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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129 case KeyEvent.VK_BACK_SPACE:
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130 case KeyEvent.VK_DELETE:
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131 alignFrame.cut_actionPerformed(null);
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142 public void fontChanged()
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144 // set idCanvas bufferedImage to null
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145 // to prevent drawing old image
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146 FontMetrics fm = getFontMetrics(av.getFont());
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148 scalePanelHolder.setPreferredSize(new Dimension(10,
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149 av.charHeight + fm.getDescent()));
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150 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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151 av.charHeight + fm.getDescent()));
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153 idPanel.idCanvas.gg = null;
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154 annotationPanel.adjustPanelHeight();
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156 Dimension d = calculateIdWidth();
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157 d.setSize(d.width + 4, d.height);
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158 idPanel.idCanvas.setPreferredSize(d);
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159 hscrollFillerPanel.setPreferredSize(d);
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166 * @return DOCUMENT ME!
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168 public Dimension calculateIdWidth()
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170 Container c = new Container();
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172 FontMetrics fm = c.getFontMetrics(av.font);
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173 AlignmentI al = av.getAlignment();
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179 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
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181 SequenceI s = al.getSequenceAt(i);
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183 if (av.getShowFullId())
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185 id = s.getDisplayId();
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192 if (fm.stringWidth(id) > idWidth)
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194 idWidth = fm.stringWidth(id);
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200 // Also check annotation label widths
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203 if (al.getAlignmentAnnotation() != null)
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205 fm = c.getFontMetrics(alabels.getFont());
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207 while (i < al.getAlignmentAnnotation().length)
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209 String label = al.getAlignmentAnnotation()[i].label;
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211 if (fm.stringWidth(label) > idWidth)
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213 idWidth = fm.stringWidth(label);
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220 return new Dimension(idWidth, 12);
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226 * @param results DOCUMENT ME!
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228 public void highlightSearchResults(int[] results)
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230 seqPanel.seqCanvas.highlightSearchResults(results);
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232 // do we need to scroll the panel?
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233 if (results != null)
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235 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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236 int start = seq.findIndex(results[1]) - 1;
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237 int end = seq.findIndex(results[2]) - 1;
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239 if ((av.getStartRes() > start) || (av.getEndRes() < end) ||
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240 ((av.getStartSeq() > results[0]) ||
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241 (av.getEndSeq() < results[0])))
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243 setScrollValues(start, results[0]);
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251 * @return DOCUMENT ME!
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253 public OverviewPanel getOverviewPanel()
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255 return overviewPanel;
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261 * @param op DOCUMENT ME!
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263 public void setOverviewPanel(OverviewPanel op)
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265 overviewPanel = op;
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271 * @param b DOCUMENT ME!
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273 public void setAnnotationVisible(boolean b)
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275 annotationSpaceFillerHolder.setVisible(b);
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276 annotationScroller.setVisible(b);
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282 * @param wrap DOCUMENT ME!
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284 public void setWrapAlignment(boolean wrap)
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286 scalePanelHolder.setVisible(!wrap);
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287 hscroll.setVisible(!wrap);
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288 idwidthAdjuster.setVisible(!wrap);
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290 av.setShowAnnotation(!wrap);
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291 annotationScroller.setVisible(!wrap);
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292 annotationSpaceFillerHolder.setVisible(!wrap);
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293 idSpaceFillerPanel1.setVisible(!wrap);
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301 public void setColourScheme()
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303 ColourSchemeI cs = av.getGlobalColourScheme();
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305 if (av.getConservationSelected())
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307 Alignment al = (Alignment) av.getAlignment();
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308 Conservation c = new Conservation("All",
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309 ResidueProperties.propHash, 3, al.getSequences(), 0,
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313 c.verdict(false, av.ConsPercGaps);
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315 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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317 av.setGlobalColourScheme(ccs);
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323 // return value is true if the scroll is valid
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324 public boolean scrollUp(boolean up)
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328 if (vscroll.getValue() < 1)
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334 vscroll.setValue(vscroll.getValue() - 1);
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338 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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344 vscroll.setValue(vscroll.getValue() + 1);
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355 * @param right DOCUMENT ME!
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357 * @return DOCUMENT ME!
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359 public boolean scrollRight(boolean right)
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363 if (hscroll.getValue() < 1)
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369 hscroll.setValue(hscroll.getValue() - 1);
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373 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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379 hscroll.setValue(hscroll.getValue() + 1);
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390 * @param x DOCUMENT ME!
