2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.api.AlignViewportI;
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24 import jalview.commands.EditCommand;
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25 import jalview.commands.EditCommand.Action;
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26 import jalview.datamodel.ColumnSelection;
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27 import jalview.datamodel.SearchResults;
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28 import jalview.datamodel.SearchResults.Match;
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29 import jalview.datamodel.Sequence;
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30 import jalview.datamodel.SequenceFeature;
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31 import jalview.datamodel.SequenceGroup;
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32 import jalview.datamodel.SequenceI;
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33 import jalview.schemes.ResidueProperties;
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34 import jalview.structure.SelectionListener;
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35 import jalview.structure.SelectionSource;
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36 import jalview.structure.SequenceListener;
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37 import jalview.structure.StructureSelectionManager;
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38 import jalview.structure.VamsasSource;
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39 import jalview.util.Comparison;
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40 import jalview.util.MappingUtils;
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41 import jalview.util.MessageManager;
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42 import jalview.viewmodel.AlignmentViewport;
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44 import java.awt.BorderLayout;
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45 import java.awt.Font;
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46 import java.awt.FontMetrics;
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47 import java.awt.Point;
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48 import java.awt.event.InputEvent;
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49 import java.awt.event.MouseEvent;
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50 import java.awt.event.MouseListener;
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51 import java.awt.event.MouseMotionListener;
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52 import java.util.List;
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53 import java.util.Vector;
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55 import javax.swing.JPanel;
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57 public class SeqPanel extends JPanel implements MouseMotionListener,
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58 MouseListener, SequenceListener, SelectionListener
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61 public SeqCanvas seqCanvas;
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63 public AlignmentPanel ap;
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65 protected int lastres;
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67 protected int startseq;
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69 protected AlignViewport av;
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71 // if character is inserted or deleted, we will need to recalculate the
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73 boolean seqEditOccurred = false;
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75 ScrollThread scrollThread = null;
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77 boolean mouseDragging = false;
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79 boolean editingSeqs = false;
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81 boolean groupEditing = false;
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85 boolean changeEndSeq = false;
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87 boolean changeStartSeq = false;
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89 boolean changeEndRes = false;
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91 boolean changeStartRes = false;
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93 SequenceGroup stretchGroup = null;
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95 StringBuffer keyboardNo1;
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97 StringBuffer keyboardNo2;
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99 boolean mouseWheelPressed = false;
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101 Point lastMousePress;
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103 EditCommand editCommand;
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105 StructureSelectionManager ssm;
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107 public SeqPanel(AlignViewport avp, AlignmentPanel p)
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111 seqCanvas = new SeqCanvas(avp);
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112 setLayout(new BorderLayout());
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117 seqCanvas.addMouseMotionListener(this);
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118 seqCanvas.addMouseListener(this);
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119 ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
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120 ssm.addStructureViewerListener(this);
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121 ssm.addSelectionListener(this);
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123 seqCanvas.repaint();
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128 if (editCommand != null && editCommand.getSize() > 0)
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130 ap.alignFrame.addHistoryItem(editCommand);
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131 av.firePropertyChange("alignment", null, av.getAlignment()
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137 editingSeqs = false;
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138 groupEditing = false;
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139 keyboardNo1 = null;
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140 keyboardNo2 = null;
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141 editCommand = null;
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144 void setCursorRow()
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146 seqCanvas.cursorY = getKeyboardNo1() - 1;
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150 void setCursorColumn()
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152 seqCanvas.cursorX = getKeyboardNo1() - 1;
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156 void setCursorRowAndColumn()
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158 if (keyboardNo2 == null)
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160 keyboardNo2 = new StringBuffer();
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164 seqCanvas.cursorX = getKeyboardNo1() - 1;
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165 seqCanvas.cursorY = getKeyboardNo2() - 1;
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170 void setCursorPosition()
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172 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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174 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
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178 void moveCursor(int dx, int dy)
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180 seqCanvas.cursorX += dx;
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181 seqCanvas.cursorY += dy;
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182 if (av.hasHiddenColumns()
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183 && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
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185 int original = seqCanvas.cursorX - dx;
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186 int maxWidth = av.getAlignment().getWidth();
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188 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
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189 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
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191 seqCanvas.cursorX += dx;
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194 if (seqCanvas.cursorX >= maxWidth
