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 groupEditing = group;
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250 startseq = seqCanvas.cursorY;
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251 lastres = seqCanvas.cursorX;
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252 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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256 void deleteGapAtCursor(boolean group)
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258 groupEditing = group;
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259 startseq = seqCanvas.cursorY;
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260 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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261 editSequence(false, seqCanvas.cursorX);
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265 void numberPressed(char value)
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267 if(keyboardNo1==null)
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268 keyboardNo1 = new StringBuffer();
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270 if(keyboardNo2!=null)
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271 keyboardNo2.append(value);
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273 keyboardNo1.append(value);
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276 int getKeyboardNo(StringBuffer kb)
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281 return Integer.parseInt(kb.toString());
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284 void setStatusMessage(SequenceI sequence, int res, int seq)
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286 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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287 sequence.getName());
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290 if (av.alignment.isNucleotide())
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292 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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295 text.append(" Nucleotide: ");
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299 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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301 text.append(" Residue: ");
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309 text.append(obj + " (" + sequence.findPosition(res) +
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314 ap.alignFrame.statusBar.setText(text.toString());
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317 public void mousePressed(MouseEvent evt)
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319 lastMousePress = evt.getPoint();
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321 //For now, ignore the mouseWheel font resizing on Macs
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322 //As the Button2_mask always seems to be true
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323 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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324 InputEvent.BUTTON2_MASK && !av.MAC)
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326 mouseWheelPressed = true;
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330 if (evt.isShiftDown()
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331 || evt.isControlDown()
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332 || evt.isAltDown())
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334 if (evt.isControlDown() || evt.isAltDown())
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336 groupEditing = true;
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338 editingSeqs = true;
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342 doMousePressedDefineMode(evt);
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347 int seq = findSeq(evt);
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348 int res = findRes(evt);
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354 if ((seq < av.getAlignment().getHeight()) &&
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355 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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369 public void mouseClicked(MouseEvent evt){}
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372 public void mouseReleased(MouseEvent evt)
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374 mouseDragging = false;
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375 mouseWheelPressed = false;
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379 doMouseReleasedDefineMode(evt);
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389 int startWrapBlock=-1;
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390 int wrappedBlock=-1;
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391 int findRes(MouseEvent evt)
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394 int x = evt.getX();
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396 if (av.wrapAlignment)
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399 int hgap = av.charHeight;
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400 if (av.scaleAboveWrapped)
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401 hgap += av.charHeight;
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403 int cHeight = av.getAlignment().getHeight() * av.charHeight
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404 + hgap + seqCanvas.getAnnotationHeight();
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406 int y = evt.getY();
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408 x -= seqCanvas.LABEL_WEST;
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411 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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415 wrappedBlock = y / cHeight;
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416 wrappedBlock += av.getStartRes() / cwidth;
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418 res = wrappedBlock * cwidth + x / av.getCharWidth();
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423 res = (x / av.getCharWidth()) + av.getStartRes();
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426 if(av.hasHiddenColumns)
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427 res = av.getColumnSelection().adjustForHiddenColumns(res);
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433 int findSeq(MouseEvent evt)
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437 int y = evt.getY();
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439 if (av.wrapAlignment)
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441 int hgap = av.charHeight;
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442 if (av.scaleAboveWrapped)
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443 hgap += av.charHeight;
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445 int cHeight = av.getAlignment().getHeight() * av.charHeight
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446 + hgap + seqCanvas.getAnnotationHeight();
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450 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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451 av.alignment.getHeight() -1);
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457 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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458 av.alignment.getHeight() -1);
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467 public void doMousePressed(MouseEvent evt)
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470 int seq = findSeq(evt);
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471 int res = findRes(evt);
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473 if (seq < av.getAlignment().getHeight() &&
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474 res < av.getAlignment().getSequenceAt(seq).getLength())
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476 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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477 // Find the residue's position in the sequence (res is the position
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478 // in the alignment
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492 public void mouseMoved(MouseEvent evt)
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494 int res = findRes(evt);
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495 int seq = findSeq(evt);
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497 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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502 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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503 if (res > sequence.getLength())
