2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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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 import java.util.Vector;
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30 public class SeqPanel
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31 extends Panel implements MouseMotionListener, MouseListener
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34 public SeqCanvas seqCanvas;
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35 public AlignmentPanel ap;
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37 protected int lastres;
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38 protected int startseq;
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40 protected AlignViewport av;
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42 // if character is inserted or deleted, we will need to recalculate the conservation
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43 boolean seqEditOccurred = false;
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45 ScrollThread scrollThread = null;
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46 boolean mouseDragging = false;
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47 boolean editingSeqs = false;
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48 boolean groupEditing = false;
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51 boolean changeEndSeq = false;
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52 boolean changeStartSeq = false;
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53 boolean changeEndRes = false;
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54 boolean changeStartRes = false;
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55 SequenceGroup stretchGroup = null;
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57 StringBuffer keyboardNo1;
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58 StringBuffer keyboardNo2;
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60 boolean mouseWheelPressed = false;
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61 Point lastMousePress;
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63 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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67 seqCanvas = new SeqCanvas(avp);
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68 setLayout(new BorderLayout());
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73 seqCanvas.addMouseMotionListener(this);
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74 seqCanvas.addMouseListener(this);
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76 seqCanvas.repaint();
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83 seqEditOccurred = false;
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84 editingSeqs = false;
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85 groupEditing = false;
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92 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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96 void setCursorColumn()
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98 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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102 void setCursorRowAndColumn()
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104 if(keyboardNo2==null)
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106 keyboardNo2 = new StringBuffer();
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110 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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111 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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116 void setCursorPosition()
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118 SequenceI sequence =
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119 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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121 seqCanvas.cursorX = sequence.findIndex(
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122 getKeyboardNo(keyboardNo1)-1
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127 void moveCursor(int dx, int dy)
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129 seqCanvas.cursorX += dx;
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130 seqCanvas.cursorY += dy;
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134 void scrollToVisible()
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136 if (seqCanvas.cursorX < 0)
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137 seqCanvas.cursorX = 0;
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138 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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139 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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141 if (seqCanvas.cursorY < 0)
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142 seqCanvas.cursorY = 0;
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143 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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144 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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148 if (av.wrapAlignment)
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150 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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154 while (seqCanvas.cursorY < av.startSeq)
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158 while (seqCanvas.cursorY + 1 > av.endSeq)
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160 ap.scrollUp(false);
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162 while (seqCanvas.cursorX < av.startRes)
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165 if (!ap.scrollRight(false))
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168 while (seqCanvas.cursorX > av.endRes)
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170 if (!ap.scrollRight(true))
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174 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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175 seqCanvas.cursorX, seqCanvas.cursorY);
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177 seqCanvas.repaint();
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180 void setSelectionAreaAtCursor(boolean topLeft)
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182 SequenceI sequence =
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183 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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185 if(av.getSelectionGroup()!=null)
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187 SequenceGroup sg = av.selectionGroup;
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188 //Find the top and bottom of this group
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189 int min = av.alignment.getHeight(), max = 0;
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190 for(int i=0; i<sg.getSize(false); i++)
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192 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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203 sg.setStartRes(seqCanvas.cursorX);
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204 if(sg.getEndRes()<seqCanvas.cursorX)
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205 sg.setEndRes(seqCanvas.cursorX);
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207 min = seqCanvas.cursorY;
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211 sg.setEndRes(seqCanvas.cursorX);
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212 if(sg.getStartRes()>seqCanvas.cursorX)
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213 sg.setStartRes(seqCanvas.cursorX);
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215 max = seqCanvas.cursorY+1;
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220 // Only the user can do this
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221 av.setSelectionGroup(null);
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225 // Now add any sequences between min and max
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226 sg.getSequences(false).removeAllElements();
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227 for (int i = min; i < max; i++)
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229 sg.addSequence(av.alignment.getSequenceAt(i), false);
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234 if (av.getSelectionGroup() == null)
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236 SequenceGroup sg = new SequenceGroup();
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237 sg.setStartRes(seqCanvas.cursorX);
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238 sg.setEndRes(seqCanvas.cursorX);
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239 sg.addSequence(sequence, false);
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240 av.setSelectionGroup(sg);
