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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20 package jalview.appletgui;
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23 import java.awt.event.*;
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25 import jalview.datamodel.*;
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26 import jalview.schemes.*;
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28 public class SeqPanel
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29 extends Panel implements MouseMotionListener, MouseListener
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32 public SeqCanvas seqCanvas;
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33 public AlignmentPanel ap;
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35 protected int lastres;
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36 protected int startseq;
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38 protected AlignViewport av;
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40 // if character is inserted or deleted, we will need to recalculate the conservation
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41 boolean seqEditOccurred = false;
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43 ScrollThread scrollThread = null;
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44 boolean mouseDragging = false;
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45 boolean editingSeqs = false;
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46 boolean groupEditing = false;
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49 boolean changeEndSeq = false;
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50 boolean changeStartSeq = false;
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51 boolean changeEndRes = false;
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52 boolean changeStartRes = false;
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53 SequenceGroup stretchGroup = null;
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55 StringBuffer keyboardNo1;
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56 StringBuffer keyboardNo2;
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58 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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62 seqCanvas = new SeqCanvas(avp);
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63 setLayout(new BorderLayout());
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68 seqCanvas.addMouseMotionListener(this);
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69 seqCanvas.addMouseListener(this);
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71 seqCanvas.repaint();
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78 seqEditOccurred = false;
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79 editingSeqs = false;
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80 groupEditing = false;
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87 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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91 void setCursorColumn()
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93 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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97 void setCursorRowAndColumn()
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99 if(keyboardNo2==null)
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101 keyboardNo2 = new StringBuffer();
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105 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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106 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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111 void setCursorPosition()
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113 SequenceI sequence =
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114 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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116 seqCanvas.cursorX = sequence.findIndex(
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117 getKeyboardNo(keyboardNo1)-1
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122 void moveCursor(int dx, int dy)
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124 seqCanvas.cursorX += dx;
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125 seqCanvas.cursorY += dy;
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129 void scrollToVisible()
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131 if (seqCanvas.cursorX < 0)
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132 seqCanvas.cursorX = 0;
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133 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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134 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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136 if (seqCanvas.cursorY < 0)
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137 seqCanvas.cursorY = 0;
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138 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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139 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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143 if (av.wrapAlignment)
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145 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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149 while (seqCanvas.cursorY < av.startSeq)
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153 while (seqCanvas.cursorY + 1 > av.endSeq)
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155 ap.scrollUp(false);
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157 while (seqCanvas.cursorX < av.startRes)
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160 if (!ap.scrollRight(false))
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163 while (seqCanvas.cursorX > av.endRes)
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165 if (!ap.scrollRight(true))
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169 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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170 seqCanvas.cursorX, seqCanvas.cursorY);
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172 seqCanvas.repaint();
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175 void setSelectionAreaAtCursor(boolean topLeft)
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177 SequenceI sequence =
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178 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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180 if(av.getSelectionGroup()!=null)
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182 SequenceGroup sg = av.selectionGroup;
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183 //Find the top and bottom of this group
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184 int min = av.alignment.getHeight(), max = 0;
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185 for(int i=0; i<sg.getSize(); i++)
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187 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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198 sg.setStartRes(seqCanvas.cursorX);
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199 if(sg.getEndRes()<seqCanvas.cursorX)
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200 sg.setEndRes(seqCanvas.cursorX);
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202 min = seqCanvas.cursorY;
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206 sg.setEndRes(seqCanvas.cursorX);
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207 if(sg.getStartRes()>seqCanvas.cursorX)
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208 sg.setStartRes(seqCanvas.cursorX);
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210 max = seqCanvas.cursorY+1;
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215 // Only the user can do this
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216 av.setSelectionGroup(null);
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220 // Now add any sequences between min and max
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221 sg.sequences.removeAllElements();
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222 for (int i = min; i < max; i++)
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224 sg.addSequence(av.alignment.getSequenceAt(i), false);
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229 if (av.getSelectionGroup() == null)
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231 SequenceGroup sg = new SequenceGroup();
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232 sg.setStartRes(seqCanvas.cursorX);
