2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.schemes.*;
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26 import java.awt.event.*;
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28 import javax.swing.*;
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30 import java.util.Vector;
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37 * @version $Revision$
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39 public class SeqPanel extends JPanel implements MouseListener,
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40 MouseMotionListener, MouseWheelListener
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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50 protected AlignViewport av;
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52 // if character is inserted or deleted, we will need to recalculate the conservation
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53 boolean seqEditOccurred = false;
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54 ScrollThread scrollThread = null;
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55 boolean mouseDragging = false;
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56 boolean editingSeqs = false;
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57 boolean groupEditing = false;
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59 //////////////////////////////////////////
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60 /////Everything below this is for defining the boundary of the rubberband
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61 //////////////////////////////////////////
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63 boolean changeEndSeq = false;
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64 boolean changeStartSeq = false;
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65 boolean changeEndRes = false;
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66 boolean changeStartRes = false;
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67 SequenceGroup stretchGroup = null;
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68 boolean remove = false;
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70 Point lastMousePress;
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71 boolean mouseWheelPressed = false;
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72 StringBuffer keyboardNo1;
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73 StringBuffer keyboardNo2;
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75 java.net.URL linkImageURL;
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78 * Creates a new SeqPanel object.
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80 * @param avp DOCUMENT ME!
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81 * @param p DOCUMENT ME!
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83 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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85 linkImageURL = getClass().getResource("/images/link.gif");
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86 ToolTipManager.sharedInstance().registerComponent(this);
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87 ToolTipManager.sharedInstance().setInitialDelay(0);
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88 ToolTipManager.sharedInstance().setDismissDelay(10000);
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90 setBackground(Color.white);
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92 seqCanvas = new SeqCanvas(avp);
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93 setLayout(new BorderLayout());
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94 add(seqCanvas, BorderLayout.CENTER);
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100 addMouseMotionListener(this);
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101 addMouseListener(this);
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102 addMouseWheelListener(this);
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106 int startWrapBlock=-1;
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107 int wrappedBlock=-1;
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108 int findRes(MouseEvent evt)
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111 int x = evt.getX();
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113 if (av.wrapAlignment)
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116 int hgap = av.charHeight;
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117 if (av.scaleAboveWrapped)
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118 hgap += av.charHeight;
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120 int cHeight = av.getAlignment().getHeight() * av.charHeight
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121 + hgap + seqCanvas.getAnnotationHeight();
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123 int y = evt.getY();
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125 x -= seqCanvas.LABEL_WEST;
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128 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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132 wrappedBlock = y / cHeight;
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133 wrappedBlock += av.getStartRes() / cwidth;
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135 res = wrappedBlock * cwidth + x / av.getCharWidth();
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140 res = (x / av.getCharWidth()) + av.getStartRes();
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143 if(av.hasHiddenColumns)
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144 res = av.getColumnSelection().adjustForHiddenColumns(res);
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150 int findSeq(MouseEvent evt)
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153 int y = evt.getY();
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155 if (av.wrapAlignment)
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157 int hgap = av.charHeight;
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158 if (av.scaleAboveWrapped)
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159 hgap += av.charHeight;
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161 int cHeight = av.getAlignment().getHeight() * av.charHeight
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162 + hgap + seqCanvas.getAnnotationHeight();
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166 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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167 av.alignment.getHeight() -1);
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171 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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172 av.alignment.getHeight() -1);
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178 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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180 Vector allFeatures = new Vector();
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182 if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
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184 while (index < seq.getSequenceFeatures().length)
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186 SequenceFeature sf = seq.getSequenceFeatures()[index];
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187 if (sf.getBegin() <= res &&
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188 sf.getEnd() >= res)
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190 if (av.featuresDisplayed.containsKey(sf.getType()))
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192 allFeatures.addElement(sf);
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198 return allFeatures;
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205 seqEditOccurred = false;
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206 editingSeqs = false;
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207 groupEditing = false;
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208 keyboardNo1 = null;
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209 keyboardNo2 = null;
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212 void setCursorRow()
