2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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23 import java.awt.event.*;
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25 import jalview.datamodel.*;
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26 import jalview.schemes.*;
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28 public class SeqPanel
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29 extends Panel implements MouseMotionListener, MouseListener
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32 public SeqCanvas seqCanvas;
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33 public AlignmentPanel ap;
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35 protected int lastres;
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36 protected int startseq;
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38 protected AlignViewport av;
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40 // if character is inserted or deleted, we will need to recalculate the conservation
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41 boolean seqEditOccurred = false;
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43 ScrollThread scrollThread = null;
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44 boolean mouseDragging = false;
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45 boolean editingSeqs = false;
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46 boolean groupEditing = false;
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49 boolean changeEndSeq = false;
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50 boolean changeStartSeq = false;
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51 boolean changeEndRes = false;
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52 boolean changeStartRes = false;
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53 SequenceGroup stretchGroup = null;
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55 StringBuffer keyboardNo1;
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56 StringBuffer keyboardNo2;
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58 boolean mouseWheelPressed = false;
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59 Point lastMousePress;
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61 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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65 seqCanvas = new SeqCanvas(avp);
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66 setLayout(new BorderLayout());
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71 seqCanvas.addMouseMotionListener(this);
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72 seqCanvas.addMouseListener(this);
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74 seqCanvas.repaint();
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81 seqEditOccurred = false;
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82 editingSeqs = false;
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83 groupEditing = false;
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90 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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94 void setCursorColumn()
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96 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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100 void setCursorRowAndColumn()
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102 if(keyboardNo2==null)
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104 keyboardNo2 = new StringBuffer();
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108 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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109 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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114 void setCursorPosition()
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116 SequenceI sequence =
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117 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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119 seqCanvas.cursorX = sequence.findIndex(
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120 getKeyboardNo(keyboardNo1)-1
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125 void moveCursor(int dx, int dy)
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127 seqCanvas.cursorX += dx;
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128 seqCanvas.cursorY += dy;
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132 void scrollToVisible()
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134 if (seqCanvas.cursorX < 0)
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135 seqCanvas.cursorX = 0;
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136 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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137 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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139 if (seqCanvas.cursorY < 0)
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140 seqCanvas.cursorY = 0;
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141 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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142 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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146 if (av.wrapAlignment)
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148 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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152 while (seqCanvas.cursorY < av.startSeq)
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156 while (seqCanvas.cursorY + 1 > av.endSeq)
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158 ap.scrollUp(false);
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160 while (seqCanvas.cursorX < av.startRes)
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163 if (!ap.scrollRight(false))
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166 while (seqCanvas.cursorX > av.endRes)
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168 if (!ap.scrollRight(true))
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172 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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173 seqCanvas.cursorX, seqCanvas.cursorY);
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175 seqCanvas.repaint();
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178 void setSelectionAreaAtCursor(boolean topLeft)
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180 SequenceI sequence =
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181 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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183 if(av.getSelectionGroup()!=null)
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185 SequenceGroup sg = av.selectionGroup;
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186 //Find the top and bottom of this group
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187 int min = av.alignment.getHeight(), max = 0;
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188 for(int i=0; i<sg.getSize(); i++)
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190 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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201 sg.setStartRes(seqCanvas.cursorX);
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202 if(sg.getEndRes()<seqCanvas.cursorX)
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203 sg.setEndRes(seqCanvas.cursorX);
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205 min = seqCanvas.cursorY;
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209 sg.setEndRes(seqCanvas.cursorX);
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210 if(sg.getStartRes()>seqCanvas.cursorX)
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211 sg.setStartRes(seqCanvas.cursorX);
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213 max = seqCanvas.cursorY+1;
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218 // Only the user can do this
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219 av.setSelectionGroup(null);
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223 // Now add any sequences between min and max
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224 sg.sequences.removeAllElements();
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225 for (int i = min; i < max; i++)
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227 sg.addSequence(av.alignment.getSequenceAt(i), false);
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232 if (av.getSelectionGroup() == null)
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234 SequenceGroup sg = new SequenceGroup();
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235 sg.setStartRes(seqCanvas.cursorX);
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236 sg.setEndRes(seqCanvas.cursorX);
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237 sg.addSequence(sequence, false);
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238 av.setSelectionGroup(sg);
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245 void insertGapAtCursor(boolean group)
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247 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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248 av.alignment, HistoryItem.EDIT));
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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 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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259 av.alignment, HistoryItem.EDIT));
