2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.jbgui.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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29 import java.awt.print.*;
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33 import javax.swing.*;
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40 * @version $Revision$
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42 public class AlignmentPanel extends GAlignmentPanel
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43 implements AdjustmentListener, Printable
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45 public AlignViewport av;
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46 OverviewPanel overviewPanel;
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49 IdwidthAdjuster idwidthAdjuster;
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51 /** DOCUMENT ME!! */
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52 public AlignFrame alignFrame;
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53 ScalePanel scalePanel;
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54 AnnotationPanel annotationPanel;
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55 AnnotationLabels alabels;
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57 // this value is set false when selection area being dragged
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58 boolean fastPaint = true;
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63 * Creates a new AlignmentPanel object.
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65 * @param af DOCUMENT ME!
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66 * @param av DOCUMENT ME!
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68 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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72 seqPanel = new SeqPanel(av, this);
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73 idPanel = new IdPanel(av, this);
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75 scalePanel = new ScalePanel(av, this);
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77 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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78 idwidthAdjuster = new IdwidthAdjuster(this);
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79 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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81 annotationPanel = new AnnotationPanel(this);
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82 alabels = new AnnotationLabels(this);
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85 annotationScroller.setViewportView(annotationPanel);
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86 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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90 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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91 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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93 setScrollValues(0, 0);
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95 annotationPanel.adjustPanelHeight();
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96 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
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97 getPreferredSize());
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98 annotationScroller.setPreferredSize(annotationPanel.
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99 getPreferredSize());
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100 setAnnotationVisible(av.getShowAnnotation());
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102 hscroll.addAdjustmentListener(this);
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103 vscroll.addAdjustmentListener(this);
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105 af.addKeyListener(new KeyAdapter()
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107 public void keyPressed(KeyEvent evt)
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110 && evt.getKeyCode()>=KeyEvent.VK_0
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111 && evt.getKeyCode()<=KeyEvent.VK_9)
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113 seqPanel.numberPressed(evt.getKeyChar());
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116 switch (evt.getKeyCode())
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118 case 27: // escape key
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119 av.setSelectionGroup(null);
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124 case KeyEvent.VK_DOWN:
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127 seqPanel.moveCursor(0,1);
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130 alignFrame.moveSelectedSequences(false);
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133 case KeyEvent.VK_UP:
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136 seqPanel.moveCursor(0,-1);
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139 alignFrame.moveSelectedSequences(true);
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142 case KeyEvent.VK_LEFT:
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145 seqPanel.moveCursor(-1,0);
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149 case KeyEvent.VK_RIGHT:
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152 seqPanel.moveCursor(1,0);
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156 case KeyEvent.VK_SPACE:
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159 seqPanel.insertGapAtCursor(evt.isControlDown());
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163 case KeyEvent.VK_DELETE:
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166 seqPanel.deleteGapAtCursor(evt.isControlDown());
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170 case KeyEvent.VK_BACK_SPACE:
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173 alignFrame.cut_actionPerformed(null);
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174 seqPanel.seqCanvas.repaint();
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178 case KeyEvent.VK_Q:
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181 seqPanel.setSelectionAreaAtCursor(true);
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184 case KeyEvent.VK_M:
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187 seqPanel.setSelectionAreaAtCursor(false);
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191 case KeyEvent.VK_F2:
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192 av.cursorMode = ! av.cursorMode;
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193 alignFrame.statusBar.setText("Keyboard editing mode is "+
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194 (av.cursorMode ? "on" : "off"));
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197 seqPanel.seqCanvas.cursorX = av.startRes;
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198 seqPanel.seqCanvas.cursorY = av.startSeq;
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200 seqPanel.seqCanvas.repaint();
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203 case KeyEvent.VK_F1:
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206 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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207 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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208 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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210 javax.help.HelpBroker hb = hs.createHelpBroker();
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211 hb.setCurrentID("home");
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212 hb.setDisplayed(true);
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214 catch (Exception ex)
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216 ex.printStackTrace();
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228 public void fontChanged()
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230 // set idCanvas bufferedImage to null
