2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.schemes.*;
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26 import java.awt.event.*;
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28 import javax.swing.*;
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35 * @version $Revision$
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37 public class SeqPanel extends JPanel implements MouseListener,
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38 MouseMotionListener, MouseWheelListener
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41 /** DOCUMENT ME!! */
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42 public SeqCanvas seqCanvas;
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44 /** DOCUMENT ME!! */
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45 public AlignmentPanel ap;
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46 protected int lastres;
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47 protected int startseq;
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48 protected AlignViewport av;
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50 // if character is inserted or deleted, we will need to recalculate the conservation
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51 boolean seqEditOccurred = false;
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52 ScrollThread scrollThread = null;
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53 boolean mouseDragging = false;
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54 boolean editingSeqs = false;
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55 boolean groupEditing = false;
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57 //////////////////////////////////////////
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58 /////Everything below this is for defining the boundary of the rubberband
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59 //////////////////////////////////////////
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61 boolean changeEndSeq = false;
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62 boolean changeStartSeq = false;
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63 boolean changeEndRes = false;
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64 boolean changeStartRes = false;
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65 SequenceGroup stretchGroup = null;
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66 boolean remove = false;
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68 boolean mouseWheelPressed = false;
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71 * Creates a new SeqPanel object.
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73 * @param avp DOCUMENT ME!
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74 * @param p DOCUMENT ME!
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76 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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78 ToolTipManager.sharedInstance().registerComponent(this);
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79 ToolTipManager.sharedInstance().setInitialDelay(0);
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80 ToolTipManager.sharedInstance().setDismissDelay(10000);
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82 setBackground(Color.white);
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84 seqCanvas = new SeqCanvas(avp);
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85 setLayout(new BorderLayout());
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86 add(seqCanvas, BorderLayout.CENTER);
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92 addMouseMotionListener(this);
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93 addMouseListener(this);
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94 addMouseWheelListener(this);
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98 int startWrapBlock=-1;
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99 int wrappedBlock=-1;
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100 int findRes(MouseEvent evt)
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103 int x = evt.getX();
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105 if (av.wrapAlignment)
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108 int hgap = av.charHeight;
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109 if (av.scaleAboveWrapped)
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110 hgap += av.charHeight;
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112 int cHeight = av.getAlignment().getHeight() * av.charHeight
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113 + hgap + seqCanvas.getAnnotationHeight();
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115 int y = evt.getY();
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117 x -= seqCanvas.LABEL_WEST;
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120 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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122 wrappedBlock = y / cHeight;
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123 wrappedBlock += av.getStartRes() / cwidth;
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125 res = wrappedBlock * cwidth + x / av.getCharWidth();
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130 res = (x / av.getCharWidth()) + av.getStartRes();
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133 if(av.hasHiddenColumns)
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134 res = av.getColumnSelection().adjustForHiddenColumns(res);
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140 int findSeq(MouseEvent evt)
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144 int y = evt.getY();
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146 if (av.wrapAlignment)
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148 int hgap = av.charHeight;
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149 if (av.scaleAboveWrapped)
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150 hgap += av.charHeight;
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152 int cHeight = av.getAlignment().getHeight() * av.charHeight
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153 + hgap + seqCanvas.getAnnotationHeight();
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157 seq = ( (y % cHeight) / av.getCharHeight());
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161 seq = (y / av.getCharHeight()) + av.getStartSeq();
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171 seqEditOccurred = false;
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172 editingSeqs = false;
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173 groupEditing = false;
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174 keyboardGaps = null;
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178 void moveCursor(int dx, int dy)
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180 seqCanvas.cursorX += dx;
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181 seqCanvas.cursorY += dy;
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183 if(seqCanvas.cursorX<0)
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184 seqCanvas.cursorX = 0;
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185 else if(seqCanvas.cursorX>av.alignment.getWidth()-1)
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186 seqCanvas.cursorX = av.alignment.getWidth()-1;
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187 if(seqCanvas.cursorX<av.startRes)
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188 ap.scrollRight(false);
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189 else if(seqCanvas.cursorX>av.endRes)
