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 lastMousePress = evt.getPoint();
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645 doMouseDraggedDefineMode(evt);
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649 int res = findRes(evt);
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656 if ((lastres == -1) || (lastres == res))
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661 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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663 // dragLeft, delete gap
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664 editSequence(false, res);
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667 editSequence(true, res);
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669 mouseDragging = true;
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670 if(scrollThread!=null)
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671 scrollThread.setEvent(evt);
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675 synchronized void editSequence(boolean insertGap, int startres)
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677 int fixedLeft = -1;
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678 int fixedRight = -1;
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679 boolean fixedColumns = false;
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680 SequenceGroup sg = av.getSelectionGroup();
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682 if(groupEditing && sg==null)
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685 if (!groupEditing && av.hasHiddenRows)
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687 //This needs to check all the sequences in a group edit,m
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688 // not just the startseq
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689 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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691 groupEditing = true;
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695 SequenceI seq = av.alignment.getSequenceAt(startseq);
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696 StringBuffer message = new StringBuffer();
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698 message.append("Edit group:");
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700 message.append("Edit sequence: "+seq.getName());
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703 message.append(" insert ");
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705 message.append(" delete ");
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707 message.append(Math.abs(startres-lastres)+" gaps.");
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708 ap.alignFrame.statusBar.setText(message.toString());
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711 //Are we editing within a selection group?
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713 || (sg != null && sg.sequences.contains(seq)))
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715 fixedColumns = true;
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717 fixedLeft = sg.getStartRes();
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718 fixedRight = sg.getEndRes();
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720 if ( (startres < fixedLeft && lastres >= fixedLeft)
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721 || (startres >= fixedLeft && lastres < fixedLeft)
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722 || (startres > fixedRight && lastres <=fixedRight)
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723 || (startres <= fixedRight && lastres > fixedRight))
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729 if (fixedLeft > startres)
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731 fixedRight = fixedLeft - 1;
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734 else if (fixedRight < startres)
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736 fixedLeft = fixedRight;
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743 if(av.hasHiddenColumns)
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745 fixedColumns = true;
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746 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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747 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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749 if( ( insertGap && startres>y1 && lastres<y1)
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750 || (!insertGap && startres<y2 && lastres>y2) )
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756 if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
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757 fixedRight = y2 -1;
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758 if(y1>fixedLeft && fixedLeft==-1)
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765 /*if (av.hasHiddenRows)
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767 //sg might be null as the user may only see 1 sequence
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770 sg = new SequenceGroup();
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771 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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774 SequenceGroup tmp = new SequenceGroup();
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776 //Do any of the sequences have hidden associates?
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777 for (int s = 0; s < sg.getSize(); s++)
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779 seq = sg.getSequenceAt(s);
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780 tmp.addSequence(seq, false);
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781 if (seq.getHiddenSequences() != null)
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783 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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784 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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791 // int blankColumn = -1;
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797 //If the user has selected the whole sequence, and is dragging to
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798 // the right, we can still extend the alignment and selectionGroup
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799 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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801 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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802 fixedRight = sg.getEndRes();
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805 // Is it valid with fixed columns??
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806 // Find the next gap before the end
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807 // of the visible region boundary
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808 boolean blank = false;
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809 for (fixedRight = fixedRight;
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810 fixedRight > lastres;
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814 for (int s = 0; s < sg.getSize(); s++)
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816 seq = sg.getSequenceAt(s);
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817 for (int j = 0; j < startres - lastres; j++)
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819 if (!jalview.util.Comparison.isGap(
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820 seq.getCharAt(fixedRight - j)))
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833 if(sg.getSize() == av.alignment.getHeight())
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835 //We can still insert gaps if the selectionGroup
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836 //contains all the sequences
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837 sg.setEndRes(sg.getEndRes()+startres-lastres);
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838 fixedRight = av.alignment.getWidth()+startres-lastres;
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850 else if(!insertGap)
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852 /// Are we able to delete?
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853 // ie are all columns blank?
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855 for (int s = 0; s < sg.getSize(); s++)
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857 seq = sg.getSequenceAt(s);
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859 for (int j = startres; j < lastres; j++)
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861 if (seq.getSequence().length() <= j)
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866 if (!jalview.util.Comparison.isGap(
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867 seq.getSequence().charAt(j)))
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869 // Not a gap, block edit not valid
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878 for (int i = 0; i < sg.getSize(); i++)
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880 seq = sg.getSequenceAt(i);
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884 // dragging to the right
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885 for (int j = lastres; j < startres; j++)
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887 if (fixedColumns && fixedRight != -1)
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889 insertChar(j, seq, fixedRight);
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892 insertChar(j, seq);
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897 // dragging to the left
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898 for (int j = lastres; j > startres; j--)
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900 if (fixedColumns && fixedRight != -1)
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902 deleteChar(startres, seq, fixedRight);
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906 deleteChar(startres, seq);
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912 else /////Editing a single sequence///////////
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916 // dragging to the right
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917 for (int j = lastres; j < startres; j++)
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919 if (fixedColumns && fixedRight != -1)
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921 if (sg.getStartRes() == 0
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922 && sg.getEndRes() + 1 == av.alignment.getWidth()
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923 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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925 //Single sequence edit, whole sequence selected,
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926 //extend the selection group
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927 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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928 fixedColumns = false;
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929 insertChar(j, seq);
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932 insertChar(j, seq, fixedRight);
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935 insertChar(j, seq);
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940 // dragging to the left
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941 for (int j = lastres; j > startres; j--)
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943 if (fixedColumns && fixedRight != -1)
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945 deleteChar(startres, seq, fixedRight);
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949 deleteChar(startres, seq);
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955 lastres = startres;
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956 seqCanvas.repaint();
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963 * @param j DOCUMENT ME!