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231 // to prevent drawing old image
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232 FontMetrics fm = getFontMetrics(av.getFont());
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234 scalePanelHolder.setPreferredSize(new Dimension(10,
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235 av.charHeight + fm.getDescent()));
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236 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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237 av.charHeight + fm.getDescent()));
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239 idPanel.idCanvas.gg = null;
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240 seqPanel.seqCanvas.img = null;
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241 annotationPanel.adjustPanelHeight();
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243 Dimension d = calculateIdWidth();
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244 d.setSize(d.width + 4, d.height);
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245 idPanel.idCanvas.setPreferredSize(d);
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246 hscrollFillerPanel.setPreferredSize(d);
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248 if (av.getWrapAlignment())
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250 int max = av.alignment.getWidth() /
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251 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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252 vscroll.setMaximum(max);
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253 vscroll.setUnitIncrement(1);
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254 vscroll.setVisibleAmount(1);
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258 setScrollValues(av.getStartRes(), av.getStartSeq());
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261 if (overviewPanel != null)
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262 overviewPanel.setBoxPosition();
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270 * @return DOCUMENT ME!
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272 public Dimension calculateIdWidth()
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274 Container c = new Container();
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276 FontMetrics fm = c.getFontMetrics(av.font);
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277 AlignmentI al = av.getAlignment();
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283 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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285 SequenceI s = al.getSequenceAt(i);
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287 id = s.getDisplayId(av.getShowJVSuffix());
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289 if (fm.stringWidth(id) > idWidth)
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291 idWidth = fm.stringWidth(id);
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297 // Also check annotation label widths
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300 if (al.getAlignmentAnnotation() != null)
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302 fm = c.getFontMetrics(alabels.getFont());
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304 while (i < al.getAlignmentAnnotation().length)
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306 String label = al.getAlignmentAnnotation()[i].label;
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308 if (fm.stringWidth(label) > idWidth)
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310 idWidth = fm.stringWidth(label);
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317 return new Dimension(idWidth, 12);
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323 * @param results DOCUMENT ME!
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325 public void highlightSearchResults(SearchResults results)
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327 seqPanel.seqCanvas.highlightSearchResults(results);
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329 // do we need to scroll the panel?
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330 if (results != null)
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332 SequenceI seq = results.getResultSequence(0);
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333 int seqIndex = av.alignment.findIndex(seq);
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334 int start = seq.findIndex(results.getResultStart(0)) - 1;
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335 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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337 if(!av.wrapAlignment)
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339 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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340 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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342 setScrollValues(start, seqIndex);
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347 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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348 if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
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350 vscroll.setValue(start / cwidth);
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351 av.startRes = vscroll.getValue() * cwidth;
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360 * @return DOCUMENT ME!
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362 public OverviewPanel getOverviewPanel()
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364 return overviewPanel;
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370 * @param op DOCUMENT ME!
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372 public void setOverviewPanel(OverviewPanel op)
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374 overviewPanel = op;
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380 * @param b DOCUMENT ME!
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382 public void setAnnotationVisible(boolean b)
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384 if (!av.wrapAlignment)
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386 annotationSpaceFillerHolder.setVisible(b);
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387 annotationScroller.setVisible(b);
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395 * @param wrap DOCUMENT ME!
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397 public void setWrapAlignment(boolean wrap)
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400 scalePanelHolder.setVisible(!wrap);
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401 hscroll.setVisible(!wrap);
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402 idwidthAdjuster.setVisible(!wrap);
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406 annotationScroller.setVisible(false);
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407 annotationSpaceFillerHolder.setVisible(false);
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409 else if (av.showAnnotation)
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411 annotationScroller.setVisible(true);
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412 annotationSpaceFillerHolder.setVisible(true);
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415 idSpaceFillerPanel1.setVisible(!wrap);
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420 // return value is true if the scroll is valid
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421 public boolean scrollUp(boolean up)
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425 if (vscroll.getValue() < 1)
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431 vscroll.setValue(vscroll.getValue() - 1);
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435 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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441 vscroll.setValue(vscroll.getValue() + 1);
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452 * @param right DOCUMENT ME!
