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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77 StringBuffer tooltipText = new StringBuffer("<html>");
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81 * Creates a new SeqPanel object.
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83 * @param avp DOCUMENT ME!
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84 * @param p DOCUMENT ME!
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86 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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88 linkImageURL = getClass().getResource("/images/link.gif");
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89 ToolTipManager.sharedInstance().registerComponent(this);
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90 ToolTipManager.sharedInstance().setInitialDelay(0);
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91 ToolTipManager.sharedInstance().setDismissDelay(10000);
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93 setBackground(Color.white);
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95 seqCanvas = new SeqCanvas(avp);
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96 setLayout(new BorderLayout());
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97 add(seqCanvas, BorderLayout.CENTER);
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101 if(!av.isDataset())
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103 addMouseMotionListener(this);
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104 addMouseListener(this);
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105 addMouseWheelListener(this);
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109 int startWrapBlock=-1;
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110 int wrappedBlock=-1;
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111 int findRes(MouseEvent evt)
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114 int x = evt.getX();
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116 if (av.wrapAlignment)
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119 int hgap = av.charHeight;
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120 if (av.scaleAboveWrapped)
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121 hgap += av.charHeight;
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123 int cHeight = av.getAlignment().getHeight() * av.charHeight
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124 + hgap + seqCanvas.getAnnotationHeight();
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126 int y = evt.getY();
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128 x -= seqCanvas.LABEL_WEST;
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131 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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135 wrappedBlock = y / cHeight;
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136 wrappedBlock += av.getStartRes() / cwidth;
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138 res = wrappedBlock * cwidth + x / av.getCharWidth();
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143 res = (x / av.getCharWidth()) + av.getStartRes();
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146 if(av.hasHiddenColumns)
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147 res = av.getColumnSelection().adjustForHiddenColumns(res);
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153 int findSeq(MouseEvent evt)
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156 int y = evt.getY();
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158 if (av.wrapAlignment)
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160 int hgap = av.charHeight;
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161 if (av.scaleAboveWrapped)
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162 hgap += av.charHeight;
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164 int cHeight = av.getAlignment().getHeight() * av.charHeight
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165 + hgap + seqCanvas.getAnnotationHeight();
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169 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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170 av.alignment.getHeight() -1);
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174 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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175 av.alignment.getHeight() -1);
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181 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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183 Vector allFeatures = new Vector();
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185 if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
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187 while (index < seq.getSequenceFeatures().length)
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189 SequenceFeature sf = seq.getSequenceFeatures()[index];
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190 if (sf.getBegin() <= res &&
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191 sf.getEnd() >= res)
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193 if (av.featuresDisplayed.containsKey(sf.getType()))
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195 allFeatures.addElement(sf);
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201 return allFeatures;
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208 seqEditOccurred = false;
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209 editingSeqs = false;
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210 groupEditing = false;
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211 keyboardNo1 = null;
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212 keyboardNo2 = null;
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215 void setCursorRow()
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217 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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221 void setCursorColumn()
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223 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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227 void setCursorRowAndColumn()
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229 if(keyboardNo2==null)
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231 keyboardNo2 = new StringBuffer();
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235 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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236 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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241 void setCursorPosition()
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243 SequenceI sequence =
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244 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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246 seqCanvas.cursorX = sequence.findIndex(
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247 getKeyboardNo(keyboardNo1)-1
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252 void moveCursor(int dx, int dy)
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254 seqCanvas.cursorX += dx;
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255 seqCanvas.cursorY += dy;
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259 void scrollToVisible()
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261 if (seqCanvas.cursorX < 0)
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262 seqCanvas.cursorX = 0;
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263 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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264 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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266 if (seqCanvas.cursorY < 0)
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267 seqCanvas.cursorY = 0;
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268 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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269 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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273 if(av.wrapAlignment)
