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.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.jbgui.*;
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27 import jalview.schemes.*;
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29 import org.jibble.epsgraphics.*;
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32 import java.awt.event.*;
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33 import java.awt.image.*;
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34 import java.awt.print.*;
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38 import javax.imageio.*;
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40 import javax.swing.*;
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47 * @version $Revision$
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49 public class AlignmentPanel extends GAlignmentPanel
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50 implements AdjustmentListener, Printable
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53 OverviewPanel overviewPanel;
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56 IdwidthAdjuster idwidthAdjuster;
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58 /** DOCUMENT ME!! */
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59 public AlignFrame alignFrame;
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60 ScalePanel scalePanel;
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61 AnnotationPanel annotationPanel;
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62 AnnotationLabels alabels;
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64 // this value is set false when selection area being dragged
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65 boolean fastPaint = true;
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70 * Creates a new AlignmentPanel object.
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72 * @param af DOCUMENT ME!
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73 * @param av DOCUMENT ME!
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75 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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79 seqPanel = new SeqPanel(av, this);
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80 idPanel = new IdPanel(av, this);
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82 scalePanel = new ScalePanel(av, this);
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84 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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85 idwidthAdjuster = new IdwidthAdjuster(this);
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86 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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88 annotationPanel = new AnnotationPanel(this);
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89 alabels = new AnnotationLabels(this);
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91 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
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92 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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93 annotationScroller.setViewportView(annotationPanel);
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94 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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98 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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99 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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101 setScrollValues(0, 0);
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103 hscroll.addAdjustmentListener(this);
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104 vscroll.addAdjustmentListener(this);
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106 setFocusable(true);
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107 addKeyListener(new KeyAdapter()
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109 public void keyPressed(KeyEvent evt)
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111 switch (evt.getKeyCode())
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113 case 27: // escape key
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114 av.setSelectionGroup(null);
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119 case KeyEvent.VK_DOWN:
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120 alignFrame.moveSelectedSequences(false);
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124 case KeyEvent.VK_UP:
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125 alignFrame.moveSelectedSequences(true);
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136 public void fontChanged()
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138 // set idCanvas bufferedImage to null
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139 // to prevent drawing old image
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140 FontMetrics fm = getFontMetrics(av.getFont());
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142 scalePanelHolder.setPreferredSize(new Dimension(10,
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143 av.charHeight + fm.getDescent()));
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144 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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145 av.charHeight + fm.getDescent()));
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147 idPanel.idCanvas.gg = null;
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148 annotationPanel.adjustPanelHeight();
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150 Dimension d = calculateIdWidth();
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151 d.setSize(d.width + 4, d.height);
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152 idPanel.idCanvas.setPreferredSize(d);
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153 hscrollFillerPanel.setPreferredSize(d);
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160 * @return DOCUMENT ME!
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162 public Dimension calculateIdWidth()
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164 Graphics g = this.getGraphics();
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168 javax.swing.JFrame f = new javax.swing.JFrame();
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170 g = f.getGraphics();
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173 FontMetrics fm = g.getFontMetrics(av.font);
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174 AlignmentI al = av.getAlignment();
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180 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
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182 SequenceI s = al.getSequenceAt(i);
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184 if (av.getShowFullId())
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186 id = s.getDisplayId();
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193 if (fm.stringWidth(id) > idWidth)
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195 idWidth = fm.stringWidth(id);
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201 // Also check annotation label widths
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204 if (al.getAlignmentAnnotation() != null)
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206 fm = g.getFontMetrics(alabels.getFont());
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208 while (i < al.getAlignmentAnnotation().length)
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210 String label = al.getAlignmentAnnotation()[i].label;
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212 if (fm.stringWidth(label) > idWidth)
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214 idWidth = fm.stringWidth(label);
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221 return new Dimension(idWidth, 12);
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227 * @param results DOCUMENT ME!
