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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30 import java.util.Vector;
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37 * @version $Revision$
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39 public class SeqPanel extends JPanel implements MouseListener,
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40 MouseMotionListener, MouseWheelListener
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43 /** DOCUMENT ME!! */
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44 public SeqCanvas seqCanvas;
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46 /** DOCUMENT ME!! */
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47 public AlignmentPanel ap;
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48 protected int lastres;
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49 protected int startseq;
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50 protected AlignViewport av;
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52 // if character is inserted or deleted, we will need to recalculate the conservation
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53 boolean seqEditOccurred = false;
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54 ScrollThread scrollThread = null;
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55 boolean mouseDragging = false;
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56 boolean editingSeqs = false;
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57 boolean groupEditing = false;
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59 //////////////////////////////////////////
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60 /////Everything below this is for defining the boundary of the rubberband
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61 //////////////////////////////////////////
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63 boolean changeEndSeq = false;
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64 boolean changeStartSeq = false;
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65 boolean changeEndRes = false;
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66 boolean changeStartRes = false;
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67 SequenceGroup stretchGroup = null;
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68 boolean remove = false;
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70 Point lastMousePress;
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71 boolean mouseWheelPressed = false;
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72 StringBuffer keyboardNo1;
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73 StringBuffer keyboardNo2;
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75 java.net.URL linkImageURL;
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78 * Creates a new SeqPanel object.
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80 * @param avp DOCUMENT ME!
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81 * @param p DOCUMENT ME!
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83 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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85 linkImageURL = getClass().getResource("/images/link.gif");
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86 ToolTipManager.sharedInstance().registerComponent(this);
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87 ToolTipManager.sharedInstance().setInitialDelay(0);
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88 ToolTipManager.sharedInstance().setDismissDelay(10000);
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90 setBackground(Color.white);
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92 seqCanvas = new SeqCanvas(avp);
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93 setLayout(new BorderLayout());
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94 add(seqCanvas, BorderLayout.CENTER);
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100 addMouseMotionListener(this);
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101 addMouseListener(this);
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102 addMouseWheelListener(this);
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106 int startWrapBlock=-1;
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107 int wrappedBlock=-1;
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108 int findRes(MouseEvent evt)
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111 int x = evt.getX();
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113 if (av.wrapAlignment)
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116 int hgap = av.charHeight;
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117 if (av.scaleAboveWrapped)
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118 hgap += av.charHeight;
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120 int cHeight = av.getAlignment().getHeight() * av.charHeight
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121 + hgap + seqCanvas.getAnnotationHeight();
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123 int y = evt.getY();
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125 x -= seqCanvas.LABEL_WEST;
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128 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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130 wrappedBlock = y / cHeight;
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131 wrappedBlock += av.getStartRes() / cwidth;
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133 res = wrappedBlock * cwidth + x / av.getCharWidth();
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138 res = (x / av.getCharWidth()) + av.getStartRes();
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141 if(av.hasHiddenColumns)
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142 res = av.getColumnSelection().adjustForHiddenColumns(res);
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148 int findSeq(MouseEvent evt)
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152 int y = evt.getY();
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154 if (av.wrapAlignment)
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156 int hgap = av.charHeight;
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157 if (av.scaleAboveWrapped)
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158 hgap += av.charHeight;
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160 int cHeight = av.getAlignment().getHeight() * av.charHeight
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161 + hgap + seqCanvas.getAnnotationHeight();
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165 seq = ( (y % cHeight) / av.getCharHeight());
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169 seq = (y / av.getCharHeight()) + av.getStartSeq();
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175 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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177 Vector allFeatures = new Vector();
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179 if(seq.getSequenceFeatures()!=null)
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181 while (index < seq.getSequenceFeatures().length)
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183 SequenceFeature sf = seq.getSequenceFeatures()[index];
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184 if (sf.getBegin() <= res &&
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185 sf.getEnd() >= res)
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187 if (av.featuresDisplayed.containsKey(sf.getType()))
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189 allFeatures.addElement(sf);
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195 return allFeatures;
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202 seqEditOccurred = false;
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203 editingSeqs = false;
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204 groupEditing = false;
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205 keyboardNo1 = null;
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206 keyboardNo2 = null;
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209 void setCursorRow()
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211 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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215 void setCursorColumn()