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233 sg.setEndRes(seqCanvas.cursorX);
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234 sg.addSequence(sequence, false);
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235 av.setSelectionGroup(sg);
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242 void insertGapAtCursor(boolean group)
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244 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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245 av.alignment, HistoryItem.EDIT));
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246 groupEditing = group;
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247 startseq = seqCanvas.cursorY;
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248 lastres = seqCanvas.cursorX;
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249 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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253 void deleteGapAtCursor(boolean group)
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255 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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256 av.alignment, HistoryItem.EDIT));
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257 groupEditing = group;
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258 startseq = seqCanvas.cursorY;
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259 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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260 editSequence(false, seqCanvas.cursorX);
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264 void numberPressed(char value)
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266 if(keyboardNo1==null)
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267 keyboardNo1 = new StringBuffer();
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269 if(keyboardNo2!=null)
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270 keyboardNo2.append(value);
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272 keyboardNo1.append(value);
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275 int getKeyboardNo(StringBuffer kb)
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280 return Integer.parseInt(kb.toString());
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283 void setStatusMessage(SequenceI sequence, int res, int seq)
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285 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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286 sequence.getName());
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289 if (av.alignment.isNucleotide())
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291 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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294 text.append(" Nucleotide: ");
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298 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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300 text.append(" Residue: ");
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308 text.append(obj + " (" + sequence.findPosition(res) +
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312 ap.alignFrame.statusBar.setText(text.toString());
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315 public void mousePressed(MouseEvent evt)
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317 if (evt.isShiftDown() || evt.isAltDown() ||
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318 evt.isControlDown())
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320 if (evt.isAltDown() || evt.isControlDown())
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322 groupEditing = true;
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324 editingSeqs = true;
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328 doMousePressedDefineMode(evt);
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333 int seq = findSeq(evt);
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334 int res = findRes(evt);
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339 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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340 av.alignment, HistoryItem.EDIT));
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342 if ((seq < av.getAlignment().getHeight()) &&
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343 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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357 public void mouseClicked(MouseEvent evt){}
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360 public void mouseReleased(MouseEvent evt)
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362 mouseDragging = false;
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366 doMouseReleasedDefineMode(evt);
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376 int startWrapBlock=-1;
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377 int wrappedBlock=-1;
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378 int findRes(MouseEvent evt)
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381 int x = evt.getX();
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383 if (av.wrapAlignment)
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386 int hgap = av.charHeight;
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387 if (av.scaleAboveWrapped)
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388 hgap += av.charHeight;
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390 int cHeight = av.getAlignment().getHeight() * av.charHeight
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391 + hgap + seqCanvas.getAnnotationHeight();
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393 int y = evt.getY();
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395 x -= seqCanvas.LABEL_WEST;
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398 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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400 wrappedBlock = y / cHeight;
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401 wrappedBlock += av.getStartRes() / cwidth;
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403 res = wrappedBlock * cwidth + x / av.getCharWidth();
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408 res = (x / av.getCharWidth()) + av.getStartRes();
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415 int findSeq(MouseEvent evt)
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419 int y = evt.getY();
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421 if (av.wrapAlignment)
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423 int hgap = av.charHeight;
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424 if (av.scaleAboveWrapped)
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425 hgap += av.charHeight;
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427 int cHeight = av.getAlignment().getHeight() * av.charHeight
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428 + hgap + seqCanvas.getAnnotationHeight();
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432 seq = ( (y % cHeight) / av.getCharHeight());
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436 seq = (y / av.getCharHeight()) + av.getStartSeq();
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443 public void doMousePressed(MouseEvent evt)
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445 ap.alignFrame.addHistoryItem(new HistoryItem(
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446 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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448 int seq = findSeq(evt);
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449 int res = findRes(evt);
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451 if (seq < av.getAlignment().getHeight() &&
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452 res < av.getAlignment().getSequenceAt(seq).getLength())
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454 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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455 // Find the residue's position in the sequence (res is the position
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456 // in the alignment
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470 public void mouseMoved(MouseEvent evt)
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472 int res = findRes(evt);
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473 int seq = findSeq(evt);
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475 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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480 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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481 if (res > sequence.getLength())