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260 groupEditing = group;
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261 startseq = seqCanvas.cursorY;
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262 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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263 editSequence(false, seqCanvas.cursorX);
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267 void numberPressed(char value)
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269 if(keyboardNo1==null)
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270 keyboardNo1 = new StringBuffer();
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272 if(keyboardNo2!=null)
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273 keyboardNo2.append(value);
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275 keyboardNo1.append(value);
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278 int getKeyboardNo(StringBuffer kb)
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283 return Integer.parseInt(kb.toString());
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286 void setStatusMessage(SequenceI sequence, int res, int seq)
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288 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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289 sequence.getName());
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292 if (av.alignment.isNucleotide())
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294 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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297 text.append(" Nucleotide: ");
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301 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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303 text.append(" Residue: ");
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311 text.append(obj + " (" + sequence.findPosition(res) +
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315 ap.alignFrame.statusBar.setText(text.toString());
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318 public void mousePressed(MouseEvent evt)
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320 lastMousePress = evt.getPoint();
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322 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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323 InputEvent.BUTTON2_MASK)
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325 mouseWheelPressed = true;
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329 if (evt.isShiftDown() || evt.isAltDown() ||
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330 evt.isControlDown())
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332 if (evt.isAltDown() || evt.isControlDown())
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334 groupEditing = true;
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336 editingSeqs = true;
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340 doMousePressedDefineMode(evt);
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345 int seq = findSeq(evt);
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346 int res = findRes(evt);
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351 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
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352 av.alignment, HistoryItem.EDIT));
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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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413 wrappedBlock = y / cHeight;
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414 wrappedBlock += av.getStartRes() / cwidth;
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416 res = wrappedBlock * cwidth + x / av.getCharWidth();
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421 res = (x / av.getCharWidth()) + av.getStartRes();
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428 int findSeq(MouseEvent evt)
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432 int y = evt.getY();
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434 if (av.wrapAlignment)
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436 int hgap = av.charHeight;
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437 if (av.scaleAboveWrapped)
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438 hgap += av.charHeight;
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440 int cHeight = av.getAlignment().getHeight() * av.charHeight
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441 + hgap + seqCanvas.getAnnotationHeight();
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445 seq = ( (y % cHeight) / av.getCharHeight());
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449 seq = (y / av.getCharHeight()) + av.getStartSeq();
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456 public void doMousePressed(MouseEvent evt)
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458 ap.alignFrame.addHistoryItem(new HistoryItem(
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459 "Edit Sequence", av.alignment, HistoryItem.EDIT));
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461 int seq = findSeq(evt);
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462 int res = findRes(evt);
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464 if (seq < av.getAlignment().getHeight() &&
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465 res < av.getAlignment().getSequenceAt(seq).getLength())
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467 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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468 // Find the residue's position in the sequence (res is the position
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469 // in the alignment
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483 public void mouseMoved(MouseEvent evt)
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485 int res = findRes(evt);
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486 int seq = findSeq(evt);
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488 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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493 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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494 if (res > sequence.getLength())
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499 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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500 sequence.getName());
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503 if (av.alignment.isNucleotide())
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505 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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508 text.append(" Nucleotide: ");
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512 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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514 text.append(" Residue: ");
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522 text.append(obj + " (" +
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523 av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
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527 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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529 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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533 // use aa to see if the mouse pointer is on a
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534 if (av.showSequenceFeatures
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535 && sequence.getSequenceFeatures()!=null
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536 && av.featuresDisplayed!=null)
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539 sequence.getSequenceFeatures();
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540 boolean first = true;
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541 while (index < sequence.getSequenceFeatures().length)
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543 SequenceFeature sf = sequence.getSequenceFeatures()[index];
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544 if (sf.getBegin() <= sequence.findPosition(res) &&
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545 sf.getEnd() >= sequence.findPosition(res))
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547 if(!av.featuresDisplayed.containsKey(sf.getType()))
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555 text.append(" Sequence Feature:");
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559 text.append(" "+sf.getType());
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561 if(sf.getDescription()!=null)
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562 text.append(" "+sf.getDescription());
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564 if (sf.getStatus()!=null && sf.getStatus().length() > 0)
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566 text.append(" (" + sf.getStatus() + ")");
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576 ap.alignFrame.statusBar.setText(text.toString());
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580 public void mouseDragged(MouseEvent evt)
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582 if (mouseWheelPressed)
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584 int oldWidth = av.charWidth;
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586 //Which is bigger, left-right or up-down?