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229 public void highlightSearchResults(int[] results)
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231 seqPanel.seqCanvas.highlightSearchResults(results);
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233 // do we need to scroll the panel?
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234 if (results != null)
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236 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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237 int start = seq.findIndex(results[1]) - 1;
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238 int end = seq.findIndex(results[2]) - 1;
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240 if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
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241 ((av.getStartSeq() > results[0]) ||
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242 (av.getEndSeq() < results[0])))
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244 setScrollValues(start, results[0]);
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252 * @return DOCUMENT ME!
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254 public OverviewPanel getOverviewPanel()
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256 return overviewPanel;
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262 * @param op DOCUMENT ME!
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264 public void setOverviewPanel(OverviewPanel op)
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266 overviewPanel = op;
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272 * @param b DOCUMENT ME!
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274 public void setAnnotationVisible(boolean b)
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276 annotationSpaceFillerHolder.setVisible(b);
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277 annotationScroller.setVisible(b);
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283 * @param wrap DOCUMENT ME!
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285 public void setWrapAlignment(boolean wrap)
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287 scalePanelHolder.setVisible(!wrap);
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288 hscroll.setVisible(!wrap);
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289 idwidthAdjuster.setVisible(!wrap);
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291 av.setShowAnnotation(!wrap);
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292 annotationScroller.setVisible(!wrap);
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293 annotationSpaceFillerHolder.setVisible(!wrap);
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294 idSpaceFillerPanel1.setVisible(!wrap);
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302 public void setColourScheme()
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304 ColourSchemeI cs = av.getGlobalColourScheme();
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306 if (av.getConservationSelected())
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308 Alignment al = (Alignment) av.getAlignment();
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309 Conservation c = new Conservation("All",
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310 ResidueProperties.propHash, 3, al.getSequences(), 0,
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314 c.verdict(false, av.ConsPercGaps);
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316 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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318 av.setGlobalColourScheme(ccs);
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324 // return value is true if the scroll is valid
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325 public boolean scrollUp(boolean up)
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329 if (vscroll.getValue() < 1)
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335 vscroll.setValue(vscroll.getValue() - 1);
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339 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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345 vscroll.setValue(vscroll.getValue() + 1);
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356 * @param right DOCUMENT ME!
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358 * @return DOCUMENT ME!
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360 public boolean scrollRight(boolean right)
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364 if (hscroll.getValue() < 1)
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370 hscroll.setValue(hscroll.getValue() - 1);
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374 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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380 hscroll.setValue(hscroll.getValue() + 1);
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391 * @param x DOCUMENT ME!
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392 * @param y DOCUMENT ME!
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394 public void setScrollValues(int x, int y)
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396 av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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399 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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400 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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402 if (hextent > av.alignment.getWidth())
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404 hextent = av.alignment.getWidth();
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407 if (vextent > av.alignment.getHeight())
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409 vextent = av.alignment.getHeight();
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412 if ((hextent + x) > av.getAlignment().getWidth())
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414 x = av.getAlignment().getWidth() - hextent;
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417 if ((vextent + y) > av.getAlignment().getHeight())
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419 y = av.getAlignment().getHeight() - vextent;
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432 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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433 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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436 public void this_mouseWheelMoved(MouseWheelEvent e)
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438 if(e.getWheelRotation()>0)
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448 * @param evt DOCUMENT ME!
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450 public void adjustmentValueChanged(AdjustmentEvent evt)
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452 int oldX = av.getStartRes();
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453 int oldY = av.getStartSeq();
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455 if (evt.getSource() == hscroll)
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457 int x = hscroll.getValue();
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460 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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463 if (evt.getSource() == vscroll)
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465 int offy = vscroll.getValue();
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467 if (av.getWrapAlignment())
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469 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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470 av.setStartRes(vscroll.getValue() * rowSize);
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471 av.setEndRes((vscroll.getValue() + 1) * rowSize);
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475 av.setStartSeq(offy);
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476 av.setEndSeq(offy +
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477 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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481 if (overviewPanel != null)
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483 overviewPanel.setBoxPosition();
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486 if (av.getWrapAlignment() || !fastPaint)
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492 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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493 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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494 av.getStartSeq() - oldY);
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496 scalePanel.repaint();
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498 if (av.getShowAnnotation())
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500 annotationPanel.fastPaint(av.getStartRes() - oldX);
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508 * @param g DOCUMENT ME!
