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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27 import org.jibble.epsgraphics.*;
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30 import java.awt.event.*;
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31 import java.awt.image.*;
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32 import java.awt.print.*;
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36 import javax.imageio.*;
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38 import javax.swing.*;
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45 * @version $Revision$
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47 public class AlignmentPanel extends GAlignmentPanel
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48 implements AdjustmentListener, Printable
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51 OverviewPanel overviewPanel;
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54 IdwidthAdjuster idwidthAdjuster;
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56 /** DOCUMENT ME!! */
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57 public AlignFrame alignFrame;
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58 ScalePanel scalePanel;
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59 AnnotationPanel annotationPanel;
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60 AnnotationLabels alabels;
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62 // this value is set false when selection area being dragged
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63 boolean fastPaint = true;
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68 * Creates a new AlignmentPanel object.
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70 * @param af DOCUMENT ME!
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71 * @param av DOCUMENT ME!
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73 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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77 seqPanel = new SeqPanel(av, this);
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78 idPanel = new IdPanel(av, this);
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80 scalePanel = new ScalePanel(av, this);
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82 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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83 idwidthAdjuster = new IdwidthAdjuster(this);
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84 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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86 annotationPanel = new AnnotationPanel(this);
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87 alabels = new AnnotationLabels(this);
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89 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
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90 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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91 annotationScroller.setViewportView(annotationPanel);
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92 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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96 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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97 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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99 setScrollValues(0, 0);
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101 hscroll.addAdjustmentListener(this);
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102 vscroll.addAdjustmentListener(this);
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104 setFocusable(true);
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105 addKeyListener(new KeyAdapter()
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107 public void keyPressed(KeyEvent evt)
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109 switch (evt.getKeyCode())
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111 case 27: // escape key
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112 av.setSelectionGroup(null);
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117 case KeyEvent.VK_DOWN:
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118 alignFrame.moveSelectedSequences(false);
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122 case KeyEvent.VK_UP:
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123 alignFrame.moveSelectedSequences(true);
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127 case KeyEvent.VK_BACK_SPACE:
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128 case KeyEvent.VK_DELETE:
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129 alignFrame.cut_actionPerformed(null);
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140 public void fontChanged()
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142 // set idCanvas bufferedImage to null
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143 // to prevent drawing old image
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144 FontMetrics fm = getFontMetrics(av.getFont());
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146 scalePanelHolder.setPreferredSize(new Dimension(10,
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147 av.charHeight + fm.getDescent()));
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148 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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149 av.charHeight + fm.getDescent()));
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151 idPanel.idCanvas.gg = null;
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152 seqPanel.seqCanvas.img = null;
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153 annotationPanel.adjustPanelHeight();
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155 Dimension d = calculateIdWidth();
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156 d.setSize(d.width + 4, d.height);
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157 idPanel.idCanvas.setPreferredSize(d);
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158 hscrollFillerPanel.setPreferredSize(d);
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160 if (av.getWrapAlignment())
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162 int max = av.alignment.getWidth() /
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163 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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164 vscroll.setMaximum(max);
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165 vscroll.setUnitIncrement(1);
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166 vscroll.setVisibleAmount(1);
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170 setScrollValues(av.getStartRes(), av.getStartSeq());
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173 if(overviewPanel!=null)
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174 overviewPanel.updateOverviewImage();
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182 * @return DOCUMENT ME!
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184 public Dimension calculateIdWidth()
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186 Container c = new Container();
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188 FontMetrics fm = c.getFontMetrics(av.font);
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189 AlignmentI al = av.getAlignment();
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195 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
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197 SequenceI s = al.getSequenceAt(i);
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199 if (av.getShowFullId())
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201 id = s.getDisplayId();
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208 if (fm.stringWidth(id) > idWidth)
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210 idWidth = fm.stringWidth(id);
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216 // Also check annotation label widths
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219 if (al.getAlignmentAnnotation() != null)
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221 fm = c.getFontMetrics(alabels.getFont());
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223 while (i < al.getAlignmentAnnotation().length)
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225 String label = al.getAlignmentAnnotation()[i].label;
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227 if (fm.stringWidth(label) > idWidth)
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229 idWidth = fm.stringWidth(label);
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236 return new Dimension(idWidth, 12);
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242 * @param results DOCUMENT ME!