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587 if (Math.abs(evt.getY() - lastMousePress.y)
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588 > Math.abs(evt.getX() - lastMousePress.x))
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590 int fontSize = av.font.getSize();
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592 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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596 else if (evt.getY() > lastMousePress.y)
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605 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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606 av.charWidth = oldWidth;
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610 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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614 else if (evt.getX() > lastMousePress.x)
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627 FontMetrics fm = getFontMetrics(av.getFont());
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628 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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630 lastMousePress = evt.getPoint();
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633 ap.annotationPanel.image = null;
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639 doMouseDraggedDefineMode(evt);
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643 int res = findRes(evt);
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650 if ((lastres == -1) || (lastres == res))
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655 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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657 // dragLeft, delete gap
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658 editSequence(false, res);
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661 editSequence(true, res);
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663 mouseDragging = true;
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664 if(scrollThread!=null)
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665 scrollThread.setEvent(evt);
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669 synchronized void editSequence(boolean insertGap, int startres)
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671 int fixedLeft = -1;
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672 int fixedRight = -1;
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673 boolean fixedColumns = false;
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674 SequenceGroup sg = av.getSelectionGroup();
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676 if(groupEditing && sg==null)
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679 SequenceI seq = av.alignment.getSequenceAt(startseq);
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680 StringBuffer message = new StringBuffer();
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682 message.append("Edit group:");
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684 message.append("Edit sequence: "+seq.getName());
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687 message.append(" insert ");
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689 message.append(" delete ");
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691 message.append(Math.abs(startres-lastres)+" gaps.");
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692 ap.alignFrame.statusBar.setText(message.toString());
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695 //Are we editing within a selection group?
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697 || (sg != null && sg.sequences.contains(seq)))
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699 fixedColumns = true;
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701 fixedLeft = sg.getStartRes();
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702 fixedRight = sg.getEndRes();
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704 if ( (startres < fixedLeft && lastres >= fixedLeft)
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705 || (startres >= fixedLeft && lastres < fixedLeft)
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706 || (startres > fixedRight && lastres <=fixedRight)
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707 || (startres <= fixedRight && lastres > fixedRight))
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713 if (fixedLeft > startres)
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715 fixedRight = fixedLeft - 1;
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718 else if (fixedRight < startres)
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720 fixedLeft = fixedRight;
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731 //If the user has selected the whole sequence, and is dragging to
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732 // the right, we can still extend the alignment and selectionGroup
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733 if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())
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735 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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736 fixedRight = sg.getEndRes();
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739 // Is it valid with fixed columns??
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740 // Find the next gap before the end
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741 // of the visible region boundary
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742 boolean blank = false;
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743 for (fixedRight = fixedRight;
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744 fixedRight > lastres;
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748 for (int s = 0; s < sg.getSize(); s++)
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750 seq = sg.getSequenceAt(s);
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751 for (int j = 0; j < startres - lastres; j++)
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753 if (!jalview.util.Comparison.isGap(
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754 seq.getCharAt(fixedRight - j)))
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767 if(sg.getSize() == av.alignment.getHeight())
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769 //We can still insert gaps if the selectionGroup
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770 //contains all the sequences
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771 sg.setEndRes(sg.getEndRes()+startres-lastres);
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772 fixedRight = av.alignment.getWidth()+startres-lastres;
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784 else if(!insertGap)
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786 /// Are we able to delete?
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787 // ie are all columns blank?
