGroup()!=null)
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280 SequenceGroup sg = av.selectionGroup;
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281 //Find the top and bottom of this group
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282 int min = av.alignment.getHeight(), max = 0;
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283 for(int i=0; i<sg.getSize(); i++)
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285 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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296 sg.setStartRes(seqCanvas.cursorX);
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297 if(sg.getEndRes()<seqCanvas.cursorX)
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298 sg.setEndRes(seqCanvas.cursorX);
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300 min = seqCanvas.cursorY;
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304 sg.setEndRes(seqCanvas.cursorX);
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305 if(sg.getStartRes()>seqCanvas.cursorX)
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306 sg.setStartRes(seqCanvas.cursorX);
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308 max = seqCanvas.cursorY+1;
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313 // Only the user can do this
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314 av.setSelectionGroup(null);
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318 // Now add any sequences between min and max
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319 sg.sequences.clear();
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320 for (int i = min; i < max; i++)
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322 sg.addSequence(av.alignment.getSequenceAt(i), false);
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327 if (av.getSelectionGroup() == null)
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329 SequenceGroup sg = new SequenceGroup();
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330 sg.setStartRes(seqCanvas.cursorX);
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331 sg.setEndRes(seqCanvas.cursorX);
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332 sg.addSequence(sequence, false);
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333 av.setSelectionGroup(sg);
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340 void insertGapAtCursor(boolean group)
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342 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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343 av.alignment, HistoryItem.EDIT));
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344 groupEditing = group;
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345 startseq = seqCanvas.cursorY;
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346 lastres = seqCanvas.cursorX;
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347 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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351 void deleteGapAtCursor(boolean group)
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353 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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354 av.alignment, HistoryItem.EDIT));
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355 groupEditing = group;
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356 startseq = seqCanvas.cursorY;
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357 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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358 editSequence(false, seqCanvas.cursorX);
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362 void numberPressed(char value)
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364 if(keyboardNo1==null)
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365 keyboardNo1 = new StringBuffer();
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367 if(keyboardNo2!=null)
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368 keyboardNo2.append(value);
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370 keyboardNo1.append(value);
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373 int getKeyboardNo(StringBuffer kb)
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378 return Integer.parseInt(kb.toString());
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385 * @param evt DOCUMENT ME!
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387 public void mouseReleased(MouseEvent evt)
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389 mouseDragging = false;
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390 mouseWheelPressed = false;
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394 doMouseReleasedDefineMode(evt);
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409 * @param evt DOCUMENT ME!
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411 public void mousePressed(MouseEvent evt)
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413 lastMousePress = evt.getPoint();
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415 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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417 mouseWheelPressed = true;
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421 if (evt.isShiftDown() || evt.isAltDown() ||
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422 evt.isControlDown())
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424 if (evt.isAltDown() || evt.isControlDown())
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426 groupEditing = true;
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428 editingSeqs = true;
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432 doMousePressedDefineMode(evt);
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438 int seq = findSeq(evt);
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439 int res = findRes(evt);
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444 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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445 av.alignment, HistoryItem.EDIT));
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447 if ((seq < av.getAlignment().getHeight()) &&
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448 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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465 * @param evt DOCUMENT ME!
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467 public void mouseMoved(MouseEvent evt)
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471 // This is because MacOSX creates a mouseMoved
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472 // If control is down, other platforms will not.