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195 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
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197 seqCanvas.cursorX = original;
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203 void scrollToVisible()
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205 if (seqCanvas.cursorX < 0)
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207 seqCanvas.cursorX = 0;
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209 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
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211 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
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214 if (seqCanvas.cursorY < 0)
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216 seqCanvas.cursorY = 0;
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218 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
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220 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
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224 if (av.getWrapAlignment())
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226 ap.scrollToWrappedVisible(seqCanvas.cursorX);
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230 while (seqCanvas.cursorY < av.startSeq)
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234 while (seqCanvas.cursorY + 1 > av.endSeq)
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236 ap.scrollUp(false);
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238 while (seqCanvas.cursorX < av.getColumnSelection()
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239 .adjustForHiddenColumns(av.startRes))
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242 if (!ap.scrollRight(false))
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247 while (seqCanvas.cursorX > av.getColumnSelection()
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248 .adjustForHiddenColumns(av.endRes))
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250 if (!ap.scrollRight(true))
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256 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
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257 seqCanvas.cursorX, seqCanvas.cursorY);
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259 seqCanvas.repaint();
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262 void setSelectionAreaAtCursor(boolean topLeft)
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264 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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266 if (av.getSelectionGroup() != null)
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268 SequenceGroup sg = av.getSelectionGroup();
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269 // Find the top and bottom of this group
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270 int min = av.getAlignment().getHeight(), max = 0;
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271 for (int i = 0; i < sg.getSize(); i++)
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273 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
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288 sg.setStartRes(seqCanvas.cursorX);
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289 if (sg.getEndRes() < seqCanvas.cursorX)
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291 sg.setEndRes(seqCanvas.cursorX);
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294 min = seqCanvas.cursorY;
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298 sg.setEndRes(seqCanvas.cursorX);
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299 if (sg.getStartRes() > seqCanvas.cursorX)
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301 sg.setStartRes(seqCanvas.cursorX);
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304 max = seqCanvas.cursorY + 1;
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309 // Only the user can do this
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310 av.setSelectionGroup(null);
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314 // Now add any sequences between min and max
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316 for (int i = min; i < max; i++)
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318 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
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323 if (av.getSelectionGroup() == null)
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325 SequenceGroup sg = new SequenceGroup();
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326 sg.setStartRes(seqCanvas.cursorX);
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327 sg.setEndRes(seqCanvas.cursorX);
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328 sg.addSequence(sequence, false);
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329 av.setSelectionGroup(sg);
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331 ap.paintAlignment(false);
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332 av.sendSelection();
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335 void insertGapAtCursor(boolean group)
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337 groupEditing = group;
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338 startseq = seqCanvas.cursorY;
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339 lastres = seqCanvas.cursorX;
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340 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
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344 void deleteGapAtCursor(boolean group)
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346 groupEditing = group;
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347 startseq = seqCanvas.cursorY;
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348 lastres = seqCanvas.cursorX + getKeyboardNo1();
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349 editSequence(false, seqCanvas.cursorX);
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353 void numberPressed(char value)
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355 if (keyboardNo1 == null)
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357 keyboardNo1 = new StringBuffer();
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360 if (keyboardNo2 != null)
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362 keyboardNo2.append(value);
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366 keyboardNo1.append(value);
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370 int getKeyboardNo1()
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374 if (keyboardNo1 != null)
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376 int value = Integer.parseInt(keyboardNo1.toString());
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377 keyboardNo1 = null;
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380 } catch (Exception x)
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383 keyboardNo1 = null;
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387 int getKeyboardNo2()
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391 if (keyboardNo2 != null)
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393 int value = Integer.parseInt(keyboardNo2.toString());
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394 keyboardNo2 = null;
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397 } catch (Exception x)
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400 keyboardNo2 = null;
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405 * Set status message in alignment panel
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408 * aligned sequence object
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412 * index of sequence in alignment
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413 * @return position of res in sequence
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415 void setStatusMessage(SequenceI sequence, int res, int seq)
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417 // TODO remove duplication of identical gui method
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418 StringBuilder text = new StringBuilder(32);
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419 String seqno = seq == -1 ? "" : " " + (seq + 1);
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420 text.append("Sequence" + seqno + " ID: " + sequence.getName());
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422 String residue = null;
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424 * Try to translate the display character to residue name (null for gap).