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190 ap.scrollRight(true);
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192 if(seqCanvas.cursorY<0)
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193 seqCanvas.cursorY=0;
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194 else if(seqCanvas.cursorY>av.alignment.getHeight()-1)
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195 seqCanvas.cursorY = av.alignment.getHeight()-1;
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196 if(seqCanvas.cursorY<av.startSeq)
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198 else if(seqCanvas.cursorY+1>av.endSeq)
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199 ap.scrollUp(false);
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201 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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202 seqCanvas.cursorX, seqCanvas.cursorY);
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203 seqCanvas.repaint();
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206 void setSelectionAreaAtCursor(boolean topLeft)
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208 SequenceI sequence =
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209 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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211 if(av.getSelectionGroup()!=null)
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213 SequenceGroup sg = av.selectionGroup;
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214 //Find the top and bottom of this group
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215 int min = av.alignment.getHeight(), max = 0;
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216 for(int i=0; i<sg.getSize(); i++)
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218 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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229 sg.setStartRes(seqCanvas.cursorX);
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230 if(sg.getEndRes()<seqCanvas.cursorX)
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231 sg.setEndRes(seqCanvas.cursorX);
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233 min = seqCanvas.cursorY;
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237 sg.setEndRes(seqCanvas.cursorX);
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238 if(sg.getStartRes()>seqCanvas.cursorX)
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239 sg.setStartRes(seqCanvas.cursorX);
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241 max = seqCanvas.cursorY+1;
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246 // Only the user can do this
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247 av.setSelectionGroup(null);
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251 // Now add any sequences between min and max
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252 sg.sequences.clear();
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253 for (int i = min; i < max; i++)
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255 sg.addSequence(av.alignment.getSequenceAt(i), false);
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260 if (av.getSelectionGroup() == null)
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262 SequenceGroup sg = new SequenceGroup();
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263 sg.setStartRes(seqCanvas.cursorX);
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264 sg.setEndRes(seqCanvas.cursorX);
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265 sg.addSequence(sequence, false);
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266 av.setSelectionGroup(sg);
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273 void insertGapAtCursor(boolean group)
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275 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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276 av.alignment, HistoryItem.EDIT));
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277 groupEditing = group;
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278 startseq = seqCanvas.cursorY;
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279 lastres = seqCanvas.cursorX;
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280 editSequence(true, seqCanvas.cursorX+getKeyboardGaps());
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284 void deleteGapAtCursor(boolean group)
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286 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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287 av.alignment, HistoryItem.EDIT));
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288 groupEditing = group;
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289 startseq = seqCanvas.cursorY;
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290 lastres = seqCanvas.cursorX+getKeyboardGaps();
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291 editSequence(false, seqCanvas.cursorX);
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295 void numberPressed(char value)
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297 if(keyboardGaps==null)
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298 keyboardGaps = new StringBuffer();
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300 keyboardGaps.append(value);
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303 StringBuffer keyboardGaps;
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304 int getKeyboardGaps()
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306 if(keyboardGaps==null)
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309 return Integer.parseInt(keyboardGaps.toString());
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316 * @param evt DOCUMENT ME!
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318 public void mouseReleased(MouseEvent evt)
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320 mouseDragging = false;
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321 mouseWheelPressed = false;
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325 doMouseReleasedDefineMode(evt);
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340 * @param evt DOCUMENT ME!
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342 public void mousePressed(MouseEvent evt)
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344 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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346 mouseWheelPressed = true;
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350 if (evt.isShiftDown() || evt.isAltDown() ||
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351 evt.isControlDown())
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353 if (evt.isAltDown() || evt.isControlDown())
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355 groupEditing = true;
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357 editingSeqs = true;
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361 doMousePressedDefineMode(evt);
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367 int seq = findSeq(evt);
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368 int res = findRes(evt);
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373 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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374 av.alignment, HistoryItem.EDIT));
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376 if ((seq < av.getAlignment().getHeight()) &&
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377 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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394 * @param evt DOCUMENT ME!