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214 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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218 void setCursorColumn()
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220 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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224 void setCursorRowAndColumn()
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226 if(keyboardNo2==null)
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228 keyboardNo2 = new StringBuffer();
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232 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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233 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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238 void setCursorPosition()
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240 SequenceI sequence =
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241 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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243 seqCanvas.cursorX = sequence.findIndex(
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244 getKeyboardNo(keyboardNo1)-1
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249 void moveCursor(int dx, int dy)
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251 seqCanvas.cursorX += dx;
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252 seqCanvas.cursorY += dy;
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256 void scrollToVisible()
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258 if (seqCanvas.cursorX < 0)
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259 seqCanvas.cursorX = 0;
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260 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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261 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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263 if (seqCanvas.cursorY < 0)
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264 seqCanvas.cursorY = 0;
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265 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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266 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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270 if(av.wrapAlignment)
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272 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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276 while (seqCanvas.cursorY < av.startSeq)
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280 while (seqCanvas.cursorY + 1 > av.endSeq)
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282 ap.scrollUp(false);
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284 if (!av.wrapAlignment)
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286 while (seqCanvas.cursorX < av.startRes)
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288 if (!ap.scrollRight(false))
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291 while (seqCanvas.cursorX > av.endRes)
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293 if (!ap.scrollRight(true))
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298 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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299 seqCanvas.cursorX, seqCanvas.cursorY);
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301 seqCanvas.repaint();
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304 void setSelectionAreaAtCursor(boolean topLeft)
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306 SequenceI sequence =
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307 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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309 if(av.getSelectionGroup()!=null)
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311 SequenceGroup sg = av.selectionGroup;
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312 //Find the top and bottom of this group
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313 int min = av.alignment.getHeight(), max = 0;
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314 for(int i=0; i<sg.getSize(false); i++)
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316 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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327 sg.setStartRes(seqCanvas.cursorX);
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328 if(sg.getEndRes()<seqCanvas.cursorX)
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329 sg.setEndRes(seqCanvas.cursorX);
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331 min = seqCanvas.cursorY;
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335 sg.setEndRes(seqCanvas.cursorX);
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336 if(sg.getStartRes()>seqCanvas.cursorX)
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337 sg.setStartRes(seqCanvas.cursorX);
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339 max = seqCanvas.cursorY+1;
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344 // Only the user can do this
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345 av.setSelectionGroup(null);
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349 // Now add any sequences between min and max
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350 sg.getSequences(false).clear();
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351 for (int i = min; i < max; i++)
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353 sg.addSequence(av.alignment.getSequenceAt(i), false);
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358 if (av.getSelectionGroup() == null)
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360 SequenceGroup sg = new SequenceGroup();
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361 sg.setStartRes(seqCanvas.cursorX);
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362 sg.setEndRes(seqCanvas.cursorX);
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363 sg.addSequence(sequence, false);
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364 av.setSelectionGroup(sg);
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371 void insertGapAtCursor(boolean group)
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373 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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374 av.alignment, HistoryItem.EDIT));
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375 groupEditing = group;
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376 startseq = seqCanvas.cursorY;
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377 lastres = seqCanvas.cursorX;
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378 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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382 void deleteGapAtCursor(boolean group)
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384 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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385 av.alignment, HistoryItem.EDIT));
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386 groupEditing = group;
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387 startseq = seqCanvas.cursorY;
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388 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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389 editSequence(false, seqCanvas.cursorX);
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393 void numberPressed(char value)
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395 if(keyboardNo1==null)
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396 keyboardNo1 = new StringBuffer();
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398 if(keyboardNo2!=null)
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399 keyboardNo2.append(value);
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401 keyboardNo1.append(value);
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404 int getKeyboardNo(StringBuffer kb)
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409 return Integer.parseInt(kb.toString());
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416 * @param evt DOCUMENT ME!