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454 * @return DOCUMENT ME!
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456 public boolean scrollRight(boolean right)
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460 if (hscroll.getValue() < 1)
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466 hscroll.setValue(hscroll.getValue() - 1);
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470 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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476 hscroll.setValue(hscroll.getValue() + 1);
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487 * @param x DOCUMENT ME!
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488 * @param y DOCUMENT ME!
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490 public void setScrollValues(int x, int y)
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493 int width = av.alignment.getWidth();
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494 int height = av.alignment.getHeight();
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496 if(av.hasHiddenColumns)
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497 width = av.getColumnSelection().findColumnPosition(width);
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499 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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501 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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502 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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504 if (hextent > width)
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509 if (vextent > height)
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514 if ( (hextent + x) > width)
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516 x = width - hextent;
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519 if ( (vextent + y) > height)
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521 y = height - vextent;
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534 hscroll.setValues(x, hextent, 0, width);
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535 vscroll.setValues(y, vextent, 0, height);
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541 * @param evt DOCUMENT ME!
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543 public void adjustmentValueChanged(AdjustmentEvent evt)
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545 int oldX = av.getStartRes();
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546 int oldY = av.getStartSeq();
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548 if (evt.getSource() == hscroll)
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550 int x = hscroll.getValue();
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553 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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556 if (evt.getSource() == vscroll)
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558 int offy = vscroll.getValue();
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560 if (av.getWrapAlignment())
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562 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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563 seqCanvas.getWidth());
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564 av.setStartRes(vscroll.getValue() * rowSize);
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565 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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569 av.setStartSeq(offy);
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570 av.setEndSeq(offy +
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571 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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575 if (overviewPanel != null)
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577 overviewPanel.setBoxPosition();
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580 int scrollX = av.startRes - oldX;
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581 int scrollY = av.startSeq - oldY;
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583 if (av.getWrapAlignment() || !fastPaint)
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589 // Make sure we're not trying to draw a panel
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590 // larger than the visible window
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591 if(scrollX>av.endRes-av.startRes)
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592 scrollX = av.endRes-av.startRes;
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593 else if(scrollX<av.startRes-av.endRes)
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594 scrollX = av.startRes - av.endRes;
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596 if(scrollX!=0 || scrollY!=0)
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598 idPanel.idCanvas.fastPaint(scrollY);
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599 seqPanel.seqCanvas.fastPaint(scrollX,
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601 scalePanel.repaint();
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603 if (av.getShowAnnotation())
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605 annotationPanel.fastPaint(scrollX);
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614 * @param g DOCUMENT ME!
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616 public void paintComponent(Graphics g)
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620 Dimension d = idPanel.idCanvas.getPreferredSize();
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621 idPanelHolder.setPreferredSize(d);
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622 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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625 if (av.getWrapAlignment())
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627 int max = av.alignment.getWidth() /
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628 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
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631 vscroll.setMaximum(max);
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632 vscroll.setUnitIncrement(1);
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633 vscroll.setVisibleAmount(1);
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637 setScrollValues(av.getStartRes(), av.getStartSeq());
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640 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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641 && overviewPanel != null)
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642 overviewPanel.updateOverviewImage();
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649 * @param pg DOCUMENT ME!
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650 * @param pf DOCUMENT ME!
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651 * @param pi DOCUMENT ME!
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653 * @return DOCUMENT ME!
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655 * @throws PrinterException DOCUMENT ME!
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657 public int print(Graphics pg, PageFormat pf, int pi)
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658 throws PrinterException
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660 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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662 int pwidth = (int) pf.getImageableWidth();
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663 int pheight = (int) pf.getImageableHeight();
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665 if (av.getWrapAlignment())
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667 return printWrappedAlignment(pg, pwidth, pheight, pi);
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671 return printUnwrapped(pg, pwidth, pheight, pi);
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678 * @param pg DOCUMENT ME!