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789 for (int s = 0; s < sg.getSize(); s++)
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791 seq = sg.getSequenceAt(s);
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793 for (int j = startres; j < lastres; j++)
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795 if (seq.getSequence().length() <= j)
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800 if (!jalview.util.Comparison.isGap(
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801 seq.getSequence().charAt(j)))
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803 // Not a gap, block edit not valid
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812 for (int i = 0; i < sg.getSize(); i++)
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814 seq = sg.getSequenceAt(i);
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818 // dragging to the right
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819 for (int j = lastres; j < startres; j++)
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821 if (fixedColumns && fixedRight != -1)
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823 insertChar(j, seq, fixedRight);
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826 insertChar(j, seq);
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831 // dragging to the left
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832 for (int j = lastres; j > startres; j--)
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834 if (fixedColumns && fixedRight != -1)
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836 deleteChar(startres, seq, fixedRight);
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840 deleteChar(startres, seq);
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846 else /////Editing a single sequence///////////
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850 // dragging to the right
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851 for (int j = lastres; j < startres; j++)
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853 if (fixedColumns && fixedRight != -1)
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855 if (sg.getStartRes() == 0
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856 && sg.getEndRes() + 1 == av.alignment.getWidth()
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857 && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
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859 //Single sequence edit, whole sequence selected,
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860 //extend the selection group
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861 sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
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862 fixedColumns = false;
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863 insertChar(j, seq);
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866 insertChar(j, seq, fixedRight);
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869 insertChar(j, seq);
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874 // dragging to the left
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875 for (int j = lastres; j > startres; j--)
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877 if (fixedColumns && fixedRight != -1)
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879 deleteChar(startres, seq, fixedRight);
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883 deleteChar(startres, seq);
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889 lastres = startres;
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890 seqCanvas.repaint();
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897 * @param j DOCUMENT ME!
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898 * @param seq DOCUMENT ME!
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900 void insertChar(int j, SequenceI seq)
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902 seq.insertCharAt(j, av.getGapCharacter());
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903 seqEditOccurred = true;
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906 void insertChar(int j, SequenceI seq, int fixedColumn)
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908 //Find the next gap before the end of the visible region boundary
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909 //If lastCol > j, theres a boundary after the gap insertion
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910 int blankColumn = fixedColumn;
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911 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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913 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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915 //Theres a space, so break and insert the gap
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920 if (blankColumn <= j)
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926 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
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929 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
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933 seq.deleteCharAt(blankColumn);
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934 seq.insertCharAt(j, av.getGapCharacter());
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935 seqEditOccurred = true;
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938 void deleteChar(int j, SequenceI seq, int fixedColumn)
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940 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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942 ap.alignFrame.statusBar.setText(
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943 "End editing: Tried removing residue " + seq.getCharAt(j));
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947 seq.deleteCharAt(j);
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948 seq.insertCharAt(fixedColumn, av.getGapCharacter());
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949 seqEditOccurred = true;
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955 * @param j DOCUMENT ME!
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956 * @param seq DOCUMENT ME!
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958 void deleteChar(int j, SequenceI seq)
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960 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
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962 ap.alignFrame.statusBar.setText(
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963 "End editing: Tried removing residue " + seq.getCharAt(j));
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967 seq.deleteCharAt(j);
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968 seqEditOccurred = true;
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969 seqCanvas.repaint();
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975 * @param i DOCUMENT ME!
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977 void editOccurred()
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979 if (!seqEditOccurred)
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981 ap.alignFrame.historyList.pop();
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982 ap.alignFrame.updateEditMenuBar();
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987 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
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991 //////////////////////////////////////////
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992 /////Everything below this is for defining the boundary of the rubberband
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993 //////////////////////////////////////////