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418 public void mouseReleased(MouseEvent evt)
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420 mouseDragging = false;
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421 mouseWheelPressed = false;
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425 doMouseReleasedDefineMode(evt);
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439 * @param evt DOCUMENT ME!
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441 public void mousePressed(MouseEvent evt)
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443 lastMousePress = evt.getPoint();
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445 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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447 mouseWheelPressed = true;
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451 if (evt.isShiftDown() || evt.isAltDown() ||
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452 evt.isControlDown())
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454 if (evt.isAltDown() || evt.isControlDown())
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456 groupEditing = true;
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458 editingSeqs = true;
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462 doMousePressedDefineMode(evt);
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468 int seq = findSeq(evt);
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469 int res = findRes(evt);
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474 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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475 av.alignment, HistoryItem.EDIT));
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477 if ((seq < av.getAlignment().getHeight()) &&
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478 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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495 * @param evt DOCUMENT ME!
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497 public void mouseMoved(MouseEvent evt)
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501 // This is because MacOSX creates a mouseMoved
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502 // If control is down, other platforms will not.
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506 int res = findRes(evt);
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507 int seq = findSeq(evt);
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510 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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513 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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515 if (res > sequence.getLength())
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520 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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522 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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525 setStatusMessage(sequence, res, seq);
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527 // use aa to see if the mouse pointer is on a
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528 if (av.showSequenceFeatures)
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530 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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533 StringBuffer sbuffer = new StringBuffer("<html>");
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534 StringBuffer seqSpecific = new StringBuffer();
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536 for (int i = 0; i < features.length; i++)
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539 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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540 (features[i].getEnd() >= sequence.findPosition(res)))
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542 if(av.featuresDisplayed==null
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543 || !av.featuresDisplayed.containsKey(features[i].getType()))
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547 if (features[i].getType().equals("disulfide bond"))
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549 if (features[i].getBegin() == sequence.findPosition(res)
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550 || features[i].getEnd() == sequence.findPosition(res))
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552 if (sbuffer.length() > 6)
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553 sbuffer.append("<br>");
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554 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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555 features[i].getEnd());
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556 if (features[i].links != null)
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557 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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562 if (sbuffer.length() > 6)
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563 sbuffer.append("<br>");
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565 sbuffer.append(features[i].getType() + " " +
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566 features[i].begin);
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567 if (features[i].begin != features[i].end)
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568 sbuffer.append(" " + features[i].end);
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570 if (features[i].getDescription() != null
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571 && !features[i].description.equals(features[i].getType()))
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572 sbuffer.append("; " + features[i].getDescription());
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574 if (features[i].getValue("status") != null)
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576 sbuffer.append("; (" + features[i].getValue("status") + ")");
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578 if (features[i].links != null)
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579 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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583 else if(features[i].begin==0 && features[i].end==0)
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585 // seqSpecific.append(features[i].featureGroup+": "
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586 // + features[i].getType()+" "
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587 // +features[i].getDescription()+"<br>");
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592 if(seqSpecific.length()>0)
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593 seqSpecific.setLength(seqSpecific.length()-4);
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595 sbuffer.append(seqSpecific);
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596 sbuffer.append("</html>");
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597 if(sbuffer.length()==13) // <html></html>
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598 setToolTipText("");
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600 setToolTipText(sbuffer.toString());
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603 setToolTipText("");
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607 void setStatusMessage(SequenceI sequence, int res, int seq)
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609 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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610 sequence.getName());
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613 if (av.alignment.isNucleotide())
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615 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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618 text.append(" Nucleotide: ");
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622 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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624 text.append(" Residue: ");
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632 text.append(obj + " (" + sequence.findPosition(res) +
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636 ap.alignFrame.statusBar.setText(text.toString());
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643 * @param evt DOCUMENT ME!
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645 public void mouseDragged(MouseEvent evt)
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647 if (mouseWheelPressed)
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649 int oldWidth = av.charWidth;
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651 //Which is bigger, left-right or up-down?