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426 final String displayChar = String.valueOf(sequence.getCharAt(res));
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427 if (av.getAlignment().isNucleotide())
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429 residue = ResidueProperties.nucleotideName.get(displayChar);
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430 if (residue != null)
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432 text.append(" Nucleotide: ").append(residue);
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437 residue = "X".equalsIgnoreCase(displayChar) ? "X"
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438 : ResidueProperties.aa2Triplet.get(displayChar);
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439 if (residue != null)
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441 text.append(" Residue: ").append(residue);
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446 if (residue != null)
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448 pos = sequence.findPosition(res);
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449 text.append(" (").append(Integer.toString(pos)).append(")");
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451 // Object obj = null;
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452 // if (av.getAlignment().isNucleotide())
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454 // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
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456 // if (obj != null)
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458 // text.append(" Nucleotide: ");
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463 // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
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464 // if (obj != null)
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466 // text.append(" Residue: ");
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470 // if (obj != null)
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475 // text.append(obj + " (" + sequence.findPosition(res) + ")");
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479 ap.alignFrame.statusBar.setText(text.toString());
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484 * Set the status bar message to highlight the first matched position in
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489 private void setStatusMessage(SearchResults results)
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491 List<Match> matches = results.getResults();
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492 if (!matches.isEmpty())
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494 Match m = matches.get(0);
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495 SequenceI seq = m.getSequence();
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496 int sequenceIndex = this.av.getAlignment().findIndex(seq);
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499 * Convert position in sequence (base 1) to sequence character array index
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502 int start = m.getStart() - 1;
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503 setStatusMessage(seq, start, sequenceIndex);
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507 public void mousePressed(MouseEvent evt)
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509 lastMousePress = evt.getPoint();
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511 // For now, ignore the mouseWheel font resizing on Macs
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512 // As the Button2_mask always seems to be true
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513 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
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516 mouseWheelPressed = true;
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520 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
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522 if (evt.isControlDown() || evt.isAltDown())
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524 groupEditing = true;
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526 editingSeqs = true;
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530 doMousePressedDefineMode(evt);
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534 int seq = findSeq(evt);
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535 int res = findRes(evt);
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537 if (seq < 0 || res < 0)
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542 if ((seq < av.getAlignment().getHeight())
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543 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
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557 public void mouseClicked(MouseEvent evt)
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559 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
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560 if (evt.getClickCount() > 1)
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562 if (av.getSelectionGroup() != null
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563 && av.getSelectionGroup().getSize() == 1
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564 && av.getSelectionGroup().getEndRes()
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565 - av.getSelectionGroup().getStartRes() < 2)
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567 av.setSelectionGroup(null);
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570 SequenceFeature[] features = findFeaturesAtRes(sequence,
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571 sequence.findPosition(findRes(evt)));
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573 if (features != null && features.length > 0)
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575 SearchResults highlight = new SearchResults();
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576 highlight.addResult(sequence, features[0].getBegin(),
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577 features[0].getEnd());
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578 seqCanvas.highlightSearchResults(highlight);
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580 if (features != null && features.length > 0)
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582 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
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583 { sequence }, features, false, ap);
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585 seqCanvas.highlightSearchResults(null);
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590 public void mouseReleased(MouseEvent evt)
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592 mouseDragging = false;
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593 mouseWheelPressed = false;
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594 ap.paintAlignment(true);
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598 doMouseReleasedDefineMode(evt);
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606 int startWrapBlock = -1;
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608 int wrappedBlock = -1;
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610 int findRes(MouseEvent evt)
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613 int x = evt.getX();
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615 if (av.getWrapAlignment())
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618 int hgap = av.getCharHeight();
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619 if (av.getScaleAboveWrapped())
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621 hgap += av.getCharHeight();
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624 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
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626 + seqCanvas.getAnnotationHeight();
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628 int y = evt.getY();
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630 x -= seqCanvas.LABEL_WEST;
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632 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
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638 wrappedBlock = y / cHeight;
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639 wrappedBlock += av.getStartRes() / cwidth;
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641 res = wrappedBlock * cwidth + x / av.getCharWidth();
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646 res = (x / av.getCharWidth()) + av.getStartRes();
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649 if (av.hasHiddenColumns())
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651 res = av.getColumnSelection().adjustForHiddenColumns(res);
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658 int findSeq(MouseEvent evt)
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660 final int sqnum = findAlRow(evt);
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661 return (sqnum < 0) ? 0 : sqnum;
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667 * @return row in alignment that was selected (or -1 for column selection)
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669 private int findAlRow(MouseEvent evt)
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672 int y = evt.getY();
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674 if (av.getWrapAlignment())
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676 int hgap = av.getCharHeight();
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677 if (av.getScaleAboveWrapped())
