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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69 StringBuffer keyboardNo1;
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70 StringBuffer keyboardNo2;
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73 * Creates a new SeqPanel object.
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75 * @param avp DOCUMENT ME!
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76 * @param p DOCUMENT ME!
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78 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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80 ToolTipManager.sharedInstance().registerComponent(this);
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81 ToolTipManager.sharedInstance().setInitialDelay(0);
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82 ToolTipManager.sharedInstance().setDismissDelay(10000);
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84 setBackground(Color.white);
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86 seqCanvas = new SeqCanvas(avp);
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87 setLayout(new BorderLayout());
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88 add(seqCanvas, BorderLayout.CENTER);
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94 addMouseMotionListener(this);
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95 addMouseListener(this);
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96 addMouseWheelListener(this);
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100 int startWrapBlock=-1;
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101 int wrappedBlock=-1;
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102 int findRes(MouseEvent evt)
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105 int x = evt.getX();
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107 if (av.wrapAlignment)
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110 int hgap = av.charHeight;
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111 if (av.scaleAboveWrapped)
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112 hgap += av.charHeight;
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114 int cHeight = av.getAlignment().getHeight() * av.charHeight
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115 + hgap + seqCanvas.getAnnotationHeight();
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117 int y = evt.getY();
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119 x -= seqCanvas.LABEL_WEST;
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122 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
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124 wrappedBlock = y / cHeight;
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125 wrappedBlock += av.getStartRes() / cwidth;
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127 res = wrappedBlock * cwidth + x / av.getCharWidth();
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132 res = (x / av.getCharWidth()) + av.getStartRes();
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135 if(av.hasHiddenColumns)
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136 res = av.getColumnSelection().adjustForHiddenColumns(res);
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142 int findSeq(MouseEvent evt)
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146 int y = evt.getY();
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148 if (av.wrapAlignment)
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150 int hgap = av.charHeight;
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151 if (av.scaleAboveWrapped)
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152 hgap += av.charHeight;
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154 int cHeight = av.getAlignment().getHeight() * av.charHeight
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155 + hgap + seqCanvas.getAnnotationHeight();
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159 seq = ( (y % cHeight) / av.getCharHeight());
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163 seq = (y / av.getCharHeight()) + av.getStartSeq();
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173 seqEditOccurred = false;
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174 editingSeqs = false;
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175 groupEditing = false;
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176 keyboardNo1 = null;
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177 keyboardNo2 = null;
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180 void setCursorRow()
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182 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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186 void setCursorColumn()
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188 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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192 void setCursorRowAndColumn()
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194 if(keyboardNo2==null)
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196 keyboardNo2 = new StringBuffer();
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200 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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201 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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206 void setCursorPosition()
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208 SequenceI sequence =
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209 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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211 seqCanvas.cursorX = sequence.findIndex(
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212 getKeyboardNo(keyboardNo1)-1
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217 void moveCursor(int dx, int dy)
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219 seqCanvas.cursorX += dx;
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220 seqCanvas.cursorY += dy;
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224 void scrollToVisible()
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226 if (seqCanvas.cursorX < 0)
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227 seqCanvas.cursorX = 0;
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228 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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229 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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231 if (seqCanvas.cursorY < 0)
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232 seqCanvas.cursorY = 0;
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233 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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234 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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238 while (seqCanvas.cursorY < av.startSeq)
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242 while (seqCanvas.cursorY + 1 > av.endSeq)
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244 ap.scrollUp(false);
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246 while (seqCanvas.cursorX < av.startRes)
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248 if(!ap.scrollRight(false))