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964 * @param seq DOCUMENT ME!
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966 void insertChar(int j, SequenceI seq)
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968 seq.insertCharAt(j, av.getGapCharacter());
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969 seqEditOccurred = true;
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972 void insertChar(int j, SequenceI seq, int fixedColumn)
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974 //Find the next gap before the end of the visible region boundary
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975 //If lastCol > j, theres a boundary after the gap insertion
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976 int blankColumn = fixedColumn;
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977 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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979 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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981 //Theres a space, so break and insert the gap
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986 if (blankColumn <= j)
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992 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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995 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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999 seq.deleteCharAt(blankColumn);
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1000 seq.insertCharAt(j, av.getGapCharacter());
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1001 seqEditOccurred = true;
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1004 void deleteChar(int j, SequenceI seq, int fixedColumn)
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1006 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1008 ap.alignFrame.statusBar.setText(
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1009 "End editing: Tried removing residue " + seq.getCharAt(j));
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1013 seq.deleteCharAt(j);
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1014 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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1015 seqEditOccurred = true;
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1021 * @param j DOCUMENT ME!
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1022 * @param seq DOCUMENT ME!
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1024 void deleteChar(int j, SequenceI seq)
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1026 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1028 ap.alignFrame.statusBar.setText(
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1029 "End editing: Tried removing residue " + seq.getCharAt(j));
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1033 seq.deleteCharAt(j);
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1034 seqEditOccurred = true;
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1035 seqCanvas.repaint();
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1040 * @param e DOCUMENT ME!
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1042 public void mouseEntered(MouseEvent e)
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1047 if (scrollThread != null)
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1049 scrollThread.running = false;
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1050 scrollThread = null;
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1057 * @param e DOCUMENT ME!
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1059 public void mouseExited(MouseEvent e)
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1061 if (av.getWrapAlignment())
\r
1066 if (mouseDragging)
\r
1068 scrollThread = new ScrollThread();
\r
1072 public void mouseClicked(MouseEvent evt)
\r
1075 public void mouseWheelMoved(MouseWheelEvent e)
\r
1078 /* if (mouseWheelPressed)
\r
1080 Font font = av.getFont();
\r
1081 int fontSize = font.getSize();
\r
1082 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1084 else if (fontSize > 1)
\r
1089 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1095 if (e.getWheelRotation() > 0)
\r
1096 ap.scrollUp(false);
\r
1098 ap.scrollUp(true);
\r
1108 * @param i DOCUMENT ME!
\r
1110 void editOccurred()
\r
1112 if (!seqEditOccurred)
\r
1114 ap.alignFrame.historyList.pop();
\r
1115 ap.alignFrame.updateEditMenuBar();
\r
1120 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1127 * @param evt DOCUMENT ME!
\r
1129 public void doMousePressedDefineMode(MouseEvent evt)
\r
1131 int res = findRes(evt);
\r
1132 int seq = findSeq(evt);
\r
1135 startWrapBlock=wrappedBlock;
\r
1137 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1139 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1140 "Cannot edit annotations in wrapped view.",
\r
1141 "Wrapped view - no edit",
\r
1142 JOptionPane.WARNING_MESSAGE);
\r
1146 if(seq<0 || res<0)
\r
1149 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1151 if ((sequence == null) || (res > sequence.getLength()))
\r
1156 stretchGroup = av.getSelectionGroup();
\r
1158 if (stretchGroup == null)
\r
1160 stretchGroup = av.alignment.findGroup(sequence);
\r
1162 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1163 (res < stretchGroup.getEndRes()))
\r
1165 av.setSelectionGroup(stretchGroup);
\r
1169 stretchGroup = null;
\r
1172 else if (!stretchGroup.sequences.contains(sequence) ||
\r
1173 (stretchGroup.getStartRes() > res) ||
\r
1174 (stretchGroup.getEndRes() < res))
\r
1176 stretchGroup = null;
\r
1178 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1180 if (allGroups != null)
\r
1182 for (int i = 0; i < allGroups.length; i++)
\r
1184 if ((allGroups[i].getStartRes() <= res) &&
\r
1185 (allGroups[i].getEndRes() >= res))
\r
1187 stretchGroup = allGroups[i];
\r
1188 av.setSelectionGroup(stretchGroup);
\r
1196 if (av.cursorMode)
\r
1198 seqCanvas.cursorX = findRes(evt);
\r
1199 seqCanvas.cursorY = findSeq(evt);
\r
1200 seqCanvas.repaint();
\r
1205 if (stretchGroup == null)
\r
1207 // define a new group here
\r
1208 SequenceGroup sg = new SequenceGroup();
\r
1209 sg.setStartRes(res);
\r
1210 sg.setEndRes(res);
\r
1211 sg.addSequence(sequence, false);
\r
1212 av.setSelectionGroup(sg);
\r
1213 stretchGroup = sg;
\r
1215 if (av.getConservationSelected())
\r
1217 SliderPanel.setConservationSlider(ap,
\r
1218 av.getGlobalColourScheme(), "Background");
\r
1221 if (av.getAbovePIDThreshold())
\r
1223 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1227 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1229 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
\r
1230 pop.show(this, evt.getX(), evt.getY());
\r
1232 // edit the properties of existing group
\r
1235 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1237 // Edit end res position of selected group
\r
1238 changeEndRes = true;
\r
1240 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
\r
1242 // Edit end res position of selected group
\r
1243 changeStartRes = true;
\r
1246 stretchGroup.getWidth();
\r
1248 seqCanvas.repaint();
\r
1254 * @param evt DOCUMENT ME!