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391 * @param y DOCUMENT ME!
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393 public void setScrollValues(int x, int y)
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395 av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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398 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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399 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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401 if (hextent > av.alignment.getWidth())
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403 hextent = av.alignment.getWidth();
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406 if (vextent > av.alignment.getHeight())
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408 vextent = av.alignment.getHeight();
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411 if ((hextent + x) > av.getAlignment().getWidth())
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413 x = av.getAlignment().getWidth() - hextent;
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416 if ((vextent + y) > av.getAlignment().getHeight())
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418 y = av.getAlignment().getHeight() - vextent;
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431 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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432 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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435 public void this_mouseWheelMoved(MouseWheelEvent e)
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437 if(e.getWheelRotation()>0)
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447 * @param evt DOCUMENT ME!
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449 public void adjustmentValueChanged(AdjustmentEvent evt)
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451 int oldX = av.getStartRes();
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452 int oldY = av.getStartSeq();
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454 if (evt.getSource() == hscroll)
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456 int x = hscroll.getValue();
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459 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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462 if (evt.getSource() == vscroll)
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464 int offy = vscroll.getValue();
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466 if (av.getWrapAlignment())
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468 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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469 av.setStartRes(vscroll.getValue() * rowSize);
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470 av.setEndRes((vscroll.getValue() + 1) * rowSize);
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474 av.setStartSeq(offy);
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475 av.setEndSeq(offy +
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476 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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480 if (overviewPanel != null)
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482 overviewPanel.setBoxPosition();
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485 if (av.getWrapAlignment() || !fastPaint)
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491 idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
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492 seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
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493 av.getStartSeq() - oldY);
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495 scalePanel.repaint();
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497 if (av.getShowAnnotation())
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499 annotationPanel.fastPaint(av.getStartRes() - oldX);
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507 * @param g DOCUMENT ME!
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509 public void paintComponent(Graphics g)
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513 Dimension d = idPanel.idCanvas.getPreferredSize();
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514 idPanelHolder.setPreferredSize(d);
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515 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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518 if (av.getWrapAlignment())
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520 int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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521 vscroll.setMaximum(max);
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522 vscroll.setUnitIncrement(1);
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523 vscroll.setVisibleAmount(1);
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527 setScrollValues(av.getStartRes(), av.getStartSeq());
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534 * @param pg DOCUMENT ME!
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535 * @param pf DOCUMENT ME!
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536 * @param pi DOCUMENT ME!
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538 * @return DOCUMENT ME!
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540 * @throws PrinterException DOCUMENT ME!
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542 public int print(Graphics pg, PageFormat pf, int pi)
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543 throws PrinterException
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545 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
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547 int pwidth = (int) pf.getImageableWidth();
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548 int pheight = (int) pf.getImageableHeight();
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550 if (av.getWrapAlignment())
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552 return printWrappedAlignment(pg, pwidth, pheight, pi);
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556 return printUnwrapped(pg, pwidth, pheight, pi);
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563 * @param pg DOCUMENT ME!
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564 * @param pwidth DOCUMENT ME!
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565 * @param pheight DOCUMENT ME!
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566 * @param pi DOCUMENT ME!
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568 * @return DOCUMENT ME!
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570 * @throws PrinterException DOCUMENT ME!
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572 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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573 throws PrinterException
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575 int idWidth = calculateIdWidth().width + 4;
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576 FontMetrics fm = getFontMetrics(av.getFont());
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577 int scaleHeight = av.charHeight + fm.getDescent();
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579 pg.setColor(Color.white);
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580 pg.fillRect(0, 0, pwidth, pheight);
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581 pg.setFont(av.getFont());
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583 ////////////////////////////////////
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584 /// How many sequences and residues can we fit on a printable page?