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679 * @param pwidth DOCUMENT ME!
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680 * @param pheight DOCUMENT ME!
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681 * @param pi DOCUMENT ME!
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683 * @return DOCUMENT ME!
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685 * @throws PrinterException DOCUMENT ME!
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687 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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688 throws PrinterException
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690 int idWidth = calculateIdWidth().width + 4;
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691 FontMetrics fm = getFontMetrics(av.getFont());
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692 int scaleHeight = av.charHeight + fm.getDescent();
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694 pg.setColor(Color.white);
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695 pg.fillRect(0, 0, pwidth, pheight);
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696 pg.setFont(av.getFont());
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698 ////////////////////////////////////
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699 /// How many sequences and residues can we fit on a printable page?
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700 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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702 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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705 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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707 /////////////////////////////
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708 /// Only print these sequences and residues on this page
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711 /////////////////////////////
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712 /// Only print these sequences and residues on this page
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715 /////////////////////////////
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716 /// Only print these sequences and residues on this page
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719 /////////////////////////////
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720 /// Only print these sequences and residues on this page
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722 startRes = (pi % pagesWide) * totalRes;
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723 endRes = (startRes + totalRes) - 1;
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725 if (endRes > (av.getAlignment().getWidth() - 1))
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727 endRes = av.getAlignment().getWidth() - 1;
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730 startSeq = (pi / pagesWide) * totalSeq;
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731 endSeq = startSeq + totalSeq;
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733 if (endSeq > av.getAlignment().getHeight())
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735 endSeq = av.getAlignment().getHeight();
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738 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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740 if (av.showAnnotation)
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742 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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745 pagesHigh /= pheight;
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747 if (pi >= (pagesWide * pagesHigh))
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749 return Printable.NO_SUCH_PAGE;
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753 pg.translate(idWidth, 0);
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754 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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755 pg.translate( -idWidth, scaleHeight);
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759 Color currentColor = null;
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760 Color currentTextColor = null;
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762 pg.setFont(new Font(av.getFont().getName(),
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764 av.getFont().getSize()));
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765 for (int i = startSeq; i < endSeq; i++)
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767 if ( (av.getSelectionGroup() != null) &&
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768 av.getSelectionGroup().sequences.contains(
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769 av.getAlignment().getSequenceAt(i)))
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771 currentColor = Color.gray;
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772 currentTextColor = Color.black;
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776 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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777 currentTextColor = Color.black;
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780 pg.setColor(currentColor);
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781 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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782 av.getCharHeight());
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784 pg.setColor(currentTextColor);
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786 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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787 ( av.getShowJVSuffix());
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789 pg.drawString(string, 0,
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790 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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791 (av.getCharHeight() / 5));
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794 pg.setFont(av.getFont());
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796 // draw main sequence panel
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797 pg.translate(idWidth, 0);
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798 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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800 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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802 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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803 alabels.drawComponent( (Graphics2D) pg, idWidth);
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804 pg.translate(idWidth+3, 0);
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805 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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809 return Printable.PAGE_EXISTS;
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815 * @param pg DOCUMENT ME!
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816 * @param pwidth DOCUMENT ME!
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817 * @param pheight DOCUMENT ME!
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818 * @param pi DOCUMENT ME!
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820 * @return DOCUMENT ME!
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822 * @throws PrinterException DOCUMENT ME!