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652 if (Math.abs(evt.getY() - lastMousePress.getY())
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653 > Math.abs(evt.getX() - lastMousePress.getX()))
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655 int fontSize = av.font.getSize();
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657 if (evt.getY() < lastMousePress.getY())
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661 else if (evt.getY() > lastMousePress.getY())
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669 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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670 av.charWidth = oldWidth;
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675 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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679 else if (evt.getX() > lastMousePress.getX())
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687 FontMetrics fm = getFontMetrics(av.getFont());
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688 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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690 lastMousePress = evt.getPoint();
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697 doMouseDraggedDefineMode(evt);
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701 int res = findRes(evt);
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708 if ((lastres == -1) || (lastres == res))
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713 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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715 // dragLeft, delete gap
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716 editSequence(false, res);
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719 editSequence(true, res);
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721 mouseDragging = true;
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722 if(scrollThread!=null)
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723 scrollThread.setEvent(evt);
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727 synchronized void editSequence(boolean insertGap, int startres)
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729 int fixedLeft = -1;
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730 int fixedRight = -1;
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731 boolean fixedColumns = false;
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732 SequenceGroup sg = av.getSelectionGroup();
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735 if (!groupEditing && av.hasHiddenRows)
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737 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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739 groupEditing = true;
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743 //No group, but the sequence may represent a group
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746 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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748 groupEditing = false;
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751 SequenceI seq = av.alignment.getSequenceAt(startseq);
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752 StringBuffer message = new StringBuffer();
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754 message.append("Edit group:");
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756 message.append("Edit sequence: "+seq.getName());
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759 message.append(" insert ");
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761 message.append(" delete ");
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763 message.append(Math.abs(startres-lastres)+" gaps.");
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764 ap.alignFrame.statusBar.setText(message.toString());
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767 //Are we editing within a selection group?
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769 || (sg != null && sg.getSequences(true).contains(seq)))
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771 fixedColumns = true;
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773 //sg might be null as the user may only see 1 sequence,
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774 //but the sequence represents a group
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777 sg = new SequenceGroup(null, null, false, false, false, 0,
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778 av.alignment.getWidth()-1);
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779 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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782 fixedLeft = sg.getStartRes();
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783 fixedRight = sg.getEndRes();
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785 if ( (startres < fixedLeft && lastres >= fixedLeft)
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786 || (startres >= fixedLeft && lastres < fixedLeft)
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787 || (startres > fixedRight && lastres <=fixedRight)
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788 || (startres <= fixedRight && lastres > fixedRight))
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794 if (fixedLeft > startres)
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796 fixedRight = fixedLeft - 1;
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799 else if (fixedRight < startres)
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801 fixedLeft = fixedRight;
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807 if(av.hasHiddenColumns )
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809 fixedColumns = true;
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810 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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811 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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813 if ( (insertGap && startres > y1 && lastres < y1)
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814 || (!insertGap && startres < y2 && lastres > y2))
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820 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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821 //Selection spans a hidden region
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822 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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830 fixedRight = y2 - 1;
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838 Vector vseqs = sg.getSequences(true);
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839 int g, groupSize = vseqs.size();
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840 SequenceI[] groupSeqs = new SequenceI[groupSize];
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841 for (g = 0; g < groupSeqs.length; g++)
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842 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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847 //If the user has selected the whole sequence, and is dragging to
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848 // the right, we can still extend the alignment and selectionGroup
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849 if( sg.getStartRes() == 0
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850 && sg.getEndRes() == fixedRight
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851 && sg.getEndRes() == av.alignment.getWidth()-1
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854 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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855 fixedRight = sg.getEndRes();
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858 // Is it valid with fixed columns??