\r
1256 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1258 if (stretchGroup == null)
\r
1264 if(stretchGroup.cs!=null)
\r
1266 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1268 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1270 stretchGroup.getWidth());
\r
1273 if (stretchGroup.cs.conservationApplied())
\r
1275 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1276 stretchGroup.getName());
\r
1277 stretchGroup.recalcConservation();
\r
1281 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1282 stretchGroup.getName());
\r
1285 changeEndRes = false;
\r
1286 changeStartRes = false;
\r
1287 stretchGroup = null;
\r
1288 PaintRefresher.Refresh(av.alignment);
\r
1294 * @param evt DOCUMENT ME!
\r
1296 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1298 int res = findRes(evt);
\r
1299 int y = findSeq(evt);
\r
1301 if(wrappedBlock!=startWrapBlock)
\r
1304 if (stretchGroup == null)
\r
1310 if(y > av.alignment.getHeight())
\r
1312 y = av.alignment.getHeight() -1;
\r
1314 if(res> av.alignment.getWidth())
\r
1316 res = av.alignment.getWidth()-1;
\r
1319 if (stretchGroup.getEndRes() == res)
\r
1321 // Edit end res position of selected group
\r
1322 changeEndRes = true;
\r
1324 else if (stretchGroup.getStartRes() == res)
\r
1326 // Edit start res position of selected group
\r
1327 changeStartRes = true;
\r
1330 if (res < av.getStartRes())
\r
1332 res = av.getStartRes();
\r
1337 if (res > (stretchGroup.getStartRes() - 1))
\r
1339 stretchGroup.setEndRes(res);
\r
1342 else if (changeStartRes)
\r
1344 if (res < (stretchGroup.getEndRes() + 1))
\r
1346 stretchGroup.setStartRes(res);
\r
1350 int dragDirection = 0;
\r
1354 dragDirection = 1;
\r
1356 else if (y < oldSeq)
\r
1358 dragDirection = -1;
\r
1362 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1364 // This routine ensures we don't skip any sequences, as the
\r
1365 // selection is quite slow.
\r
1366 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1368 oldSeq += dragDirection;
\r
1373 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1375 if (stretchGroup.sequences.contains(nextSeq))
\r
1377 stretchGroup.deleteSequence(seq, false);
\r
1383 stretchGroup.addSequence(seq, false);
\r
1386 stretchGroup.addSequence(nextSeq, false);
\r
1393 mouseDragging = true;
\r
1395 if (scrollThread != null)
\r
1397 scrollThread.setEvent(evt);
\r
1400 seqCanvas.repaint();
\r
1403 void scrollCanvas(MouseEvent evt)
\r
1407 if(scrollThread!=null)
\r
1409 scrollThread.running = false;
\r
1410 scrollThread = null;
\r
1412 mouseDragging = false;
\r
1416 if (scrollThread == null)
\r
1417 scrollThread = new ScrollThread();
\r
1419 mouseDragging = true;
\r
1420 scrollThread.setEvent(evt);
\r
1426 // this class allows scrolling off the bottom of the visible alignment
\r
1427 class ScrollThread extends Thread
\r
1430 boolean running = false;
\r
1432 public ScrollThread()
\r
1437 public void setEvent(MouseEvent e)
\r
1442 public void stopScrolling()
\r
1455 if (mouseDragging && (evt.getY() < 0) &&
\r
1456 (av.getStartSeq() > 0))
\r
1458 running = ap.scrollUp(true);
\r
1461 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1462 (av.alignment.getHeight() > av.getEndSeq()))
\r
1464 running = ap.scrollUp(false);
\r
1467 if (mouseDragging && (evt.getX() < 0))
\r
1469 running = ap.scrollRight(false);
\r
1471 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1473 running = ap.scrollRight(true);
\r
1481 catch (Exception ex)
\r