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510 public void paintComponent(Graphics g)
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514 Dimension d = idPanel.idCanvas.getPreferredSize();
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515 idPanelHolder.setPreferredSize(d);
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516 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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519 if (av.getWrapAlignment())
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521 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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522 vscroll.setMaximum(max);
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523 vscroll.setUnitIncrement(1);
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524 vscroll.setVisibleAmount(1);
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528 setScrollValues(av.getStartRes(), av.getStartSeq());
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535 * @param pg DOCUMENT ME!
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536 * @param pf DOCUMENT ME!
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537 * @param pi DOCUMENT ME!
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539 * @return DOCUMENT ME!
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541 * @throws PrinterException DOCUMENT ME!
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543 public int print(Graphics pg, PageFormat pf, int pi)
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544 throws PrinterException
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546 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
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548 int pwidth = (int) pf.getImageableWidth();
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549 int pheight = (int) pf.getImageableHeight();
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551 if (av.getWrapAlignment())
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553 return printWrappedAlignment(pg, pwidth, pheight, pi);
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557 return printUnwrapped(pg, pwidth, pheight, pi);
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564 * @param pg DOCUMENT ME!
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565 * @param pwidth DOCUMENT ME!
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566 * @param pheight DOCUMENT ME!
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567 * @param pi DOCUMENT ME!
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569 * @return DOCUMENT ME!
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571 * @throws PrinterException DOCUMENT ME!
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573 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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574 throws PrinterException
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576 int idWidth = calculateIdWidth().width + 4;
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577 FontMetrics fm = getFontMetrics(av.getFont());
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578 int scaleHeight = av.charHeight + fm.getDescent();
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580 pg.setColor(Color.white);
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581 pg.fillRect(0, 0, pwidth, pheight);
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582 pg.setFont(av.getFont());
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584 ////////////////////////////////////
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585 /// How many sequences and residues can we fit on a printable page?
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586 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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588 int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
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591 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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593 /////////////////////////////
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594 /// Only print these sequences and residues on this page
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597 /////////////////////////////
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598 /// Only print these sequences and residues on this page
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601 /////////////////////////////
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602 /// Only print these sequences and residues on this page
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605 /////////////////////////////
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606 /// Only print these sequences and residues on this page
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608 startRes = (pi % pagesWide) * totalRes;
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609 endRes = (startRes + totalRes) - 1;
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611 if (endRes > (av.getAlignment().getWidth() - 1))
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613 endRes = av.getAlignment().getWidth() - 1;
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616 startSeq = (pi / pagesWide) * totalSeq;
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617 endSeq = startSeq + totalSeq;
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619 if (endSeq > av.getAlignment().getHeight())
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621 endSeq = av.getAlignment().getHeight();
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624 int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
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626 if (av.showAnnotation)
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628 pagesHigh += annotationPanel.getHeight();
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631 pagesHigh /= pheight;
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633 if (pi >= (pagesWide * pagesHigh))
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635 return Printable.NO_SUCH_PAGE;
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639 pg.translate(idWidth, 0);
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640 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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641 pg.translate(-idWidth, scaleHeight);
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645 Color currentColor = null;
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646 Color currentTextColor = null;
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648 for (int i = startSeq; i < endSeq; i++)
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650 if ((av.getSelectionGroup() != null) &&
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651 av.getSelectionGroup().sequences.contains(
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652 av.getAlignment().getSequenceAt(i)))
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654 currentColor = Color.gray;
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655 currentTextColor = Color.black;
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659 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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660 currentTextColor = Color.black;
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663 pg.setColor(currentColor);
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664 pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,
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665 av.getCharHeight());
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667 pg.setColor(currentTextColor);
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669 String string = av.getAlignment().getSequenceAt(i).getName();
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671 if (av.getShowFullId())
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673 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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676 pg.drawString(string, 0,
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677 (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
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678 (av.getCharHeight() / 5));
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681 // draw main sequence panel
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682 pg.translate(idWidth, 0);
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683 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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684 startRes, startSeq, 0);
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686 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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688 pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
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689 alabels.drawComponent((Graphics2D) pg);
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690 pg.translate(idWidth, 0);
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691 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
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695 return Printable.PAGE_EXISTS;
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701 * @param pg DOCUMENT ME!
