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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22 import javax.imageio.*;
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25 import java.awt.event.*;
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26 import java.awt.image.*;
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27 import java.awt.print.*;
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28 import javax.swing.*;
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30 import org.jibble.epsgraphics.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.jbgui.*;
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34 import jalview.schemes.*;
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36 public class AlignmentPanel
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37 extends GAlignmentPanel implements AdjustmentListener, Printable
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40 OverviewPanel overviewPanel;
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43 IdwidthAdjuster idwidthAdjuster;
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44 public AlignFrame alignFrame;
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45 ScalePanel scalePanel;
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46 AnnotationPanel annotationPanel;
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47 AnnotationLabels alabels;
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49 // this value is set false when selection area being dragged
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50 boolean fastPaint = false;
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54 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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58 seqPanel = new SeqPanel(av, this);
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59 idPanel = new IdPanel(av, this);
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61 scalePanel = new ScalePanel(av, this);
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63 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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64 idwidthAdjuster = new IdwidthAdjuster(this);
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65 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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67 annotationPanel = new AnnotationPanel(this);
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68 alabels = new AnnotationLabels(this);
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70 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
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71 getPreferredSize());
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72 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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73 annotationScroller.setViewportView(annotationPanel);
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74 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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78 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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79 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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81 setScrollValues(0, 0);
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83 hscroll.addAdjustmentListener(this);
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84 vscroll.addAdjustmentListener(this);
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87 addKeyListener(new KeyAdapter()
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89 public void keyPressed(KeyEvent evt)
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91 switch (evt.getKeyCode())
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93 case 27: // escape key
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94 av.setSelectionGroup(null);
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99 case KeyEvent.VK_DOWN:
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100 alignFrame.moveSelectedSequences(false);
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104 case KeyEvent.VK_UP:
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105 alignFrame.moveSelectedSequences(true);
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113 public void fontChanged()
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115 // set idCanvas bufferedImage to null
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116 // to prevent drawing old image
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117 FontMetrics fm = getFontMetrics(av.getFont());
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119 scalePanelHolder.setPreferredSize(new Dimension(10,
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120 av.charHeight + fm.getDescent()));
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121 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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122 av.charHeight + fm.getDescent()));
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124 idPanel.idCanvas.gg = null;
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125 annotationPanel.adjustPanelHeight();
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127 Dimension d = calculateIdWidth();
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128 d.setSize(d.width + 4, d.height);
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129 idPanel.idCanvas.setPreferredSize(d);
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130 hscrollFillerPanel.setPreferredSize(d);
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134 Dimension calculateIdWidth()
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136 Graphics g = this.getGraphics();
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140 javax.swing.JFrame f = new javax.swing.JFrame();
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142 g = f.getGraphics();
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145 FontMetrics fm = g.getFontMetrics(av.font);
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146 AlignmentI al = av.getAlignment();
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152 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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154 SequenceI s = al.getSequenceAt(i);
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156 if (av.getShowFullId())
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158 id = s.getDisplayId();
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165 if (fm.stringWidth(id) > idWidth)
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167 idWidth = fm.stringWidth(id);
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173 // Also check annotation label widths
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176 if (al.getAlignmentAnnotation() != null)
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178 fm = g.getFontMetrics(alabels.getFont());
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180 while (i < al.getAlignmentAnnotation().length)
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182 String label = al.getAlignmentAnnotation()[i].label;
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184 if (fm.stringWidth(label) > idWidth)
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186 idWidth = fm.stringWidth(label);
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193 return new Dimension(idWidth, 12);
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196 public void highlightSearchResults(int[] results)
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198 seqPanel.seqCanvas.highlightSearchResults(results);
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200 // do we need to scroll the panel?