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247 void insertGapAtCursor(boolean group)
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249 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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250 av.alignment, HistoryItem.EDIT));
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251 groupEditing = group;
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252 startseq = seqCanvas.cursorY;
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253 lastres = seqCanvas.cursorX;
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254 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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258 void deleteGapAtCursor(boolean group)
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260 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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261 av.alignment, HistoryItem.EDIT));
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262 groupEditing = group;
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263 startseq = seqCanvas.cursorY;
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264 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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265 editSequence(false, seqCanvas.cursorX);
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269 void numberPressed(char value)
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271 if(keyboardNo1==null)
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272 keyboardNo1 = new StringBuffer();
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274 if(keyboardNo2!=null)
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275 keyboardNo2.append(value);
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277 keyboardNo1.append(value);
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280 int getKeyboardNo(StringBuffer kb)
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285 return Integer.parseInt(kb.toString());
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288 void setStatusMessage(SequenceI sequence, int res, int seq)
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290 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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291 sequence.getName());
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294 if (av.alignment.isNucleotide())
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296 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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299 text.append(" Nucleotide: ");
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303 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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305 text.append(" Residue: ");
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313 text.append(obj + " (" + sequence.findPosition(res) +
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318 ap.alignFrame.statusBar.setText(text.toString());
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321 public void mousePressed(MouseEvent evt)
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323 lastMousePress = evt.getPoint();
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325 //For now, ignore the mouseWheel font resizing on Macs
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326 //As the Button2_mask always seems to be true
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327 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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328 InputEvent.BUTTON2_MASK && !av.MAC)
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330 mouseWheelPressed = true;
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334 if (evt.isShiftDown()
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335 || evt.isControlDown()
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336 || evt.isAltDown())
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338 if (evt.isControlDown() || evt.isAltDown())
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340 groupEditing = true;
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342 editingSeqs = true;
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346 doMousePressedDefineMode(evt);
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351 int seq = findSeq(evt);
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352 int res = findRes(evt);
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357 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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358 av.alignment, HistoryItem.EDIT));
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360 if ((seq < av.getAlignment().getHeight()) &&
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361 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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375 public void mouseClicked(MouseEvent evt){}
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378 public void mouseReleased(MouseEvent evt)
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380 mouseDragging = false;
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381 mouseWheelPressed = false;
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385 doMouseReleasedDefineMode(evt);
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395 int startWrapBlock=-1;
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396 int wrappedBlock=-1;
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397 int findRes(MouseEvent evt)
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400 int x = evt.getX();
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402 if (av.wrapAlignment)
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405 int hgap = av.charHeight;
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406 if (av.scaleAboveWrapped)
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407 hgap += av.charHeight;
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409 int cHeight = av.getAlignment().getHeight() * av.charHeight
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410 + hgap + seqCanvas.getAnnotationHeight();
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412 int y = evt.getY();
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414 x -= seqCanvas.LABEL_WEST;
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417 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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421 wrappedBlock = y / cHeight;
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422 wrappedBlock += av.getStartRes() / cwidth;
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424 res = wrappedBlock * cwidth + x / av.getCharWidth();
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429 res = (x / av.getCharWidth()) + av.getStartRes();
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432 if(av.hasHiddenColumns)
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433 res = av.getColumnSelection().adjustForHiddenColumns(res);
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439 int findSeq(MouseEvent evt)
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443 int y = evt.getY();
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445 if (av.wrapAlignment)
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447 int hgap = av.charHeight;
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448 if (av.scaleAboveWrapped)
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449 hgap += av.charHeight;
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451 int cHeight = av.getAlignment().getHeight() * av.charHeight
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452 + hgap + seqCanvas.getAnnotationHeight();
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456 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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457 av.alignment.getHeight() -1);
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463 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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464 av.alignment.getHeight() -1);
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473 public void doMousePressed(MouseEvent evt)
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475 ap.alignFrame.addHistoryItem(new HistoryItem(
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476 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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478 int seq = findSeq(evt);
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479 int res = findRes(evt);
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481 if (seq < av.getAlignment().getHeight() &&
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482 res < av.getAlignment().getSequenceAt(seq).getLength())
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484 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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485 // Find the residue's position in the sequence (res is the position
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486 // in the alignment