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217 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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221 void setCursorRowAndColumn()
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223 if(keyboardNo2==null)
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225 keyboardNo2 = new StringBuffer();
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229 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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230 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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235 void setCursorPosition()
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237 SequenceI sequence =
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238 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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240 seqCanvas.cursorX = sequence.findIndex(
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241 getKeyboardNo(keyboardNo1)-1
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246 void moveCursor(int dx, int dy)
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248 seqCanvas.cursorX += dx;
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249 seqCanvas.cursorY += dy;
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253 void scrollToVisible()
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255 if (seqCanvas.cursorX < 0)
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256 seqCanvas.cursorX = 0;
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257 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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258 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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260 if (seqCanvas.cursorY < 0)
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261 seqCanvas.cursorY = 0;
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262 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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263 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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267 if(av.wrapAlignment)
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269 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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273 while (seqCanvas.cursorY < av.startSeq)
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277 while (seqCanvas.cursorY + 1 > av.endSeq)
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279 ap.scrollUp(false);
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281 if (!av.wrapAlignment)
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283 while (seqCanvas.cursorX < av.startRes)
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285 if (!ap.scrollRight(false))
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288 while (seqCanvas.cursorX > av.endRes)
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290 if (!ap.scrollRight(true))
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295 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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296 seqCanvas.cursorX, seqCanvas.cursorY);
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298 seqCanvas.repaint();
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301 void setSelectionAreaAtCursor(boolean topLeft)
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303 SequenceI sequence =
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304 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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306 if(av.getSelectionGroup()!=null)
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308 SequenceGroup sg = av.selectionGroup;
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309 //Find the top and bottom of this group
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310 int min = av.alignment.getHeight(), max = 0;
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311 for(int i=0; i<sg.getSize(); i++)
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313 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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324 sg.setStartRes(seqCanvas.cursorX);
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325 if(sg.getEndRes()<seqCanvas.cursorX)
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326 sg.setEndRes(seqCanvas.cursorX);
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328 min = seqCanvas.cursorY;
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332 sg.setEndRes(seqCanvas.cursorX);
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333 if(sg.getStartRes()>seqCanvas.cursorX)
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334 sg.setStartRes(seqCanvas.cursorX);
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336 max = seqCanvas.cursorY+1;
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341 // Only the user can do this
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342 av.setSelectionGroup(null);
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346 // Now add any sequences between min and max
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347 sg.sequences.clear();
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348 for (int i = min; i < max; i++)
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350 sg.addSequence(av.alignment.getSequenceAt(i), false);
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355 if (av.getSelectionGroup() == null)
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357 SequenceGroup sg = new SequenceGroup();
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358 sg.setStartRes(seqCanvas.cursorX);
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359 sg.setEndRes(seqCanvas.cursorX);
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360 sg.addSequence(sequence, false);
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361 av.setSelectionGroup(sg);
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368 void insertGapAtCursor(boolean group)
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370 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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371 av.alignment, HistoryItem.EDIT));
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372 groupEditing = group;
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373 startseq = seqCanvas.cursorY;
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374 lastres = seqCanvas.cursorX;
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375 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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379 void deleteGapAtCursor(boolean group)
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381 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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382 av.alignment, HistoryItem.EDIT));
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383 groupEditing = group;
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384 startseq = seqCanvas.cursorY;
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385 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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386 editSequence(false, seqCanvas.cursorX);
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390 void numberPressed(char value)
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392 if(keyboardNo1==null)
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393 keyboardNo1 = new StringBuffer();
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395 if(keyboardNo2!=null)
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396 keyboardNo2.append(value);
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398 keyboardNo1.append(value);
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401 int getKeyboardNo(StringBuffer kb)
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406 return Integer.parseInt(kb.toString());
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413 * @param evt DOCUMENT ME!
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415 public void mouseReleased(MouseEvent evt)
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417 mouseDragging = false;
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418 mouseWheelPressed = false;
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422 doMouseReleasedDefineMode(evt);
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437 * @param evt DOCUMENT ME!