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508 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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509 sequence.getName());
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512 if (av.alignment.isNucleotide())
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514 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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517 text.append(" Nucleotide: ");
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521 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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523 text.append(" Residue: ");
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530 text.append(obj + " (" + sequence.findPosition(res) + ")");
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534 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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536 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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539 ap.alignFrame.statusBar.setText(text.toString());
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542 // use aa to see if the mouse pointer is on a
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543 if (av.showSequenceFeatures
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544 && sequence.getSequenceFeatures()!=null
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545 && av.featuresDisplayed!=null)
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547 StringBuffer featureText = new StringBuffer();
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548 Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
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551 while (index < allFeatures.size())
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553 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
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555 featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
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557 if (sf.getDescription() != null)
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558 featureText.append(" " + sf.getDescription());
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560 if (sf.getValue("status") != null )
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562 String status = sf.getValue("status").toString();
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563 if(status.length()>0)
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564 featureText.append(" (" + sf.getValue("status") + ")");
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566 featureText.append("\n");
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572 if (tooltip == null)
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573 tooltip = new Tooltip(featureText.toString(), seqCanvas);
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575 tooltip.setTip(featureText.toString());
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580 else if (tooltip != null)
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582 tooltip.setTip("");
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586 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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588 Vector allFeatures = new Vector();
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590 if(seq.getSequenceFeatures()!=null)
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592 while (index < seq.getSequenceFeatures().length)
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594 SequenceFeature sf = seq.getSequenceFeatures()[index];
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595 if (sf.getBegin() <= res &&
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596 sf.getEnd() >= res)
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598 if (av.featuresDisplayed.containsKey(sf.getType()))
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600 allFeatures.addElement(sf);
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606 return allFeatures;
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611 public void mouseDragged(MouseEvent evt)
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613 if (mouseWheelPressed)
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615 int oldWidth = av.charWidth;
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617 //Which is bigger, left-right or up-down?
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618 if (Math.abs(evt.getY() - lastMousePress.y)
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619 > Math.abs(evt.getX() - lastMousePress.x))
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621 int fontSize = av.font.getSize();
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623 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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627 else if (evt.getY() > lastMousePress.y)
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636 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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637 av.charWidth = oldWidth;
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641 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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645 else if (evt.getX() > lastMousePress.x)
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658 FontMetrics fm = getFontMetrics(av.getFont());
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659 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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661 lastMousePress = evt.getPoint();
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664 ap.annotationPanel.image = null;
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670 doMouseDraggedDefineMode(evt);
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674 int res = findRes(evt);
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681 if ((lastres == -1) || (lastres == res))
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686 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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688 // dragLeft, delete gap
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689 editSequence(false, res);
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692 editSequence(true, res);
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694 mouseDragging = true;
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695 if(scrollThread!=null)
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696 scrollThread.setEvent(evt);
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700 synchronized void editSequence(boolean insertGap, int startres)
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702 int fixedLeft = -1;
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703 int fixedRight = -1;
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704 boolean fixedColumns = false;
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705 SequenceGroup sg = av.getSelectionGroup();
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708 if (!groupEditing && av.hasHiddenRows)
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710 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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712 groupEditing = true;
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716 //No group, but the sequence may represent a group
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719 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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721 groupEditing = false;
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724 SequenceI seq = av.alignment.getSequenceAt(startseq);
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725 StringBuffer message = new StringBuffer();
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727 message.append("Edit group:");
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729 message.append("Edit sequence: "+seq.getName());
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732 message.append(" insert ");
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734 message.append(" delete ");
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736 message.append(Math.abs(startres-lastres)+" gaps.");
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737 ap.alignFrame.statusBar.setText(message.toString());
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740 //Are we editing within a selection group?