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201 if (results != null)
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203 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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204 int start = seq.findIndex(results[1]) - 1;
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205 int end = seq.findIndex(results[2]) - 1;
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207 if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
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208 ( (av.getStartSeq() > results[0]) ||
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209 (av.getEndSeq() < results[0])))
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211 setScrollValues(start, results[0]);
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216 public OverviewPanel getOverviewPanel()
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218 return overviewPanel;
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221 public void setOverviewPanel(OverviewPanel op)
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223 overviewPanel = op;
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226 public void setAnnotationVisible(boolean b)
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228 annotationSpaceFillerHolder.setVisible(b);
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229 annotationScroller.setVisible(b);
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232 public void setWrapAlignment(boolean wrap)
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234 scalePanelHolder.setVisible(!wrap);
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235 hscroll.setVisible(!wrap);
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236 idwidthAdjuster.setVisible(!wrap);
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238 av.setShowAnnotation(!wrap);
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239 annotationScroller.setVisible(!wrap);
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240 annotationSpaceFillerHolder.setVisible(!wrap);
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241 idSpaceFillerPanel1.setVisible(!wrap);
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246 public void setColourScheme()
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248 ColourSchemeI cs = av.getGlobalColourScheme();
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250 if (av.getConservationSelected())
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252 Alignment al = (Alignment) av.getAlignment();
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253 Conservation c = new Conservation("All",
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254 ResidueProperties.propHash, 3,
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255 al.getSequences(), 0,
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259 c.verdict(false, av.ConsPercGaps);
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261 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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263 av.setGlobalColourScheme(ccs);
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269 // return value is true if the scroll is valid
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270 public boolean scrollUp(boolean up)
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274 if (vscroll.getValue() < 1)
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280 vscroll.setValue(vscroll.getValue() - 1);
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284 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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290 vscroll.setValue(vscroll.getValue() + 1);
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298 public boolean scrollRight(boolean right)
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302 if (hscroll.getValue() < 1)
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308 hscroll.setValue(hscroll.getValue() - 1);
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312 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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318 hscroll.setValue(hscroll.getValue() + 1);
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326 public void setScrollValues(int x, int y)
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328 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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331 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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332 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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334 if (hextent > av.alignment.getWidth())
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336 hextent = av.alignment.getWidth();
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339 if (vextent > av.alignment.getHeight())
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341 vextent = av.alignment.getHeight();
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344 if ( (hextent + x) > av.getAlignment().getWidth())
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346 x = av.getAlignment().getWidth() - hextent;
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349 if ( (vextent + y) > av.getAlignment().getHeight())
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351 y = av.getAlignment().getHeight() - vextent;
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364 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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365 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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368 public void adjustmentValueChanged(AdjustmentEvent evt)
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370 int oldX = av.getStartRes();
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371 int oldY = av.getStartSeq();
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373 if (evt.getSource() == hscroll)
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375 int x = hscroll.getValue();
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378 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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381 if (evt.getSource() == vscroll)
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383 int offy = vscroll.getValue();
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385 if (av.getWrapAlignment())
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387 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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388 seqCanvas.getWidth());
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389 av.setStartRes(vscroll.getValue() * rowSize);
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390 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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394 av.setStartSeq(offy);
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395 av.setEndSeq(offy +
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396 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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400 if (overviewPanel != null)
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402 overviewPanel.setBoxPosition();
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405 if (av.getWrapAlignment() || !fastPaint)
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411 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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412 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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413 av.getStartSeq() - oldY);
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415 scalePanel.repaint();
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417 if (av.getShowAnnotation())
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419 annotationPanel.fastPaint(av.getStartRes() - oldX);
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424 public void paintComponent(Graphics g)
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428 Dimension d = idPanel.idCanvas.getPreferredSize();
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429 idPanelHolder.setPreferredSize(d);
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430 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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433 if (av.getWrapAlignment())
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435 int max = av.alignment.getWidth() /
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436 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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437 vscroll.setMaximum(max);
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438 vscroll.setUnitIncrement(1);
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439 vscroll.setVisibleAmount(1);
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443 setScrollValues(av.getStartRes(), av.getStartSeq());
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447 public int print(Graphics pg, PageFormat pf, int pi)
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448 throws PrinterException
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450 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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452 int pwidth = (int) pf.getImageableWidth();
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453 int pheight = (int) pf.getImageableHeight();
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455 if (av.getWrapAlignment())
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457 return printWrappedAlignment(pg, pwidth, pheight, pi);
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461 return printUnwrapped(pg, pwidth, pheight, pi);
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465 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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466 throws PrinterException
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468 int idWidth = calculateIdWidth().width + 4;
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469 FontMetrics fm = getFontMetrics(av.getFont());
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470 int scaleHeight = av.charHeight + fm.getDescent();
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472 pg.setColor(Color.white);
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473 pg.fillRect(0, 0, pwidth, pheight);
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474 pg.setFont(av.getFont());
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476 ////////////////////////////////////
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477 /// How many sequences and residues can we fit on a printable page?