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500 public void mouseMoved(MouseEvent evt)
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502 int res = findRes(evt);
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503 int seq = findSeq(evt);
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505 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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510 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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511 if (res > sequence.getLength())
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516 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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517 sequence.getName());
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520 if (av.alignment.isNucleotide())
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522 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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525 text.append(" Nucleotide: ");
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529 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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531 text.append(" Residue: ");
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538 text.append(obj + " (" + sequence.findPosition(res) + ")");
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542 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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544 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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547 ap.alignFrame.statusBar.setText(text.toString());
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550 // use aa to see if the mouse pointer is on a
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551 if (av.showSequenceFeatures
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552 && sequence.getSequenceFeatures()!=null
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553 && av.featuresDisplayed!=null)
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555 StringBuffer featureText = new StringBuffer();
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556 Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
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559 while (index < allFeatures.size())
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561 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
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563 featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
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565 if (sf.getDescription() != null)
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566 featureText.append(" " + sf.getDescription());
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568 if (sf.getValue("status") != null )
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570 String status = sf.getValue("status").toString();
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571 if(status.length()>0)
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572 featureText.append(" (" + sf.getValue("status") + ")");
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574 featureText.append("\n");
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580 if (tooltip == null)
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581 tooltip = new Tooltip(featureText.toString(), seqCanvas);
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583 tooltip.setTip(featureText.toString());
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588 else if (tooltip != null)
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590 tooltip.setTip("");
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594 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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596 Vector allFeatures = new Vector();
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598 if(seq.getSequenceFeatures()!=null)
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600 while (index < seq.getSequenceFeatures().length)
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602 SequenceFeature sf = seq.getSequenceFeatures()[index];
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603 if (sf.getBegin() <= res &&
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604 sf.getEnd() >= res)
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606 if (av.featuresDisplayed.containsKey(sf.getType()))
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608 allFeatures.addElement(sf);
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614 return allFeatures;
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619 public void mouseDragged(MouseEvent evt)
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621 if (mouseWheelPressed)
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623 int oldWidth = av.charWidth;
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625 //Which is bigger, left-right or up-down?
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626 if (Math.abs(evt.getY() - lastMousePress.y)
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627 > Math.abs(evt.getX() - lastMousePress.x))
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629 int fontSize = av.font.getSize();
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631 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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635 else if (evt.getY() > lastMousePress.y)
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644 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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645 av.charWidth = oldWidth;
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649 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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653 else if (evt.getX() > lastMousePress.x)
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666 FontMetrics fm = getFontMetrics(av.getFont());
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667 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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669 lastMousePress = evt.getPoint();
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672 ap.annotationPanel.image = null;
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678 doMouseDraggedDefineMode(evt);
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682 int res = findRes(evt);
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689 if ((lastres == -1) || (lastres == res))
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694 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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696 // dragLeft, delete gap
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697 editSequence(false, res);
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700 editSequence(true, res);
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702 mouseDragging = true;
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703 if(scrollThread!=null)
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704 scrollThread.setEvent(evt);
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708 synchronized void editSequence(boolean insertGap, int startres)
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710 int fixedLeft = -1;
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711 int fixedRight = -1;
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712 boolean fixedColumns = false;
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713 SequenceGroup sg = av.getSelectionGroup();
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716 if (!groupEditing && av.hasHiddenRows)
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718 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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720 groupEditing = true;
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724 //No group, but the sequence may represent a group
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727 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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729 groupEditing = false;
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732 SequenceI seq = av.alignment.getSequenceAt(startseq);
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733 StringBuffer message = new StringBuffer();
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735 message.append("Edit group:");
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737 message.append("Edit sequence: "+seq.getName());
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740 message.append(" insert ");
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742 message.append(" delete ");
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744 message.append(Math.abs(startres-lastres)+" gaps.");
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745 ap.alignFrame.statusBar.setText(message.toString());
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748 //Are we editing within a selection group?