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824 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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826 throws PrinterException
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829 int annotationHeight = 0;
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830 AnnotationLabels labels = null;
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831 if (av.showAnnotation)
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833 annotationHeight = annotationPanel.adjustPanelHeight();
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834 labels = new AnnotationLabels(av);
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837 int hgap = av.charHeight;
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838 if (av.scaleAboveWrapped)
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839 hgap += av.charHeight;
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841 int cHeight = av.getAlignment().getHeight() * av.charHeight
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843 + annotationHeight;
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845 int idWidth = calculateIdWidth().width + 4;
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847 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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850 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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852 pg.setColor(Color.white);
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853 pg.fillRect(0, 0, pwidth, pheight);
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854 pg.setFont(av.getFont());
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858 pg.setColor(Color.black);
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860 pg.translate(0, -pi * pheight);
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862 pg.setClip(0, pi * pheight, pwidth, pheight);
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865 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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866 av.getFont().getSize());
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867 pg.setFont(italic);
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871 for (int i = 0; i < av.alignment.getHeight(); i++)
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873 SequenceI s = av.alignment.getSequenceAt(i);
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874 String string = s.getDisplayId( av.getShowJVSuffix());
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876 pg.drawString(string, 0,
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877 ( (i * av.charHeight) + ypos + av.charHeight) -
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878 (av.charHeight / 5));
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880 if (labels != null)
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884 (av.getAlignment().getHeight() * av.charHeight));
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886 pg.setFont(av.getFont());
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887 labels.drawComponent(pg, idWidth);
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888 pg.setFont(italic);
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891 (av.getAlignment().getHeight() * av.charHeight));
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896 while (ypos < totalHeight);
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898 pg.translate(idWidth, 0);
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900 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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902 if ( (pi * pheight) < totalHeight)
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904 return Printable.PAGE_EXISTS;
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909 return Printable.NO_SUCH_PAGE;
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913 void makeAlignmentImage(int type, File file)
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915 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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916 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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918 if (idPanel.getWidth() == 0)
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920 width += calculateIdWidth().getWidth() + 4;
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923 if (av.getWrapAlignment())
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925 height = getWrappedHeight();
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926 width = seqPanel.getWidth() + idPanel.getWidth();
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928 else if (av.getShowAnnotation())
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930 height += annotationPanel.adjustPanelHeight() + 3;
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933 jalview.util.ImageMaker im;
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934 if(type==jalview.util.ImageMaker.PNG)
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935 im = new jalview.util.ImageMaker(this,
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936 jalview.util.ImageMaker.PNG,
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937 "Create PNG image from alignment",
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938 width, height, file, null);
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940 im = new jalview.util.ImageMaker(this,
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941 jalview.util.ImageMaker.EPS,
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942 "Create EPS file from alignment",
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943 width, height, file, alignFrame.getTitle() );
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947 if (av.getWrapAlignment())
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949 if(im.getGraphics()!=null)
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951 printWrappedAlignment(im.getGraphics(), width, height, 0);
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957 if(im.getGraphics()!=null)
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959 printUnwrapped(im.getGraphics(), width, height, 0);
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964 catch (OutOfMemoryError err)
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966 System.out.println("########################\n"
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967 + "OUT OF MEMORY " + file + "\n"
\r
968 + "########################");
\r
970 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
971 "Out of Memory Creating Image!!"
\r
973 "\nSee help files for increasing Java Virtual Machine memory."
