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.setBoxPosition();
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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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309 annotationScroller.setVisible(false);
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310 annotationSpaceFillerHolder.setVisible(false);
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312 else if(av.showAnnotation)
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314 annotationScroller.setVisible(true);
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315 annotationSpaceFillerHolder.setVisible(true);
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318 idSpaceFillerPanel1.setVisible(!wrap);
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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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440 * @param evt DOCUMENT ME!
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442 public void adjustmentValueChanged(AdjustmentEvent evt)
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445 int oldX = av.getStartRes();
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446 int oldY = av.getStartSeq();
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448 if (evt.getSource() == hscroll)
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450 int x = hscroll.getValue();
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453 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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456 if (evt.getSource() == vscroll)
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458 int offy = vscroll.getValue();
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460 if (av.getWrapAlignment())
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462 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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463 av.setStartRes(vscroll.getValue() * rowSize);
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464 av.setEndRes((vscroll.getValue() + 1) * rowSize);
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468 av.setStartSeq(offy);
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469 av.setEndSeq(offy +
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470 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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474 if (overviewPanel != null)
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476 overviewPanel.setBoxPosition();
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479 int xShift = av.getStartRes() - oldX;
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480 int yShift = av.getStartSeq() - oldY;
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482 if ( (xShift != 0 && yShift != 0) ||
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483 (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
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484 || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
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485 || av.getWrapAlignment()
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488 // Either no shift at all, or shift greater than visible amount
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493 idPanel.idCanvas.fastPaint(yShift);
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494 seqPanel.seqCanvas.fastPaint(xShift, yShift);
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496 scalePanel.repaint();
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498 if (av.getShowAnnotation())
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500 annotationPanel.fastPaint(xShift);
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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 boolean accurateText = true;
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776 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
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777 "Prompt each time");
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779 // If we need to prompt, and if the GUI is visible then
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780 // Prompt for EPS rendering style
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781 if (renderStyle.equalsIgnoreCase("Prompt each time")
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783 (System.getProperty("java.awt.headless") != null
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784 && System.getProperty("java.awt.headless").equals("true")))
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786 EPSOptions eps = new EPSOptions();
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787 renderStyle = eps.getValue();
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789 if(eps.cancelled || renderStyle==null)
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792 renderStyle = eps.getValue();
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795 if (renderStyle.equalsIgnoreCase("text"))
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797 accurateText = false;
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801 if(epsFile == null)
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803 jalview.io.JalviewFileChooser chooser = new jalview.io.
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804 JalviewFileChooser(jalview.bin.Cache.getProperty(
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805 "LAST_DIRECTORY"), new String[]
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808 {"Encapsulated Postscript"},
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809 "Encapsulated Postscript");
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810 chooser.setFileView(new jalview.io.JalviewFileView());
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811 chooser.setDialogTitle("Create EPS file from alignment");
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812 chooser.setToolTipText("Save");
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814 int value = chooser.showSaveDialog(this);
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816 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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821 epsFile = chooser.getSelectedFile();
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823 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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824 chooser.getSelectedFile().getParent());
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827 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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828 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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830 if (av.getWrapAlignment())
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832 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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834 width = seqPanel.getWidth() + idPanel.getWidth();
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839 if (av.getShowAnnotation())
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841 height += annotationPanel.getPreferredSize().height;
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846 FileOutputStream out = new FileOutputStream(epsFile);
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847 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
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850 pg.setAccurateTextMode(accurateText);
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852 if (av.getWrapAlignment())
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854 printWrappedAlignment(pg, width, height, 0);
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858 printUnwrapped(pg, width, height, 0);
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864 catch (Exception ex)
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866 ex.printStackTrace();
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871 public void makePNGImageMap(File imgMapFile, String imageName)
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873 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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874 //////////////////////////////////////////////
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875 int idWidth = calculateIdWidth().width + 4;