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750 || (sg != null && sg.getSequences(true).contains(seq)))
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752 fixedColumns = true;
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754 //sg might be null as the user may only see 1 sequence,
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755 //but the sequence represents a group
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758 sg = new SequenceGroup(null, null, false, false, false, 0,
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759 av.alignment.getWidth()-1);
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760 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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763 fixedLeft = sg.getStartRes();
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764 fixedRight = sg.getEndRes();
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766 if ( (startres < fixedLeft && lastres >= fixedLeft)
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767 || (startres >= fixedLeft && lastres < fixedLeft)
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768 || (startres > fixedRight && lastres <=fixedRight)
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769 || (startres <= fixedRight && lastres > fixedRight))
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775 if (fixedLeft > startres)
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777 fixedRight = fixedLeft - 1;
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780 else if (fixedRight < startres)
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782 fixedLeft = fixedRight;
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788 if(av.hasHiddenColumns )
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790 fixedColumns = true;
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791 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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792 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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794 if ( (insertGap && startres > y1 && lastres < y1)
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795 || (!insertGap && startres < y2 && lastres > y2))
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801 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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802 //Selection spans a hidden region
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803 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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811 fixedRight = y2 - 1;
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822 //If the user has selected the whole sequence, and is dragging to
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823 // the right, we can still extend the alignment and selectionGroup
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824 if( sg.getStartRes() == 0
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825 && sg.getEndRes() == fixedRight
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826 && sg.getEndRes() == av.alignment.getWidth()-1
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829 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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830 fixedRight = sg.getEndRes();
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833 // Is it valid with fixed columns??
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834 // Find the next gap before the end
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835 // of the visible region boundary
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836 boolean blank = false;
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837 for (fixedRight = fixedRight;
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838 fixedRight > lastres;
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842 for (int s = 0; s < sg.getSize(true); s++)
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844 seq = (SequenceI)sg.getSequences(true).elementAt(s);
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845 for (int j = 0; j < startres - lastres; j++)
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847 if (!jalview.util.Comparison.isGap(
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848 seq.getCharAt(fixedRight - j)))
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861 if(sg.getSize(false) == av.alignment.getHeight() )
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863 if((av.hasHiddenColumns
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864 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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870 int alWidth = av.alignment.getWidth();
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871 if(av.hasHiddenRows)
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873 int hwidth = av.alignment.getHiddenSequences().getWidth();
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877 //We can still insert gaps if the selectionGroup
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878 //contains all the sequences
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879 sg.setEndRes(sg.getEndRes()+startres-lastres);
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880 fixedRight = alWidth+startres-lastres;
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892 else if(!insertGap)
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894 /// Are we able to delete?
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895 // ie are all columns blank?
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897 for (int s = 0; s < sg.getSize(true); s++)
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899 seq = (SequenceI)sg.getSequences(true).elementAt(s);
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901 for (int j = startres; j < lastres; j++)
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903 if (seq.getSequence().length() <= j)
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908 if (!jalview.util.Comparison.isGap(
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909 seq.getSequence().charAt(j)))
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911 // Not a gap, block edit not valid
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920 for (int i = 0; i < sg.getSize(true); i++)
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922 seq = (SequenceI) sg.getSequences(true).elementAt(i);
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926 // dragging to the right
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927 for (int j = lastres; j < startres; j++)
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929 if (fixedColumns && fixedRight != -1)
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931 insertChar(j, seq, fixedRight);
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934 insertChar(j, seq);
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939 // dragging to the left
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940 for (int j = lastres; j > startres; j--)
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942 if (fixedColumns && fixedRight != -1)
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944 deleteChar(startres, seq, fixedRight);
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948 deleteChar(startres, seq);
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954 else /////Editing a single sequence///////////
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958 // dragging to the right
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959 for (int j = lastres; j < startres; j++)
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961 if (fixedColumns && fixedRight != -1)
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963 insertChar(j, seq, fixedRight);
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966 insertChar(j, seq);
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971 // dragging to the left
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972 for (int j = lastres; j > startres; j--)
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974 if (fixedColumns && fixedRight != -1)
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976 deleteChar(startres, seq, fixedRight);
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980 deleteChar(startres, seq);
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986 lastres = startres;
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987 seqCanvas.repaint();
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994 * @param j DOCUMENT ME!
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995 * @param seq DOCUMENT ME!