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702 * @param pwidth DOCUMENT ME!
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703 * @param pheight DOCUMENT ME!
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704 * @param pi DOCUMENT ME!
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706 * @return DOCUMENT ME!
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708 * @throws PrinterException DOCUMENT ME!
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710 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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711 int pi) throws PrinterException
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713 int idWidth = calculateIdWidth().width + 4;
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715 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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717 int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
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718 1) * av.charHeight;
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720 pg.setColor(Color.white);
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721 pg.fillRect(0, 0, pwidth, pheight);
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722 pg.setFont(av.getFont());
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726 pg.setColor(Color.black);
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728 pg.translate(0, -pi * pheight);
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730 pg.setClip(0, pi * pheight, pwidth, pheight);
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732 int ypos = 2 * av.charHeight;
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736 for (int i = 0; i < av.alignment.getHeight(); i++)
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738 SequenceI s = av.alignment.getSequenceAt(i);
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739 String string = s.getName();
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741 if (av.getShowFullId())
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743 string = s.getDisplayId();
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746 pg.drawString(string, 0,
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747 ((i * av.charHeight) + ypos + av.charHeight) -
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748 (av.charHeight / 5));
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751 ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
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753 while (ypos < totalHeight);
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755 pg.translate(idWidth, 0);
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757 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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759 if ((pi * pheight) < totalHeight)
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761 return Printable.PAGE_EXISTS;
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765 return Printable.NO_SUCH_PAGE;
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772 public void makeEPS(File epsFile)
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774 if(epsFile == null)
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776 jalview.io.JalviewFileChooser chooser = new jalview.io.
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777 JalviewFileChooser(jalview.bin.Cache.getProperty(
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778 "LAST_DIRECTORY"), new String[]
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781 {"Encapsulated Postscript"},
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782 "Encapsulated Postscript");
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783 chooser.setFileView(new jalview.io.JalviewFileView());
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784 chooser.setDialogTitle("Create EPS file from alignment");
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785 chooser.setToolTipText("Save");
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787 int value = chooser.showSaveDialog(this);
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789 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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794 epsFile = chooser.getSelectedFile();
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796 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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797 chooser.getSelectedFile().getParent());
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800 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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801 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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803 if (av.getWrapAlignment())
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805 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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807 width = seqPanel.getWidth() + idPanel.getWidth();
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812 if (av.getShowAnnotation())
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814 height += annotationPanel.getPreferredSize().height;
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819 FileOutputStream out = new FileOutputStream(epsFile);
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820 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
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823 if (av.getWrapAlignment())
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825 printWrappedAlignment(pg, width, height, 0);
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829 printUnwrapped(pg, width, height, 0);
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835 catch (Exception ex)
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837 ex.printStackTrace();
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842 public void makePNGImageMap(File imgMapFile, String imageName)
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844 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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845 //////////////////////////////////////////////
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846 int idWidth = calculateIdWidth().width + 4;
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847 FontMetrics fm = getFontMetrics(av.getFont());
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848 int scaleHeight = av.charHeight + fm.getDescent();
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851 //////////////////////////////////
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852 if(imgMapFile!=null)
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856 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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857 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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858 out.println("<img src=\"" + imageName +
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859 "\" border=\"0\" usemap=\"#Map\" >"
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860 +"<map name=\"Map\">");
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862 for (int s = 0; s < av.alignment.getHeight(); s++)
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864 SequenceI seq = av.alignment.getSequenceAt(s);