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476 int res = findRes(evt);
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477 int seq = findSeq(evt);
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480 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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483 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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485 if (res > sequence.getLength())
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490 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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492 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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495 setStatusMessage(sequence, res, seq);
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497 // use aa to see if the mouse pointer is on a
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498 if (av.showSequenceFeatures)
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500 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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503 StringBuffer sbuffer = new StringBuffer("<html>");
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505 for (int i = 0; i < features.length; i++)
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508 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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509 (features[i].getEnd() >= sequence.findPosition(res)))
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511 if(av.featuresDisplayed==null
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512 || !av.featuresDisplayed.containsKey(features[i].getType()))
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516 if (features[i].getType().equals("disulfide bond"))
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518 if (features[i].getBegin() == sequence.findPosition(res)
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519 || features[i].getEnd() == sequence.findPosition(res))
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521 if (sbuffer.length() > 6)
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522 sbuffer.append("<br>");
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523 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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524 features[i].getEnd());
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529 if (sbuffer.length() > 6)
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530 sbuffer.append("<br>");
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531 if(features[i].featureGroup!=null)
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532 sbuffer.append(features[i].featureGroup+";");
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534 sbuffer.append(features[i].getType());
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536 if (features[i].getDescription() != null
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537 && !features[i].description.equals(features[i].getType()))
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538 sbuffer.append("; " + features[i].getDescription());
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540 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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542 sbuffer.append("; (" + features[i].getStatus() + ")");
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549 sbuffer.append("</html>");
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550 if(sbuffer.length()==13) // <html></html>
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551 setToolTipText("");
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553 setToolTipText(sbuffer.toString());
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556 setToolTipText("");
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560 void setStatusMessage(SequenceI sequence, int res, int seq)
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562 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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563 sequence.getName());
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566 if (av.alignment.isNucleotide())
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568 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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571 text.append(" Nucleotide: ");
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575 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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577 text.append(" Residue: ");
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585 text.append(obj + " (" + sequence.findPosition(res) +
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589 ap.alignFrame.statusBar.setText(text.toString());
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596 * @param evt DOCUMENT ME!
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598 public void mouseDragged(MouseEvent evt)
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600 if (mouseWheelPressed)
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602 int oldWidth = av.charWidth;
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604 //Which is bigger, left-right or up-down?
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605 if (Math.abs(evt.getY() - lastMousePress.getY())
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606 > Math.abs(evt.getX() - lastMousePress.getX()))
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608 int fontSize = av.font.getSize();
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610 if (evt.getY() < lastMousePress.getY() && av.charHeight > 1)
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614 else if (evt.getY() > lastMousePress.getY())
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619 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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620 av.charWidth = oldWidth;
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626 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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630 else if (evt.getX() > lastMousePress.getX())
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638 FontMetrics fm = getFontMetrics(av.getFont());
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639 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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641 lastMousePress = evt.getPoint();
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648 doMouseDraggedDefineMode(evt);
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652 int res = findRes(evt);
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659 if ((lastres == -1) || (lastres == res))
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664 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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666 // dragLeft, delete gap
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667 editSequence(false, res);
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670 editSequence(true, res);
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672 mouseDragging = true;
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673 if(scrollThread!=null)
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674 scrollThread.setEvent(evt);
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678 synchronized void editSequence(boolean insertGap, int startres)
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680 int fixedLeft = -1;
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681 int fixedRight = -1;
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682 boolean fixedColumns = false;
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683 SequenceGroup sg = av.getSelectionGroup();
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685 if(groupEditing && sg==null)
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688 if (!groupEditing && av.hasHiddenRows)
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690 //This needs to check all the sequences in a group edit,m
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691 // not just the startseq
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692 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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694 groupEditing = true;
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698 SequenceI seq = av.alignment.getSequenceAt(startseq);
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699 StringBuffer message = new StringBuffer();
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701 message.append("Edit group:");
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703 message.append("Edit sequence: "+seq.getName());
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706 message.append(" insert ");
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708 message.append(" delete ");
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710 message.append(Math.abs(startres-lastres)+" gaps.");
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711 ap.alignFrame.statusBar.setText(message.toString());
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714 //Are we editing within a selection group?
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716 || (sg != null && sg.sequences.contains(seq)))
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718 fixedColumns = true;
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720 fixedLeft = sg.getStartRes();
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721 fixedRight = sg.getEndRes();
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723 if ( (startres < fixedLeft && lastres >= fixedLeft)
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724 || (startres >= fixedLeft && lastres < fixedLeft)
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725 || (startres > fixedRight && lastres <=fixedRight)
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726 || (startres <= fixedRight && lastres > fixedRight))
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732 if (fixedLeft > startres)
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734 fixedRight = fixedLeft - 1;
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737 else if (fixedRight < startres)
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739 fixedLeft = fixedRight;
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746 if(av.hasHiddenColumns)
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748 fixedColumns = true;
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749 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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750 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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752 if( ( insertGap && startres>y1 && lastres<y1)
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753 || (!insertGap && startres<y2 && lastres>y2) )
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759 if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
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760 fixedRight = y2 -1;
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761 if(y1>fixedLeft && fixedLeft==-1)
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768 /*if (av.hasHiddenRows)
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770 //sg might be null as the user may only see 1 sequence
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773 sg = new SequenceGroup();
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774 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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777 SequenceGroup tmp = new SequenceGroup();
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779 //Do any of the sequences have hidden associates?