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997 void insertChar(int j, SequenceI seq)
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999 seq.insertCharAt(j, av.getGapCharacter());
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1000 seqEditOccurred = true;
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1003 void insertChar(int j, SequenceI seq, int fixedColumn)
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1005 //Find the next gap before the end of the visible region boundary
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1006 //If lastCol > j, theres a boundary after the gap insertion
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1007 int blankColumn = fixedColumn;
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1008 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1010 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1012 //Theres a space, so break and insert the gap
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1017 if (blankColumn <= j)
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1023 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1026 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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1030 seq.deleteCharAt(blankColumn);
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1031 seq.insertCharAt(j, av.getGapCharacter());
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1032 seqEditOccurred = true;
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1035 void deleteChar(int j, SequenceI seq, int fixedColumn)
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1037 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1039 ap.alignFrame.statusBar.setText(
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1040 "End editing: Tried removing residue " + seq.getCharAt(j));
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1043 seq.deleteCharAt(j);
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1044 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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1045 seqEditOccurred = true;
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1051 * @param j DOCUMENT ME!
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1052 * @param seq DOCUMENT ME!
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1054 void deleteChar(int j, SequenceI seq)
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1056 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1058 ap.alignFrame.statusBar.setText(
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1059 "End editing: Tried removing residue " + seq.getCharAt(j));
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1063 seq.deleteCharAt(j);
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1064 seqEditOccurred = true;
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1065 seqCanvas.repaint();
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1071 * @param i DOCUMENT ME!
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1073 void editOccurred()
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1075 if (!seqEditOccurred)
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1077 ap.alignFrame.historyList.pop();
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1078 ap.alignFrame.updateEditMenuBar();
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1083 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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1087 //////////////////////////////////////////
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1088 /////Everything below this is for defining the boundary of the rubberband
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1089 //////////////////////////////////////////
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1090 public void doMousePressedDefineMode(MouseEvent evt)
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1094 if (scrollThread != null)
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1096 scrollThread.running = false;
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1097 scrollThread = null;
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1100 int res = findRes(evt);
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1101 int seq = findSeq(evt);
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1103 startWrapBlock=wrappedBlock;
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1108 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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1110 if (sequence == null || res > sequence.getLength())
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1115 stretchGroup = av.getSelectionGroup();
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1117 if (stretchGroup == null)
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1119 stretchGroup = av.alignment.findGroup(sequence);
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1120 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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1121 res < stretchGroup.getEndRes())
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1123 av.setSelectionGroup(stretchGroup);
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1127 stretchGroup = null;
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1131 else if (!stretchGroup.getSequences(false).contains(sequence)
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1132 || stretchGroup.getStartRes() > res
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1133 || stretchGroup.getEndRes() < res)
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1135 stretchGroup = null;
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1137 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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1139 if (allGroups != null)
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1141 for (int i = 0; i < allGroups.length; i++)
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1143 if (allGroups[i].getStartRes() <= res &&
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1144 allGroups[i].getEndRes() >= res)
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1146 stretchGroup = allGroups[i];
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1151 av.setSelectionGroup(stretchGroup);
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1155 // DETECT RIGHT MOUSE BUTTON IN AWT
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1156 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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1157 InputEvent.BUTTON3_MASK)
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1159 Vector allFeatures = getAllFeaturesAtRes(sequence,
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1160 sequence.findPosition(res));
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1162 Vector links = null;
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1163 if(allFeatures!=null)
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1165 for (int i = 0; i < allFeatures.size(); i++)
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1167 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
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1168 if (sf.links != null)
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1170 links = new Vector();
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1171 for (int j = 0; j < sf.links.size(); j++)
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1173 links.addElement(sf.links.elementAt(j));
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1178 APopupMenu popup = new APopupMenu(ap, null, links);
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1180 popup.show(this, evt.getX(), evt.getY());
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1185 if (av.cursorMode)
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1187 seqCanvas.cursorX = findRes(evt);
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1188 seqCanvas.cursorY = findSeq(evt);
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1189 seqCanvas.repaint();
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1193 //Only if left mouse button do we want to change group sizes
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1195 if (stretchGroup == null)
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1197 // define a new group here
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1198 SequenceGroup sg = new SequenceGroup();
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1199 sg.setStartRes(res);
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1200 sg.setEndRes(res);
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1201 sg.addSequence(sequence, false);
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1202 av.setSelectionGroup(sg);
