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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27 import jalview.commands.*;
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29 import java.util.Vector;
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31 public class SeqPanel
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32 extends Panel implements MouseMotionListener, MouseListener
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35 public SeqCanvas seqCanvas;
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36 public AlignmentPanel ap;
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38 protected int lastres;
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39 protected int startseq;
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41 protected AlignViewport av;
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43 // if character is inserted or deleted, we will need to recalculate the conservation
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44 boolean seqEditOccurred = false;
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46 ScrollThread scrollThread = null;
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47 boolean mouseDragging = false;
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48 boolean editingSeqs = false;
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49 boolean groupEditing = false;
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52 boolean changeEndSeq = false;
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53 boolean changeStartSeq = false;
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54 boolean changeEndRes = false;
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55 boolean changeStartRes = false;
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56 SequenceGroup stretchGroup = null;
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58 StringBuffer keyboardNo1;
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59 StringBuffer keyboardNo2;
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61 boolean mouseWheelPressed = false;
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62 Point lastMousePress;
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64 EditCommand editCommand;
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66 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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70 seqCanvas = new SeqCanvas(avp);
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71 setLayout(new BorderLayout());
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76 seqCanvas.addMouseMotionListener(this);
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77 seqCanvas.addMouseListener(this);
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79 seqCanvas.repaint();
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84 if (editCommand!=null && editCommand.getSize() > 0)
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86 ap.alignFrame.addHistoryItem(editCommand);
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87 av.firePropertyChange("alignment", null,
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88 av.getAlignment().getSequences());
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93 editingSeqs = false;
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94 groupEditing = false;
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100 void setCursorRow()
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102 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
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106 void setCursorColumn()
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108 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
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112 void setCursorRowAndColumn()
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114 if(keyboardNo2==null)
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116 keyboardNo2 = new StringBuffer();
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120 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
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121 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
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126 void setCursorPosition()
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128 SequenceI sequence =
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129 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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131 seqCanvas.cursorX = sequence.findIndex(
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132 getKeyboardNo(keyboardNo1)-1
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137 void moveCursor(int dx, int dy)
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139 seqCanvas.cursorX += dx;
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140 seqCanvas.cursorY += dy;
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141 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
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143 int original = seqCanvas.cursorX - dx;
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144 int maxWidth = av.alignment.getWidth();
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146 while(!av.colSel.isVisible(seqCanvas.cursorX)
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147 && seqCanvas.cursorX<maxWidth
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148 && seqCanvas.cursorX>0)
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150 seqCanvas.cursorX += dx;
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153 if(seqCanvas.cursorX>=maxWidth
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154 || !av.colSel.isVisible(seqCanvas.cursorX) )
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156 seqCanvas.cursorX = original;
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162 void scrollToVisible()
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164 if (seqCanvas.cursorX < 0)
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165 seqCanvas.cursorX = 0;
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166 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
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167 seqCanvas.cursorX = av.alignment.getWidth() - 1;
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169 if (seqCanvas.cursorY < 0)
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170 seqCanvas.cursorY = 0;
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171 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
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172 seqCanvas.cursorY = av.alignment.getHeight() - 1;
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176 if (av.wrapAlignment)
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178 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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182 while (seqCanvas.cursorY < av.startSeq)
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186 while (seqCanvas.cursorY + 1 > av.endSeq)
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188 ap.scrollUp(false);
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190 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
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193 if (!ap.scrollRight(false))
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196 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
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198 if (!ap.scrollRight(true))
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202 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
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203 seqCanvas.cursorX, seqCanvas.cursorY);
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205 seqCanvas.repaint();
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208 void setSelectionAreaAtCursor(boolean topLeft)
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210 SequenceI sequence =
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211 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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213 if(av.getSelectionGroup()!=null)
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215 SequenceGroup sg = av.selectionGroup;
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216 //Find the top and bottom of this group
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217 int min = av.alignment.getHeight(), max = 0;
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218 for(int i=0; i<sg.getSize(false); i++)
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220 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
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231 sg.setStartRes(seqCanvas.cursorX);
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232 if(sg.getEndRes()<seqCanvas.cursorX)
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233 sg.setEndRes(seqCanvas.cursorX);
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235 min = seqCanvas.cursorY;
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239 sg.setEndRes(seqCanvas.cursorX);
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240 if(sg.getStartRes()>seqCanvas.cursorX)
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241 sg.setStartRes(seqCanvas.cursorX);
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243 max = seqCanvas.cursorY+1;
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248 // Only the user can do this