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439 public void mousePressed(MouseEvent evt)
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441 lastMousePress = evt.getPoint();
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443 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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445 mouseWheelPressed = true;
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449 if (evt.isShiftDown() || evt.isAltDown() ||
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450 evt.isControlDown())
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452 if (evt.isAltDown() || evt.isControlDown())
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454 groupEditing = true;
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456 editingSeqs = true;
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460 doMousePressedDefineMode(evt);
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466 int seq = findSeq(evt);
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467 int res = findRes(evt);
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472 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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473 av.alignment, HistoryItem.EDIT));
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475 if ((seq < av.getAlignment().getHeight()) &&
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476 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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493 * @param evt DOCUMENT ME!
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495 public void mouseMoved(MouseEvent evt)
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499 // This is because MacOSX creates a mouseMoved
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500 // If control is down, other platforms will not.
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504 int res = findRes(evt);
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505 int seq = findSeq(evt);
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508 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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511 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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513 if (res > sequence.getLength())
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518 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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520 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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523 setStatusMessage(sequence, res, seq);
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525 // use aa to see if the mouse pointer is on a
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526 if (av.showSequenceFeatures)
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528 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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531 StringBuffer sbuffer = new StringBuffer("<html>");
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532 StringBuffer seqSpecific = new StringBuffer();
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534 for (int i = 0; i < features.length; i++)
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537 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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538 (features[i].getEnd() >= sequence.findPosition(res)))
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540 if(av.featuresDisplayed==null
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541 || !av.featuresDisplayed.containsKey(features[i].getType()))
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545 if (features[i].getType().equals("disulfide bond"))
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547 if (features[i].getBegin() == sequence.findPosition(res)
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548 || features[i].getEnd() == sequence.findPosition(res))
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550 if (sbuffer.length() > 6)
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551 sbuffer.append("<br>");
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552 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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553 features[i].getEnd());
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554 if (features[i].links != null)
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555 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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560 if (sbuffer.length() > 6)
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561 sbuffer.append("<br>");
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563 sbuffer.append(features[i].getType() + " " +
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564 features[i].begin);
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565 if (features[i].begin != features[i].end)
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566 sbuffer.append(" " + features[i].end);
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568 if (features[i].getDescription() != null
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569 && !features[i].description.equals(features[i].getType()))
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570 sbuffer.append("; " + features[i].getDescription());
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572 if (features[i].getValue("status") != null)
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574 sbuffer.append("; (" + features[i].getValue("status") + ")");
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576 if (features[i].links != null)
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577 sbuffer.append(" <img src=\"" + linkImageURL + "\">");
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581 else if(features[i].begin==0 && features[i].end==0)
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583 // seqSpecific.append(features[i].featureGroup+": "
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584 // + features[i].getType()+" "
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585 // +features[i].getDescription()+"<br>");
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590 if(seqSpecific.length()>0)
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591 seqSpecific.setLength(seqSpecific.length()-4);
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593 sbuffer.append(seqSpecific);
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594 sbuffer.append("</html>");
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595 if(sbuffer.length()==13) // <html></html>
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596 setToolTipText("");
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598 setToolTipText(sbuffer.toString());
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601 setToolTipText("");
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605 void setStatusMessage(SequenceI sequence, int res, int seq)
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607 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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608 sequence.getName());
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611 if (av.alignment.isNucleotide())
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613 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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616 text.append(" Nucleotide: ");
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620 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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622 text.append(" Residue: ");
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630 text.append(obj + " (" + sequence.findPosition(res) +
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634 ap.alignFrame.statusBar.setText(text.toString());
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641 * @param evt DOCUMENT ME!
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643 public void mouseDragged(MouseEvent evt)
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645 if (mouseWheelPressed)
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647 int oldWidth = av.charWidth;
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649 //Which is bigger, left-right or up-down?