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679 hgap += av.getCharHeight();
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682 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
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684 + seqCanvas.getAnnotationHeight();
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688 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
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697 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
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698 .getAlignment().getHeight() - 1);
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708 public void doMousePressed(MouseEvent evt)
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711 int seq = findSeq(evt);
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712 int res = findRes(evt);
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714 if (seq < av.getAlignment().getHeight()
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715 && res < av.getAlignment().getSequenceAt(seq).getLength())
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717 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
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718 // Find the residue's position in the sequence (res is the position
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719 // in the alignment
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733 String lastMessage;
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735 public void mouseOverSequence(SequenceI sequence, int index, int pos)
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737 String tmp = sequence.hashCode() + index + "";
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738 if (lastMessage == null || !lastMessage.equals(tmp))
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740 ssm.mouseOverSequence(sequence, index, pos, av);
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746 public void highlightSequence(SearchResults results)
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748 if (av.isFollowHighlight())
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750 if (ap.scrollToPosition(results, true))
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752 ap.alignFrame.repaint();
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755 setStatusMessage(results);
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756 seqCanvas.highlightSearchResults(results);
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761 public VamsasSource getVamsasSource()
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763 return this.ap == null ? null : this.ap.av;
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766 public void updateColours(SequenceI seq, int index)
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768 System.out.println("update the seqPanel colours");
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772 public void mouseMoved(MouseEvent evt)
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774 int res = findRes(evt);
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775 int seq = findSeq(evt);
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777 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
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779 if (tooltip != null)
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781 tooltip.setTip("");
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786 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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787 if (res > sequence.getLength())
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789 if (tooltip != null)
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791 tooltip.setTip("");
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796 int respos = sequence.findPosition(res);
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799 mouseOverSequence(sequence, res, respos);
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802 StringBuilder text = new StringBuilder();
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803 text.append("Sequence ").append(Integer.toString(seq + 1))
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804 .append(" ID: ").append(sequence.getName());
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807 final String ch = String.valueOf(sequence.getCharAt(res));
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808 if (av.getAlignment().isNucleotide())
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810 obj = ResidueProperties.nucleotideName.get(ch);
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813 text.append(" Nucleotide: ").append(obj);
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818 obj = "X".equalsIgnoreCase(ch) ? "X"
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819 : ResidueProperties.aa2Triplet.get(ch);
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822 text.append(" Residue: ").append(obj);
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828 text.append(" (").append(Integer.toString(respos)).append(")");
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831 ap.alignFrame.statusBar.setText(text.toString());
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833 StringBuilder tooltipText = new StringBuilder();
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834 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
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835 if (groups != null)
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837 for (int g = 0; g < groups.length; g++)
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839 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
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841 if (!groups[g].getName().startsWith("JTreeGroup")
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842 && !groups[g].getName().startsWith("JGroup"))
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844 tooltipText.append(groups[g].getName()).append(" ");
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846 if (groups[g].getDescription() != null)
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848 tooltipText.append(groups[g].getDescription());
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850 tooltipText.append("\n");
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855 // use aa to see if the mouse pointer is on a
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856 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
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857 sequence.findPosition(res));
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860 while (index < allFeatures.length)
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862 SequenceFeature sf = allFeatures[index];
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864 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
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866 if (sf.getDescription() != null)
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868 tooltipText.append(" " + sf.getDescription());
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871 if (sf.getValue("status") != null)
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873 String status = sf.getValue("status").toString();
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874 if (status.length() > 0)
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876 tooltipText.append(" (" + sf.getValue("status") + ")");
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879 tooltipText.append("\n");
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884 if (tooltip == null)
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886 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
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890 tooltip.setTip(tooltipText.toString());
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894 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
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896 Vector tmp = new Vector();
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897 SequenceFeature[] features = sequence.getSequenceFeatures();
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898 if (features != null)
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900 for (int i = 0; i < features.length; i++)
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902 if (av.getFeaturesDisplayed() == null
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903 || !av.getFeaturesDisplayed().isVisible(features[i].getType()))
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908 if (features[i].featureGroup != null
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909 && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false))
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914 if ((features[i].getBegin() <= res)
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915 && (features[i].getEnd() >= res))
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917 tmp.addElement(features[i]);
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922 features = new SequenceFeature[tmp.size()];
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923 tmp.copyInto(features);
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930 public void mouseDragged(MouseEvent evt)
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932 if (mouseWheelPressed)
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934 int oldWidth = av.getCharWidth();
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936 // Which is bigger, left-right or up-down?