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251 while (seqCanvas.cursorX > av.endRes)
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253 if(!ap.scrollRight(true))
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257 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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258 seqCanvas.cursorX, seqCanvas.cursorY);
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260 seqCanvas.repaint();
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263 void setSelectionAreaAtCursor(boolean topLeft)
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265 SequenceI sequence =
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266 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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268 if(av.getSelectionGroup()!=null)
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270 SequenceGroup sg = av.selectionGroup;
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271 //Find the top and bottom of this group
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272 int min = av.alignment.getHeight(), max = 0;
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273 for(int i=0; i<sg.getSize(); i++)
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275 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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286 sg.setStartRes(seqCanvas.cursorX);
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287 if(sg.getEndRes()<seqCanvas.cursorX)
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288 sg.setEndRes(seqCanvas.cursorX);
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290 min = seqCanvas.cursorY;
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294 sg.setEndRes(seqCanvas.cursorX);
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295 if(sg.getStartRes()>seqCanvas.cursorX)
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296 sg.setStartRes(seqCanvas.cursorX);
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298 max = seqCanvas.cursorY+1;
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303 // Only the user can do this
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304 av.setSelectionGroup(null);
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308 // Now add any sequences between min and max
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309 sg.sequences.clear();
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310 for (int i = min; i < max; i++)
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312 sg.addSequence(av.alignment.getSequenceAt(i), false);
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317 if (av.getSelectionGroup() == null)
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319 SequenceGroup sg = new SequenceGroup();
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320 sg.setStartRes(seqCanvas.cursorX);
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321 sg.setEndRes(seqCanvas.cursorX);
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322 sg.addSequence(sequence, false);
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323 av.setSelectionGroup(sg);
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330 void insertGapAtCursor(boolean group)
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332 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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333 av.alignment, HistoryItem.EDIT));
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334 groupEditing = group;
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335 startseq = seqCanvas.cursorY;
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336 lastres = seqCanvas.cursorX;
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337 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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341 void deleteGapAtCursor(boolean group)
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343 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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344 av.alignment, HistoryItem.EDIT));
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345 groupEditing = group;
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346 startseq = seqCanvas.cursorY;
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347 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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348 editSequence(false, seqCanvas.cursorX);
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352 void numberPressed(char value)
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354 if(keyboardNo1==null)
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355 keyboardNo1 = new StringBuffer();
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357 if(keyboardNo2!=null)
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358 keyboardNo2.append(value);
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360 keyboardNo1.append(value);
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363 int getKeyboardNo(StringBuffer kb)
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368 return Integer.parseInt(kb.toString());
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375 * @param evt DOCUMENT ME!
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377 public void mouseReleased(MouseEvent evt)
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379 mouseDragging = false;
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380 mouseWheelPressed = false;
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384 doMouseReleasedDefineMode(evt);
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399 * @param evt DOCUMENT ME!
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401 public void mousePressed(MouseEvent evt)
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403 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
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405 mouseWheelPressed = true;
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409 if (evt.isShiftDown() || evt.isAltDown() ||
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410 evt.isControlDown())
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412 if (evt.isAltDown() || evt.isControlDown())
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414 groupEditing = true;
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416 editingSeqs = true;
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420 doMousePressedDefineMode(evt);
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426 int seq = findSeq(evt);
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427 int res = findRes(evt);
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432 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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433 av.alignment, HistoryItem.EDIT));
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435 if ((seq < av.getAlignment().getHeight()) &&
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436 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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453 * @param evt DOCUMENT ME!
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455 public void mouseMoved(MouseEvent evt)
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459 // This is because MacOSX creates a mouseMoved
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460 // If control is down, other platforms will not.