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975 JOptionPane.WARNING_MESSAGE);
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976 System.out.println("Create IMAGE: " + err);
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980 catch (Exception ex)
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982 ex.printStackTrace();
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988 public void makeEPS(File epsFile)
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990 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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996 public void makePNG(File pngFile)
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998 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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1001 public void makePNGImageMap(File imgMapFile, String imageName)
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1003 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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1004 //////////////////////////////////////////////
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1005 int idWidth = calculateIdWidth().width + 4;
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1006 FontMetrics fm = getFontMetrics(av.getFont());
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1007 int scaleHeight = av.charHeight + fm.getDescent();
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1010 //////////////////////////////////
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1011 if (imgMapFile != null)
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1015 int s, sSize = av.alignment.getHeight(),
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1016 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
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1017 StringBuffer text = new StringBuffer();
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1018 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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1019 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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1020 out.println("<img src=\"" + imageName +
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1021 "\" border=\"0\" usemap=\"#Map\" >"
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1022 + "<map name=\"Map\">");
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1024 for (s = 0; s < sSize; s++)
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1026 sy = s * av.charHeight + scaleHeight;
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1028 SequenceI seq = av.alignment.getSequenceAt(s);
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1029 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
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1030 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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1031 for(res =0; res<alwidth; res++)
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1033 text = new StringBuffer();
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1034 Object obj = null;
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1035 if(av.alignment.isNucleotide())
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1036 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
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1038 obj = ResidueProperties.aa2Triplet.get(
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1039 seq.getCharAt(res) + "");
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1044 String triplet = obj.toString();
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1045 int alIndex = seq.findPosition(res);
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1046 gSize = groups.length;
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1047 for (g = 0; g < gSize; g++)
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1049 if(text.length()<1)
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1051 text.append("<area shape=\"rect\" coords=\""
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1052 + (idWidth + res * av.charWidth) + ","
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1054 + (idWidth + (res + 1) * av.charWidth) + ","
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1055 + (av.charHeight + sy) + "\""
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1056 + " onMouseOver=\"toolTip('"
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1057 + alIndex + " " + triplet );
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1060 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
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1061 text.append("<br><em>" + groups[g].getName() + "</em>");
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1064 if (features != null)
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1066 if(text.length()<1)
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1068 text.append("<area shape=\"rect\" coords=\""
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1069 + (idWidth + res * av.charWidth) + ","
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1071 + (idWidth + (res + 1) * av.charWidth) + ","
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1072 + (av.charHeight + sy) + "\""
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1073 + " onMouseOver=\"toolTip('"
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1074 + alIndex + " " + triplet );
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1076 fSize = features.length;
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1077 for (f = 0; f < fSize; f++)
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1080 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
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1081 (features[f].getEnd() >= seq.findPosition(res)))
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1083 if (features[f].getType().equals("disulfide bond"))
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1085 if (features[f].getBegin() == seq.findPosition(res)
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1086 || features[f].getEnd() == seq.findPosition(res))
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1088 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
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1089 features[f].getEnd());
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1094 text.append("<br>");
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1095 text.append(features[f].getType());
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1096 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
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1097 text.append(" " + features[f].getDescription());
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1099 if (features[f].getStatus() != null && features[f].getStatus().length()>0)
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1101 text.append(" (" + features[f].getStatus() + ")");
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1108 if(text.length()>1)
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1110 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
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1111 out.println(text.toString());
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1115 out.println("</map></body></html>");
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1119 catch (Exception ex)
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1121 ex.printStackTrace();
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1123 } ///////////END OF IMAGE MAP
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1127 int getWrappedHeight()
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1130 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
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1131 seqPanel.seqCanvas.getWidth());
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1133 int hgap = av.charHeight;
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1134 if (av.scaleAboveWrapped)
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1135 hgap += av.charHeight;
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1137 int annotationHeight = 0;
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1138 if (av.showAnnotation)
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1140 annotationHeight = annotationPanel.adjustPanelHeight();
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1143 int cHeight = av.getAlignment().getHeight() * av.charHeight
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1145 + annotationHeight;
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1147 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
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1155 * @author $author$
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1156 * @version $Revision$
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1162 * Creates a new Preview object.
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1164 * @param image DOCUMENT ME!
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1166 public Preview(Image image)
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1168 setResizable(true);
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1169 setSize(image.getWidth(this), image.getHeight(this));
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1171 getContentPane().setLayout(new BorderLayout());
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1172 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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1181 * @author $author$
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1182 * @version $Revision$
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1184 class PreviewPanel
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1190 * Creates a new PreviewPanel object.
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1192 * @param image DOCUMENT ME!
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1194 public PreviewPanel(Image image)
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1196 this.image = image;
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1202 * @param g DOCUMENT ME!
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1204 public void paintComponent(Graphics g)
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1206 if (image != null)
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1208 g.drawImage(image, 0, 0, this);
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1212 System.out.println("DEBUG:image is null");
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