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937 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
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938 - lastMousePress.x))
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940 int fontSize = av.font.getSize();
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942 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
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946 else if (evt.getY() > lastMousePress.y)
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956 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
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957 av.setCharWidth(oldWidth);
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961 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
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963 av.setCharWidth(av.getCharWidth() - 1);
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965 else if (evt.getX() > lastMousePress.x)
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967 av.setCharWidth(av.getCharWidth() + 1);
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970 if (av.getCharWidth() < 1)
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972 av.setCharWidth(1);
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978 FontMetrics fm = getFontMetrics(av.getFont());
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979 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
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981 lastMousePress = evt.getPoint();
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983 ap.paintAlignment(false);
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984 ap.annotationPanel.image = null;
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990 doMouseDraggedDefineMode(evt);
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994 int res = findRes(evt);
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1001 if ((lastres == -1) || (lastres == res))
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1006 if ((res < av.getAlignment().getWidth()) && (res < lastres))
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1008 // dragLeft, delete gap
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1009 editSequence(false, res);
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1013 editSequence(true, res);
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1016 mouseDragging = true;
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1017 if (scrollThread != null)
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1019 scrollThread.setEvent(evt);
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1024 synchronized void editSequence(boolean insertGap, int startres)
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1026 int fixedLeft = -1;
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1027 int fixedRight = -1;
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1028 boolean fixedColumns = false;
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1029 SequenceGroup sg = av.getSelectionGroup();
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1031 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
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1033 if (!groupEditing && av.hasHiddenRows())
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1035 if (av.isHiddenRepSequence(seq))
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1037 sg = av.getRepresentedSequences(seq);
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1038 groupEditing = true;
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1042 StringBuffer message = new StringBuffer();
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1045 message.append(MessageManager.getString("action.edit_group")).append(
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1047 if (editCommand == null)
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1049 editCommand = new EditCommand(
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1050 MessageManager.getString("action.edit_group"));
\r
1055 message.append(MessageManager.getString("label.edit_sequence"))
\r
1056 .append(" " + seq.getName());
\r
1057 String label = seq.getName();
\r
1058 if (label.length() > 10)
\r
1060 label = label.substring(0, 10);
\r
1062 if (editCommand == null)
\r
1064 editCommand = new EditCommand(MessageManager.formatMessage(
\r
1065 "label.edit_params", new String[]
\r
1072 message.append(" insert ");
\r
1076 message.append(" delete ");
\r
1079 message.append(Math.abs(startres - lastres) + " gaps.");
\r
1080 ap.alignFrame.statusBar.setText(message.toString());
\r
1082 // Are we editing within a selection group?
\r
1084 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
\r
1087 fixedColumns = true;
\r
1089 // sg might be null as the user may only see 1 sequence,
\r
1090 // but the sequence represents a group
\r
1093 if (!av.isHiddenRepSequence(seq))
\r
1099 sg = av.getRepresentedSequences(seq);
\r
1102 fixedLeft = sg.getStartRes();
\r
1103 fixedRight = sg.getEndRes();
\r
1105 if ((startres < fixedLeft && lastres >= fixedLeft)
\r
1106 || (startres >= fixedLeft && lastres < fixedLeft)
\r
1107 || (startres > fixedRight && lastres <= fixedRight)
\r
1108 || (startres <= fixedRight && lastres > fixedRight))
\r
1114 if (fixedLeft > startres)
\r
1116 fixedRight = fixedLeft - 1;
\r
1119 else if (fixedRight < startres)
\r
1121 fixedLeft = fixedRight;
\r
1126 if (av.hasHiddenColumns())
\r
1128 fixedColumns = true;
\r
1129 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
\r
1130 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
\r
1132 if ((insertGap && startres > y1 && lastres < y1)
\r
1133 || (!insertGap && startres < y2 && lastres > y2))
\r
1139 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
\r
1140 // Selection spans a hidden region
\r
1141 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
\r
1143 if (startres >= y2)
\r
1149 fixedRight = y2 - 1;
\r
1156 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
\r
1157 .toArray(new SequenceI[0]);
\r
1162 // If the user has selected the whole sequence, and is dragging to
\r
1163 // the right, we can still extend the alignment and selectionGroup
\r
1164 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
\r
1165 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
\r
1167 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
\r
1168 fixedRight = sg.getEndRes();
\r
1171 // Is it valid with fixed columns??
\r
1172 // Find the next gap before the end
\r
1173 // of the visible region boundary
\r
1174 boolean blank = false;
\r
1175 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
\r
1179 for (SequenceI gs : groupSeqs)
\r
1181 for (int j = 0; j < startres - lastres; j++)
\r
1183 if (!Comparison.isGap(gs.getCharAt(fixedRight
\r
1199 if (sg.getSize() == av.getAlignment().getHeight())
\r
1201 if ((av.hasHiddenColumns() && startres < av
\r
1202 .getColumnSelection().getHiddenBoundaryRight(startres)))
\r
1208 int alWidth = av.getAlignment().getWidth();
\r
1209 if (av.hasHiddenRows())
\r
1211 int hwidth = av.getAlignment().getHiddenSequences()
\r
1213 if (hwidth > alWidth)
\r
1218 // We can still insert gaps if the selectionGroup
\r
1219 // contains all the sequences
\r
1220 sg.setEndRes(sg.getEndRes() + startres - lastres);
\r
1221 fixedRight = alWidth + startres - lastres;
\r
1232 else if (!insertGap)
\r
1234 // / Are we able to delete?
\r
1235 // ie are all columns blank?