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650 if (Math.abs(evt.getY() - lastMousePress.getY())
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651 > Math.abs(evt.getX() - lastMousePress.getX()))
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653 int fontSize = av.font.getSize();
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655 if (evt.getY() < lastMousePress.getY())
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659 else if (evt.getY() > lastMousePress.getY())
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667 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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668 av.charWidth = oldWidth;
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673 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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677 else if (evt.getX() > lastMousePress.getX())
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685 FontMetrics fm = getFontMetrics(av.getFont());
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686 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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688 lastMousePress = evt.getPoint();
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695 doMouseDraggedDefineMode(evt);
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699 int res = findRes(evt);
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706 if ((lastres == -1) || (lastres == res))
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711 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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713 // dragLeft, delete gap
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714 editSequence(false, res);
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717 editSequence(true, res);
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719 mouseDragging = true;
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720 if(scrollThread!=null)
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721 scrollThread.setEvent(evt);
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725 synchronized void editSequence(boolean insertGap, int startres)
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727 int fixedLeft = -1;
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728 int fixedRight = -1;
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729 boolean fixedColumns = false;
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730 SequenceGroup sg = av.getSelectionGroup();
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732 if(groupEditing && sg==null)
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735 if (!groupEditing && av.hasHiddenRows)
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737 //This needs to check all the sequences in a group edit,m
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738 // not just the startseq
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739 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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741 groupEditing = true;
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745 SequenceI seq = av.alignment.getSequenceAt(startseq);
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746 StringBuffer message = new StringBuffer();
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748 message.append("Edit group:");
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750 message.append("Edit sequence: "+seq.getName());
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753 message.append(" insert ");
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755 message.append(" delete ");
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757 message.append(Math.abs(startres-lastres)+" gaps.");
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758 ap.alignFrame.statusBar.setText(message.toString());
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761 //Are we editing within a selection group?
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763 || (sg != null && sg.sequences.contains(seq)))
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765 fixedColumns = true;
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767 fixedLeft = sg.getStartRes();
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768 fixedRight = sg.getEndRes();
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770 if ( (startres < fixedLeft && lastres >= fixedLeft)
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771 || (startres >= fixedLeft && lastres < fixedLeft)
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772 || (startres > fixedRight && lastres <=fixedRight)
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773 || (startres <= fixedRight && lastres > fixedRight))
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779 if (fixedLeft > startres)
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781 fixedRight = fixedLeft - 1;
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784 else if (fixedRight < startres)
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786 fixedLeft = fixedRight;
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793 if(av.hasHiddenColumns)
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795 fixedColumns = true;
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796 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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797 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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799 if( ( insertGap && startres>y1 && lastres<y1)
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800 || (!insertGap && startres<y2 && lastres>y2) )
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806 if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
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807 fixedRight = y2 -1;
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808 if(y1>fixedLeft && fixedLeft==-1)
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815 /*if (av.hasHiddenRows)
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817 //sg might be null as the user may only see 1 sequence
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820 sg = new SequenceGroup();
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821 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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824 SequenceGroup tmp = new SequenceGroup();
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826 //Do any of the sequences have hidden associates?
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827 for (int s = 0; s < sg.getSize(); s++)
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829 seq = sg.getSequenceAt(s);
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830 tmp.addSequence(seq, false);
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831 if (seq.getHiddenSequences() != null)
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833 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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834 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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841 // int blankColumn = -1;
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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 && sg.getEndRes() + 1 == av.alignment.getWidth())
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851 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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852 fixedRight = sg.getEndRes();
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855 // Is it valid with fixed columns??
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856 // Find the next gap before the end
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857 // of the visible region boundary
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858 boolean blank = false;
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859 for (fixedRight = fixedRight;
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860 fixedRight > lastres;
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864 for (int s = 0; s < sg.getSize(); s++)
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866 seq = sg.getSequenceAt(s);
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867 for (int j = 0; j < startres - lastres; j++)
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869 if (!jalview.util.Comparison.isGap(
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870 seq.getCharAt(fixedRight - j)))
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883 if(sg.getSize() == av.alignment.getHeight())
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885 //We can still insert gaps if the selectionGroup
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886 //contains all the sequences
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887 sg.setEndRes(sg.getEndRes()+startres-lastres);
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888 fixedRight = av.alignment.getWidth()+startres-lastres;
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900 else if(!insertGap)
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902 /// Are we able to delete?
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903 // ie are all columns blank?