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249 av.setSelectionGroup(null);
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253 // Now add any sequences between min and max
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254 sg.getSequences(false).removeAllElements();
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255 for (int i = min; i < max; i++)
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257 sg.addSequence(av.alignment.getSequenceAt(i), false);
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262 if (av.getSelectionGroup() == null)
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264 SequenceGroup sg = new SequenceGroup();
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265 sg.setStartRes(seqCanvas.cursorX);
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266 sg.setEndRes(seqCanvas.cursorX);
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267 sg.addSequence(sequence, false);
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268 av.setSelectionGroup(sg);
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275 void insertGapAtCursor(boolean group)
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277 groupEditing = group;
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278 startseq = seqCanvas.cursorY;
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279 lastres = seqCanvas.cursorX;
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280 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
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284 void deleteGapAtCursor(boolean group)
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286 groupEditing = group;
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287 startseq = seqCanvas.cursorY;
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288 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
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289 editSequence(false, seqCanvas.cursorX);
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293 void numberPressed(char value)
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295 if(keyboardNo1==null)
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296 keyboardNo1 = new StringBuffer();
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298 if(keyboardNo2!=null)
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299 keyboardNo2.append(value);
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301 keyboardNo1.append(value);
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304 int getKeyboardNo(StringBuffer kb)
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309 return Integer.parseInt(kb.toString());
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312 void setStatusMessage(SequenceI sequence, int res, int seq)
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314 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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315 sequence.getName());
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318 if (av.alignment.isNucleotide())
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320 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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323 text.append(" Nucleotide: ");
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327 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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329 text.append(" Residue: ");
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337 text.append(obj + " (" + sequence.findPosition(res) +
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342 ap.alignFrame.statusBar.setText(text.toString());
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345 public void mousePressed(MouseEvent evt)
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347 lastMousePress = evt.getPoint();
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349 //For now, ignore the mouseWheel font resizing on Macs
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350 //As the Button2_mask always seems to be true
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351 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
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352 InputEvent.BUTTON2_MASK && !av.MAC)
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354 mouseWheelPressed = true;
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358 if (evt.isShiftDown()
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359 || evt.isControlDown()
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360 || evt.isAltDown())
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362 if (evt.isControlDown() || evt.isAltDown())
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364 groupEditing = true;
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366 editingSeqs = true;
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370 doMousePressedDefineMode(evt);
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375 int seq = findSeq(evt);
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376 int res = findRes(evt);
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382 if ((seq < av.getAlignment().getHeight()) &&
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383 (res < av.getAlignment().getSequenceAt(seq).getLength()))
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397 public void mouseClicked(MouseEvent evt){}
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400 public void mouseReleased(MouseEvent evt)
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402 mouseDragging = false;
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403 mouseWheelPressed = false;
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407 doMouseReleasedDefineMode(evt);
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415 int startWrapBlock=-1;
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416 int wrappedBlock=-1;
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417 int findRes(MouseEvent evt)
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420 int x = evt.getX();
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422 if (av.wrapAlignment)
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425 int hgap = av.charHeight;
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426 if (av.scaleAboveWrapped)
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427 hgap += av.charHeight;
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429 int cHeight = av.getAlignment().getHeight() * av.charHeight
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430 + hgap + seqCanvas.getAnnotationHeight();
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432 int y = evt.getY();
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434 x -= seqCanvas.LABEL_WEST;
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437 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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441 wrappedBlock = y / cHeight;
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442 wrappedBlock += av.getStartRes() / cwidth;
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444 res = wrappedBlock * cwidth + x / av.getCharWidth();
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449 res = (x / av.getCharWidth()) + av.getStartRes();
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452 if(av.hasHiddenColumns)
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453 res = av.getColumnSelection().adjustForHiddenColumns(res);
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459 int findSeq(MouseEvent evt)
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463 int y = evt.getY();
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465 if (av.wrapAlignment)
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467 int hgap = av.charHeight;
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468 if (av.scaleAboveWrapped)
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469 hgap += av.charHeight;
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471 int cHeight = av.getAlignment().getHeight() * av.charHeight
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472 + hgap + seqCanvas.getAnnotationHeight();
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476 seq = Math.min( (y % cHeight) / av.getCharHeight(),
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477 av.alignment.getHeight() -1);
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483 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
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484 av.alignment.getHeight() -1);
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493 public void doMousePressed(MouseEvent evt)
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496 int seq = findSeq(evt);
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497 int res = findRes(evt);
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499 if (seq < av.getAlignment().getHeight() &&
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500 res < av.getAlignment().getSequenceAt(seq).getLength())
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502 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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503 // Find the residue's position in the sequence (res is the position
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504 // in the alignment
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518 public void mouseMoved(MouseEvent evt)
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520 int res = findRes(evt);