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585 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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587 int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -
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590 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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592 /////////////////////////////
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593 /// Only print these sequences and residues on this page
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596 /////////////////////////////
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597 /// Only print these sequences and residues on this page
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600 /////////////////////////////
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601 /// Only print these sequences and residues on this page
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604 /////////////////////////////
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605 /// Only print these sequences and residues on this page
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607 startRes = (pi % pagesWide) * totalRes;
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608 endRes = (startRes + totalRes) - 1;
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610 if (endRes > (av.getAlignment().getWidth() - 1))
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612 endRes = av.getAlignment().getWidth() - 1;
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615 startSeq = (pi / pagesWide) * totalSeq;
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616 endSeq = startSeq + totalSeq;
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618 if (endSeq > av.getAlignment().getHeight())
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620 endSeq = av.getAlignment().getHeight();
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623 int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
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625 if (av.showAnnotation)
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627 pagesHigh += annotationPanel.getHeight();
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630 pagesHigh /= pheight;
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632 if (pi >= (pagesWide * pagesHigh))
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634 return Printable.NO_SUCH_PAGE;
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638 pg.translate(idWidth, 0);
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639 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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640 pg.translate(-idWidth, scaleHeight);
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644 Color currentColor = null;
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645 Color currentTextColor = null;
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647 for (int i = startSeq; i < endSeq; i++)
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649 if ((av.getSelectionGroup() != null) &&
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650 av.getSelectionGroup().sequences.contains(
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651 av.getAlignment().getSequenceAt(i)))
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653 currentColor = Color.gray;
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654 currentTextColor = Color.black;
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658 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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659 currentTextColor = Color.black;
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662 pg.setColor(currentColor);
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663 pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,
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664 av.getCharHeight());
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666 pg.setColor(currentTextColor);
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668 String string = av.getAlignment().getSequenceAt(i).getName();
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670 if (av.getShowFullId())
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672 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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675 pg.drawString(string, 0,
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676 (((i-startSeq) * av.charHeight) + av.getCharHeight()) -
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677 (av.getCharHeight() / 5));
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680 // draw main sequence panel
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681 pg.translate(idWidth, 0);
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682 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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683 startRes, startSeq, 0);
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685 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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687 pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);
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688 alabels.drawComponent((Graphics2D) pg);
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689 pg.translate(idWidth, 0);
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690 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +
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694 return Printable.PAGE_EXISTS;
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700 * @param pg DOCUMENT ME!
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701 * @param pwidth DOCUMENT ME!
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702 * @param pheight DOCUMENT ME!
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703 * @param pi DOCUMENT ME!
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705 * @return DOCUMENT ME!
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707 * @throws PrinterException DOCUMENT ME!
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709 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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710 int pi) throws PrinterException
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712 int idWidth = calculateIdWidth().width + 4;
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714 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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716 int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +
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717 1) * av.charHeight;
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719 pg.setColor(Color.white);
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720 pg.fillRect(0, 0, pwidth, pheight);
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721 pg.setFont(av.getFont());
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725 pg.setColor(Color.black);
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727 pg.translate(0, -pi * pheight);
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729 pg.setClip(0, pi * pheight, pwidth, pheight);
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731 int ypos = 2 * av.charHeight;
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735 for (int i = 0; i < av.alignment.getHeight(); i++)
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737 SequenceI s = av.alignment.getSequenceAt(i);
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738 String string = s.getName();
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740 if (av.getShowFullId())
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742 string = s.getDisplayId();
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745 pg.drawString(string, 0,
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746 ((i * av.charHeight) + ypos + av.charHeight) -
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747 (av.charHeight / 5));
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750 ypos += ((av.alignment.getHeight() + 2) * av.charHeight);
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752 while (ypos < totalHeight);
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754 pg.translate(idWidth, 0);
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756 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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758 if ((pi * pheight) < totalHeight)
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760 return Printable.PAGE_EXISTS;
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764 return Printable.NO_SUCH_PAGE;
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771 public void makeEPS(File epsFile)
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773 if(epsFile == null)
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775 jalview.io.JalviewFileChooser chooser = new jalview.io.