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275 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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279 while (seqCanvas.cursorY < av.startSeq)
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283 while (seqCanvas.cursorY + 1 > av.endSeq)
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285 ap.scrollUp(false);
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287 if (!av.wrapAlignment)
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289 while (seqCanvas.cursorX < av.startRes)
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291 if (!ap.scrollRight(false))
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294 while (seqCanvas.cursorX > av.endRes)
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296 if (!ap.scrollRight(true))
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301 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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302 seqCanvas.cursorX, seqCanvas.cursorY);
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304 seqCanvas.repaint();
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307 void setSelectionAreaAtCursor(boolean topLeft)
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309 SequenceI sequence =
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310 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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312 if(av.getSelectionGroup()!=null)
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314 SequenceGroup sg = av.selectionGroup;
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315 //Find the top and bottom of this group
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316 int min = av.alignment.getHeight(), max = 0;
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317 for(int i=0; i<sg.getSize(false); i++)
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319 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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330 sg.setStartRes(seqCanvas.cursorX);
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331 if(sg.getEndRes()<seqCanvas.cursorX)
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332 sg.setEndRes(seqCanvas.cursorX);
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334 min = seqCanvas.cursorY;
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338 sg.setEndRes(seqCanvas.cursorX);
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339 if(sg.getStartRes()>seqCanvas.cursorX)
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340 sg.setStartRes(seqCanvas.cursorX);
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342 max = seqCanvas.cursorY+1;
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347 // Only the user can do this
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348 av.setSelectionGroup(null);
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352 // Now add any sequences between min and max
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353 sg.getSequences(false).clear();
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354 for (int i = min; i < max; i++)
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356 sg.addSequence(av.alignment.getSequenceAt(i), false);
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361 if (av.getSelectionGroup() == null)
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363 SequenceGroup sg = new SequenceGroup();
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364 sg.setStartRes(seqCanvas.cursorX);
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365 sg.setEndRes(seqCanvas.cursorX);
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366 sg.addSequence(sequence, false);
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367 av.setSelectionGroup(sg);
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374 void insertGapAtCursor(boolean group)
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376 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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377 av.alignment, HistoryItem.EDIT));
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378 groupEditing = group;
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379 startseq = seqCanvas.cursorY;
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380 lastres = seqCanvas.cursorX;
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381 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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385 void deleteGapAtCursor(boolean group)
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387 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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388 av.alignment, HistoryItem.EDIT));
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389 groupEditing = group;
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390 startseq = seqCanvas.cursorY;
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391 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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392 editSequence(false, seqCanvas.cursorX);
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396 void numberPressed(char value)
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398 if(keyboardNo1==null)
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399 keyboardNo1 = new StringBuffer();
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401 if(keyboardNo2!=null)
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402 keyboardNo2.append(value);
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404 keyboardNo1.append(value);
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407 int getKeyboardNo(StringBuffer kb)
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412 return Integer.parseInt(kb.toString());
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419 * @param evt DOCUMENT ME!
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421 public void mouseReleased(MouseEvent evt)
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423 mouseDragging = false;
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424 mouseWheelPressed = false;
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428 doMouseReleasedDefineMode(evt);
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442 * @param evt DOCUMENT ME!
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444 public void mousePressed(MouseEvent evt)
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446 lastMousePress = evt.getPoint();
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448 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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450 mouseWheelPressed = true;
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454 if (evt.isShiftDown() || evt.isAltDown() ||
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455 evt.isControlDown())
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457 if (evt.isAltDown() || evt.isControlDown())
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459 groupEditing = true;
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461 editingSeqs = true;
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465 doMousePressedDefineMode(evt);
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471 int seq = findSeq(evt);
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472 int res = findRes(evt);
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477 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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478 av.alignment, HistoryItem.EDIT));
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480 if ((seq < av.getAlignment().getHeight()) &&
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481 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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498 * @param evt DOCUMENT ME!
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500 public void mouseMoved(MouseEvent evt)
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504 // This is because MacOSX creates a mouseMoved
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505 // If control is down, other platforms will not.