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780 for (int s = 0; s < sg.getSize(); s++)
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782 seq = sg.getSequenceAt(s);
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783 tmp.addSequence(seq, false);
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784 if (seq.getHiddenSequences() != null)
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786 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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787 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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794 // int blankColumn = -1;
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800 //If the user has selected the whole sequence, and is dragging to
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801 // the right, we can still extend the alignment and selectionGroup
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802 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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804 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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805 fixedRight = sg.getEndRes();
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808 // Is it valid with fixed columns??
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809 // Find the next gap before the end
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810 // of the visible region boundary
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811 boolean blank = false;
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812 for (fixedRight = fixedRight;
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813 fixedRight > lastres;
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817 for (int s = 0; s < sg.getSize(); s++)
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819 seq = sg.getSequenceAt(s);
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820 for (int j = 0; j < startres - lastres; j++)
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822 if (!jalview.util.Comparison.isGap(
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823 seq.getCharAt(fixedRight - j)))
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836 if(sg.getSize() == av.alignment.getHeight())
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838 //We can still insert gaps if the selectionGroup
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839 //contains all the sequences
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840 sg.setEndRes(sg.getEndRes()+startres-lastres);
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841 fixedRight = av.alignment.getWidth()+startres-lastres;
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853 else if(!insertGap)
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855 /// Are we able to delete?
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856 // ie are all columns blank?
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858 for (int s = 0; s < sg.getSize(); s++)
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860 seq = sg.getSequenceAt(s);
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862 for (int j = startres; j < lastres; j++)
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864 if (seq.getSequence().length() <= j)
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869 if (!jalview.util.Comparison.isGap(
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870 seq.getSequence().charAt(j)))
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872 // Not a gap, block edit not valid
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881 for (int i = 0; i < sg.getSize(); i++)
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883 seq = sg.getSequenceAt(i);
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887 // dragging to the right
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888 for (int j = lastres; j < startres; j++)
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890 if (fixedColumns && fixedRight != -1)
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892 insertChar(j, seq, fixedRight);
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895 insertChar(j, seq);
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900 // dragging to the left
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901 for (int j = lastres; j > startres; j--)
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903 if (fixedColumns && fixedRight != -1)
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905 deleteChar(startres, seq, fixedRight);
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909 deleteChar(startres, seq);
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915 else /////Editing a single sequence///////////
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919 // dragging to the right
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920 for (int j = lastres; j < startres; j++)
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922 if (fixedColumns && fixedRight != -1)
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924 if (sg.getStartRes() == 0
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925 && sg.getEndRes() + 1 == av.alignment.getWidth()
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926 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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928 //Single sequence edit, whole sequence selected,
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929 //extend the selection group
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930 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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931 fixedColumns = false;
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932 insertChar(j, seq);
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935 insertChar(j, seq, fixedRight);
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938 insertChar(j, seq);
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943 // dragging to the left
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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 deleteChar(startres, seq, fixedRight);
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952 deleteChar(startres, seq);
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958 lastres = startres;
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959 seqCanvas.repaint();
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966 * @param j DOCUMENT ME!
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967 * @param seq DOCUMENT ME!
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969 void insertChar(int j, SequenceI seq)
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971 seq.insertCharAt(j, av.getGapCharacter());
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972 seqEditOccurred = true;
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975 void insertChar(int j, SequenceI seq, int fixedColumn)
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977 //Find the next gap before the end of the visible region boundary
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978 //If lastCol > j, theres a boundary after the gap insertion
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979 int blankColumn = fixedColumn;
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980 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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982 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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984 //Theres a space, so break and insert the gap
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989 if (blankColumn <= j)
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995 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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998 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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1002 seq.deleteCharAt(blankColumn);
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1003 seq.insertCharAt(j, av.getGapCharacter());
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1004 seqEditOccurred = true;
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1007 void deleteChar(int j, SequenceI seq, int fixedColumn)
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1009 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1011 ap.alignFrame.statusBar.setText(
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1012 "End editing: Tried removing residue " + seq.getCharAt(j));
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1016 seq.deleteCharAt(j);
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1017 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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1018 seqEditOccurred = true;
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1024 * @param j DOCUMENT ME!