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742 || (sg != null && sg.getSequences(true).contains(seq)))
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744 fixedColumns = true;
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746 //sg might be null as the user may only see 1 sequence,
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747 //but the sequence represents a group
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750 sg = new SequenceGroup(null, null, false, false, false, 0,
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751 av.alignment.getWidth()-1);
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752 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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755 fixedLeft = sg.getStartRes();
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756 fixedRight = sg.getEndRes();
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758 if ( (startres < fixedLeft && lastres >= fixedLeft)
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759 || (startres >= fixedLeft && lastres < fixedLeft)
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760 || (startres > fixedRight && lastres <=fixedRight)
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761 || (startres <= fixedRight && lastres > fixedRight))
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767 if (fixedLeft > startres)
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769 fixedRight = fixedLeft - 1;
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772 else if (fixedRight < startres)
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774 fixedLeft = fixedRight;
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780 if(av.hasHiddenColumns )
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782 fixedColumns = true;
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783 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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784 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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786 if ( (insertGap && startres > y1 && lastres < y1)
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787 || (!insertGap && startres < y2 && lastres > y2))
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793 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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794 //Selection spans a hidden region
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795 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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803 fixedRight = y2 - 1;
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812 Vector vseqs = sg.getSequences(true);
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813 int g, groupSize = vseqs.size();
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814 SequenceI[] groupSeqs = new SequenceI[groupSize];
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815 for (g = 0; g < groupSeqs.length; g++)
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816 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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821 //If the user has selected the whole sequence, and is dragging to
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822 // the right, we can still extend the alignment and selectionGroup
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823 if( sg.getStartRes() == 0
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824 && sg.getEndRes() == fixedRight
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825 && sg.getEndRes() == av.alignment.getWidth()-1
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828 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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829 fixedRight = sg.getEndRes();
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832 // Is it valid with fixed columns??
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833 // Find the next gap before the end
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834 // of the visible region boundary
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835 boolean blank = false;
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836 for (fixedRight = fixedRight;
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837 fixedRight > lastres;
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842 for (g = 0; g < groupSize; g++)
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844 for (int j = 0; j < startres - lastres; j++)
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846 if (!jalview.util.Comparison.isGap(
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847 groupSeqs[g].getCharAt(fixedRight - j)))
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860 if(sg.getSize(false) == av.alignment.getHeight() )
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862 if((av.hasHiddenColumns
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863 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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869 int alWidth = av.alignment.getWidth();
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870 if(av.hasHiddenRows)
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872 int hwidth = av.alignment.getHiddenSequences().getWidth();
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876 //We can still insert gaps if the selectionGroup
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877 //contains all the sequences
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878 sg.setEndRes(sg.getEndRes()+startres-lastres);
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879 fixedRight = alWidth+startres-lastres;
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891 else if(!insertGap)
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893 /// Are we able to delete?
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894 // ie are all columns blank?
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896 for (g = 0; g < groupSize; g++)
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898 for (int j = startres; j < lastres; j++)
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900 if (groupSeqs[g].getLength() <= j)
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905 if (!jalview.util.Comparison.isGap(
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906 groupSeqs[g].getCharAt(j)))
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908 // Not a gap, block edit not valid
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917 for (g = 0; g < groupSize; g++)
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921 // dragging to the right
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922 for (int j = lastres; j < startres; j++)
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924 if (fixedColumns && fixedRight != -1)
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926 insertChar(j, groupSeqs[g], fixedRight);
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929 insertChar(j, groupSeqs[g]);
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934 // dragging to the left
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935 for (int j = lastres; j > startres; j--)
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937 if (fixedColumns && fixedRight != -1)
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939 deleteChar(startres, groupSeqs[g], fixedRight);
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943 deleteChar(startres, groupSeqs[g]);
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948 } else /////Editing a single sequence///////////
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952 // dragging to the right
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953 for (int j = lastres; j < startres; j++)
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955 if (fixedColumns && fixedRight != -1)
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957 insertChar(j, seq, fixedRight);
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960 insertChar(j, seq);
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965 // dragging to the left
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966 for (int j = lastres; j > startres; j--)
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968 if (fixedColumns && fixedRight != -1)
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970 deleteChar(startres, seq, fixedRight);
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974 deleteChar(startres, seq);
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980 lastres = startres;
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981 seqCanvas.repaint();
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988 * @param j DOCUMENT ME!
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989 * @param seq DOCUMENT ME!