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859 // Find the next gap before the end
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860 // of the visible region boundary
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861 boolean blank = false;
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862 for (fixedRight = fixedRight;
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863 fixedRight > lastres;
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868 for (g = 0; g < groupSize; g++)
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870 for (int j = 0; j < startres - lastres; j++)
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872 if (!jalview.util.Comparison.isGap(
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873 groupSeqs[g].getCharAt(fixedRight - j)))
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886 if(sg.getSize(false) == av.alignment.getHeight() )
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888 if((av.hasHiddenColumns
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889 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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895 int alWidth = av.alignment.getWidth();
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896 if(av.hasHiddenRows)
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898 int hwidth = av.alignment.getHiddenSequences().getWidth();
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902 //We can still insert gaps if the selectionGroup
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903 //contains all the sequences
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904 sg.setEndRes(sg.getEndRes()+startres-lastres);
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905 fixedRight = alWidth+startres-lastres;
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917 else if(!insertGap)
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919 /// Are we able to delete?
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920 // ie are all columns blank?
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922 for (g = 0; g < groupSize; g++)
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924 for (int j = startres; j < lastres; j++)
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926 if (groupSeqs[g].getLength() <= j)
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931 if (!jalview.util.Comparison.isGap(
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932 groupSeqs[g].getCharAt(j)))
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934 // Not a gap, block edit not valid
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943 for (g = 0; g < groupSize; g++)
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947 // dragging to the right
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948 for (int j = lastres; j < startres; j++)
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950 if (fixedColumns && fixedRight != -1)
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952 insertChar(j, groupSeqs[g], fixedRight);
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955 insertChar(j, groupSeqs[g]);
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960 // dragging to the left
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961 for (int j = lastres; j > startres; j--)
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963 if (fixedColumns && fixedRight != -1)
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965 deleteChar(startres, groupSeqs[g], fixedRight);
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969 deleteChar(startres, groupSeqs[g]);
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975 else /////Editing a single sequence///////////
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979 // dragging to the right
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980 for (int j = lastres; j < startres; j++)
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982 if (fixedColumns && fixedRight != -1)
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984 insertChar(j, seq, fixedRight);
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987 insertChar(j, seq);
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992 // dragging to the left
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993 for (int j = lastres; j > startres; j--)
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995 if (fixedColumns && fixedRight != -1)
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997 deleteChar(startres, seq, fixedRight);
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1001 deleteChar(startres, seq);
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1007 lastres = startres;
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1008 seqCanvas.repaint();
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1015 * @param j DOCUMENT ME!
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1016 * @param seq DOCUMENT ME!
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1018 void insertChar(int j, SequenceI seq)
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1020 seq.insertCharAt(j, av.getGapCharacter());
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1021 seqEditOccurred = true;
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1024 void insertChar(int j, SequenceI seq, int fixedColumn)
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1026 //Find the next gap before the end of the visible region boundary
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1027 //If lastCol > j, theres a boundary after the gap insertion
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1028 int blankColumn = fixedColumn;
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1029 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1031 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1033 //Theres a space, so break and insert the gap
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1038 if (blankColumn <= j)
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1040 blankColumn = fixedColumn;
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1045 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1048 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
\r
1052 seq.deleteCharAt(blankColumn);
\r
1053 seq.insertCharAt(j, av.getGapCharacter());
\r
1054 seqEditOccurred = true;
\r
1057 void deleteChar(int j, SequenceI seq, int fixedColumn)
\r
1059 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1061 ap.alignFrame.statusBar.setText(
\r
1062 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1066 seq.deleteCharAt(j);
\r
1067 seq.insertCharAt(fixedColumn, av.getGapCharacter());
\r
1068 seqEditOccurred = true;
\r
1074 * @param j DOCUMENT ME!
\r
1075 * @param seq DOCUMENT ME!
\r
1077 void deleteChar(int j, SequenceI seq)
\r
1079 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1081 ap.alignFrame.statusBar.setText(
\r
1082 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1086 seq.deleteCharAt(j);
\r
1087 seqEditOccurred = true;
\r
1088 seqCanvas.repaint();
\r
1093 * @param e DOCUMENT ME!
\r
1095 public void mouseEntered(MouseEvent e)
\r
1100 if (scrollThread != null)
\r
1102 scrollThread.running = false;
\r
1103 scrollThread = null;
\r
1110 * @param e DOCUMENT ME!