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1203 stretchGroup = sg;
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1205 if (av.getConservationSelected())
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1207 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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1210 if (av.getAbovePIDThreshold())
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1212 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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1219 public void doMouseReleasedDefineMode(MouseEvent evt)
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1221 if (stretchGroup == null)
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1226 if(stretchGroup.cs!=null)
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1228 if (stretchGroup.cs instanceof ClustalxColourScheme)
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1230 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
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1231 stretchGroup.getSequences(true),
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1232 stretchGroup.getWidth());
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1235 if (stretchGroup.cs.conservationApplied())
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1237 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
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1238 stretchGroup.getName());
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1239 stretchGroup.recalcConservation();
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1243 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
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1244 stretchGroup.getName());
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1247 changeEndRes = false;
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1248 changeStartRes = false;
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1249 stretchGroup = null;
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1250 PaintRefresher.Refresh(av.alignment);
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1254 public void doMouseDraggedDefineMode(MouseEvent evt)
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1256 int res = findRes(evt);
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1257 int y = findSeq(evt);
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1259 if(wrappedBlock!=startWrapBlock)
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1262 if (stretchGroup == null)
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1267 mouseDragging = true;
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1270 if(y > av.alignment.getHeight())
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1272 y = av.alignment.getHeight() -1;
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1275 if(res>av.alignment.getWidth())
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1276 res = av.alignment.getWidth()-1;
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1278 if (stretchGroup.getEndRes() == res)
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1280 // Edit end res position of selected group
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1281 changeEndRes = true;
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1283 else if (stretchGroup.getStartRes() == res)
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1285 // Edit start res position of selected group
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1286 changeStartRes = true;
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1296 if (res > (stretchGroup.getStartRes() - 1))
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1298 stretchGroup.setEndRes(res);
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1301 else if (changeStartRes)
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1303 if (res < (stretchGroup.getEndRes() + 1))
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1305 stretchGroup.setStartRes(res);
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1309 int dragDirection = 0;
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1313 dragDirection = 1;
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1315 else if (y < oldSeq)
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1317 dragDirection = -1;
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1321 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
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1323 // This routine ensures we don't skip any sequences, as the
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1324 // selection is quite slow.
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1325 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1327 oldSeq += dragDirection;
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1332 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
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1334 if (stretchGroup.getSequences(false).contains(nextSeq))
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1336 stretchGroup.deleteSequence(seq, false);
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1342 stretchGroup.addSequence(seq, false);
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1345 stretchGroup.addSequence(nextSeq, false);
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1353 if(res>av.endRes || res<av.startRes
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1354 || y<av.startSeq || y>av.endSeq)
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1359 if (scrollThread != null)
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1361 scrollThread.setEvent(evt);
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1364 seqCanvas.repaint();
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1367 public void mouseEntered(MouseEvent e)
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1372 if (scrollThread != null)
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1374 scrollThread.running = false;
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1375 scrollThread = null;
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1379 public void mouseExited(MouseEvent e)
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1381 if (av.getWrapAlignment())
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1386 if (mouseDragging && scrollThread==null)
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1388 scrollThread = new ScrollThread();
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1392 void scrollCanvas(MouseEvent evt)
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1396 if(scrollThread!=null)
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1398 scrollThread.running = false;
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1399 scrollThread = null;
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1401 mouseDragging = false;
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1405 if (scrollThread == null)
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1406 scrollThread = new ScrollThread();
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1408 mouseDragging = true;
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1409 scrollThread.setEvent(evt);
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1414 // this class allows scrolling off the bottom of the visible alignment
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1415 class ScrollThread
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1419 boolean running = false;
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1420 public ScrollThread()
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1425 public void setEvent(MouseEvent e)
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1430 public void stopScrolling()
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1444 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
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1446 running = ap.scrollUp(true);
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1449 if (mouseDragging && evt.getY() >= getSize().height &&
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1450 av.alignment.getHeight() > av.getEndSeq())
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1452 running = ap.scrollUp(false);
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1455 if (mouseDragging && evt.getX() < 0)
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1457 running = ap.scrollRight(false);
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1460 else if (mouseDragging && evt.getX() >= getSize().width)
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1462 running = ap.scrollRight(true);
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1470 catch (Exception ex)
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