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991 void insertChar(int j, SequenceI seq)
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993 seq.insertCharAt(j, av.getGapCharacter());
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994 seqEditOccurred = true;
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997 void insertChar(int j, SequenceI seq, int fixedColumn)
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999 //Find the next gap before the end of the visible region boundary
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1000 //If lastCol > j, theres a boundary after the gap insertion
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1001 int blankColumn = fixedColumn;
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1002 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1004 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1006 //Theres a space, so break and insert the gap
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1011 if (blankColumn <= j)
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1017 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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1020 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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1024 seq.deleteCharAt(blankColumn);
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1025 seq.insertCharAt(j, av.getGapCharacter());
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1026 seqEditOccurred = true;
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1029 void deleteChar(int j, SequenceI seq, int fixedColumn)
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1031 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1033 ap.alignFrame.statusBar.setText(
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1034 "End editing: Tried removing residue " + seq.getCharAt(j));
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1037 seq.deleteCharAt(j);
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1038 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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1039 seqEditOccurred = true;
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1045 * @param j DOCUMENT ME!
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1046 * @param seq DOCUMENT ME!
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1048 void deleteChar(int j, SequenceI seq)
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1050 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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1052 ap.alignFrame.statusBar.setText(
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1053 "End editing: Tried removing residue " + seq.getCharAt(j));
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1057 seq.deleteCharAt(j);
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1058 seqEditOccurred = true;
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1059 seqCanvas.repaint();
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1065 * @param i DOCUMENT ME!
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1067 void editOccurred()
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1069 if (!seqEditOccurred)
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1071 ap.alignFrame.historyList.pop();
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1072 ap.alignFrame.updateEditMenuBar();
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1077 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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1081 //////////////////////////////////////////
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1082 /////Everything below this is for defining the boundary of the rubberband
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1083 //////////////////////////////////////////
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1084 public void doMousePressedDefineMode(MouseEvent evt)
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1088 if (scrollThread != null)
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1090 scrollThread.running = false;
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1091 scrollThread = null;
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1094 int res = findRes(evt);
\r
1095 int seq = findSeq(evt);
\r
1097 startWrapBlock=wrappedBlock;
\r
1102 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1104 if (sequence == null || res > sequence.getLength())
\r
1109 stretchGroup = av.getSelectionGroup();
\r
1111 if (stretchGroup == null)
\r
1113 stretchGroup = av.alignment.findGroup(sequence);
\r
1114 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1115 res < stretchGroup.getEndRes())
\r
1117 av.setSelectionGroup(stretchGroup);
\r
1121 stretchGroup = null;
\r
1125 else if (!stretchGroup.getSequences(false).contains(sequence)
\r
1126 || stretchGroup.getStartRes() > res
\r
1127 || stretchGroup.getEndRes() < res)
\r
1129 stretchGroup = null;
\r
1131 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1133 if (allGroups != null)
\r
1135 for (int i = 0; i < allGroups.length; i++)
\r
1137 if (allGroups[i].getStartRes() <= res &&
\r
1138 allGroups[i].getEndRes() >= res)