\r
1237 for (SequenceI gs : groupSeqs)
\r
1239 for (int j = startres; j < lastres; j++)
\r
1241 if (gs.getLength() <= j)
\r
1246 if (!Comparison.isGap(gs.getCharAt(j)))
\r
1248 // Not a gap, block edit not valid
\r
1258 // dragging to the right
\r
1259 if (fixedColumns && fixedRight != -1)
\r
1261 for (int j = lastres; j < startres; j++)
\r
1263 insertChar(j, groupSeqs, fixedRight);
\r
1268 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
\r
1269 startres - lastres, av.getAlignment(), true);
\r
1274 // dragging to the left
\r
1275 if (fixedColumns && fixedRight != -1)
\r
1277 for (int j = lastres; j > startres; j--)
\r
1279 deleteChar(startres, groupSeqs, fixedRight);
\r
1284 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
\r
1285 lastres - startres, av.getAlignment(), true);
\r
1291 // ///Editing a single sequence///////////
\r
1295 // dragging to the right
\r
1296 if (fixedColumns && fixedRight != -1)
\r
1298 for (int j = lastres; j < startres; j++)
\r
1300 insertChar(j, new SequenceI[]
\r
1301 { seq }, fixedRight);
\r
1306 editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
\r
1307 { seq }, lastres, startres - lastres, av.getAlignment(), true);
\r
1312 // dragging to the left
\r
1313 if (fixedColumns && fixedRight != -1)
\r
1315 for (int j = lastres; j > startres; j--)
\r
1317 if (!Comparison.isGap(seq.getCharAt(startres)))
\r
1322 deleteChar(startres, new SequenceI[]
\r
1323 { seq }, fixedRight);
\r
1328 // could be a keyboard edit trying to delete none gaps
\r
1330 for (int m = startres; m < lastres; m++)
\r
1332 if (!Comparison.isGap(seq.getCharAt(m)))
\r
1341 editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
\r
1342 { seq }, startres, max, av.getAlignment(), true);
\r
1348 lastres = startres;
\r
1349 seqCanvas.repaint();
\r
1352 void insertChar(int j, SequenceI[] seq, int fixedColumn)
\r
1354 int blankColumn = fixedColumn;
\r
1355 for (int s = 0; s < seq.length; s++)
\r
1357 // Find the next gap before the end of the visible region boundary
\r
1358 // If lastCol > j, theres a boundary after the gap insertion
\r
1360 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1362 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1364 // Theres a space, so break and insert the gap
\r
1369 if (blankColumn <= j)
\r
1371 blankColumn = fixedColumn;
\r
1377 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
\r
1378 av.getAlignment(), true);
\r
1380 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
\r
1385 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
\r
1388 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
\r
1391 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
\r
1392 av.getAlignment(), true);
\r
1395 // ////////////////////////////////////////
\r
1396 // ///Everything below this is for defining the boundary of the rubberband
\r
1397 // ////////////////////////////////////////
\r
1398 public void doMousePressedDefineMode(MouseEvent evt)
\r
1400 if (scrollThread != null)
\r
1402 scrollThread.running = false;
\r
1403 scrollThread = null;
\r
1406 int res = findRes(evt);
\r
1407 int seq = findSeq(evt);
\r
1409 startWrapBlock = wrappedBlock;
\r
1416 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
\r
1418 if (sequence == null || res > sequence.getLength())
\r
1423 stretchGroup = av.getSelectionGroup();
\r
1425 if (stretchGroup == null)
\r
1427 stretchGroup = av.getAlignment().findGroup(sequence);
\r
1428 if (stretchGroup != null && res > stretchGroup.getStartRes()
\r
1429 && res < stretchGroup.getEndRes())
\r
1431 av.setSelectionGroup(stretchGroup);
\r
1435 stretchGroup = null;
\r
1439 else if (!stretchGroup.getSequences(null).contains(sequence)
\r
1440 || stretchGroup.getStartRes() > res
\r
1441 || stretchGroup.getEndRes() < res)
\r
1443 stretchGroup = null;
\r
1445 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
\r
1447 if (allGroups != null)
\r
1449 for (int i = 0; i < allGroups.length; i++)
\r
1451 if (allGroups[i].getStartRes() <= res
\r
1452 && allGroups[i].getEndRes() >= res)
\r
1454 stretchGroup = allGroups[i];
\r
1459 av.setSelectionGroup(stretchGroup);
\r
1462 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1463 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
\r
1465 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
\r
1466 sequence.findPosition(res));
\r
1468 Vector<String> links = null;
\r
1469 if (allFeatures != null)
\r
1471 for (int i = 0; i < allFeatures.length; i++)
\r
1473 if (allFeatures[i].links != null)
\r
1475 if (links == null)
\r
1477 links = new Vector<String>();
\r
1479 for (int j = 0; j < allFeatures[i].links.size(); j++)
\r
1481 links.addElement(allFeatures[i].links.elementAt(j));
\r