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464 int res = findRes(evt);
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465 int seq = findSeq(evt);
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468 if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
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471 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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473 if (res > sequence.getLength())
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478 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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480 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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483 setStatusMessage(sequence, res, seq);
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485 // use aa to see if the mouse pointer is on a
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486 if (av.showSequenceFeatures)
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488 SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
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491 StringBuffer sbuffer = new StringBuffer("<html>");
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493 for (int i = 0; i < features.length; i++)
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496 if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
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497 (features[i].getEnd() >= sequence.findPosition(res)))
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499 if(av.featuresDisplayed==null
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500 || !av.featuresDisplayed.containsKey(features[i].getType()))
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504 if (features[i].getType().equals("disulfide bond"))
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506 if (features[i].getBegin() == sequence.findPosition(res)
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507 || features[i].getEnd() == sequence.findPosition(res))
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509 if (sbuffer.length() > 6)
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510 sbuffer.append("<br>");
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511 sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
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512 features[i].getEnd());
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517 if (sbuffer.length() > 6)
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518 sbuffer.append("<br>");
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519 if(features[i].featureGroup!=null)
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520 sbuffer.append(features[i].featureGroup+";");
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522 sbuffer.append(features[i].getType());
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524 if (features[i].getDescription() != null
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525 && !features[i].description.equals(features[i].getType()))
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526 sbuffer.append("; " + features[i].getDescription());
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528 if (features[i].getStatus() != null && features[i].getStatus().length()>0)
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530 sbuffer.append("; (" + features[i].getStatus() + ")");
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537 sbuffer.append("</html>");
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538 if(sbuffer.length()==13) // <html></html>
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539 setToolTipText("");
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541 setToolTipText(sbuffer.toString());
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544 setToolTipText("");
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548 void setStatusMessage(SequenceI sequence, int res, int seq)
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550 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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551 sequence.getName());
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554 if (av.alignment.isNucleotide())
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556 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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559 text.append(" Nucleotide: ");
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563 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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565 text.append(" Residue: ");
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573 text.append(obj + " (" + sequence.findPosition(res) +
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577 ap.alignFrame.statusBar.setText(text.toString());
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584 * @param evt DOCUMENT ME!
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586 public void mouseDragged(MouseEvent evt)
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590 doMouseDraggedDefineMode(evt);
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594 int res = findRes(evt);
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601 if ((lastres == -1) || (lastres == res))
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606 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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608 // dragLeft, delete gap
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609 editSequence(false, res);
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612 editSequence(true, res);
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614 mouseDragging = true;
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615 if(scrollThread!=null)
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616 scrollThread.setEvent(evt);
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620 synchronized void editSequence(boolean insertGap, int startres)
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622 int fixedLeft = -1;
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623 int fixedRight = -1;
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624 boolean fixedColumns = false;
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625 SequenceGroup sg = av.getSelectionGroup();
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627 if(groupEditing && sg==null)
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630 if (!groupEditing && av.hasHiddenRows)
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632 //This needs to check all the sequences in a group edit,m
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633 // not just the startseq
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634 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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636 groupEditing = true;
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640 SequenceI seq = av.alignment.getSequenceAt(startseq);
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641 StringBuffer message = new StringBuffer();
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643 message.append("Edit group:");
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645 message.append("Edit sequence: "+seq.getName());
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648 message.append(" insert ");
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650 message.append(" delete ");
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652 message.append(Math.abs(startres-lastres)+" gaps.");
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653 ap.alignFrame.statusBar.setText(message.toString());
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656 //Are we editing within a selection group?
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658 || (sg != null && sg.sequences.contains(seq)))
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660 fixedColumns = true;
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662 fixedLeft = sg.getStartRes();
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663 fixedRight = sg.getEndRes();
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665 if ( (startres < fixedLeft && lastres >= fixedLeft)
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666 || (startres >= fixedLeft && lastres < fixedLeft)
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667 || (startres > fixedRight && lastres <=fixedRight)
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668 || (startres <= fixedRight && lastres > fixedRight))
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674 if (fixedLeft > startres)
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676 fixedRight = fixedLeft - 1;
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679 else if (fixedRight < startres)
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681 fixedLeft = fixedRight;
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688 if(av.hasHiddenColumns)
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690 fixedColumns = true;
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691 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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692 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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694 if( ( insertGap && startres>y1 && lastres<y1)
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695 || (!insertGap && startres<y2 && lastres>y2) )
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701 if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
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702 fixedRight = y2 -1;
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703 if(y1>fixedLeft && fixedLeft==-1)
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710 /*if (av.hasHiddenRows)
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712 //sg might be null as the user may only see 1 sequence
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715 sg = new SequenceGroup();
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716 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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719 SequenceGroup tmp = new SequenceGroup();
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721 //Do any of the sequences have hidden associates?
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722 for (int s = 0; s < sg.getSize(); s++)
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724 seq = sg.getSequenceAt(s);
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725 tmp.addSequence(seq, false);
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726 if (seq.getHiddenSequences() != null)
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728 for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
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729 tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
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736 // int blankColumn = -1;
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742 //If the user has selected the whole sequence, and is dragging to
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743 // the right, we can still extend the alignment and selectionGroup
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744 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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746 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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747 fixedRight = sg.getEndRes();
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750 // Is it valid with fixed columns??