\r
1140 stretchGroup = allGroups[i];
\r
1145 av.setSelectionGroup(stretchGroup);
\r
1149 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1150 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1151 InputEvent.BUTTON3_MASK)
\r
1153 Vector allFeatures = getAllFeaturesAtRes(sequence,
\r
1154 sequence.findPosition(res));
\r
1156 Vector links = null;
\r
1157 if(allFeatures!=null)
\r
1159 for (int i = 0; i < allFeatures.size(); i++)
\r
1161 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1162 if (sf.links != null)
\r
1164 links = new Vector();
\r
1165 for (int j = 0; j < sf.links.size(); j++)
\r
1167 links.addElement(sf.links.elementAt(j));
\r
1172 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1174 popup.show(this, evt.getX(), evt.getY());
\r
1179 if (av.cursorMode)
\r
1181 seqCanvas.cursorX = findRes(evt);
\r
1182 seqCanvas.cursorY = findSeq(evt);
\r
1183 seqCanvas.repaint();
\r
1187 //Only if left mouse button do we want to change group sizes
\r
1189 if (stretchGroup == null)
\r
1191 // define a new group here
\r
1192 SequenceGroup sg = new SequenceGroup();
\r
1193 sg.setStartRes(res);
\r
1194 sg.setEndRes(res);
\r
1195 sg.addSequence(sequence, false);
\r
1196 av.setSelectionGroup(sg);
\r
1197 stretchGroup = sg;
\r
1199 if (av.getConservationSelected())
\r
1201 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1204 if (av.getAbovePIDThreshold())
\r
1206 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1213 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1215 if (stretchGroup == null)
\r
1220 if(stretchGroup.cs!=null)
\r
1222 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1224 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1225 stretchGroup.getSequences(true),
\r
1226 stretchGroup.getWidth());
\r
1229 if (stretchGroup.cs.conservationApplied())
\r
1231 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1232 stretchGroup.getName());
\r
1233 stretchGroup.recalcConservation();
\r
1237 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1238 stretchGroup.getName());
\r
1241 changeEndRes = false;
\r
1242 changeStartRes = false;
\r
1243 stretchGroup = null;
\r
1244 PaintRefresher.Refresh(av.alignment);
\r
1248 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1250 int res = findRes(evt);
\r
1251 int y = findSeq(evt);
\r
1253 if(wrappedBlock!=startWrapBlock)
\r
1256 if (stretchGroup == null)
\r
1261 mouseDragging = true;
\r
1264 if(y > av.alignment.getHeight())
\r
1266 y = av.alignment.getHeight() -1;
\r
1269 if(res>=av.alignment.getWidth())
\r
1270 res = av.alignment.getWidth()-1;
\r
1272 if (stretchGroup.getEndRes() == res)
\r
1274 // Edit end res position of selected group
\r
1275 changeEndRes = true;
\r
1277 else if (stretchGroup.getStartRes() == res)
\r
1279 // Edit start res position of selected group
\r
1280 changeStartRes = true;
\r
1290 if (res > (stretchGroup.getStartRes() - 1))
\r
1292 stretchGroup.setEndRes(res);
\r
1295 else if (changeStartRes)
\r
1297 if (res < (stretchGroup.getEndRes() + 1))
\r
1299 stretchGroup.setStartRes(res);
\r
1303 int dragDirection = 0;
\r
1307 dragDirection = 1;
\r
1309 else if (y < oldSeq)
\r
1311 dragDirection = -1;
\r
1315 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1317 // This routine ensures we don't skip any sequences, as the
\r
1318 // selection is quite slow.
\r
1319 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1321 oldSeq += dragDirection;
\r
1326 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1328 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1330 stretchGroup.deleteSequence(seq, false);
\r
1336 stretchGroup.addSequence(seq, false);
\r
1339 stretchGroup.addSequence(nextSeq, false);
\r
1347 if(res>av.endRes || res<av.startRes
\r
1348 || y<av.startSeq || y>av.endSeq)
\r
1353 if (scrollThread != null)
\r
1355 scrollThread.setEvent(evt);
\r
1358 seqCanvas.repaint();
\r
1361 public void mouseEntered(MouseEvent e)
\r
1366 if (scrollThread != null)
\r
1368 scrollThread.running = false;
\r
1369 scrollThread = null;
\r
1373 public void mouseExited(MouseEvent e)
\r
1375 if (av.getWrapAlignment())
\r
1380 if (mouseDragging && scrollThread==null)
\r
1382 scrollThread = new ScrollThread();
\r
1386 void scrollCanvas(MouseEvent evt)
\r
1390 if(scrollThread!=null)
\r
1392 scrollThread.running = false;
\r
1393 scrollThread = null;
\r
1395 mouseDragging = false;
\r
1399 if (scrollThread == null)
\r
1400 scrollThread = new ScrollThread();
\r
1402 mouseDragging = true;
\r
1403 scrollThread.setEvent(evt);
\r
1408 // this class allows scrolling off the bottom of the visible alignment
\r
1409 class ScrollThread
\r
1413 boolean running = false;
\r
1414 public ScrollThread()
\r
1419 public void setEvent(MouseEvent e)
\r
1424 public void stopScrolling()
\r
1438 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1440 running = ap.scrollUp(true);
\r
1443 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1444 av.alignment.getHeight() > av.getEndSeq())
\r
1446 running = ap.scrollUp(false);
\r
1449 if (mouseDragging && evt.getX() < 0)
\r
1451 running = ap.scrollRight(false);
\r
1454 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1456 running = ap.scrollRight(true);
\r
1464 catch (Exception ex)
\r