\r
1112 public void mouseExited(MouseEvent e)
\r
1114 if (av.getWrapAlignment())
\r
1119 if (mouseDragging)
\r
1121 scrollThread = new ScrollThread();
\r
1125 public void mouseClicked(MouseEvent evt)
\r
1128 public void mouseWheelMoved(MouseWheelEvent e)
\r
1131 /* if (mouseWheelPressed)
\r
1133 Font font = av.getFont();
\r
1134 int fontSize = font.getSize();
\r
1135 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1137 else if (fontSize > 1)
\r
1142 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1148 if (e.getWheelRotation() > 0)
\r
1149 ap.scrollUp(false);
\r
1151 ap.scrollUp(true);
\r
1161 * @param i DOCUMENT ME!
\r
1163 void editOccurred()
\r
1165 if (!seqEditOccurred)
\r
1167 ap.alignFrame.historyList.pop();
\r
1168 ap.alignFrame.updateEditMenuBar();
\r
1173 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1180 * @param evt DOCUMENT ME!
\r
1182 public void doMousePressedDefineMode(MouseEvent evt)
\r
1184 int res = findRes(evt);
\r
1185 int seq = findSeq(evt);
\r
1188 startWrapBlock=wrappedBlock;
\r
1190 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1192 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1193 "Cannot edit annotations in wrapped view.",
\r
1194 "Wrapped view - no edit",
\r
1195 JOptionPane.WARNING_MESSAGE);
\r
1199 if(seq<0 || res<0)
\r
1202 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1204 if ((sequence == null) || (res > sequence.getLength()))
\r
1209 stretchGroup = av.getSelectionGroup();
\r
1211 if (stretchGroup == null)
\r
1213 stretchGroup = av.alignment.findGroup(sequence);
\r
1215 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1216 (res < stretchGroup.getEndRes()))
\r
1218 av.setSelectionGroup(stretchGroup);
\r
1222 stretchGroup = null;
\r
1225 else if (!stretchGroup.getSequences(false).contains(sequence) ||
\r
1226 (stretchGroup.getStartRes() > res) ||
\r
1227 (stretchGroup.getEndRes() < res))
\r
1229 stretchGroup = null;
\r
1231 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1233 if (allGroups != null)
\r
1235 for (int i = 0; i < allGroups.length; i++)
\r
1237 if ((allGroups[i].getStartRes() <= res) &&
\r
1238 (allGroups[i].getEndRes() >= res))
\r
1240 stretchGroup = allGroups[i];
\r
1246 av.setSelectionGroup(stretchGroup);
\r
1251 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1253 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1254 sequence.findPosition(res));
\r
1255 Vector links = new Vector();
\r
1256 for (int i = 0; i < allFeatures.size(); i++)
\r
1258 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1259 if (sf.links != null)
\r
1261 for (int j = 0; j < sf.links.size(); j++)
\r
1263 links.addElement(sf.links.elementAt(j));
\r
1268 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1269 pop.show(this, evt.getX(), evt.getY());
\r
1273 if (av.cursorMode)
\r
1275 seqCanvas.cursorX = findRes(evt);
\r
1276 seqCanvas.cursorY = findSeq(evt);
\r
1277 seqCanvas.repaint();
\r
1281 if (stretchGroup == null)
\r
1283 //Only if left mouse button do we want to change group sizes
\r
1285 // define a new group here
\r
1286 SequenceGroup sg = new SequenceGroup();
\r
1287 sg.setStartRes(res);
\r
1288 sg.setEndRes(res);
\r
1289 sg.addSequence(sequence, false);
\r
1290 av.setSelectionGroup(sg);
\r
1291 stretchGroup = sg;
\r
1293 if (av.getConservationSelected())
\r
1295 SliderPanel.setConservationSlider(ap,
\r
1296 av.getGlobalColourScheme(),
\r
1300 if (av.getAbovePIDThreshold())
\r
1302 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1305 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1307 // Edit end res position of selected group
\r
1308 changeEndRes = true;
\r
1310 else if ( (stretchGroup != null) &&
\r
1311 (stretchGroup.getStartRes() == res))
\r
1313 // Edit end res position of selected group
\r
1314 changeStartRes = true;
\r
1316 stretchGroup.getWidth();
\r
1319 seqCanvas.repaint();
\r
1325 * @param evt DOCUMENT ME!