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509 int res = findRes(evt);
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510 int seq = findSeq(evt);
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513 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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516 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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518 if (res > sequence.getLength())
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523 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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525 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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528 setStatusMessage(sequence, res, seq);
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530 // use aa to see if the mouse pointer is on a
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531 if (av.showSequenceFeatures)
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533 tooltipText.setLength(6); // Cuts the buffer back to <html>
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535 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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538 for (int i = 0; i < features.length; i++)
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541 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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542 (features[i].getEnd() >= sequence.findPosition(res)))
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544 if(av.featuresDisplayed==null
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545 || !av.featuresDisplayed.containsKey(features[i].getType()))
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549 if (features[i].getType().equals("disulfide bond"))
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551 if (features[i].getBegin() == sequence.findPosition(res)
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552 || features[i].getEnd() == sequence.findPosition(res))
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554 if (tooltipText.length() > 6)
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555 tooltipText.append("<br>");
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556 tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +
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557 features[i].getEnd());
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558 if (features[i].links != null)
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559 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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564 if (tooltipText.length() > 6)
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565 tooltipText.append("<br>");
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567 tooltipText.append(features[i].getType() + " " +
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568 features[i].begin);
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569 if (features[i].begin != features[i].end)
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570 tooltipText.append(" " + features[i].end);
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572 if (features[i].getDescription() != null
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573 && !features[i].description.equals(features[i].getType()))
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575 tmpString = features[i].getDescription();
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576 int startTag=tmpString.toUpperCase().indexOf("<HTML>");
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579 tmpString = tmpString.substring(startTag + 6);
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581 int endTag=tmpString.toUpperCase().indexOf("</BODY>");
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584 tmpString = tmpString.substring(0, endTag);
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586 endTag = tmpString.toUpperCase().indexOf("</HTML>");
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589 tmpString = tmpString.substring(0, endTag);
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594 tooltipText.append("; " + tmpString);
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598 if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
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600 //The description does not specify html is to
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601 //be used, so we must remove < > symbols
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602 tmpString = tmpString.replaceAll("<", "<");
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603 tmpString = tmpString.replaceAll(">", ">");
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605 tooltipText.append("; ");
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606 tooltipText.append(tmpString);
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610 tooltipText.append("; "+tmpString);
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613 if (features[i].getValue("status") != null )
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615 String status = features[i].getValue("status").toString();
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616 if(status.length()>0)
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617 tooltipText.append("; (" + features[i].getValue("status") + ")");
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620 if (features[i].links != null)
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621 tooltipText.append(" <img src=\"" + linkImageURL + "\">");
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625 else if(features[i].begin==0 && features[i].end==0)
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627 // seqSpecific.append(features[i].featureGroup+": "
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628 // + features[i].getType()+" "
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629 // +features[i].getDescription()+"<br>");
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636 if(tooltipText.length()==6) // <html></html>
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639 setToolTipText("");
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643 tooltipText.append("</html>");
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644 setToolTipText(tooltipText.toString());
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648 setToolTipText("");
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652 void setStatusMessage(SequenceI sequence, int res, int seq)
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654 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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655 sequence.getName());
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658 if (av.alignment.isNucleotide())
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660 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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663 text.append(" Nucleotide: ");
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667 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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669 text.append(" Residue: ");
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677 text.append(obj + " (" + sequence.findPosition(res) +
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681 ap.alignFrame.statusBar.setText(text.toString());
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688 * @param evt DOCUMENT ME!
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690 public void mouseDragged(MouseEvent evt)
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692 if (mouseWheelPressed)
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694 int oldWidth = av.charWidth;
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696 //Which is bigger, left-right or up-down?