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521 int seq = findSeq(evt);
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523 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
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528 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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529 if (res > sequence.getLength())
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534 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
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535 sequence.getName());
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538 if (av.alignment.isNucleotide())
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540 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
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543 text.append(" Nucleotide: ");
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547 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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549 text.append(" Residue: ");
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556 text.append(obj + " (" + sequence.findPosition(res) + ")");
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560 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
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562 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
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565 ap.alignFrame.statusBar.setText(text.toString());
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568 // use aa to see if the mouse pointer is on a
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569 if (av.showSequenceFeatures
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570 && sequence.getSequenceFeatures()!=null
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571 && av.featuresDisplayed!=null)
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573 StringBuffer featureText = new StringBuffer();
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574 Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
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577 while (index < allFeatures.size())
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579 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
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581 featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
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583 if (sf.getDescription() != null)
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584 featureText.append(" " + sf.getDescription());
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586 if (sf.getValue("status") != null )
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588 String status = sf.getValue("status").toString();
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589 if(status.length()>0)
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590 featureText.append(" (" + sf.getValue("status") + ")");
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592 featureText.append("\n");
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598 if (tooltip == null)
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599 tooltip = new Tooltip(featureText.toString(), seqCanvas);
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601 tooltip.setTip(featureText.toString());
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606 else if (tooltip != null)
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608 tooltip.setTip("");
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612 Vector getAllFeaturesAtRes(SequenceI seq, int res)
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614 Vector allFeatures = new Vector();
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616 if(seq.getSequenceFeatures()!=null)
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618 while (index < seq.getSequenceFeatures().length)
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620 SequenceFeature sf = seq.getSequenceFeatures()[index];
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621 if (sf.getBegin() <= res &&
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622 sf.getEnd() >= res)
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624 if (av.featuresDisplayed.containsKey(sf.getType()))
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626 allFeatures.addElement(sf);
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632 return allFeatures;
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637 public void mouseDragged(MouseEvent evt)
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639 if (mouseWheelPressed)
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641 int oldWidth = av.charWidth;
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643 //Which is bigger, left-right or up-down?
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644 if (Math.abs(evt.getY() - lastMousePress.y)
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645 > Math.abs(evt.getX() - lastMousePress.x))
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647 int fontSize = av.font.getSize();
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649 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
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653 else if (evt.getY() > lastMousePress.y)
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662 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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663 av.charWidth = oldWidth;
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667 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
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671 else if (evt.getX() > lastMousePress.x)
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684 FontMetrics fm = getFontMetrics(av.getFont());
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685 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
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687 lastMousePress = evt.getPoint();
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690 ap.annotationPanel.image = null;
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696 doMouseDraggedDefineMode(evt);
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700 int res = findRes(evt);
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707 if ((lastres == -1) || (lastres == res))
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712 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
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714 // dragLeft, delete gap
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715 editSequence(false, res);
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718 editSequence(true, res);
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720 mouseDragging = true;
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721 if(scrollThread!=null)
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722 scrollThread.setEvent(evt);
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726 synchronized void editSequence(boolean insertGap, int startres)
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728 int fixedLeft = -1;
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729 int fixedRight = -1;
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730 boolean fixedColumns = false;
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731 SequenceGroup sg = av.getSelectionGroup();
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734 if (!groupEditing && av.hasHiddenRows)
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736 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
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738 groupEditing = true;
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742 //No group, but the sequence may represent a group
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745 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
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747 groupEditing = false;
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750 SequenceI seq = av.alignment.getSequenceAt(startseq);
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751 StringBuffer message = new StringBuffer();
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754 message.append("Edit group:");
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755 if (editCommand == null)
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756 editCommand = new EditCommand("Edit Group");
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760 message.append("Edit sequence: " + seq.getName());
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761 String label = seq.getName();
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762 if(label.length()>10)
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763 label = label.substring(0,10);
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764 if(editCommand==null)
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765 editCommand = new EditCommand("Edit "+label);
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769 message.append(" insert ");
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771 message.append(" delete ");
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773 message.append(Math.abs(startres-lastres)+" gaps.");
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774 ap.alignFrame.statusBar.setText(message.toString());
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777 //Are we editing within a selection group?