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1025 * @param seq DOCUMENT ME!
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1027 void deleteChar(int j, SequenceI seq)
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1029 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1031 ap.alignFrame.statusBar.setText(
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1032 "End editing: Tried removing residue " + seq.getCharAt(j));
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1036 seq.deleteCharAt(j);
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1037 seqEditOccurred = true;
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1038 seqCanvas.repaint();
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1043 * @param e DOCUMENT ME!
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1045 public void mouseEntered(MouseEvent e)
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1050 if (scrollThread != null)
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1052 scrollThread.running = false;
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1053 scrollThread = null;
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1060 * @param e DOCUMENT ME!
\r
1062 public void mouseExited(MouseEvent e)
\r
1064 if (av.getWrapAlignment())
\r
1069 if (mouseDragging)
\r
1071 scrollThread = new ScrollThread();
\r
1075 public void mouseClicked(MouseEvent evt)
\r
1078 public void mouseWheelMoved(MouseWheelEvent e)
\r
1081 /* if (mouseWheelPressed)
\r
1083 Font font = av.getFont();
\r
1084 int fontSize = font.getSize();
\r
1085 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1087 else if (fontSize > 1)
\r
1092 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1098 if (e.getWheelRotation() > 0)
\r
1099 ap.scrollUp(false);
\r
1101 ap.scrollUp(true);
\r
1111 * @param i DOCUMENT ME!
\r
1113 void editOccurred()
\r
1115 if (!seqEditOccurred)
\r
1117 ap.alignFrame.historyList.pop();
\r
1118 ap.alignFrame.updateEditMenuBar();
\r
1123 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1130 * @param evt DOCUMENT ME!
\r
1132 public void doMousePressedDefineMode(MouseEvent evt)
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1134 int res = findRes(evt);
\r
1135 int seq = findSeq(evt);
\r
1138 startWrapBlock=wrappedBlock;
\r
1140 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1142 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1143 "Cannot edit annotations in wrapped view.",
\r
1144 "Wrapped view - no edit",
\r
1145 JOptionPane.WARNING_MESSAGE);
\r
1149 if(seq<0 || res<0)
\r
1152 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1154 if ((sequence == null) || (res > sequence.getLength()))
\r
1159 stretchGroup = av.getSelectionGroup();
\r
1161 if (stretchGroup == null)
\r
1163 stretchGroup = av.alignment.findGroup(sequence);
\r
1165 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1166 (res < stretchGroup.getEndRes()))
\r
1168 av.setSelectionGroup(stretchGroup);
\r
1172 stretchGroup = null;
\r
1175 else if (!stretchGroup.sequences.contains(sequence) ||
\r
1176 (stretchGroup.getStartRes() > res) ||
\r
1177 (stretchGroup.getEndRes() < res))
\r
1179 stretchGroup = null;
\r
1181 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1183 if (allGroups != null)
\r
1185 for (int i = 0; i < allGroups.length; i++)
\r
1187 if ((allGroups[i].getStartRes() <= res) &&
\r
1188 (allGroups[i].getEndRes() >= res))
\r
1190 stretchGroup = allGroups[i];
\r
1191 av.setSelectionGroup(stretchGroup);
\r
1199 if (av.cursorMode)
\r
1201 seqCanvas.cursorX = findRes(evt);
\r
1202 seqCanvas.cursorY = findSeq(evt);
\r
1203 seqCanvas.repaint();
\r
1208 if (stretchGroup == null)
\r
1210 // define a new group here
\r
1211 SequenceGroup sg = new SequenceGroup();
\r
1212 sg.setStartRes(res);
\r
1213 sg.setEndRes(res);
\r
1214 sg.addSequence(sequence, false);
\r
1215 av.setSelectionGroup(sg);
\r
1216 stretchGroup = sg;
\r
1218 if (av.getConservationSelected())
\r
1220 SliderPanel.setConservationSlider(ap,
\r
1221 av.getGlobalColourScheme(), "Background");
\r
1224 if (av.getAbovePIDThreshold())
\r
1226 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1230 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1232 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
\r
1233 pop.show(this, evt.getX(), evt.getY());
\r
1235 // edit the properties of existing group
\r
1238 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1240 // Edit end res position of selected group
\r
1241 changeEndRes = true;
\r
1243 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
\r
1245 // Edit end res position of selected group
\r
1246 changeStartRes = true;
\r
1249 stretchGroup.getWidth();
\r
1251 seqCanvas.repaint();
\r
1257 * @param evt DOCUMENT ME!