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697 if (Math.abs(evt.getY() - lastMousePress.getY())
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698 > Math.abs(evt.getX() - lastMousePress.getX()))
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700 int fontSize = av.font.getSize();
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702 if (evt.getY() < lastMousePress.getY())
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706 else if (evt.getY() > lastMousePress.getY())
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714 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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715 av.charWidth = oldWidth;
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720 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
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724 else if (evt.getX() > lastMousePress.getX())
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732 FontMetrics fm = getFontMetrics(av.getFont());
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733 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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735 lastMousePress = evt.getPoint();
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742 doMouseDraggedDefineMode(evt);
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746 int res = findRes(evt);
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753 if ((lastres == -1) || (lastres == res))
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758 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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760 // dragLeft, delete gap
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761 editSequence(false, res);
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764 editSequence(true, res);
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766 mouseDragging = true;
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767 if(scrollThread!=null)
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768 scrollThread.setEvent(evt);
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772 synchronized void editSequence(boolean insertGap, int startres)
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774 int fixedLeft = -1;
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775 int fixedRight = -1;
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776 boolean fixedColumns = false;
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777 SequenceGroup sg = av.getSelectionGroup();
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780 if (!groupEditing && av.hasHiddenRows)
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782 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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784 groupEditing = true;
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788 //No group, but the sequence may represent a group
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791 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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793 groupEditing = false;
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796 SequenceI seq = av.alignment.getSequenceAt(startseq);
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797 StringBuffer message = new StringBuffer();
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799 message.append("Edit group:");
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801 message.append("Edit sequence: "+seq.getName());
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804 message.append(" insert ");
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806 message.append(" delete ");
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808 message.append(Math.abs(startres-lastres)+" gaps.");
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809 ap.alignFrame.statusBar.setText(message.toString());
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812 //Are we editing within a selection group?
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814 || (sg != null && sg.getSequences(true).contains(seq)))
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816 fixedColumns = true;
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818 //sg might be null as the user may only see 1 sequence,
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819 //but the sequence represents a group
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822 sg = new SequenceGroup(null, null, false, false, false, 0,
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823 av.alignment.getWidth()-1);
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824 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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827 fixedLeft = sg.getStartRes();
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828 fixedRight = sg.getEndRes();
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830 if ( (startres < fixedLeft && lastres >= fixedLeft)
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831 || (startres >= fixedLeft && lastres < fixedLeft)
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832 || (startres > fixedRight && lastres <=fixedRight)
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833 || (startres <= fixedRight && lastres > fixedRight))
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839 if (fixedLeft > startres)
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841 fixedRight = fixedLeft - 1;
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844 else if (fixedRight < startres)
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846 fixedLeft = fixedRight;
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852 if(av.hasHiddenColumns )
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854 fixedColumns = true;
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855 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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856 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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858 if ( (insertGap && startres > y1 && lastres < y1)
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859 || (!insertGap && startres < y2 && lastres > y2))
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865 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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866 //Selection spans a hidden region
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867 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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875 fixedRight = y2 - 1;
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883 Vector vseqs = sg.getSequences(true);
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884 int g, groupSize = vseqs.size();
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885 SequenceI[] groupSeqs = new SequenceI[groupSize];
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886 for (g = 0; g < groupSeqs.length; g++)
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887 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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892 //If the user has selected the whole sequence, and is dragging to
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893 // the right, we can still extend the alignment and selectionGroup
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894 if( sg.getStartRes() == 0
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895 && sg.getEndRes() == fixedRight
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896 && sg.getEndRes() == av.alignment.getWidth()-1
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899 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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900 fixedRight = sg.getEndRes();
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903 // Is it valid with fixed columns??
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904 // Find the next gap before the end
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905 // of the visible region boundary
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906 boolean blank = false;
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907 for (fixedRight = fixedRight;
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908 fixedRight > lastres;
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913 for (g = 0; g < groupSize; g++)
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915 for (int j = 0; j < startres - lastres; j++)
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917 if (!jalview.util.Comparison.isGap(
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918 groupSeqs[g].getCharAt(fixedRight - j)))
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931 if(sg.getSize(false) == av.alignment.getHeight() )
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933 if((av.hasHiddenColumns
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934 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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940 int alWidth = av.alignment.getWidth();
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941 if(av.hasHiddenRows)
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943 int hwidth = av.alignment.getHiddenSequences().getWidth();
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947 //We can still insert gaps if the selectionGroup
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948 //contains all the sequences
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949 sg.setEndRes(sg.getEndRes()+startres-lastres);
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950 fixedRight = alWidth+startres-lastres;
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962 else if(!insertGap)
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964 /// Are we able to delete?