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486 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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487 sequence.getName());
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490 if (av.alignment.isNucleotide())
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492 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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495 text.append(" Nucleotide: ");
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499 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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501 text.append(" Residue: ");
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509 text.append(obj + " (" +
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510 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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514 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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516 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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520 // use aa to see if the mouse pointer is on a
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521 if (av.showSequenceFeatures
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522 && sequence.getSequenceFeatures()!=null
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523 && av.featuresDisplayed!=null)
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526 sequence.getSequenceFeatures();
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527 boolean first = true;
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528 while (index < sequence.getSequenceFeatures().length)
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530 SequenceFeature sf = sequence.getSequenceFeatures()[index];
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531 if (sf.getBegin() <= sequence.findPosition(res) &&
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532 sf.getEnd() >= sequence.findPosition(res))
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534 if(!av.featuresDisplayed.containsKey(sf.getType()))
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542 text.append(" Sequence Feature:");
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546 text.append(" "+sf.getType());
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548 if(sf.getDescription()!=null)
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549 text.append(" "+sf.getDescription());
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551 if (sf.getStatus()!=null && sf.getStatus().length() > 0)
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553 text.append(" (" + sf.getStatus() + ")");
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563 ap.alignFrame.statusBar.setText(text.toString());
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567 public void mouseDragged(MouseEvent evt)
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571 doMouseDraggedDefineMode(evt);
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575 int res = findRes(evt);
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582 if ((lastres == -1) || (lastres == res))
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587 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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589 // dragLeft, delete gap
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590 editSequence(false, res);
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593 editSequence(true, res);
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595 mouseDragging = true;
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596 if(scrollThread!=null)
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597 scrollThread.setEvent(evt);
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601 synchronized void editSequence(boolean insertGap, int startres)
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603 int fixedLeft = -1;
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604 int fixedRight = -1;
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605 boolean fixedColumns = false;
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606 SequenceGroup sg = av.getSelectionGroup();
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608 if(groupEditing && sg==null)
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611 SequenceI seq = av.alignment.getSequenceAt(startseq);
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612 StringBuffer message = new StringBuffer();
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614 message.append("Edit group:");
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616 message.append("Edit sequence: "+seq.getName());
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619 message.append(" insert ");
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621 message.append(" delete ");
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623 message.append(Math.abs(startres-lastres)+" gaps.");
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624 ap.alignFrame.statusBar.setText(message.toString());
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627 //Are we editing within a selection group?
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629 || (sg != null && sg.sequences.contains(seq)))
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631 fixedColumns = true;
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633 fixedLeft = sg.getStartRes();
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634 fixedRight = sg.getEndRes();
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636 if ( (startres < fixedLeft && lastres >= fixedLeft)
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637 || (startres >= fixedLeft && lastres < fixedLeft)
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638 || (startres > fixedRight && lastres <=fixedRight)
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639 || (startres <= fixedRight && lastres > fixedRight))
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645 if (fixedLeft > startres)
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647 fixedRight = fixedLeft - 1;
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650 else if (fixedRight < startres)
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652 fixedLeft = fixedRight;
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663 //If the user has selected the whole sequence, and is dragging to
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664 // the right, we can still extend the alignment and selectionGroup
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665 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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667 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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668 fixedRight = sg.getEndRes();
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671 // Is it valid with fixed columns??
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672 // Find the next gap before the end
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673 // of the visible region boundary
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674 boolean blank = false;
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675 for (fixedRight = fixedRight;
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676 fixedRight > lastres;
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680 for (int s = 0; s < sg.getSize(); s++)
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682 seq = sg.getSequenceAt(s);
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683 for (int j = 0; j < startres - lastres; j++)
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685 if (!jalview.util.Comparison.isGap(
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686 seq.getCharAt(fixedRight - j)))
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699 if(sg.getSize() == av.alignment.getHeight())
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701 //We can still insert gaps if the selectionGroup
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702 //contains all the sequences
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703 sg.setEndRes(sg.getEndRes()+startres-lastres);
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704 fixedRight = av.alignment.getWidth()+startres-lastres;
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716 else if(!insertGap)
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718 /// Are we able to delete?
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719 // ie are all columns blank?