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876 FontMetrics fm = getFontMetrics(av.getFont());
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877 int scaleHeight = av.charHeight + fm.getDescent();
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880 //////////////////////////////////
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881 if(imgMapFile!=null)
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885 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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886 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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887 out.println("<img src=\"" + imageName +
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888 "\" border=\"0\" usemap=\"#Map\" >"
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889 +"<map name=\"Map\">");
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891 for (int s = 0; s < av.alignment.getHeight(); s++)
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893 SequenceI seq = av.alignment.getSequenceAt(s);
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894 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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895 for (int i = 0; i < groups.length; i++)
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897 int sy = s * av.charHeight + scaleHeight;
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898 for (int res = groups[i].getStartRes();
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899 res < groups[i].getEndRes() + 1; res++)
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901 int alIndex = seq.findPosition(res);
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902 Object obj = ResidueProperties.aa2Triplet.get(
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903 seq.getCharAt(res) + "");
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907 String triplet = obj.toString();
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910 "<area shape=\"rect\" coords=\""
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911 + (idWidth + res * av.charWidth) + ","
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913 + (idWidth + (res + 1) * av.charWidth) + ","
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914 + (av.charHeight + sy) + "\""
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915 + " onMouseOver=\"toolTip('"
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916 + alIndex + " " + triplet +
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917 "<br><em>" + groups[i].getName() +
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918 "</em>')\"; onMouseOut=\"toolTip()\"; "
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924 out.println("</map></body></html>");
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928 catch (Exception ex)
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930 ex.printStackTrace();
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932 }///////////END OF IMAGE MAP
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939 public void makePNG(File pngFile)
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943 jalview.io.JalviewFileChooser chooser = new jalview.io.
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944 JalviewFileChooser(jalview.bin.Cache.getProperty(
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945 "LAST_DIRECTORY"), new String[]
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948 {"Portable network graphics"},
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949 "Portable network graphics");
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950 chooser.setFileView(new jalview.io.JalviewFileView());
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951 chooser.setDialogTitle("Create EPS file from alignment");
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952 chooser.setToolTipText("Save");
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954 int value = chooser.showSaveDialog(this);
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956 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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961 pngFile = chooser.getSelectedFile();
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963 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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964 chooser.getSelectedFile().getParent());
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969 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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970 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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972 if (av.getWrapAlignment())
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974 height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *
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976 width = seqPanel.getWidth() + idPanel.getWidth();
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981 if (av.getShowAnnotation())
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983 height += annotationPanel.getPreferredSize().height;
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989 FileOutputStream out = new FileOutputStream(pngFile);
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991 BufferedImage bi = new BufferedImage(width, height,
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992 BufferedImage.TYPE_INT_RGB);
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993 Graphics2D png = (Graphics2D) bi.getGraphics();
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995 png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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996 RenderingHints.VALUE_ANTIALIAS_ON);
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998 if (av.getWrapAlignment())
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1000 printWrappedAlignment(png, width, height, 0);
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1004 printUnwrapped(png, width, height, 0);
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1007 ImageIO.write(bi, "png", out);
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1010 catch(OutOfMemoryError err)
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1012 System.out.println("########################\n"
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1013 +"OUT OF MEMORY "+pngFile+"\n"
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1014 +"########################");
\r
1017 catch (Exception ex)
\r
1019 ex.printStackTrace();
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1028 * @author $author$
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1029 * @version $Revision$
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1031 class Preview extends JFrame
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1034 * Creates a new Preview object.
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1036 * @param image DOCUMENT ME!
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1038 public Preview(Image image)
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1040 setResizable(true);
\r
1041 setSize(image.getWidth(this), image.getHeight(this));
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1043 getContentPane().setLayout(new BorderLayout());
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1044 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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1054 * @author $author$
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1055 * @version $Revision$
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1057 class PreviewPanel extends JPanel
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1062 * Creates a new PreviewPanel object.
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1064 * @param image DOCUMENT ME!
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1066 public PreviewPanel(Image image)
\r
1068 this.image = image;
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1074 * @param g DOCUMENT ME!
\r
1076 public void paintComponent(Graphics g)
\r
1078 if (image != null)
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1080 g.drawImage(image, 0, 0, this);
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1084 System.out.println("DEBUG:image is null");
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