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776 JalviewFileChooser(jalview.bin.Cache.getProperty(
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777 "LAST_DIRECTORY"), new String[]
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780 {"Encapsulated Postscript"},
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781 "Encapsulated Postscript");
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782 chooser.setFileView(new jalview.io.JalviewFileView());
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783 chooser.setDialogTitle("Create EPS file from alignment");
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784 chooser.setToolTipText("Save");
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786 int value = chooser.showSaveDialog(this);
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788 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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793 epsFile = chooser.getSelectedFile();
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795 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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796 chooser.getSelectedFile().getParent());
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799 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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800 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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802 if (av.getWrapAlignment())
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804 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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806 width = seqPanel.getWidth() + idPanel.getWidth();
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811 if (av.getShowAnnotation())
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813 height += annotationPanel.getPreferredSize().height;
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818 FileOutputStream out = new FileOutputStream(epsFile);
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819 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
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822 if (av.getWrapAlignment())
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824 printWrappedAlignment(pg, width, height, 0);
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828 printUnwrapped(pg, width, height, 0);
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834 catch (Exception ex)
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836 ex.printStackTrace();
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841 public void makePNGImageMap(File imgMapFile, String imageName)
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843 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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844 //////////////////////////////////////////////
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845 int idWidth = calculateIdWidth().width + 4;
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846 FontMetrics fm = getFontMetrics(av.getFont());
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847 int scaleHeight = av.charHeight + fm.getDescent();
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850 //////////////////////////////////
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851 if(imgMapFile!=null)
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855 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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856 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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857 out.println("<img src=\"" + imageName +
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858 "\" border=\"0\" usemap=\"#Map\" >"
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859 +"<map name=\"Map\">");
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861 for (int s = 0; s < av.alignment.getHeight(); s++)
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863 SequenceI seq = av.alignment.getSequenceAt(s);
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864 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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865 for (int i = 0; i < groups.length; i++)
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867 int sy = s * av.charHeight + scaleHeight;
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868 for (int res = groups[i].getStartRes();
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869 res < groups[i].getEndRes() + 1; res++)
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871 int alIndex = seq.findPosition(res);
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872 Object obj = ResidueProperties.aa2Triplet.get(
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873 seq.getCharAt(res) + "");
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877 String triplet = obj.toString();
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880 "<area shape=\"rect\" coords=\""
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881 + (idWidth + res * av.charWidth) + ","
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883 + (idWidth + (res + 1) * av.charWidth) + ","
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884 + (av.charHeight + sy) + "\""
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885 + " onMouseOver=\"toolTip('"
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886 + alIndex + " " + triplet +
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887 "<br><em>" + groups[i].getName() +
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888 "</em>')\"; onMouseOut=\"toolTip()\"; "
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894 out.println("</map></body></html>");
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898 catch (Exception ex)
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900 ex.printStackTrace();
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902 }///////////END OF IMAGE MAP
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909 public void makePNG(File pngFile)
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913 jalview.io.JalviewFileChooser chooser = new jalview.io.
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914 JalviewFileChooser(jalview.bin.Cache.getProperty(
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915 "LAST_DIRECTORY"), new String[]
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918 {"Portable network graphics"},
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919 "Portable network graphics");
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920 chooser.setFileView(new jalview.io.JalviewFileView());
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921 chooser.setDialogTitle("Create EPS file from alignment");
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922 chooser.setToolTipText("Save");
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924 int value = chooser.showSaveDialog(this);
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926 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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931 pngFile = chooser.getSelectedFile();
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933 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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934 chooser.getSelectedFile().getParent());
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939 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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940 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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942 if (av.getWrapAlignment())
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944 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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946 width = seqPanel.getWidth() + idPanel.getWidth();
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951 if (av.getShowAnnotation())
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953 height += annotationPanel.getPreferredSize().height;
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959 FileOutputStream out = new FileOutputStream(pngFile);
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961 BufferedImage bi = new BufferedImage(width, height,
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962 BufferedImage.TYPE_INT_RGB);
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963 Graphics2D png = (Graphics2D) bi.getGraphics();
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965 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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966 RenderingHints.VALUE_ANTIALIAS_ON);
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968 if (av.getWrapAlignment())
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970 printWrappedAlignment(png, width, height, 0);
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974 printUnwrapped(png, width, height, 0);
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977 ImageIO.write(bi, "png", out);
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980 catch(OutOfMemoryError err)
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982 System.out.println("########################\n"
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983 +"OUT OF MEMORY "+pngFile+"\n"
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984 +"########################");
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986 catch (Exception ex)
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988 ex.printStackTrace();
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998 * @version $Revision$
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1000 class Preview extends JFrame
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1003 * Creates a new Preview object.
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1005 * @param image DOCUMENT ME!
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1007 public Preview(Image image)
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1009 setResizable(true);
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1010 setSize(image.getWidth(this), image.getHeight(this));
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1012 getContentPane().setLayout(new BorderLayout());
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1013 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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1023 * @author $author$
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1024 * @version $Revision$
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1026 class PreviewPanel extends JPanel
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1031 * Creates a new PreviewPanel object.
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1033 * @param image DOCUMENT ME!
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1035 public PreviewPanel(Image image)
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1037 this.image = image;
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1043 * @param g DOCUMENT ME!
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1045 public void paintComponent(Graphics g)
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1047 if (image != null)
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1049 g.drawImage(image, 0, 0, this);
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1053 System.out.println("DEBUG:image is null");
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