\r
1327 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1329 if (stretchGroup == null)
\r
1335 if(stretchGroup.cs!=null)
\r
1337 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1339 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1340 stretchGroup.getSequences(true),
\r
1341 stretchGroup.getWidth());
\r
1344 if (stretchGroup.cs.conservationApplied())
\r
1346 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1347 stretchGroup.getName());
\r
1348 stretchGroup.recalcConservation();
\r
1352 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1353 stretchGroup.getName());
\r
1356 changeEndRes = false;
\r
1357 changeStartRes = false;
\r
1358 stretchGroup = null;
\r
1360 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1366 * @param evt DOCUMENT ME!
\r
1368 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1370 int res = findRes(evt);
\r
1371 int y = findSeq(evt);
\r
1373 if(wrappedBlock!=startWrapBlock)
\r
1376 if (stretchGroup == null)
\r
1381 if(res> av.alignment.getWidth())
\r
1383 res = av.alignment.getWidth()-1;
\r
1386 if (stretchGroup.getEndRes() == res)
\r
1388 // Edit end res position of selected group
\r
1389 changeEndRes = true;
\r
1391 else if (stretchGroup.getStartRes() == res)
\r
1393 // Edit start res position of selected group
\r
1394 changeStartRes = true;
\r
1397 if (res < av.getStartRes())
\r
1399 res = av.getStartRes();
\r
1404 if (res > (stretchGroup.getStartRes() - 1))
\r
1406 stretchGroup.setEndRes(res);
\r
1409 else if (changeStartRes)
\r
1411 if (res < (stretchGroup.getEndRes() + 1))
\r
1413 stretchGroup.setStartRes(res);
\r
1417 int dragDirection = 0;
\r
1421 dragDirection = 1;
\r
1423 else if (y < oldSeq)
\r
1425 dragDirection = -1;
\r
1429 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1431 // This routine ensures we don't skip any sequences, as the
\r
1432 // selection is quite slow.
\r
1433 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1435 oldSeq += dragDirection;
\r
1440 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1442 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1444 stretchGroup.deleteSequence(seq, false);
\r
1450 stretchGroup.addSequence(seq, false);
\r
1453 stretchGroup.addSequence(nextSeq, false);
\r
1460 mouseDragging = true;
\r
1462 if (scrollThread != null)
\r
1464 scrollThread.setEvent(evt);
\r
1467 seqCanvas.repaint();
\r
1470 void scrollCanvas(MouseEvent evt)
\r
1474 if(scrollThread!=null)
\r
1476 scrollThread.running = false;
\r
1477 scrollThread = null;
\r
1479 mouseDragging = false;
\r
1483 if (scrollThread == null)
\r
1484 scrollThread = new ScrollThread();
\r
1486 mouseDragging = true;
\r
1487 scrollThread.setEvent(evt);
\r
1493 // this class allows scrolling off the bottom of the visible alignment
\r
1494 class ScrollThread extends Thread
\r
1497 boolean running = false;
\r
1499 public ScrollThread()
\r
1504 public void setEvent(MouseEvent e)
\r
1509 public void stopScrolling()
\r
1522 if (mouseDragging && (evt.getY() < 0) &&
\r
1523 (av.getStartSeq() > 0))
\r
1525 running = ap.scrollUp(true);
\r
1528 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1529 (av.alignment.getHeight() > av.getEndSeq()))
\r
1531 running = ap.scrollUp(false);
\r
1534 if (mouseDragging && (evt.getX() < 0))
\r
1536 running = ap.scrollRight(false);
\r
1538 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1540 running = ap.scrollRight(true);
\r
1548 catch (Exception ex)
\r