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244 public void highlightSearchResults(int[] results)
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246 seqPanel.seqCanvas.highlightSearchResults(results);
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248 // do we need to scroll the panel?
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249 if (results != null)
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251 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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252 int start = seq.findIndex(results[1]) - 1;
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253 int end = seq.findIndex(results[2]) - 1;
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255 if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
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256 ((av.getStartSeq() > results[0]) ||
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257 (av.getEndSeq() < results[0])))
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259 setScrollValues(start, results[0]);
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267 * @return DOCUMENT ME!
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269 public OverviewPanel getOverviewPanel()
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271 return overviewPanel;
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277 * @param op DOCUMENT ME!
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279 public void setOverviewPanel(OverviewPanel op)
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281 overviewPanel = op;
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287 * @param b DOCUMENT ME!
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289 public void setAnnotationVisible(boolean b)
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291 annotationSpaceFillerHolder.setVisible(b);
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292 annotationScroller.setVisible(b);
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298 * @param wrap DOCUMENT ME!
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300 public void setWrapAlignment(boolean wrap)
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303 scalePanelHolder.setVisible(!wrap);
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304 hscroll.setVisible(!wrap);
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305 idwidthAdjuster.setVisible(!wrap);
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307 av.setShowAnnotation(!wrap);
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308 annotationScroller.setVisible(!wrap);
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309 annotationSpaceFillerHolder.setVisible(!wrap);
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310 idSpaceFillerPanel1.setVisible(!wrap);
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316 // return value is true if the scroll is valid
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317 public boolean scrollUp(boolean up)
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321 if (vscroll.getValue() < 1)
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327 vscroll.setValue(vscroll.getValue() - 1);
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331 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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337 vscroll.setValue(vscroll.getValue() + 1);
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348 * @param right DOCUMENT ME!
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350 * @return DOCUMENT ME!
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352 public boolean scrollRight(boolean right)
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356 if (hscroll.getValue() < 1)
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362 hscroll.setValue(hscroll.getValue() - 1);
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366 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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372 hscroll.setValue(hscroll.getValue() + 1);
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383 * @param x DOCUMENT ME!
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384 * @param y DOCUMENT ME!
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386 public void setScrollValues(int x, int y)
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388 av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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391 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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392 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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394 if (hextent > av.alignment.getWidth())
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396 hextent = av.alignment.getWidth();
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399 if (vextent > av.alignment.getHeight())
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401 vextent = av.alignment.getHeight();
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404 if ((hextent + x) > av.getAlignment().getWidth())
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406 x = av.getAlignment().getWidth() - hextent;
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409 if ((vextent + y) > av.getAlignment().getHeight())
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411 y = av.getAlignment().getHeight() - vextent;
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424 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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425 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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432 * @param evt DOCUMENT ME!
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434 public void adjustmentValueChanged(AdjustmentEvent evt)
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436 int oldX = av.getStartRes();
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437 int oldY = av.getStartSeq();
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439 if (evt.getSource() == hscroll)
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441 int x = hscroll.getValue();
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444 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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447 if (evt.getSource() == vscroll)
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449 int offy = vscroll.getValue();
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451 if (av.getWrapAlignment())
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453 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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454 av.setStartRes(vscroll.getValue() * rowSize);
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455 av.setEndRes((vscroll.getValue() + 1) * rowSize);
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459 av.setStartSeq(offy);
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460 av.setEndSeq(offy +
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461 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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465 if (overviewPanel != null)
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467 overviewPanel.setBoxPosition();
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470 if (av.getWrapAlignment() || !fastPaint)
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476 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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477 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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478 av.getStartSeq() - oldY);
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480 scalePanel.repaint();
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482 if (av.getShowAnnotation())
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484 annotationPanel.fastPaint(av.getStartRes() - oldX);
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492 * @param g DOCUMENT ME!