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779 || (sg != null && sg.getSequences(true).contains(seq)))
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781 fixedColumns = true;
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783 //sg might be null as the user may only see 1 sequence,
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784 //but the sequence represents a group
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787 sg = new SequenceGroup(null, null, false, false, false, 0,
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788 av.alignment.getWidth()-1);
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789 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
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792 fixedLeft = sg.getStartRes();
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793 fixedRight = sg.getEndRes();
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795 if ( (startres < fixedLeft && lastres >= fixedLeft)
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796 || (startres >= fixedLeft && lastres < fixedLeft)
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797 || (startres > fixedRight && lastres <=fixedRight)
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798 || (startres <= fixedRight && lastres > fixedRight))
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804 if (fixedLeft > startres)
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806 fixedRight = fixedLeft - 1;
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809 else if (fixedRight < startres)
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811 fixedLeft = fixedRight;
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817 if(av.hasHiddenColumns )
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819 fixedColumns = true;
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820 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
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821 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
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823 if ( (insertGap && startres > y1 && lastres < y1)
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824 || (!insertGap && startres < y2 && lastres > y2))
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830 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
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831 //Selection spans a hidden region
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832 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
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840 fixedRight = y2 - 1;
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848 Vector vseqs = sg.getSequences(true);
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849 int g, groupSize = vseqs.size();
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850 SequenceI[] groupSeqs = new SequenceI[groupSize];
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851 for (g = 0; g < groupSeqs.length; g++)
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852 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
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857 //If the user has selected the whole sequence, and is dragging to
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858 // the right, we can still extend the alignment and selectionGroup
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859 if( sg.getStartRes() == 0
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860 && sg.getEndRes() == fixedRight
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861 && sg.getEndRes() == av.alignment.getWidth()-1
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864 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
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865 fixedRight = sg.getEndRes();
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868 // Is it valid with fixed columns??
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869 // Find the next gap before the end
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870 // of the visible region boundary
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871 boolean blank = false;
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872 for (fixedRight = fixedRight;
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873 fixedRight > lastres;
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878 for (g = 0; g < groupSize; g++)
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880 for (int j = 0; j < startres - lastres; j++)
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882 if (!jalview.util.Comparison.isGap(
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883 groupSeqs[g].getCharAt(fixedRight - j)))
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896 if(sg.getSize(false) == av.alignment.getHeight() )
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898 if((av.hasHiddenColumns
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899 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
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905 int alWidth = av.alignment.getWidth();
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906 if(av.hasHiddenRows)
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908 int hwidth = av.alignment.getHiddenSequences().getWidth();
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912 //We can still insert gaps if the selectionGroup
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913 //contains all the sequences
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914 sg.setEndRes(sg.getEndRes()+startres-lastres);
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915 fixedRight = alWidth+startres-lastres;
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927 else if(!insertGap)
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929 /// Are we able to delete?
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930 // ie are all columns blank?
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932 for (g = 0; g < groupSize; g++)