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721 for (int s = 0; s < sg.getSize(); s++)
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723 seq = sg.getSequenceAt(s);
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725 for (int j = startres; j < lastres; j++)
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727 if (seq.getSequence().length() <= j)
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732 if (!jalview.util.Comparison.isGap(
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733 seq.getSequence().charAt(j)))
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735 // Not a gap, block edit not valid
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744 for (int i = 0; i < sg.getSize(); i++)
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746 seq = sg.getSequenceAt(i);
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750 // dragging to the right
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751 for (int j = lastres; j < startres; j++)
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753 if (fixedColumns && fixedRight != -1)
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755 insertChar(j, seq, fixedRight);
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758 insertChar(j, seq);
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763 // dragging to the left
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764 for (int j = lastres; j > startres; j--)
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766 if (fixedColumns && fixedRight != -1)
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768 deleteChar(startres, seq, fixedRight);
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772 deleteChar(startres, seq);
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778 else /////Editing a single sequence///////////
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782 // dragging to the right
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783 for (int j = lastres; j < startres; j++)
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785 if (fixedColumns && fixedRight != -1)
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787 if (sg.getStartRes() == 0
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788 && sg.getEndRes() + 1 == av.alignment.getWidth()
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789 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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791 //Single sequence edit, whole sequence selected,
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792 //extend the selection group
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793 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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794 fixedColumns = false;
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795 insertChar(j, seq);
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798 insertChar(j, seq, fixedRight);
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801 insertChar(j, seq);
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806 // dragging to the left
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807 for (int j = lastres; j > startres; j--)
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809 if (fixedColumns && fixedRight != -1)
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811 deleteChar(startres, seq, fixedRight);
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815 deleteChar(startres, seq);
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821 lastres = startres;
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822 seqCanvas.repaint();
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829 * @param j DOCUMENT ME!
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830 * @param seq DOCUMENT ME!
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832 void insertChar(int j, SequenceI seq)
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834 seq.insertCharAt(j, av.getGapCharacter());
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835 seqEditOccurred = true;
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838 void insertChar(int j, SequenceI seq, int fixedColumn)
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840 //Find the next gap before the end of the visible region boundary
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841 //If lastCol > j, theres a boundary after the gap insertion
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842 int blankColumn = fixedColumn;
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843 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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845 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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847 //Theres a space, so break and insert the gap
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852 if (blankColumn <= j)
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858 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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861 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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865 seq.deleteCharAt(blankColumn);
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866 seq.insertCharAt(j, av.getGapCharacter());
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867 seqEditOccurred = true;
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870 void deleteChar(int j, SequenceI seq, int fixedColumn)
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872 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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874 ap.alignFrame.statusBar.setText(
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875 "End editing: Tried removing residue " + seq.getCharAt(j));
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879 seq.deleteCharAt(j);
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880 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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881 seqEditOccurred = true;
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887 * @param j DOCUMENT ME!
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888 * @param seq DOCUMENT ME!
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890 void deleteChar(int j, SequenceI seq)
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892 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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894 ap.alignFrame.statusBar.setText(
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895 "End editing: Tried removing residue " + seq.getCharAt(j));
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899 seq.deleteCharAt(j);
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900 seqEditOccurred = true;
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901 seqCanvas.repaint();
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907 * @param i DOCUMENT ME!
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909 void editOccurred()
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911 if (!seqEditOccurred)
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913 ap.alignFrame.historyList.pop();
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914 ap.alignFrame.updateEditMenuBar();
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919 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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923 //////////////////////////////////////////
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924 /////Everything below this is for defining the boundary of the rubberband
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925 //////////////////////////////////////////
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926 public void doMousePressedDefineMode(MouseEvent evt)
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928 if (scrollThread != null)
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930 scrollThread.running = false;
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931 scrollThread = null;
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934 int res = findRes(evt);
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935 int seq = findSeq(evt);
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937 startWrapBlock=wrappedBlock;