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905 for (int s = 0; s < sg.getSize(); s++)
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907 seq = sg.getSequenceAt(s);
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909 for (int j = startres; j < lastres; j++)
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911 if (seq.getSequence().length() <= j)
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916 if (!jalview.util.Comparison.isGap(
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917 seq.getSequence().charAt(j)))
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919 // Not a gap, block edit not valid
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928 for (int i = 0; i < sg.getSize(); i++)
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930 seq = sg.getSequenceAt(i);
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934 // dragging to the right
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935 for (int j = lastres; j < startres; j++)
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937 if (fixedColumns && fixedRight != -1)
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939 insertChar(j, seq, fixedRight);
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942 insertChar(j, seq);
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947 // dragging to the left
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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 deleteChar(startres, seq, fixedRight);
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956 deleteChar(startres, seq);
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962 else /////Editing a single sequence///////////
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966 // dragging to the right
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967 for (int j = lastres; j < startres; j++)
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969 if (fixedColumns && fixedRight != -1)
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971 if (sg.getStartRes() == 0
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972 && sg.getEndRes() + 1 == av.alignment.getWidth()
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973 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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975 //Single sequence edit, whole sequence selected,
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976 //extend the selection group
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977 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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978 fixedColumns = false;
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979 insertChar(j, seq);
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982 insertChar(j, seq, fixedRight);
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985 insertChar(j, seq);
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990 // dragging to the left
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991 for (int j = lastres; j > startres; j--)
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993 if (fixedColumns && fixedRight != -1)
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995 deleteChar(startres, seq, fixedRight);
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999 deleteChar(startres, seq);
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1005 lastres = startres;
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1006 seqCanvas.repaint();
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1013 * @param j DOCUMENT ME!
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1014 * @param seq DOCUMENT ME!
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1016 void insertChar(int j, SequenceI seq)
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1018 seq.insertCharAt(j, av.getGapCharacter());
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1019 seqEditOccurred = true;
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1022 void insertChar(int j, SequenceI seq, int fixedColumn)
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1024 //Find the next gap before the end of the visible region boundary
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1025 //If lastCol > j, theres a boundary after the gap insertion
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1026 int blankColumn = fixedColumn;
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1027 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1029 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1031 //Theres a space, so break and insert the gap
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1036 if (blankColumn <= j)
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1042 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1045 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
\r
1049 seq.deleteCharAt(blankColumn);
\r
1050 seq.insertCharAt(j, av.getGapCharacter());
\r
1051 seqEditOccurred = true;
\r
1054 void deleteChar(int j, SequenceI seq, int fixedColumn)
\r
1056 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1058 ap.alignFrame.statusBar.setText(
\r
1059 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1063 seq.deleteCharAt(j);
\r
1064 seq.insertCharAt(fixedColumn, av.getGapCharacter());
\r
1065 seqEditOccurred = true;
\r
1071 * @param j DOCUMENT ME!
\r
1072 * @param seq DOCUMENT ME!
\r
1074 void deleteChar(int j, SequenceI seq)
\r
1076 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1078 ap.alignFrame.statusBar.setText(
\r
1079 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1083 seq.deleteCharAt(j);
\r
1084 seqEditOccurred = true;
\r
1085 seqCanvas.repaint();
\r
1090 * @param e DOCUMENT ME!
\r
1092 public void mouseEntered(MouseEvent e)
\r
1097 if (scrollThread != null)
\r
1099 scrollThread.running = false;
\r
1100 scrollThread = null;
\r
1107 * @param e DOCUMENT ME!
\r
1109 public void mouseExited(MouseEvent e)
\r
1111 if (av.getWrapAlignment())
\r
1116 if (mouseDragging)
\r
1118 scrollThread = new ScrollThread();
\r
1122 public void mouseClicked(MouseEvent evt)
\r
1125 public void mouseWheelMoved(MouseWheelEvent e)
\r
1128 /* if (mouseWheelPressed)
\r
1130 Font font = av.getFont();
\r
1131 int fontSize = font.getSize();
\r
1132 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1134 else if (fontSize > 1)
\r
1139 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1145 if (e.getWheelRotation() > 0)
\r
1146 ap.scrollUp(false);
\r
1148 ap.scrollUp(true);
\r
1158 * @param i DOCUMENT ME!
\r
1160 void editOccurred()
\r
1162 if (!seqEditOccurred)
\r
1164 ap.alignFrame.historyList.pop();
\r
1165 ap.alignFrame.updateEditMenuBar();
\r
1170 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1177 * @param evt DOCUMENT ME!