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934 for (int j = startres; j < lastres; j++)
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936 if (groupSeqs[g].getLength() <= j)
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941 if (!jalview.util.Comparison.isGap(
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942 groupSeqs[g].getCharAt(j)))
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944 // Not a gap, block edit not valid
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954 // dragging to the right
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955 if (fixedColumns && fixedRight != -1)
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957 for (int j = lastres; j < startres; j++)
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959 insertChar(j, groupSeqs, fixedRight);
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964 editCommand.appendEdit(EditCommand.INSERT_GAP,
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966 startres, startres-lastres,
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967 av.getGapCharacter(),
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973 // dragging to the left
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974 if (fixedColumns && fixedRight != -1)
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976 for (int j = lastres; j > startres; j--)
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978 deleteChar(startres, groupSeqs, fixedRight);
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982 editCommand.appendEdit(EditCommand.DELETE_GAP,
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984 startres, lastres - startres,
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985 av.getGapCharacter(),
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990 else /////Editing a single sequence///////////
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994 // dragging to the right
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995 if (fixedColumns && fixedRight != -1)
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997 for (int j = lastres; j < startres; j++)
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999 insertChar(j, new SequenceI[]{seq}, fixedRight);
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1004 editCommand.appendEdit(EditCommand.INSERT_GAP,
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1007 lastres, startres-lastres,
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1008 av.getGapCharacter(),
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1014 // dragging to the left
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1015 if (fixedColumns && fixedRight != -1)
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1017 for (int j = lastres; j > startres; j--)
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1019 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
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1024 deleteChar(startres, new SequenceI[]{seq}, fixedRight);
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1029 //could be a keyboard edit trying to delete none gaps
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1031 for(int m = startres; m<lastres; m++)
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1033 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
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1040 editCommand.appendEdit(EditCommand.DELETE_GAP,
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1044 av.getGapCharacter(),
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1051 lastres = startres;
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1052 seqCanvas.repaint();
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1057 void insertChar(int j, SequenceI [] seq, int fixedColumn)
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1059 int blankColumn = fixedColumn;
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1060 for(int s=0; s<seq.length; s++)
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1062 //Find the next gap before the end of the visible region boundary
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1063 //If lastCol > j, theres a boundary after the gap insertion
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1065 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
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1067 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
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1069 //Theres a space, so break and insert the gap
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1074 if (blankColumn <= j)
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1076 blankColumn = fixedColumn;
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1082 editCommand.appendEdit(EditCommand.DELETE_GAP,
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1084 blankColumn, 1, av.getGapCharacter(), true);
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1086 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1088 j, 1, av.getGapCharacter(),
\r
1093 void deleteChar(int j, SequenceI [] seq, int fixedColumn)
\r
1096 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1098 j, 1, av.getGapCharacter(), true);
\r
1100 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1102 fixedColumn, 1, av.getGapCharacter(), true);
\r
1106 //////////////////////////////////////////
\r
1107 /////Everything below this is for defining the boundary of the rubberband
\r
1108 //////////////////////////////////////////
\r
1109 public void doMousePressedDefineMode(MouseEvent evt)
\r
1111 if (scrollThread != null)
\r
1113 scrollThread.running = false;
\r
1114 scrollThread = null;
\r
1117 int res = findRes(evt);
\r
1118 int seq = findSeq(evt);
\r
1120 startWrapBlock=wrappedBlock;
\r
1125 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1127 if (sequence == null || res > sequence.getLength())
\r
1132 stretchGroup = av.getSelectionGroup();
\r
1134 if (stretchGroup == null)
\r
1136 stretchGroup = av.alignment.findGroup(sequence);