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396 public void mouseMoved(MouseEvent evt)
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400 // This is because MacOSX creates a mouseMoved
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401 // If control is down, other platforms will not.
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405 int res = findRes(evt);
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406 int seq = findSeq(evt);
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409 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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412 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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414 if (res > sequence.getLength())
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419 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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421 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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424 setStatusMessage(sequence, res, seq);
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426 // use aa to see if the mouse pointer is on a
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427 if (av.showSequenceFeatures)
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429 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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432 StringBuffer sbuffer = new StringBuffer("<html>");
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434 for (int i = 0; i < features.length; i++)
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437 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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438 (features[i].getEnd() >= sequence.findPosition(res)))
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440 if(av.featuresDisplayed==null
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441 || !av.featuresDisplayed.containsKey(features[i].getType()))
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445 if (features[i].getType().equals("disulfide bond"))
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447 if (features[i].getBegin() == sequence.findPosition(res)
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448 || features[i].getEnd() == sequence.findPosition(res))
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450 if (sbuffer.length() > 6)
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451 sbuffer.append("<br>");
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452 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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453 features[i].getEnd());
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458 if (sbuffer.length() > 6)
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459 sbuffer.append("<br>");
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460 if(features[i].featureGroup!=null)
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461 sbuffer.append(features[i].featureGroup+";");
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463 sbuffer.append(features[i].getType());
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465 if (features[i].getDescription() != null
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466 && !features[i].description.equals(features[i].getType()))
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467 sbuffer.append("; " + features[i].getDescription());
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469 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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471 sbuffer.append("; (" + features[i].getStatus() + ")");
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478 sbuffer.append("</html>");
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479 if(sbuffer.length()==13) // <html></html>
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480 setToolTipText("");
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482 setToolTipText(sbuffer.toString());
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485 setToolTipText("");
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489 void setStatusMessage(SequenceI sequence, int res, int seq)
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491 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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492 sequence.getName());
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495 if (av.alignment.isNucleotide())
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497 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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500 text.append(" Nucleotide: ");
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504 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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506 text.append(" Residue: ");
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514 text.append(obj + " (" + sequence.findPosition(res) +
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518 ap.alignFrame.statusBar.setText(text.toString());
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525 * @param evt DOCUMENT ME!
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527 public void mouseDragged(MouseEvent evt)
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531 doMouseDraggedDefineMode(evt);
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535 int res = findRes(evt);
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542 if ((lastres == -1) || (lastres == res))
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547 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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549 // dragLeft, delete gap
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550 editSequence(false, res);
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553 editSequence(true, res);
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555 mouseDragging = true;
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556 if(scrollThread!=null)
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557 scrollThread.setEvent(evt);
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561 void editSequence(boolean insertGap, int startres)
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563 int fixedLeft = -1;
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564 int fixedRight = -1;
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565 boolean fixedColumns = false;
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567 if(insertGap && av.hasHiddenColumns)
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569 //Stop editing if the user has dragged beyond hiddenBoundary
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570 fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);
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571 if( fixedRight < lastres)
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573 if(lastres!=fixedRight)
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581 if (!groupEditing && av.hasHiddenRows)
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583 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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585 groupEditing = true;
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590 SequenceI seq = av.alignment.getSequenceAt(startseq);
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591 StringBuffer message = new StringBuffer();
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593 message.append("Edit group:");
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595 message.append("Edit sequence: "+seq.getName());
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598 message.append(" insert ");
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600 message.append(" delete ");
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602 message.append(Math.abs(startres-lastres)+" gaps.");
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603 ap.alignFrame.statusBar.setText(message.toString());
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606 //Are we editing within a selection group?