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865 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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866 for (int i = 0; i < groups.length; i++)
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868 int sy = s * av.charHeight + scaleHeight;
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869 for (int res = groups[i].getStartRes();
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870 res < groups[i].getEndRes() + 1; res++)
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872 int alIndex = seq.findPosition(res);
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873 Object obj = ResidueProperties.aa2Triplet.get(
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874 seq.getCharAt(res) + "");
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878 String triplet = obj.toString();
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881 "<area shape=\"rect\" coords=\""
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882 + (idWidth + res * av.charWidth) + ","
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884 + (idWidth + (res + 1) * av.charWidth) + ","
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885 + (av.charHeight + sy) + "\""
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886 + " onMouseOver=\"toolTip('"
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887 + alIndex + " " + triplet +
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888 "<br><em>" + groups[i].getName() +
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889 "</em>')\"; onMouseOut=\"toolTip()\"; "
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895 out.println("</map></body></html>");
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899 catch (Exception ex)
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901 ex.printStackTrace();
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903 }///////////END OF IMAGE MAP
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910 public void makePNG(File pngFile)
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914 jalview.io.JalviewFileChooser chooser = new jalview.io.
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915 JalviewFileChooser(jalview.bin.Cache.getProperty(
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916 "LAST_DIRECTORY"), new String[]
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919 {"Portable network graphics"},
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920 "Portable network graphics");
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921 chooser.setFileView(new jalview.io.JalviewFileView());
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922 chooser.setDialogTitle("Create EPS file from alignment");
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923 chooser.setToolTipText("Save");
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925 int value = chooser.showSaveDialog(this);
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927 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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932 pngFile = chooser.getSelectedFile();
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934 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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935 chooser.getSelectedFile().getParent());
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940 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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941 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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943 if (av.getWrapAlignment())
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945 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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947 width = seqPanel.getWidth() + idPanel.getWidth();
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952 if (av.getShowAnnotation())
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954 height += annotationPanel.getPreferredSize().height;
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960 FileOutputStream out = new FileOutputStream(pngFile);
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962 BufferedImage bi = new BufferedImage(width, height,
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963 BufferedImage.TYPE_INT_RGB);
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964 Graphics2D png = (Graphics2D) bi.getGraphics();
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966 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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967 RenderingHints.VALUE_ANTIALIAS_ON);
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969 if (av.getWrapAlignment())
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971 printWrappedAlignment(png, width, height, 0);
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975 printUnwrapped(png, width, height, 0);
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978 ImageIO.write(bi, "png", out);
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981 catch(OutOfMemoryError err)
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983 System.out.println("########################\n"
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984 +"OUT OF MEMORY "+pngFile+"\n"
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985 +"########################");
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987 catch (Exception ex)
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989 ex.printStackTrace();
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999 * @version $Revision$
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1001 class Preview extends JFrame
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1004 * Creates a new Preview object.
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1006 * @param image DOCUMENT ME!
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1008 public Preview(Image image)
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1010 setResizable(true);
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1011 setSize(image.getWidth(this), image.getHeight(this));
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1013 getContentPane().setLayout(new BorderLayout());
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1014 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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1024 * @author $author$
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1025 * @version $Revision$
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1027 class PreviewPanel extends JPanel
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1032 * Creates a new PreviewPanel object.
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1034 * @param image DOCUMENT ME!
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1036 public PreviewPanel(Image image)
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1038 this.image = image;
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1044 * @param g DOCUMENT ME!
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1046 public void paintComponent(Graphics g)
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1048 if (image != null)
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1050 g.drawImage(image, 0, 0, this);
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1054 System.out.println("DEBUG:image is null");
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