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478 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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480 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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483 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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485 /////////////////////////////
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486 /// Only print these sequences and residues on this page
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489 /////////////////////////////
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490 /// Only print these sequences and residues on this page
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493 /////////////////////////////
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494 /// Only print these sequences and residues on this page
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497 /////////////////////////////
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498 /// Only print these sequences and residues on this page
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500 startRes = (pi % pagesWide) * totalRes;
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501 endRes = (startRes + totalRes) - 1;
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503 if (endRes > (av.getAlignment().getWidth() - 1))
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505 endRes = av.getAlignment().getWidth() - 1;
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508 startSeq = (pi / pagesWide) * totalSeq;
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509 endSeq = startSeq + totalSeq;
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511 if (endSeq > av.getAlignment().getHeight())
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513 endSeq = av.getAlignment().getHeight();
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516 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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518 if (av.showAnnotation)
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520 pagesHigh += annotationPanel.getHeight();
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523 pagesHigh /= pheight;
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525 if (pi >= (pagesWide * pagesHigh))
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527 return Printable.NO_SUCH_PAGE;
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531 pg.translate(idWidth, 0);
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532 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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533 pg.translate( -idWidth, scaleHeight);
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537 Color currentColor = null;
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538 Color currentTextColor = null;
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540 for (int i = startSeq; i < endSeq; i++)
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542 if ( (av.getSelectionGroup() != null) &&
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543 av.getSelectionGroup().sequences.contains(
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544 av.getAlignment().getSequenceAt(i)))
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546 currentColor = Color.gray;
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547 currentTextColor = Color.black;
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551 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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552 currentTextColor = Color.black;
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555 pg.setColor(currentColor);
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557 jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
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558 av.getCharHeight()), idWidth, av.getCharHeight());
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560 pg.setColor(currentTextColor);
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562 String string = av.getAlignment().getSequenceAt(i).getName();
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564 if (av.getShowFullId())
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566 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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569 pg.drawString(string, 0,
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570 (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
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571 av.getCharHeight()) + av.getCharHeight()) -
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572 (av.getCharHeight() / 5));
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575 // draw main sequence panel
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576 pg.translate(idWidth, 0);
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577 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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578 startRes, startSeq, 0);
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580 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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582 pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
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583 alabels.drawComponent( (Graphics2D) pg);
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584 pg.translate(idWidth, 0);
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585 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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589 return Printable.PAGE_EXISTS;
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592 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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594 throws PrinterException
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596 int idWidth = calculateIdWidth().width + 4;
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598 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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600 int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
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601 ( (av.alignment.getWidth() / resWidth) +
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602 1) * av.charHeight;
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604 pg.setColor(Color.white);
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605 pg.fillRect(0, 0, pwidth, pheight);
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606 pg.setFont(av.getFont());
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610 pg.setColor(Color.black);
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612 pg.translate(0, -pi * pheight);
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614 pg.setClip(0, pi * pheight, pwidth, pheight);
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616 int ypos = 2 * av.charHeight;
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620 for (int i = 0; i < av.alignment.getHeight(); i++)
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622 SequenceI s = av.alignment.getSequenceAt(i);
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623 String string = s.getName();
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625 if (av.getShowFullId())
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627 string = s.getDisplayId();
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630 pg.drawString(string, 0,
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631 (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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632 av.charHeight) - (av.charHeight / 5));
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635 ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);
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637 while (ypos < totalHeight);
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639 pg.translate(idWidth, 0);
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641 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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643 if ( (pi * pheight) < totalHeight)
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645 return Printable.PAGE_EXISTS;
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649 return Printable.NO_SUCH_PAGE;
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653 public void makeEPS()
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655 int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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657 int width = seqPanel.getWidth() + idPanel.getWidth();
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659 if (!av.getWrapAlignment())
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661 height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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662 width = idPanel.getWidth() +
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663 (av.alignment.getWidth() * av.charWidth);
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666 if (av.getShowAnnotation())
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668 height += annotationPanel.getPreferredSize().height;
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673 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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674 jalview.bin.Cache.getProperty(
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675 "LAST_DIRECTORY"), new String[]
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678 {"Encapsulated Postscript"},
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679 "Encapsulated Postscript");
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680 chooser.setFileView(new jalview.io.JalviewFileView());
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681 chooser.setDialogTitle("Create EPS file from alignment");
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682 chooser.setToolTipText("Save");
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684 int value = chooser.showSaveDialog(this);
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686 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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691 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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692 chooser.getSelectedFile().getParent());
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694 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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695 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
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698 if (av.getWrapAlignment())
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700 printWrappedAlignment(pg, width, height, 0);
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704 printUnwrapped(pg, width, height, 0);
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710 catch (Exception ex)
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712 ex.printStackTrace();
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716 public void makePNG()
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718 int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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720 int width = seqPanel.getWidth() + idPanel.getWidth();
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722 if (!av.getWrapAlignment())
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724 height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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725 width = idPanel.getWidth() +
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726 (av.alignment.getWidth() * av.charWidth);
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729 if (av.getShowAnnotation())
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731 height += annotationPanel.getPreferredSize().height;
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736 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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737 jalview.bin.Cache.getProperty(
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738 "LAST_DIRECTORY"), new String[]
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741 {"Portable network graphics"},
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742 "Portable network graphics");
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743 chooser.setFileView(new jalview.io.JalviewFileView());
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744 chooser.setDialogTitle("Create EPS file from alignment");
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745 chooser.setToolTipText("Save");
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747 int value = chooser.showSaveDialog(this);
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749 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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754 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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755 chooser.getSelectedFile().getParent());
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757 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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759 BufferedImage bi = new BufferedImage(width, height,
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760 BufferedImage.TYPE_INT_RGB);
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761 Graphics2D png = (Graphics2D) bi.getGraphics();
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763 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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764 RenderingHints.VALUE_ANTIALIAS_ON);
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766 if (av.getWrapAlignment())
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768 printWrappedAlignment(png, width, height, 0);
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772 printUnwrapped(png, width, height, 0);
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775 ImageIO.write(bi, "png", out);
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778 catch (Exception ex)
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780 ex.printStackTrace();
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788 public Preview(Image image)
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790 setResizable(true);
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791 setSize(image.getWidth(this), image.getHeight(this));
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793 getContentPane().setLayout(new BorderLayout());
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794 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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805 public PreviewPanel(Image image)
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807 this.image = image;
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810 public void paintComponent(Graphics g)
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814 g.drawImage(image, 0, 0, this);
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818 System.out.println("DEBUG:image is null");
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