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494 public void paintComponent(Graphics g)
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498 Dimension d = idPanel.idCanvas.getPreferredSize();
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499 idPanelHolder.setPreferredSize(d);
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500 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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503 if (av.getWrapAlignment())
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505 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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506 vscroll.setMaximum(max);
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507 vscroll.setUnitIncrement(1);
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508 vscroll.setVisibleAmount(1);
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512 setScrollValues(av.getStartRes(), av.getStartSeq());
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519 * @param pg DOCUMENT ME!
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520 * @param pf DOCUMENT ME!
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521 * @param pi DOCUMENT ME!
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523 * @return DOCUMENT ME!
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525 * @throws PrinterException DOCUMENT ME!
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527 public int print(Graphics pg, PageFormat pf, int pi)
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528 throws PrinterException
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530 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
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532 int pwidth = (int) pf.getImageableWidth();
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533 int pheight = (int) pf.getImageableHeight();
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535 if (av.getWrapAlignment())
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537 return printWrappedAlignment(pg, pwidth, pheight, pi);
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541 return printUnwrapped(pg, pwidth, pheight, pi);
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548 * @param pg DOCUMENT ME!
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549 * @param pwidth DOCUMENT ME!
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550 * @param pheight DOCUMENT ME!
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551 * @param pi DOCUMENT ME!
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553 * @return DOCUMENT ME!
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555 * @throws PrinterException DOCUMENT ME!
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557 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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558 throws PrinterException
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560 int idWidth = calculateIdWidth().width + 4;
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561 FontMetrics fm = getFontMetrics(av.getFont());
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562 int scaleHeight = av.charHeight + fm.getDescent();
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564 pg.setColor(Color.white);
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565 pg.fillRect(0, 0, pwidth, pheight);
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566 pg.setFont(av.getFont());
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568 ////////////////////////////////////
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569 /// How many sequences and residues can we fit on a printable page?
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570 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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572 int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
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575 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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577 /////////////////////////////
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578 /// Only print these sequences and residues on this page
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581 /////////////////////////////
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582 /// Only print these sequences and residues on this page
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585 /////////////////////////////
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586 /// Only print these sequences and residues on this page
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589 /////////////////////////////
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590 /// Only print these sequences and residues on this page
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592 startRes = (pi % pagesWide) * totalRes;
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593 endRes = (startRes + totalRes) - 1;
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595 if (endRes > (av.getAlignment().getWidth() - 1))
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597 endRes = av.getAlignment().getWidth() - 1;
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600 startSeq = (pi / pagesWide) * totalSeq;
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601 endSeq = startSeq + totalSeq;
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603 if (endSeq > av.getAlignment().getHeight())
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605 endSeq = av.getAlignment().getHeight();
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608 int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
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610 if (av.showAnnotation)
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612 pagesHigh += annotationPanel.getHeight();
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615 pagesHigh /= pheight;
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617 if (pi >= (pagesWide * pagesHigh))
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619 return Printable.NO_SUCH_PAGE;
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623 pg.translate(idWidth, 0);
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624 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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625 pg.translate(-idWidth, scaleHeight);
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629 Color currentColor = null;
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630 Color currentTextColor = null;
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632 for (int i = startSeq; i < endSeq; i++)
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634 if ((av.getSelectionGroup() != null) &&
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635 av.getSelectionGroup().sequences.contains(
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636 av.getAlignment().getSequenceAt(i)))
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638 currentColor = Color.gray;
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639 currentTextColor = Color.black;
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643 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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644 currentTextColor = Color.black;
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647 pg.setColor(currentColor);
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648 pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,
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649 av.getCharHeight());
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651 pg.setColor(currentTextColor);
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653 String string = av.getAlignment().getSequenceAt(i).getName();
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655 if (av.getShowFullId())
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657 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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660 pg.drawString(string, 0,
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661 (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
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662 (av.getCharHeight() / 5));
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665 // draw main sequence panel
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666 pg.translate(idWidth, 0);
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667 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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668 startRes, startSeq, 0);
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670 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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672 pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
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673 alabels.drawComponent((Graphics2D) pg);
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674 pg.translate(idWidth, 0);
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675 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
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679 return Printable.PAGE_EXISTS;
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685 * @param pg DOCUMENT ME!