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608 || (av.getSelectionGroup() != null &&
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609 av.getSelectionGroup().sequences.contains(seq)))
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611 fixedColumns = true;
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613 fixedLeft = av.getSelectionGroup().getStartRes();
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614 fixedRight = av.getSelectionGroup().getEndRes();
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616 if ( (startres < fixedLeft && lastres >= fixedLeft)
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617 || (startres >= fixedLeft && lastres < fixedLeft)
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618 || (startres > fixedRight && lastres <=fixedRight)
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619 || (startres <= fixedRight && lastres > fixedRight))
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625 if (fixedLeft > startres)
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627 fixedRight = fixedLeft - 1;
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630 else if (fixedRight < startres)
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632 fixedLeft = fixedRight;
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639 SequenceGroup sg = av.getSelectionGroup();
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640 if(fixedLeft>sg.getEndRes()
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641 ||fixedRight<sg.getStartRes())
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647 if (av.hasHiddenRows)
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649 //sg might be null as the user may only see 1 sequence
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652 sg = new SequenceGroup();
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653 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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656 SequenceGroup tmp = new SequenceGroup();
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658 //Do any of the sequences have hidden associates?
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659 for (int s = 0; s < sg.getSize(); s++)
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661 seq = sg.getSequenceAt(s);
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662 tmp.addSequence(seq, false);
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663 if (seq.getHiddenSequences() != null)
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665 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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666 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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680 // int blankColumn = -1;
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686 // Find the next gap before the end
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687 // of the visible region boundary
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688 if (av.hasHiddenColumns)
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690 // int lastCol = av.getColumnSelection().
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691 // getHiddenRegionBoundary(res);
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695 if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)
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697 for (fixedRight = fixedRight;
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698 fixedRight > lastres;
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701 boolean blank = true;
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702 for (int s = 0; s < sg.getSize(); s++)
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704 seq = sg.getSequenceAt(s);
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706 if (seq.getSequence().length() <= fixedRight)
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711 if (!jalview.util.Comparison.isGap(
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712 seq.getCharAt(fixedRight)))
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723 if (fixedRight <= startres)
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734 /// Are we able to delete?
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735 // ie are all columns blank?
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737 for (int s = 0; s < sg.getSize(); s++)
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739 seq = sg.getSequenceAt(s);
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741 for (int j = startres; j < lastres; j++)
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743 if (seq.getSequence().length() <= j)
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748 if (!jalview.util.Comparison.isGap(
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749 seq.getSequence().charAt(j)))
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751 // Not a gap, block edit not valid
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760 for (int i = 0; i < sg.getSize(); i++)
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762 seq = sg.getSequenceAt(i);
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766 // dragging to the right
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767 for (int j = lastres; j < startres; j++)
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769 if (fixedColumns && fixedRight != -1)
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771 insertChar(j, seq, fixedRight);
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774 insertChar(j, seq);
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779 // dragging to the left
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780 for (int j = lastres; j > startres; j--)
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782 if (fixedColumns && fixedRight != -1)
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784 deleteChar(startres, seq, fixedRight);
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788 deleteChar(startres, seq);
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794 else /////Editing a single sequence///////////
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799 // dragging to the right
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800 for (int j = lastres; j < startres; j++)
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802 if (fixedColumns && fixedRight != -1)
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803 insertChar(j, seq, fixedRight);
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805 insertChar(j, seq);
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810 // dragging to the left
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811 for (int j = lastres; j > startres; j--)
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813 if (fixedColumns && fixedRight != -1)
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815 deleteChar(startres, seq, fixedRight);
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819 deleteChar(startres, seq);
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825 lastres = startres;
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826 seqCanvas.repaint();
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833 * @param j DOCUMENT ME!
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834 * @param seq DOCUMENT ME!