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751 // Find the next gap before the end
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752 // of the visible region boundary
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753 boolean blank = false;
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754 for (fixedRight = fixedRight;
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755 fixedRight > lastres;
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759 for (int s = 0; s < sg.getSize(); s++)
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761 seq = sg.getSequenceAt(s);
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762 for (int j = 0; j < startres - lastres; j++)
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764 if (!jalview.util.Comparison.isGap(
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765 seq.getCharAt(fixedRight - j)))
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778 if(sg.getSize() == av.alignment.getHeight())
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780 //We can still insert gaps if the selectionGroup
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781 //contains all the sequences
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782 sg.setEndRes(sg.getEndRes()+1+startres-lastres);
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783 fixedRight = av.alignment.getWidth()+startres-lastres;
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795 else if(!insertGap)
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797 /// Are we able to delete?
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798 // ie are all columns blank?
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800 for (int s = 0; s < sg.getSize(); s++)
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802 seq = sg.getSequenceAt(s);
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804 for (int j = startres; j < lastres; j++)
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806 if (seq.getSequence().length() <= j)
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811 if (!jalview.util.Comparison.isGap(
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812 seq.getSequence().charAt(j)))
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814 // Not a gap, block edit not valid
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823 for (int i = 0; i < sg.getSize(); i++)
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825 seq = sg.getSequenceAt(i);
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829 // dragging to the right
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830 for (int j = lastres; j < startres; j++)
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832 if (fixedColumns && fixedRight != -1)
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834 insertChar(j, seq, fixedRight);
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837 insertChar(j, seq);
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842 // dragging to the left
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843 for (int j = lastres; j > startres; j--)
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845 if (fixedColumns && fixedRight != -1)
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847 deleteChar(startres, seq, fixedRight);
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851 deleteChar(startres, seq);
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857 else /////Editing a single sequence///////////
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861 // dragging to the right
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862 for (int j = lastres; j < startres; j++)
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864 if (fixedColumns && fixedRight != -1)
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866 if (sg.getStartRes() == 0
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867 && sg.getEndRes() + 1 == av.alignment.getWidth()
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868 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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870 //Single sequence edit, whole sequence selected,
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871 //extend the selection group
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872 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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873 fixedColumns = false;
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874 insertChar(j, seq);
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877 insertChar(j, seq, fixedRight);
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880 insertChar(j, seq);
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885 // dragging to the left
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886 for (int j = lastres; j > startres; j--)
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888 if (fixedColumns && fixedRight != -1)
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890 deleteChar(startres, seq, fixedRight);
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894 deleteChar(startres, seq);
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900 lastres = startres;
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901 seqCanvas.repaint();
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908 * @param j DOCUMENT ME!
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909 * @param seq DOCUMENT ME!
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911 void insertChar(int j, SequenceI seq)
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913 seq.insertCharAt(j, av.getGapCharacter());
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914 seqEditOccurred = true;
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917 void insertChar(int j, SequenceI seq, int fixedColumn)
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919 //Find the next gap before the end of the visible region boundary
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920 //If lastCol > j, theres a boundary after the gap insertion
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921 int blankColumn = fixedColumn;
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922 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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924 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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926 //Theres a space, so break and insert the gap
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931 if (blankColumn <= j)
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937 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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940 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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944 seq.deleteCharAt(blankColumn);
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945 seq.insertCharAt(j, av.getGapCharacter());
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946 seqEditOccurred = true;
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949 void deleteChar(int j, SequenceI seq, int fixedColumn)
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951 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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953 ap.alignFrame.statusBar.setText(
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954 "End editing: Tried removing residue " + seq.getCharAt(j));
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958 seq.deleteCharAt(j);
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959 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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960 seqEditOccurred = true;
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966 * @param j DOCUMENT ME!
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967 * @param seq DOCUMENT ME!
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969 void deleteChar(int j, SequenceI seq)
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971 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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973 ap.alignFrame.statusBar.setText(
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974 "End editing: Tried removing residue " + seq.getCharAt(j));
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978 seq.deleteCharAt(j);
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979 seqEditOccurred = true;
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980 seqCanvas.repaint();
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985 * @param e DOCUMENT ME!