1486 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1488 popup.show(this, evt.getX(), evt.getY());
\r
1492 if (av.cursorMode)
\r
1494 seqCanvas.cursorX = findRes(evt);
\r
1495 seqCanvas.cursorY = findSeq(evt);
\r
1496 seqCanvas.repaint();
\r
1500 // Only if left mouse button do we want to change group sizes
\r
1502 if (stretchGroup == null)
\r
1504 // define a new group here
\r
1505 SequenceGroup sg = new SequenceGroup();
\r
1506 sg.setStartRes(res);
\r
1507 sg.setEndRes(res);
\r
1508 sg.addSequence(sequence, false);
\r
1509 av.setSelectionGroup(sg);
\r
1510 stretchGroup = sg;
\r
1512 if (av.getConservationSelected())
\r
1514 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1517 if (av.getAbovePIDThreshold())
\r
1519 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1526 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1528 if (stretchGroup == null)
\r
1533 stretchGroup.recalcConservation(); // always do this - annotation has own
\r
1535 if (stretchGroup.cs != null)
\r
1537 stretchGroup.cs.alignmentChanged(stretchGroup,
\r
1538 av.getHiddenRepSequences());
\r
1540 if (stretchGroup.cs.conservationApplied())
\r
1542 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1543 stretchGroup.getName());
\r
1547 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1548 stretchGroup.getName());
\r
1551 changeEndRes = false;
\r
1552 changeStartRes = false;
\r
1553 stretchGroup = null;
\r
1554 PaintRefresher.Refresh(ap, av.getSequenceSetId());
\r
1555 ap.paintAlignment(true);
\r
1556 av.sendSelection();
\r
1559 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1561 int res = findRes(evt);
\r
1562 int y = findSeq(evt);
\r
1564 if (wrappedBlock != startWrapBlock)
\r
1569 if (stretchGroup == null)
\r
1574 mouseDragging = true;
\r
1576 if (y > av.getAlignment().getHeight())
\r
1578 y = av.getAlignment().getHeight() - 1;
\r
1581 if (res >= av.getAlignment().getWidth())
\r
1583 res = av.getAlignment().getWidth() - 1;
\r
1586 if (stretchGroup.getEndRes() == res)
\r
1588 // Edit end res position of selected group
\r
1589 changeEndRes = true;
\r
1591 else if (stretchGroup.getStartRes() == res)
\r
1593 // Edit start res position of selected group
\r
1594 changeStartRes = true;
\r
1604 if (res > (stretchGroup.getStartRes() - 1))
\r
1606 stretchGroup.setEndRes(res);
\r
1609 else if (changeStartRes)
\r
1611 if (res < (stretchGroup.getEndRes() + 1))
\r
1613 stretchGroup.setStartRes(res);
\r
1617 int dragDirection = 0;
\r
1621 dragDirection = 1;
\r
1623 else if (y < oldSeq)
\r
1625 dragDirection = -1;
\r
1628 while ((y != oldSeq) && (oldSeq > -1)
\r
1629 && (y < av.getAlignment().getHeight()))
\r
1631 // This routine ensures we don't skip any sequences, as the
\r
1632 // selection is quite slow.
\r
1633 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1635 oldSeq += dragDirection;
\r
1642 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1644 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1646 stretchGroup.deleteSequence(seq, false);
\r
1652 stretchGroup.addSequence(seq, false);
\r
1655 stretchGroup.addSequence(nextSeq, false);
\r
1664 if (res > av.endRes || res < av.startRes || y < av.startSeq
\r
1670 if (scrollThread != null)
\r
1672 scrollThread.setEvent(evt);
\r
1675 seqCanvas.repaint();
\r
1678 public void mouseEntered(MouseEvent e)
\r
1685 if (scrollThread != null)
\r
1687 scrollThread.running = false;
\r
1688 scrollThread = null;
\r
1692 public void mouseExited(MouseEvent e)
\r
1694 if (av.getWrapAlignment())
\r
1699 if (mouseDragging && scrollThread == null)
\r
1701 scrollThread = new ScrollThread();
\r
1705 void scrollCanvas(MouseEvent evt)
\r
1709 if (scrollThread != null)
\r
1711 scrollThread.running = false;
\r
1712 scrollThread = null;
\r
1714 mouseDragging = false;
\r
1718 if (scrollThread == null)
\r
1720 scrollThread = new ScrollThread();
\r
1723 mouseDragging = true;
\r
1724 scrollThread.setEvent(evt);
\r
1729 // this class allows scrolling off the bottom of the visible alignment
\r
1730 class ScrollThread extends Thread
\r
1734 boolean running = false;
\r
1736 public ScrollThread()
\r
1741 public void setEvent(MouseEvent e)
\r
1746 public void stopScrolling()
\r
1760 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1762 running = ap.scrollUp(true);
\r
1765 if (mouseDragging && evt.getY() >= getSize().height
\r
1766 && av.getAlignment().getHeight() > av.getEndSeq())
\r
1768 running = ap.scrollUp(false);
\r
1771 if (mouseDragging && evt.getX() < 0)
\r
1773 running = ap.scrollRight(false);
\r
1776 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1778 running = ap.scrollRight(true);
\r
1785 } catch (Exception ex)
\r
1793 * modify current selection according to a received message.