\r
1137 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1138 res < stretchGroup.getEndRes())
\r
1140 av.setSelectionGroup(stretchGroup);
\r
1144 stretchGroup = null;
\r
1148 else if (!stretchGroup.getSequences(false).contains(sequence)
\r
1149 || stretchGroup.getStartRes() > res
\r
1150 || stretchGroup.getEndRes() < res)
\r
1152 stretchGroup = null;
\r
1154 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1156 if (allGroups != null)
\r
1158 for (int i = 0; i < allGroups.length; i++)
\r
1160 if (allGroups[i].getStartRes() <= res &&
\r
1161 allGroups[i].getEndRes() >= res)
\r
1163 stretchGroup = allGroups[i];
\r
1168 av.setSelectionGroup(stretchGroup);
\r
1172 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1173 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1174 InputEvent.BUTTON3_MASK)
\r
1176 Vector allFeatures = getAllFeaturesAtRes(sequence,
\r
1177 sequence.findPosition(res));
\r
1179 Vector links = null;
\r
1180 if(allFeatures!=null)
\r
1182 for (int i = 0; i < allFeatures.size(); i++)
\r
1184 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1185 if (sf.links != null)
\r
1187 links = new Vector();
\r
1188 for (int j = 0; j < sf.links.size(); j++)
\r
1190 links.addElement(sf.links.elementAt(j));
\r
1195 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1197 popup.show(this, evt.getX(), evt.getY());
\r
1202 if (av.cursorMode)
\r
1204 seqCanvas.cursorX = findRes(evt);
\r
1205 seqCanvas.cursorY = findSeq(evt);
\r
1206 seqCanvas.repaint();
\r
1210 //Only if left mouse button do we want to change group sizes
\r
1212 if (stretchGroup == null)
\r
1214 // define a new group here
\r
1215 SequenceGroup sg = new SequenceGroup();
\r
1216 sg.setStartRes(res);
\r
1217 sg.setEndRes(res);
\r
1218 sg.addSequence(sequence, false);
\r
1219 av.setSelectionGroup(sg);
\r
1220 stretchGroup = sg;
\r
1222 if (av.getConservationSelected())
\r
1224 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1227 if (av.getAbovePIDThreshold())
\r
1229 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1236 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1238 if (stretchGroup == null)
\r
1243 if(stretchGroup.cs!=null)
\r
1245 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1247 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1248 stretchGroup.getSequences(true),
\r
1249 stretchGroup.getWidth());
\r
1252 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1253 || stretchGroup.cs instanceof PIDColourScheme
\r
1254 || stretchGroup.cs.conservationApplied()
\r
1255 || stretchGroup.cs.getThreshold() > 0)
\r
1256 stretchGroup.recalcConservation();
\r
1259 if (stretchGroup.cs.conservationApplied())
\r
1261 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1262 stretchGroup.getName());
\r
1263 stretchGroup.recalcConservation();
\r
1267 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1268 stretchGroup.getName());
\r
1271 changeEndRes = false;
\r
1272 changeStartRes = false;
\r
1273 stretchGroup = null;
\r
1274 PaintRefresher.Refresh(ap, av.getSequenceSetId());
\r
1278 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1280 int res = findRes(evt);
\r
1281 int y = findSeq(evt);
\r
1283 if(wrappedBlock!=startWrapBlock)
\r
1286 if (stretchGroup == null)
\r
1291 mouseDragging = true;
\r
1294 if(y > av.alignment.getHeight())
\r
1296 y = av.alignment.getHeight() -1;
\r
1299 if(res>=av.alignment.getWidth())
\r
1300 res = av.alignment.getWidth()-1;
\r
1302 if (stretchGroup.getEndRes() == res)
\r
1304 // Edit end res position of selected group
\r
1305 changeEndRes = true;
\r
1307 else if (stretchGroup.getStartRes() == res)
\r
1309 // Edit start res position of selected group
\r
1310 changeStartRes = true;
\r
1320 if (res > (stretchGroup.getStartRes() - 1))
\r
1322 stretchGroup.setEndRes(res);
\r
1325 else if (changeStartRes)
\r
1327 if (res < (stretchGroup.getEndRes() + 1))
\r
1329 stretchGroup.setStartRes(res);
\r
1333 int dragDirection = 0;
\r
1337 dragDirection = 1;
\r
1339 else if (y < oldSeq)
\r
1341 dragDirection = -1;
\r
1345 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1347 // This routine ensures we don't skip any sequences, as the
\r
1348 // selection is quite slow.
\r
1349 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1351 oldSeq += dragDirection;
\r
1356 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1358 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1360 stretchGroup.deleteSequence(seq, false);
\r
1366 stretchGroup.addSequence(seq, false);
\r
1369 stretchGroup.addSequence(nextSeq, false);
\r
1377 if(res>av.endRes || res<av.startRes
\r
1378 || y<av.startSeq || y>av.endSeq)
\r
1383 if (scrollThread != null)
\r
1385 scrollThread.setEvent(evt);
\r
1388 seqCanvas.repaint();
\r
1391 public void mouseEntered(MouseEvent e)
\r
1396 if (scrollThread != null)
\r
1398 scrollThread.running = false;
\r
1399 scrollThread = null;
\r
1403 public void mouseExited(MouseEvent e)
\r
1405 if (av.getWrapAlignment())
\r
1410 if (mouseDragging && scrollThread==null)
\r
1412 scrollThread = new ScrollThread();
\r
1416 void scrollCanvas(MouseEvent evt)
\r
1420 if(scrollThread!=null)
\r
1422 scrollThread.running = false;
\r
1423 scrollThread = null;
\r
1425 mouseDragging = false;
\r
1429 if (scrollThread == null)
\r
1430 scrollThread = new ScrollThread();
\r
1432 mouseDragging = true;
\r
1433 scrollThread.setEvent(evt);
\r
1438 // this class allows scrolling off the bottom of the visible alignment
\r
1439 class ScrollThread
\r
1443 boolean running = false;
\r
1444 public ScrollThread()
\r
1449 public void setEvent(MouseEvent e)
\r
1454 public void stopScrolling()
\r
1468 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1470 running = ap.scrollUp(true);
\r
1473 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1474 av.alignment.getHeight() > av.getEndSeq())
\r
1476 running = ap.scrollUp(false);
\r
1479 if (mouseDragging && evt.getX() < 0)
\r
1481 running = ap.scrollRight(false);
\r
1484 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1486 running = ap.scrollRight(true);
\r
1494 catch (Exception ex)
\r