\r
1259 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1261 if (stretchGroup == null)
\r
1267 if(stretchGroup.cs!=null)
\r
1269 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1271 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1273 stretchGroup.getWidth());
\r
1276 if (stretchGroup.cs.conservationApplied())
\r
1278 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1279 stretchGroup.getName());
\r
1280 stretchGroup.recalcConservation();
\r
1284 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1285 stretchGroup.getName());
\r
1288 changeEndRes = false;
\r
1289 changeStartRes = false;
\r
1290 stretchGroup = null;
\r
1291 PaintRefresher.Refresh(av.alignment);
\r
1297 * @param evt DOCUMENT ME!
\r
1299 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1301 int res = findRes(evt);
\r
1302 int y = findSeq(evt);
\r
1304 if(wrappedBlock!=startWrapBlock)
\r
1307 if (stretchGroup == null)
\r
1313 if(y > av.alignment.getHeight())
\r
1315 y = av.alignment.getHeight() -1;
\r
1317 if(res> av.alignment.getWidth())
\r
1319 res = av.alignment.getWidth()-1;
\r
1322 if (stretchGroup.getEndRes() == res)
\r
1324 // Edit end res position of selected group
\r
1325 changeEndRes = true;
\r
1327 else if (stretchGroup.getStartRes() == res)
\r
1329 // Edit start res position of selected group
\r
1330 changeStartRes = true;
\r
1333 if (res < av.getStartRes())
\r
1335 res = av.getStartRes();
\r
1340 if (res > (stretchGroup.getStartRes() - 1))
\r
1342 stretchGroup.setEndRes(res);
\r
1345 else if (changeStartRes)
\r
1347 if (res < (stretchGroup.getEndRes() + 1))
\r
1349 stretchGroup.setStartRes(res);
\r
1353 int dragDirection = 0;
\r
1357 dragDirection = 1;
\r
1359 else if (y < oldSeq)
\r
1361 dragDirection = -1;
\r
1365 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1367 // This routine ensures we don't skip any sequences, as the
\r
1368 // selection is quite slow.
\r
1369 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1371 oldSeq += dragDirection;
\r
1376 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1378 if (stretchGroup.sequences.contains(nextSeq))
\r
1380 stretchGroup.deleteSequence(seq, false);
\r
1386 stretchGroup.addSequence(seq, false);
\r
1389 stretchGroup.addSequence(nextSeq, false);
\r
1396 mouseDragging = true;
\r
1398 if (scrollThread != null)
\r
1400 scrollThread.setEvent(evt);
\r
1403 seqCanvas.repaint();
\r
1406 void scrollCanvas(MouseEvent evt)
\r
1410 if(scrollThread!=null)
\r
1412 scrollThread.running = false;
\r
1413 scrollThread = null;
\r
1415 mouseDragging = false;
\r
1419 if (scrollThread == null)
\r
1420 scrollThread = new ScrollThread();
\r
1422 mouseDragging = true;
\r
1423 scrollThread.setEvent(evt);
\r
1429 // this class allows scrolling off the bottom of the visible alignment
\r
1430 class ScrollThread extends Thread
\r
1433 boolean running = false;
\r
1435 public ScrollThread()
\r
1440 public void setEvent(MouseEvent e)
\r
1445 public void stopScrolling()
\r
1458 if (mouseDragging && (evt.getY() < 0) &&
\r
1459 (av.getStartSeq() > 0))
\r
1461 running = ap.scrollUp(true);
\r
1464 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1465 (av.alignment.getHeight() > av.getEndSeq()))
\r
1467 running = ap.scrollUp(false);
\r
1470 if (mouseDragging && (evt.getX() < 0))
\r
1472 running = ap.scrollRight(false);
\r
1474 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1476 running = ap.scrollRight(true);
\r
1484 catch (Exception ex)
\r