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686 * @param pwidth DOCUMENT ME!
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687 * @param pheight DOCUMENT ME!
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688 * @param pi DOCUMENT ME!
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690 * @return DOCUMENT ME!
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692 * @throws PrinterException DOCUMENT ME!
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694 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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695 int pi) throws PrinterException
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697 int idWidth = calculateIdWidth().width + 4;
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699 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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701 int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
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702 1) * av.charHeight;
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704 pg.setColor(Color.white);
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705 pg.fillRect(0, 0, pwidth, pheight);
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706 pg.setFont(av.getFont());
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710 pg.setColor(Color.black);
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712 pg.translate(0, -pi * pheight);
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714 pg.setClip(0, pi * pheight, pwidth, pheight);
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716 int ypos = 2 * av.charHeight;
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720 for (int i = 0; i < av.alignment.getHeight(); i++)
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722 SequenceI s = av.alignment.getSequenceAt(i);
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723 String string = s.getName();
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725 if (av.getShowFullId())
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727 string = s.getDisplayId();
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730 pg.drawString(string, 0,
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731 ((i * av.charHeight) + ypos + av.charHeight) -
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732 (av.charHeight / 5));
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735 ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
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737 while (ypos < totalHeight);
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739 pg.translate(idWidth, 0);
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741 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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743 if ((pi * pheight) < totalHeight)
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745 return Printable.PAGE_EXISTS;
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749 return Printable.NO_SUCH_PAGE;
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756 public void makeEPS(File epsFile)
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758 if(epsFile == null)
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760 jalview.io.JalviewFileChooser chooser = new jalview.io.
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761 JalviewFileChooser(jalview.bin.Cache.getProperty(
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762 "LAST_DIRECTORY"), new String[]
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765 {"Encapsulated Postscript"},
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766 "Encapsulated Postscript");
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767 chooser.setFileView(new jalview.io.JalviewFileView());
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768 chooser.setDialogTitle("Create EPS file from alignment");
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769 chooser.setToolTipText("Save");
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771 int value = chooser.showSaveDialog(this);
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773 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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778 epsFile = chooser.getSelectedFile();
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780 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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781 chooser.getSelectedFile().getParent());
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784 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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785 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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787 if (av.getWrapAlignment())
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789 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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791 width = seqPanel.getWidth() + idPanel.getWidth();
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796 if (av.getShowAnnotation())
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798 height += annotationPanel.getPreferredSize().height;
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803 FileOutputStream out = new FileOutputStream(epsFile);
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804 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
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807 if (av.getWrapAlignment())
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809 printWrappedAlignment(pg, width, height, 0);
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813 printUnwrapped(pg, width, height, 0);
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819 catch (Exception ex)
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821 ex.printStackTrace();
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826 public void makePNGImageMap(File imgMapFile, String imageName)
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828 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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829 //////////////////////////////////////////////
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830 int idWidth = calculateIdWidth().width + 4;
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831 FontMetrics fm = getFontMetrics(av.getFont());
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832 int scaleHeight = av.charHeight + fm.getDescent();
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835 //////////////////////////////////
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836 if(imgMapFile!=null)
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840 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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841 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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842 out.println("<img src=\"" + imageName +
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843 "\" border=\"0\" usemap=\"#Map\" >"
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844 +"<map name=\"Map\">");
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846 for (int s = 0; s < av.alignment.getHeight(); s++)
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848 SequenceI seq = av.alignment.getSequenceAt(s);