\r
1179 public void doMousePressedDefineMode(MouseEvent evt)
\r
1181 int res = findRes(evt);
\r
1182 int seq = findSeq(evt);
\r
1185 startWrapBlock=wrappedBlock;
\r
1187 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1189 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1190 "Cannot edit annotations in wrapped view.",
\r
1191 "Wrapped view - no edit",
\r
1192 JOptionPane.WARNING_MESSAGE);
\r
1196 if(seq<0 || res<0)
\r
1199 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1201 if ((sequence == null) || (res > sequence.getLength()))
\r
1206 stretchGroup = av.getSelectionGroup();
\r
1208 if (stretchGroup == null)
\r
1210 stretchGroup = av.alignment.findGroup(sequence);
\r
1212 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1213 (res < stretchGroup.getEndRes()))
\r
1215 av.setSelectionGroup(stretchGroup);
\r
1219 stretchGroup = null;
\r
1222 else if (!stretchGroup.sequences.contains(sequence) ||
\r
1223 (stretchGroup.getStartRes() > res) ||
\r
1224 (stretchGroup.getEndRes() < res))
\r
1226 stretchGroup = null;
\r
1228 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1230 if (allGroups != null)
\r
1232 for (int i = 0; i < allGroups.length; i++)
\r
1234 if ((allGroups[i].getStartRes() <= res) &&
\r
1235 (allGroups[i].getEndRes() >= res))
\r
1237 stretchGroup = allGroups[i];
\r
1243 av.setSelectionGroup(stretchGroup);
\r
1247 if (av.cursorMode)
\r
1249 seqCanvas.cursorX = findRes(evt);
\r
1250 seqCanvas.cursorY = findSeq(evt);
\r
1251 seqCanvas.repaint();
\r
1256 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1258 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1259 sequence.findPosition(res));
\r
1260 Vector links = new Vector();;
\r
1261 for (int i = 0; i < allFeatures.size(); i++)
\r
1263 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1264 if (sf.links != null)
\r
1266 for (int j = 0; j < sf.links.size(); j++)
\r
1268 links.addElement(sf.links.elementAt(j));
\r
1274 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1275 pop.show(this, evt.getX(), evt.getY());
\r
1277 else if (stretchGroup == null)
\r
1279 //Only if left mouse button do we want to change group sizes
\r
1281 // define a new group here
\r
1282 SequenceGroup sg = new SequenceGroup();
\r
1283 sg.setStartRes(res);
\r
1284 sg.setEndRes(res);
\r
1285 sg.addSequence(sequence, false);
\r
1286 av.setSelectionGroup(sg);
\r
1287 stretchGroup = sg;
\r
1289 if (av.getConservationSelected())
\r
1291 SliderPanel.setConservationSlider(ap,
\r
1292 av.getGlobalColourScheme(),
\r
1296 if (av.getAbovePIDThreshold())
\r
1298 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1301 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1303 // Edit end res position of selected group
\r
1304 changeEndRes = true;
\r
1306 else if ( (stretchGroup != null) &&
\r
1307 (stretchGroup.getStartRes() == res))
\r
1309 // Edit end res position of selected group
\r
1310 changeStartRes = true;
\r
1312 stretchGroup.getWidth();
\r
1315 seqCanvas.repaint();
\r
1321 * @param evt DOCUMENT ME!
\r
1323 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1325 if (stretchGroup == null)
\r
1331 if(stretchGroup.cs!=null)
\r
1333 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1335 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1337 stretchGroup.getWidth());
\r
1340 if (stretchGroup.cs.conservationApplied())
\r
1342 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1343 stretchGroup.getName());
\r
1344 stretchGroup.recalcConservation();
\r
1348 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1349 stretchGroup.getName());
\r
1352 changeEndRes = false;
\r
1353 changeStartRes = false;
\r
1354 stretchGroup = null;
\r
1355 PaintRefresher.Refresh(av.alignment);
\r
1361 * @param evt DOCUMENT ME!
\r
1363 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1365 int res = findRes(evt);
\r
1366 int y = findSeq(evt);
\r
1368 if(wrappedBlock!=startWrapBlock)
\r
1371 if (stretchGroup == null)
\r
1377 if(y > av.alignment.getHeight())
\r
1379 y = av.alignment.getHeight() -1;
\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.sequences.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