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965 // ie are all columns blank?
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967 for (g = 0; g < groupSize; g++)
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969 for (int j = startres; j < lastres; j++)
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971 if (groupSeqs[g].getLength() <= j)
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976 if (!jalview.util.Comparison.isGap(
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977 groupSeqs[g].getCharAt(j)))
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979 // Not a gap, block edit not valid
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988 for (g = 0; g < groupSize; g++)
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992 // dragging to the right
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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 insertChar(j, groupSeqs[g], fixedRight);
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1000 insertChar(j, groupSeqs[g]);
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1005 // dragging to the left
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1006 for (int j = lastres; j > startres; j--)
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1008 if (fixedColumns && fixedRight != -1)
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1010 deleteChar(startres, groupSeqs[g], fixedRight);
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1014 deleteChar(startres, groupSeqs[g]);
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1020 else /////Editing a single sequence///////////
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1024 // dragging to the right
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1025 for (int j = lastres; j < startres; j++)
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1027 if (fixedColumns && fixedRight != -1)
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1029 insertChar(j, seq, fixedRight);
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1032 insertChar(j, seq);
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1037 // dragging to the left
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1038 for (int j = lastres; j > startres; j--)
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1040 if (fixedColumns && fixedRight != -1)
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1042 deleteChar(startres, seq, fixedRight);
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1046 deleteChar(startres, seq);
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1052 lastres = startres;
\r
1053 seqCanvas.repaint();
\r
1060 * @param j DOCUMENT ME!
\r
1061 * @param seq DOCUMENT ME!
\r
1063 void insertChar(int j, SequenceI seq)
\r
1065 seq.insertCharAt(j, av.getGapCharacter());
\r
1066 seqEditOccurred = true;
\r
1069 void insertChar(int j, SequenceI seq, int fixedColumn)
\r
1071 //Find the next gap before the end of the visible region boundary
\r
1072 //If lastCol > j, theres a boundary after the gap insertion
\r
1073 int blankColumn = fixedColumn;
\r
1074 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1076 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1078 //Theres a space, so break and insert the gap
\r
1083 if (blankColumn <= j)
\r
1085 blankColumn = fixedColumn;
\r
1090 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1093 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
\r
1097 seq.deleteCharAt(blankColumn);
\r
1098 seq.insertCharAt(j, av.getGapCharacter());
\r
1099 seqEditOccurred = true;
\r
1102 void deleteChar(int j, SequenceI seq, int fixedColumn)
\r
1104 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1106 ap.alignFrame.statusBar.setText(
\r
1107 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1111 seq.deleteCharAt(j);
\r
1112 seq.insertCharAt(fixedColumn, av.getGapCharacter());
\r
1113 seqEditOccurred = true;
\r
1119 * @param j DOCUMENT ME!
\r
1120 * @param seq DOCUMENT ME!
\r
1122 void deleteChar(int j, SequenceI seq)
\r
1124 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1126 ap.alignFrame.statusBar.setText(
\r
1127 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1131 seq.deleteCharAt(j);
\r
1132 seqEditOccurred = true;
\r
1133 seqCanvas.repaint();
\r
1138 * @param e DOCUMENT ME!
\r
1140 public void mouseEntered(MouseEvent e)
\r
1145 if (scrollThread != null)
\r
1147 scrollThread.running = false;
\r
1148 scrollThread = null;
\r
1155 * @param e DOCUMENT ME!