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942 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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944 if (sequence == null || res > sequence.getLength())
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949 stretchGroup = av.getSelectionGroup();
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951 if (stretchGroup == null)
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953 stretchGroup = av.alignment.findGroup(sequence);
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954 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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955 res < stretchGroup.getEndRes())
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957 av.setSelectionGroup(stretchGroup);
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961 stretchGroup = null;
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965 else if (!stretchGroup.sequences.contains(sequence)
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966 || stretchGroup.getStartRes() > res
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967 || stretchGroup.getEndRes() < res)
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969 stretchGroup = null;
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971 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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973 if (allGroups != null)
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975 for (int i = 0; i < allGroups.length; i++)
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977 if (allGroups[i].getStartRes() <= res &&
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978 allGroups[i].getEndRes() >= res)
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980 stretchGroup = allGroups[i];
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981 av.setSelectionGroup(stretchGroup);
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988 if (stretchGroup == null)
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990 // define a new group here
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991 SequenceGroup sg = new SequenceGroup();
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992 sg.setStartRes(res);
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994 sg.addSequence(sequence, false);
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995 av.setSelectionGroup(sg);
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998 if (av.getConservationSelected())
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1000 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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1003 if (av.getAbovePIDThreshold())
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1005 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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1011 // DETECT RIGHT MOUSE BUTTON IN AWT
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1012 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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1013 InputEvent.BUTTON3_MASK)
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1015 APopupMenu popup = new APopupMenu(ap, null, null);
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1017 popup.show(this, evt.getX(), evt.getY());
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1020 if (stretchGroup != null && stretchGroup.getEndRes() == res)
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1022 // Edit end res position of selected group
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1023 changeEndRes = true;
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1026 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
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1028 // Edit end res position of selected group
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1029 changeStartRes = true;
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1034 public void doMouseReleasedDefineMode(MouseEvent evt)
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1036 if (stretchGroup == null)
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1041 if(stretchGroup.cs!=null)
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1043 if (stretchGroup.cs instanceof ClustalxColourScheme)
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1045 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
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1047 stretchGroup.getWidth());
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1050 if (stretchGroup.cs.conservationApplied())
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1052 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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1053 stretchGroup.getName());
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1054 stretchGroup.recalcConservation();
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1058 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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1059 stretchGroup.getName());
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1062 changeEndRes = false;
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1063 changeStartRes = false;
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1064 stretchGroup = null;
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1065 PaintRefresher.Refresh(av.alignment);
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1069 public void doMouseDraggedDefineMode(MouseEvent evt)
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1071 int res = findRes(evt);
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1072 int y = findSeq(evt);
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1074 if(wrappedBlock!=startWrapBlock)
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1077 if (stretchGroup == null)
\r
1082 mouseDragging = true;
\r
1085 if(y > av.alignment.getHeight())
\r
1087 y = av.alignment.getHeight() -1;
\r
1090 if(res>av.alignment.getWidth())
\r
1091 res = av.alignment.getWidth()-1;
\r
1093 if (stretchGroup.getEndRes() == res)
\r
1095 // Edit end res position of selected group
\r
1096 changeEndRes = true;
\r
1098 else if (stretchGroup.getStartRes() == res)
\r
1100 // Edit start res position of selected group
\r
1101 changeStartRes = true;
\r
1111 if (res > (stretchGroup.getStartRes() - 1))
\r
1113 stretchGroup.setEndRes(res);
\r
1116 else if (changeStartRes)
\r
1118 if (res < (stretchGroup.getEndRes() + 1))
\r
1120 stretchGroup.setStartRes(res);
\r
1124 int dragDirection = 0;
\r
1128 dragDirection = 1;
\r
1130 else if (y < oldSeq)
\r
1132 dragDirection = -1;
\r
1136 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1138 // This routine ensures we don't skip any sequences, as the
\r
1139 // selection is quite slow.
\r
1140 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1142 oldSeq += dragDirection;
\r
1147 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1149 if (stretchGroup.sequences.contains(nextSeq))
\r
1151 stretchGroup.deleteSequence(seq, false);
\r
1157 stretchGroup.addSequence(seq, false);
\r
1160 stretchGroup.addSequence(nextSeq, false);
\r
1168 if(res>av.endRes || res<av.startRes
\r
1169 || y<av.startSeq || y>av.endSeq)
\r
1174 if (scrollThread != null)
\r
1176 scrollThread.setEvent(evt);
\r
1179 seqCanvas.repaint();
\r
1182 public void mouseEntered(MouseEvent e)
\r
1187 if (scrollThread != null)
\r
1189 scrollThread.running = false;
\r
1190 scrollThread = null;
\r
1194 public void mouseExited(MouseEvent e)
\r
1196 if (av.getWrapAlignment())
\r
1201 if (mouseDragging && scrollThread==null)
\r
1203 scrollThread = new ScrollThread();
\r
1207 // this class allows scrolling off the bottom of the visible alignment
\r
1208 class ScrollThread
\r
1212 boolean running = false;
\r
1213 public ScrollThread()
\r
1218 public void setEvent(MouseEvent e)
\r
1223 public void stopScrolling()
\r
1237 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1239 running = ap.scrollUp(true);
\r
1242 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1243 av.alignment.getHeight() > av.getEndSeq())
\r
1245 running = ap.scrollUp(false);
\r
1248 if (mouseDragging && evt.getX() < 0)
\r
1250 running = ap.scrollRight(true);
\r
1253 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1255 running = ap.scrollRight(false);
\r
1263 catch (Exception ex)
\r