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849 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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850 for (int i = 0; i < groups.length; i++)
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852 int sy = s * av.charHeight + scaleHeight;
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853 for (int res = groups[i].getStartRes();
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854 res < groups[i].getEndRes() + 1; res++)
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856 int alIndex = seq.findPosition(res);
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857 Object obj = ResidueProperties.aa2Triplet.get(
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858 seq.getCharAt(res) + "");
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862 String triplet = obj.toString();
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865 "<area shape=\"rect\" coords=\""
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866 + (idWidth + res * av.charWidth) + ","
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868 + (idWidth + (res + 1) * av.charWidth) + ","
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869 + (av.charHeight + sy) + "\""
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870 + " onMouseOver=\"toolTip('"
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871 + alIndex + " " + triplet +
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872 "<br><em>" + groups[i].getName() +
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873 "</em>')\"; onMouseOut=\"toolTip()\"; "
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879 out.println("</map></body></html>");
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883 catch (Exception ex)
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885 ex.printStackTrace();
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887 }///////////END OF IMAGE MAP
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894 public void makePNG(File pngFile)
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898 jalview.io.JalviewFileChooser chooser = new jalview.io.
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899 JalviewFileChooser(jalview.bin.Cache.getProperty(
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900 "LAST_DIRECTORY"), new String[]
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903 {"Portable network graphics"},
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904 "Portable network graphics");
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905 chooser.setFileView(new jalview.io.JalviewFileView());
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906 chooser.setDialogTitle("Create EPS file from alignment");
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907 chooser.setToolTipText("Save");
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909 int value = chooser.showSaveDialog(this);
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911 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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916 pngFile = chooser.getSelectedFile();
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918 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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919 chooser.getSelectedFile().getParent());
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924 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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925 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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927 if (av.getWrapAlignment())
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929 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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931 width = seqPanel.getWidth() + idPanel.getWidth();
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936 if (av.getShowAnnotation())
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938 height += annotationPanel.getPreferredSize().height;
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944 FileOutputStream out = new FileOutputStream(pngFile);
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946 BufferedImage bi = new BufferedImage(width, height,
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947 BufferedImage.TYPE_INT_RGB);
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948 Graphics2D png = (Graphics2D) bi.getGraphics();
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950 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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951 RenderingHints.VALUE_ANTIALIAS_ON);
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953 if (av.getWrapAlignment())
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955 printWrappedAlignment(png, width, height, 0);
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959 printUnwrapped(png, width, height, 0);
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962 ImageIO.write(bi, "png", out);
\r
965 catch(OutOfMemoryError err)
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967 System.out.println("########################\n"
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968 +"OUT OF MEMORY "+pngFile+"\n"
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969 +"########################");
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971 catch (Exception ex)
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973 ex.printStackTrace();
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983 * @version $Revision$
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985 class Preview extends JFrame
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988 * Creates a new Preview object.
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990 * @param image DOCUMENT ME!
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992 public Preview(Image image)
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994 setResizable(true);
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995 setSize(image.getWidth(this), image.getHeight(this));
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997 getContentPane().setLayout(new BorderLayout());
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998 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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1008 * @author $author$
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1009 * @version $Revision$
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1011 class PreviewPanel extends JPanel
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1016 * Creates a new PreviewPanel object.
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1018 * @param image DOCUMENT ME!
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1020 public PreviewPanel(Image image)
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1022 this.image = image;
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1028 * @param g DOCUMENT ME!
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1030 public void paintComponent(Graphics g)
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1032 if (image != null)
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1034 g.drawImage(image, 0, 0, this);
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1038 System.out.println("DEBUG:image is null");
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