\r
1157 public void mouseExited(MouseEvent e)
\r
1159 if (av.getWrapAlignment())
\r
1164 if (mouseDragging)
\r
1166 scrollThread = new ScrollThread();
\r
1170 public void mouseClicked(MouseEvent evt)
\r
1173 public void mouseWheelMoved(MouseWheelEvent e)
\r
1176 /* if (mouseWheelPressed)
\r
1178 Font font = av.getFont();
\r
1179 int fontSize = font.getSize();
\r
1180 if (e.getWheelRotation() > 0 && fontSize < 51)
\r
1182 else if (fontSize > 1)
\r
1187 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
\r
1193 if (e.getWheelRotation() > 0)
\r
1194 ap.scrollUp(false);
\r
1196 ap.scrollUp(true);
\r
1206 * @param i DOCUMENT ME!
\r
1208 void editOccurred()
\r
1210 if (!seqEditOccurred)
\r
1212 ap.alignFrame.historyList.pop();
\r
1213 ap.alignFrame.updateEditMenuBar();
\r
1218 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1225 * @param evt DOCUMENT ME!
\r
1227 public void doMousePressedDefineMode(MouseEvent evt)
\r
1229 int res = findRes(evt);
\r
1230 int seq = findSeq(evt);
\r
1233 startWrapBlock=wrappedBlock;
\r
1235 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1237 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1238 "Cannot edit annotations in wrapped view.",
\r
1239 "Wrapped view - no edit",
\r
1240 JOptionPane.WARNING_MESSAGE);
\r
1244 if(seq<0 || res<0)
\r
1247 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1249 if ((sequence == null) || (res > sequence.getLength()))
\r
1254 stretchGroup = av.getSelectionGroup();
\r
1256 if (stretchGroup == null)
\r
1258 stretchGroup = av.alignment.findGroup(sequence);
\r
1260 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1261 (res < stretchGroup.getEndRes()))
\r
1263 av.setSelectionGroup(stretchGroup);
\r
1267 stretchGroup = null;
\r
1270 else if (!stretchGroup.getSequences(false).contains(sequence) ||
\r
1271 (stretchGroup.getStartRes() > res) ||
\r
1272 (stretchGroup.getEndRes() < res))
\r
1274 stretchGroup = null;
\r
1276 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1278 if (allGroups != null)
\r
1280 for (int i = 0; i < allGroups.length; i++)
\r
1282 if ((allGroups[i].getStartRes() <= res) &&
\r
1283 (allGroups[i].getEndRes() >= res))
\r
1285 stretchGroup = allGroups[i];
\r
1291 av.setSelectionGroup(stretchGroup);
\r
1296 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1298 Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
\r
1299 sequence.findPosition(res));
\r
1300 Vector links = new Vector();
\r
1301 for (int i = 0; i < allFeatures.size(); i++)
\r
1303 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1304 if (sf.links != null)
\r
1306 for (int j = 0; j < sf.links.size(); j++)
\r
1308 links.addElement(sf.links.elementAt(j));
\r
1313 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
\r
1314 pop.show(this, evt.getX(), evt.getY());
\r
1318 if (av.cursorMode)
\r
1320 seqCanvas.cursorX = findRes(evt);
\r
1321 seqCanvas.cursorY = findSeq(evt);
\r
1322 seqCanvas.repaint();
\r
1326 if (stretchGroup == null)
\r
1328 //Only if left mouse button do we want to change group sizes
\r
1330 // define a new group here
\r
1331 SequenceGroup sg = new SequenceGroup();
\r
1332 sg.setStartRes(res);
\r
1333 sg.setEndRes(res);
\r
1334 sg.addSequence(sequence, false);
\r
1335 av.setSelectionGroup(sg);
\r
1336 stretchGroup = sg;
\r
1338 if (av.getConservationSelected())
\r
1340 SliderPanel.setConservationSlider(ap,
\r
1341 av.getGlobalColourScheme(),
\r
1345 if (av.getAbovePIDThreshold())
\r
1347 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1350 if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1352 // Edit end res position of selected group
\r
1353 changeEndRes = true;
\r
1355 else if ( (stretchGroup != null) &&
\r
1356 (stretchGroup.getStartRes() == res))
\r
1358 // Edit end res position of selected group
\r
1359 changeStartRes = true;
\r
1361 stretchGroup.getWidth();
\r
1364 seqCanvas.repaint();
\r
1370 * @param evt DOCUMENT ME!