\r
1795 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
\r
1796 SelectionSource source)
\r
1798 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
\r
1799 // handles selection messages...
\r
1800 // TODO: extend config options to allow user to control if selections may be
\r
1801 // shared between viewports.
\r
1803 && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
\r
1804 .getSequenceSetId().equals(av.getSequenceSetId()))))
\r
1810 * Check for selection in a view of which this one is a dna/protein
\r
1813 if (selectionFromTranslation(seqsel, colsel, source))
\r
1818 // do we want to thread this ? (contention with seqsel and colsel locks, I
\r
1820 // rules are: colsel is copied if there is a real intersection between
\r
1821 // sequence selection
\r
1822 boolean repaint = false, copycolsel = true;
\r
1823 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
\r
1825 SequenceGroup sgroup = null;
\r
1826 if (seqsel != null && seqsel.getSize() > 0)
\r
1828 if (av.getAlignment() == null)
\r
1831 .println("Selection message: alignviewport av SeqSetId="
\r
1832 + av.getSequenceSetId() + " ViewId="
\r
1834 + " 's alignment is NULL! returning immediatly.");
\r
1837 sgroup = seqsel.intersect(av.getAlignment(),
\r
1838 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
\r
1839 if ((sgroup == null || sgroup.getSize() == 0)
\r
1840 && (colsel == null || colsel.size() == 0))
\r
1842 // don't copy columns if the region didn't intersect.
\r
1843 copycolsel = false;
\r
1846 if (sgroup != null && sgroup.getSize() > 0)
\r
1848 av.setSelectionGroup(sgroup);
\r
1852 av.setSelectionGroup(null);
\r
1854 repaint = av.isSelectionGroupChanged(true);
\r
1857 && (av.getColumnSelection() == null || !av
\r
1858 .isColSelChanged(true)))
\r
1860 // the current selection is unset or from a previous message
\r
1861 // so import the new colsel.
\r
1862 if (colsel == null || colsel.size() == 0)
\r
1864 if (av.getColumnSelection() != null)
\r
1866 av.getColumnSelection().clear();
\r
1871 // TODO: shift colSel according to the intersecting sequences
\r
1872 if (av.getColumnSelection() == null)
\r
1874 av.setColumnSelection(new ColumnSelection(colsel));
\r
1878 av.getColumnSelection().setElementsFrom(colsel);
\r
1881 repaint |= av.isColSelChanged(true);
\r
1884 && av.hasHiddenColumns()
\r
1885 && (av.getColumnSelection() == null || av.getColumnSelection()
\r
1886 .getHiddenColumns() == null))
\r
1888 System.err.println("Bad things");
\r
1892 ap.scalePanelHolder.repaint();
\r
1898 * scroll to the given row/column - or nearest visible location
\r
1903 public void scrollTo(int row, int column)
\r
1906 row = row < 0 ? ap.av.startSeq : row;
\r
1907 column = column < 0 ? ap.av.startRes : column;
\r
1908 ap.scrollTo(column, column, row, true, true);
\r
1912 * scroll to the given row - or nearest visible location
\r
1916 public void scrollToRow(int row)
\r
1919 row = row < 0 ? ap.av.startSeq : row;
\r
1920 ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
\r
1924 * scroll to the given column - or nearest visible location
\r
1928 public void scrollToColumn(int column)
\r
1931 column = column < 0 ? ap.av.startRes : column;
\r
1932 ap.scrollTo(column, column, ap.av.startSeq, true, true);
\r
1936 * If this panel is a cdna/protein translation view of the selection source,
\r
1937 * tries to map the source selection to a local one, and returns true. Else
\r
1944 protected boolean selectionFromTranslation(SequenceGroup seqsel,
\r
1945 ColumnSelection colsel, SelectionSource source)
\r
1947 if (!(source instanceof AlignViewportI)) {
\r
1950 final AlignViewportI sourceAv = (AlignViewportI) source;
\r
1951 if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
\r
1957 * Map sequence selection
\r
1959 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
\r
1960 av.setSelectionGroup(sg);
\r
1961 av.isSelectionGroupChanged(true);
\r
1964 * Map column selection
\r
1966 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
\r
1968 av.setColumnSelection(cs);
\r
1969 av.isColSelChanged(true);
\r
1971 ap.scalePanelHolder.repaint();
\r