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994 public void doMousePressedDefineMode(MouseEvent evt)
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998 if (scrollThread != null)
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1000 scrollThread.running = false;
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1001 scrollThread = null;
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1004 int res = findRes(evt);
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1005 int seq = findSeq(evt);
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1007 startWrapBlock=wrappedBlock;
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1012 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
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1014 if (sequence == null || res > sequence.getLength())
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1019 stretchGroup = av.getSelectionGroup();
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1021 if (stretchGroup == null)
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1023 stretchGroup = av.alignment.findGroup(sequence);
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1024 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
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1025 res < stretchGroup.getEndRes())
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1027 av.setSelectionGroup(stretchGroup);
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1031 stretchGroup = null;
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1035 else if (!stretchGroup.sequences.contains(sequence)
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1036 || stretchGroup.getStartRes() > res
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1037 || stretchGroup.getEndRes() < res)
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1039 stretchGroup = null;
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1041 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
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1043 if (allGroups != null)
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1045 for (int i = 0; i < allGroups.length; i++)
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1047 if (allGroups[i].getStartRes() <= res &&
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1048 allGroups[i].getEndRes() >= res)
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1050 stretchGroup = allGroups[i];
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1051 av.setSelectionGroup(stretchGroup);
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1058 if (stretchGroup == null)
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1060 // define a new group here
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1061 SequenceGroup sg = new SequenceGroup();
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1062 sg.setStartRes(res);
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1063 sg.setEndRes(res);
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1064 sg.addSequence(sequence, false);
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1065 av.setSelectionGroup(sg);
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1066 stretchGroup = sg;
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1068 if (av.getConservationSelected())
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1070 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
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1073 if (av.getAbovePIDThreshold())
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1075 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
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1081 // DETECT RIGHT MOUSE BUTTON IN AWT
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1082 else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
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1083 InputEvent.BUTTON3_MASK)
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1085 APopupMenu popup = new APopupMenu(ap, null, null);
\r
1087 popup.show(this, evt.getX(), evt.getY());
\r
1090 if (stretchGroup != null && stretchGroup.getEndRes() == res)
\r
1092 // Edit end res position of selected group
\r
1093 changeEndRes = true;
\r
1096 else if (stretchGroup != null && stretchGroup.getStartRes() == res)
\r
1098 // Edit end res position of selected group
\r
1099 changeStartRes = true;
\r
1104 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1106 if (stretchGroup == null)
\r
1111 if(stretchGroup.cs!=null)
\r
1113 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1115 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
\r
1117 stretchGroup.getWidth());
\r
1120 if (stretchGroup.cs.conservationApplied())
\r
1122 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1123 stretchGroup.getName());
\r
1124 stretchGroup.recalcConservation();
\r
1128 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1129 stretchGroup.getName());
\r
1132 changeEndRes = false;
\r
1133 changeStartRes = false;
\r
1134 stretchGroup = null;
\r
1135 PaintRefresher.Refresh(av.alignment);
\r
1139 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1141 int res = findRes(evt);
\r
1142 int y = findSeq(evt);
\r
1144 if(wrappedBlock!=startWrapBlock)
\r
1147 if (stretchGroup == null)
\r
1152 mouseDragging = true;
\r
1155 if(y > av.alignment.getHeight())
\r
1157 y = av.alignment.getHeight() -1;
\r
1160 if(res>av.alignment.getWidth())
\r
1161 res = av.alignment.getWidth()-1;
\r
1163 if (stretchGroup.getEndRes() == res)
\r
1165 // Edit end res position of selected group
\r
1166 changeEndRes = true;
\r
1168 else if (stretchGroup.getStartRes() == res)
\r
1170 // Edit start res position of selected group
\r
1171 changeStartRes = true;
\r
1181 if (res > (stretchGroup.getStartRes() - 1))
\r
1183 stretchGroup.setEndRes(res);
\r
1186 else if (changeStartRes)
\r
1188 if (res < (stretchGroup.getEndRes() + 1))
\r
1190 stretchGroup.setStartRes(res);
\r
1194 int dragDirection = 0;
\r
1198 dragDirection = 1;
\r
1200 else if (y < oldSeq)
\r
1202 dragDirection = -1;
\r
1206 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1208 // This routine ensures we don't skip any sequences, as the
\r
1209 // selection is quite slow.
\r
1210 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1212 oldSeq += dragDirection;
\r
1217 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1219 if (stretchGroup.sequences.contains(nextSeq))
\r
1221 stretchGroup.deleteSequence(seq, false);
\r
1227 stretchGroup.addSequence(seq, false);
\r
1230 stretchGroup.addSequence(nextSeq, false);
\r
1238 if(res>av.endRes || res<av.startRes
\r
1239 || y<av.startSeq || y>av.endSeq)
\r
1244 if (scrollThread != null)
\r
1246 scrollThread.setEvent(evt);
\r
1249 seqCanvas.repaint();
\r
1252 public void mouseEntered(MouseEvent e)
\r
1257 if (scrollThread != null)
\r
1259 scrollThread.running = false;
\r
1260 scrollThread = null;
\r
1264 public void mouseExited(MouseEvent e)
\r
1266 if (av.getWrapAlignment())
\r
1271 if (mouseDragging && scrollThread==null)
\r
1273 scrollThread = new ScrollThread();
\r
1277 // this class allows scrolling off the bottom of the visible alignment
\r
1278 class ScrollThread
\r
1282 boolean running = false;
\r
1283 public ScrollThread()
\r
1288 public void setEvent(MouseEvent e)
\r
1293 public void stopScrolling()
\r
1307 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1309 running = ap.scrollUp(true);
\r
1312 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1313 av.alignment.getHeight() > av.getEndSeq())
\r
1315 running = ap.scrollUp(false);
\r
1318 if (mouseDragging && evt.getX() < 0)
\r
1320 running = ap.scrollRight(true);
\r
1323 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1325 running = ap.scrollRight(false);
\r
1333 catch (Exception ex)
\r