\r
1372 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1374 if (stretchGroup == null)
\r
1380 if(stretchGroup.cs!=null)
\r
1382 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1384 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1385 stretchGroup.getSequences(true),
\r
1386 stretchGroup.getWidth());
\r
1389 if (stretchGroup.cs.conservationApplied())
\r
1391 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1392 stretchGroup.getName());
\r
1393 stretchGroup.recalcConservation();
\r
1397 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1398 stretchGroup.getName());
\r
1401 changeEndRes = false;
\r
1402 changeStartRes = false;
\r
1403 stretchGroup = null;
\r
1405 PaintRefresher.Refresh(this, av.getSequenceSetId());
\r
1411 * @param evt DOCUMENT ME!
\r
1413 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1415 int res = findRes(evt);
\r
1416 int y = findSeq(evt);
\r
1418 if(wrappedBlock!=startWrapBlock)
\r
1421 if (stretchGroup == null)
\r
1426 if(res> av.alignment.getWidth())
\r
1428 res = av.alignment.getWidth()-1;
\r
1431 if (stretchGroup.getEndRes() == res)
\r
1433 // Edit end res position of selected group
\r
1434 changeEndRes = true;
\r
1436 else if (stretchGroup.getStartRes() == res)
\r
1438 // Edit start res position of selected group
\r
1439 changeStartRes = true;
\r
1442 if (res < av.getStartRes())
\r
1444 res = av.getStartRes();
\r
1449 if (res > (stretchGroup.getStartRes() - 1))
\r
1451 stretchGroup.setEndRes(res);
\r
1454 else if (changeStartRes)
\r
1456 if (res < (stretchGroup.getEndRes() + 1))
\r
1458 stretchGroup.setStartRes(res);
\r
1462 int dragDirection = 0;
\r
1466 dragDirection = 1;
\r
1468 else if (y < oldSeq)
\r
1470 dragDirection = -1;
\r
1474 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1476 // This routine ensures we don't skip any sequences, as the
\r
1477 // selection is quite slow.
\r
1478 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1480 oldSeq += dragDirection;
\r
1485 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1487 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1489 stretchGroup.deleteSequence(seq, false);
\r
1495 stretchGroup.addSequence(seq, false);
\r
1498 stretchGroup.addSequence(nextSeq, false);
\r
1505 mouseDragging = true;
\r
1507 if (scrollThread != null)
\r
1509 scrollThread.setEvent(evt);
\r
1512 seqCanvas.repaint();
\r
1515 void scrollCanvas(MouseEvent evt)
\r
1519 if(scrollThread!=null)
\r
1521 scrollThread.running = false;
\r
1522 scrollThread = null;
\r
1524 mouseDragging = false;
\r
1528 if (scrollThread == null)
\r
1529 scrollThread = new ScrollThread();
\r
1531 mouseDragging = true;
\r
1532 scrollThread.setEvent(evt);
\r
1538 // this class allows scrolling off the bottom of the visible alignment
\r
1539 class ScrollThread extends Thread
\r
1542 boolean running = false;
\r
1544 public ScrollThread()
\r
1549 public void setEvent(MouseEvent e)
\r
1554 public void stopScrolling()
\r
1567 if (mouseDragging && (evt.getY() < 0) &&
\r
1568 (av.getStartSeq() > 0))
\r
1570 running = ap.scrollUp(true);
\r
1573 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1574 (av.alignment.getHeight() > av.getEndSeq()))
\r
1576 running = ap.scrollUp(false);
\r
1579 if (mouseDragging && (evt.getX() < 0))
\r
1581 running = ap.scrollRight(false);
\r
1583 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1585 running = ap.scrollRight(true);
\r
1593 catch (Exception ex)
\r