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987 public void mouseEntered(MouseEvent e)
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992 if (scrollThread != null)
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994 scrollThread.running = false;
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995 scrollThread = null;
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1002 * @param e DOCUMENT ME!
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1004 public void mouseExited(MouseEvent e)
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1006 if (av.getWrapAlignment())
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1011 if (mouseDragging)
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1013 scrollThread = new ScrollThread();
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1017 public void mouseClicked(MouseEvent evt)
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1020 public void mouseWheelMoved(MouseWheelEvent e)
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1023 if (mouseWheelPressed)
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1025 Font font = av.getFont();
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1026 int fontSize = font.getSize();
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1027 if (e.getWheelRotation() > 0 && fontSize < 51)
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1029 else if (fontSize > 1)
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1032 av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
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1037 if (e.getWheelRotation() > 0)
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1038 ap.scrollUp(false);
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1040 ap.scrollUp(true);
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1050 * @param i DOCUMENT ME!
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1052 void editOccurred()
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1054 if (!seqEditOccurred)
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1056 ap.alignFrame.historyList.pop();
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1057 ap.alignFrame.updateEditMenuBar();
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1062 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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1069 * @param evt DOCUMENT ME!
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1071 public void doMousePressedDefineMode(MouseEvent evt)
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1073 int res = findRes(evt);
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1074 int seq = findSeq(evt);
\r
1077 startWrapBlock=wrappedBlock;
\r
1079 if(av.wrapAlignment && seq>av.alignment.getHeight())
\r
1081 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1082 "Cannot edit annotations in wrapped view.",
\r
1083 "Wrapped view - no edit",
\r
1084 JOptionPane.WARNING_MESSAGE);
\r
1088 if(seq<0 || res<0)
\r
1091 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1093 if ((sequence == null) || (res > sequence.getLength()))
\r
1098 stretchGroup = av.getSelectionGroup();
\r
1100 if (stretchGroup == null)
\r
1102 stretchGroup = av.alignment.findGroup(sequence);
\r
1104 if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
\r
1105 (res < stretchGroup.getEndRes()))
\r
1107 av.setSelectionGroup(stretchGroup);
\r
1111 stretchGroup = null;
\r
1114 else if (!stretchGroup.sequences.contains(sequence) ||
\r
1115 (stretchGroup.getStartRes() > res) ||
\r
1116 (stretchGroup.getEndRes() < res))
\r
1118 stretchGroup = null;
\r
1120 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1122 if (allGroups != null)
\r
1124 for (int i = 0; i < allGroups.length; i++)
\r
1126 if ((allGroups[i].getStartRes() <= res) &&
\r
1127 (allGroups[i].getEndRes() >= res))
\r
1129 stretchGroup = allGroups[i];
\r
1130 av.setSelectionGroup(stretchGroup);
\r
1138 if (av.cursorMode)
\r
1140 seqCanvas.cursorX = findRes(evt);
\r
1141 seqCanvas.cursorY = findSeq(evt);
\r
1142 seqCanvas.repaint();
\r
1147 if (stretchGroup == null)
\r
1149 // define a new group here
\r
1150 SequenceGroup sg = new SequenceGroup();
\r
1151 sg.setStartRes(res);
\r
1152 sg.setEndRes(res);
\r
1153 sg.addSequence(sequence, false);
\r
1154 av.setSelectionGroup(sg);
\r
1155 stretchGroup = sg;
\r
1157 if (av.getConservationSelected())
\r
1159 SliderPanel.setConservationSlider(ap,
\r
1160 av.getGlobalColourScheme(), "Background");
\r
1163 if (av.getAbovePIDThreshold())
\r
1165 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1169 else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
\r
1171 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
\r
1172 pop.show(this, evt.getX(), evt.getY());
\r
1174 // edit the properties of existing group
\r
1177 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
\r
1179 // Edit end res position of selected group
\r
1180 changeEndRes = true;
\r
1182 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
\r
1184 // Edit end res position of selected group
\r
1185 changeStartRes = true;
\r
1188 stretchGroup.getWidth();
\r
1190 seqCanvas.repaint();
\r
1196 * @param evt DOCUMENT ME!