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836 void insertChar(int j, SequenceI seq)
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838 seq.insertCharAt(j, av.getGapCharacter());
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839 seqEditOccurred = true;
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842 void insertChar(int j, SequenceI seq, int fixedColumn)
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844 //Find the next gap before the end of the visible region boundary
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845 //If lastCol > j, theres a boundary after the gap insertion
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846 int blankColumn = fixedColumn;
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847 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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849 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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851 //Theres a space, so break and insert the gap
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856 if (blankColumn <= j)
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862 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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865 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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869 seq.deleteCharAt(blankColumn);
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870 seq.insertCharAt(j, av.getGapCharacter());
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871 seqEditOccurred = true;
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874 void deleteChar(int j, SequenceI seq, int fixedColumn)
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876 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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878 ap.alignFrame.statusBar.setText(
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879 "End editing: Tried removing residue " + seq.getCharAt(j));
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883 seq.deleteCharAt(j);
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884 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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885 seqEditOccurred = true;
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891 * @param j DOCUMENT ME!
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892 * @param seq DOCUMENT ME!
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894 void deleteChar(int j, SequenceI seq)
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896 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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898 ap.alignFrame.statusBar.setText(
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899 "End editing: Tried removing residue " + seq.getCharAt(j));
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903 seq.deleteCharAt(j);
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904 seqEditOccurred = true;
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905 seqCanvas.repaint();
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910 * @param e DOCUMENT ME!
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912 public void mouseEntered(MouseEvent e)
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917 if (scrollThread != null)
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919 scrollThread.running = false;
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920 scrollThread = null;
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927 * @param e DOCUMENT ME!
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929 public void mouseExited(MouseEvent e)
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931 if (av.getWrapAlignment())
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938 scrollThread = new ScrollThread();
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942 public void mouseClicked(MouseEvent evt)
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945 public void mouseWheelMoved(MouseWheelEvent e)
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948 if (mouseWheelPressed)
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950 Font font = av.getFont();
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951 int fontSize = font.getSize();
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952 if (e.getWheelRotation() > 0 && fontSize < 51)
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954 else if (fontSize > 1)
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957 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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962 if (e.getWheelRotation() > 0)
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963 ap.scrollUp(false);
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975 * @param i DOCUMENT ME!
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977 void editOccurred()
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979 if (!seqEditOccurred)
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981 ap.alignFrame.historyList.pop();
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982 ap.alignFrame.updateEditMenuBar();
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987 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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994 * @param evt DOCUMENT ME!
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996 public void doMousePressedDefineMode(MouseEvent evt)
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998 int res = findRes(evt);
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999 int seq = findSeq(evt);
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1002 startWrapBlock=wrappedBlock;
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1004 if(av.wrapAlignment && seq>av.alignment.getHeight())
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1006 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1007 "Cannot edit annotations in wrapped view.",
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1008 "Wrapped view - no edit",
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1009 JOptionPane.WARNING_MESSAGE);
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1013 if(seq<0 || res<0)
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1016 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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1018 if ((sequence == null) || (res > sequence.getLength()))
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1023 stretchGroup = av.getSelectionGroup();
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1025 if (stretchGroup == null)
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1027 stretchGroup = av.alignment.findGroup(sequence);
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1029 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
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1030 (res < stretchGroup.getEndRes()))
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1032 av.setSelectionGroup(stretchGroup);
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1036 stretchGroup = null;
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1039 else if (!stretchGroup.sequences.contains(sequence) ||
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1040 (stretchGroup.getStartRes() > res) ||
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1041 (stretchGroup.getEndRes() < res))
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1043 stretchGroup = null;
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1045 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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1047 if (allGroups != null)
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1049 for (int i = 0; i < allGroups.length; i++)
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1051 if ((allGroups[i].getStartRes() <= res) &&
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1052 (allGroups[i].getEndRes() >= res))
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1054 stretchGroup = allGroups[i];
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1055 av.setSelectionGroup(stretchGroup);
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1063 if (av.cursorMode)
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1065 seqCanvas.cursorX = findRes(evt);
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1066 seqCanvas.cursorY = findSeq(evt);
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1067 seqCanvas.repaint();
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1072 if (stretchGroup == null)
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1074 // define a new group here
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1075 SequenceGroup sg = new SequenceGroup();
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1076 sg.setStartRes(res);
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1077 sg.setEndRes(res);
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1078 sg.addSequence(sequence, false);
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1079 av.setSelectionGroup(sg);
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1080 stretchGroup = sg;
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1082 if (av.getConservationSelected())
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1084 SliderPanel.setConservationSlider(ap,
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1085 av.getGlobalColourScheme(), "Background");
\r
1088 if (av.getAbovePIDThreshold())
\r
1090 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1094 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1096 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
\r
1097 pop.show(this, evt.getX(), evt.getY());
\r
1099 // edit the properties of existing group
\r
1102 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1104 // Edit end res position of selected group
\r
1105 changeEndRes = true;
\r
1107 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
\r
1109 // Edit end res position of selected group
\r
1110 changeStartRes = true;
\r
1113 stretchGroup.getWidth();
\r
1115 seqCanvas.repaint();
\r
1121 * @param evt DOCUMENT ME!
\r
1123 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1125 if (stretchGroup == null)
\r
1131 if(stretchGroup.cs!=null)
\r
1133 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1135 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1137 stretchGroup.getWidth());
\r
1140 if (stretchGroup.cs.conservationApplied())
\r
1142 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1143 stretchGroup.getName());
\r
1144 stretchGroup.recalcConservation();
\r
1148 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1149 stretchGroup.getName());
\r
1152 changeEndRes = false;
\r
1153 changeStartRes = false;
\r
1154 stretchGroup = null;
\r
1155 PaintRefresher.Refresh(av.alignment);
\r
1161 * @param evt DOCUMENT ME!
\r
1163 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1165 int res = findRes(evt);
\r
1166 int y = findSeq(evt);
\r
1168 if(wrappedBlock!=startWrapBlock)
\r
1171 if (stretchGroup == null)
\r
1177 if(y > av.alignment.getHeight())
\r
1179 y = av.alignment.getHeight() -1;
\r
1182 if (stretchGroup.getEndRes() == res)
\r
1184 // Edit end res position of selected group
\r
1185 changeEndRes = true;
\r
1187 else if (stretchGroup.getStartRes() == res)
\r
1189 // Edit start res position of selected group
\r
1190 changeStartRes = true;
\r
1193 if (res < av.getStartRes())
\r
1195 res = av.getStartRes();
\r
1200 if (res > (stretchGroup.getStartRes() - 1))
\r
1202 stretchGroup.setEndRes(res);
\r
1205 else if (changeStartRes)
\r
1207 if (res < (stretchGroup.getEndRes() + 1))
\r
1209 stretchGroup.setStartRes(res);
\r
1213 int dragDirection = 0;
\r
1217 dragDirection = 1;
\r
1219 else if (y < oldSeq)
\r
1221 dragDirection = -1;
\r
1225 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1227 // This routine ensures we don't skip any sequences, as the
\r
1228 // selection is quite slow.
\r
1229 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1231 oldSeq += dragDirection;
\r
1236 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1238 if (stretchGroup.sequences.contains(nextSeq))
\r
1240 stretchGroup.deleteSequence(seq, false);
\r
1246 stretchGroup.addSequence(seq, false);
\r
1249 stretchGroup.addSequence(nextSeq, false);
\r
1256 mouseDragging = true;
\r
1258 if (scrollThread != null)
\r
1260 scrollThread.setEvent(evt);
\r
1263 seqCanvas.repaint();
\r
1268 // this class allows scrolling off the bottom of the visible alignment
\r
1269 class ScrollThread extends Thread
\r
1272 boolean running = false;
\r
1274 public ScrollThread()
\r
1279 public void setEvent(MouseEvent e)
\r
1284 public void stopScrolling()
\r
1297 if (mouseDragging && (evt.getY() < 0) &&
\r
1298 (av.getStartSeq() > 0))
\r
1300 running = ap.scrollUp(true);
\r
1303 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1304 (av.alignment.getHeight() > av.getEndSeq()))
\r
1306 running = ap.scrollUp(false);
\r
1309 if (mouseDragging && (evt.getX() < 0))
\r
1311 running = ap.scrollRight(false);
\r
1313 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1315 running = ap.scrollRight(true);
\r
1323 catch (Exception ex)
\r