\r
1198 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1200 if (stretchGroup == null)
\r
1206 if(stretchGroup.cs!=null)
\r
1208 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1210 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1212 stretchGroup.getWidth());
\r
1215 if (stretchGroup.cs.conservationApplied())
\r
1217 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1218 stretchGroup.getName());
\r
1219 stretchGroup.recalcConservation();
\r
1223 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1224 stretchGroup.getName());
\r
1227 changeEndRes = false;
\r
1228 changeStartRes = false;
\r
1229 stretchGroup = null;
\r
1230 PaintRefresher.Refresh(av.alignment);
\r
1236 * @param evt DOCUMENT ME!
\r
1238 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1240 int res = findRes(evt);
\r
1241 int y = findSeq(evt);
\r
1243 if(wrappedBlock!=startWrapBlock)
\r
1246 if (stretchGroup == null)
\r
1252 if(y > av.alignment.getHeight())
\r
1254 y = av.alignment.getHeight() -1;
\r
1256 if(res> av.alignment.getWidth())
\r
1258 res = av.alignment.getWidth()-1;
\r
1261 if (stretchGroup.getEndRes() == res)
\r
1263 // Edit end res position of selected group
\r
1264 changeEndRes = true;
\r
1266 else if (stretchGroup.getStartRes() == res)
\r
1268 // Edit start res position of selected group
\r
1269 changeStartRes = true;
\r
1272 if (res < av.getStartRes())
\r
1274 res = av.getStartRes();
\r
1279 if (res > (stretchGroup.getStartRes() - 1))
\r
1281 stretchGroup.setEndRes(res);
\r
1284 else if (changeStartRes)
\r
1286 if (res < (stretchGroup.getEndRes() + 1))
\r
1288 stretchGroup.setStartRes(res);
\r
1292 int dragDirection = 0;
\r
1296 dragDirection = 1;
\r
1298 else if (y < oldSeq)
\r
1300 dragDirection = -1;
\r
1304 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1306 // This routine ensures we don't skip any sequences, as the
\r
1307 // selection is quite slow.
\r
1308 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1310 oldSeq += dragDirection;
\r
1315 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1317 if (stretchGroup.sequences.contains(nextSeq))
\r
1319 stretchGroup.deleteSequence(seq, false);
\r
1325 stretchGroup.addSequence(seq, false);
\r
1328 stretchGroup.addSequence(nextSeq, false);
\r
1335 mouseDragging = true;
\r
1337 if (scrollThread != null)
\r
1339 scrollThread.setEvent(evt);
\r
1342 seqCanvas.repaint();
\r
1345 void scrollCanvas(MouseEvent evt)
\r
1349 if(scrollThread!=null)
\r
1351 scrollThread.running = false;
\r
1352 scrollThread = null;
\r
1354 mouseDragging = false;
\r
1358 if (scrollThread == null)
\r
1359 scrollThread = new ScrollThread();
\r
1361 mouseDragging = true;
\r
1362 scrollThread.setEvent(evt);
\r
1368 // this class allows scrolling off the bottom of the visible alignment
\r
1369 class ScrollThread extends Thread
\r
1372 boolean running = false;
\r
1374 public ScrollThread()
\r
1379 public void setEvent(MouseEvent e)
\r
1384 public void stopScrolling()
\r
1397 if (mouseDragging && (evt.getY() < 0) &&
\r
1398 (av.getStartSeq() > 0))
\r
1400 running = ap.scrollUp(true);
\r
1403 if (mouseDragging && (evt.getY() >= getHeight()) &&
\r
1404 (av.alignment.getHeight() > av.getEndSeq()))
\r
1406 running = ap.scrollUp(false);
\r
1409 if (mouseDragging && (evt.getX() < 0))
\r
1411 running = ap.scrollRight(false);
\r
1413 else if (mouseDragging && (evt.getX() >= getWidth()))
\r
1415 running = ap.scrollRight(true);
\r
1423 catch (Exception ex)
\r