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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28 import java.awt.event.*;
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29 import java.awt.print.*;
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33 import javax.swing.*;
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40 * @version $Revision$
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42 public class AlignmentPanel extends GAlignmentPanel
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43 implements AdjustmentListener, Printable
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45 public AlignViewport av;
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46 OverviewPanel overviewPanel;
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49 IdwidthAdjuster idwidthAdjuster;
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51 /** DOCUMENT ME!! */
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52 public AlignFrame alignFrame;
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53 ScalePanel scalePanel;
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54 AnnotationPanel annotationPanel;
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55 AnnotationLabels alabels;
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57 // this value is set false when selection area being dragged
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58 boolean fastPaint = true;
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63 * Creates a new AlignmentPanel object.
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65 * @param af DOCUMENT ME!
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66 * @param av DOCUMENT ME!
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68 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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72 seqPanel = new SeqPanel(av, this);
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73 idPanel = new IdPanel(av, this);
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75 scalePanel = new ScalePanel(av, this);
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77 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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78 idwidthAdjuster = new IdwidthAdjuster(this);
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79 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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81 annotationPanel = new AnnotationPanel(this);
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82 alabels = new AnnotationLabels(this);
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84 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
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85 getPreferredSize());
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86 annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
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87 annotationScroller.setViewportView(annotationPanel);
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88 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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92 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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93 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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95 setScrollValues(0, 0);
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97 annotationPanel.adjustPanelHeight();
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98 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
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99 getPreferredSize());
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100 annotationScroller.setPreferredSize(annotationPanel.
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101 getPreferredSize());
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102 setAnnotationVisible(av.getShowAnnotation());
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104 hscroll.addAdjustmentListener(this);
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105 vscroll.addAdjustmentListener(this);
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107 af.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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134 case KeyEvent.VK_P:
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135 seqPanel.seqCanvas.increaseAARatio();
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137 case KeyEvent.VK_L:
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138 seqPanel.seqCanvas.decreaseAARation();
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148 public void fontChanged()
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150 // set idCanvas bufferedImage to null
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151 // to prevent drawing old image
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152 FontMetrics fm = getFontMetrics(av.getFont());
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154 scalePanelHolder.setPreferredSize(new Dimension(10,
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155 av.charHeight + fm.getDescent()));
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156 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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157 av.charHeight + fm.getDescent()));
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159 idPanel.idCanvas.gg = null;
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160 seqPanel.seqCanvas.img = null;
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161 annotationPanel.adjustPanelHeight();
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163 Dimension d = calculateIdWidth();
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164 d.setSize(d.width + 4, d.height);
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165 idPanel.idCanvas.setPreferredSize(d);
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166 hscrollFillerPanel.setPreferredSize(d);
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168 if (av.getWrapAlignment())
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170 int max = av.alignment.getWidth() /
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171 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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172 vscroll.setMaximum(max);
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173 vscroll.setUnitIncrement(1);
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174 vscroll.setVisibleAmount(1);
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178 setScrollValues(av.getStartRes(), av.getStartSeq());
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181 if (overviewPanel != null)
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182 overviewPanel.setBoxPosition();
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190 * @return DOCUMENT ME!
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192 public Dimension calculateIdWidth()
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194 Container c = new Container();
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196 FontMetrics fm = c.getFontMetrics(av.font);
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197 AlignmentI al = av.getAlignment();
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203 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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205 SequenceI s = al.getSequenceAt(i);
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207 id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
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209 if (fm.stringWidth(id) > idWidth)
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211 idWidth = fm.stringWidth(id);
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217 // Also check annotation label widths
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220 if (al.getAlignmentAnnotation() != null)
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222 fm = c.getFontMetrics(alabels.getFont());
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224 while (i < al.getAlignmentAnnotation().length)
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226 String label = al.getAlignmentAnnotation()[i].label;
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228 if (fm.stringWidth(label) > idWidth)
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230 idWidth = fm.stringWidth(label);
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237 return new Dimension(idWidth, 12);
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243 * @param results DOCUMENT ME!
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245 public void highlightSearchResults(int[] results)
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247 seqPanel.seqCanvas.highlightSearchResults(results);
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249 // do we need to scroll the panel?
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250 if (results != null)
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252 SequenceI seq = av.alignment.getSequenceAt(results[0]);
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253 int start = seq.findIndex(results[1]) - 1;
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254 int end = seq.findIndex(results[2]) - 1;
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256 if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
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257 ( (av.getStartSeq() > results[0]) ||
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258 (av.getEndSeq() < results[0])))
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260 setScrollValues(start, results[0]);
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268 * @return DOCUMENT ME!
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270 public OverviewPanel getOverviewPanel()
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272 return overviewPanel;
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278 * @param op DOCUMENT ME!
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280 public void setOverviewPanel(OverviewPanel op)
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282 overviewPanel = op;
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288 * @param b DOCUMENT ME!
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290 public void setAnnotationVisible(boolean b)
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292 if (!av.wrapAlignment)
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294 annotationSpaceFillerHolder.setVisible(b);
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295 annotationScroller.setVisible(b);
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303 * @param wrap DOCUMENT ME!
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305 public void setWrapAlignment(boolean wrap)
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308 scalePanelHolder.setVisible(!wrap);
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309 hscroll.setVisible(!wrap);
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310 idwidthAdjuster.setVisible(!wrap);
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314 annotationScroller.setVisible(false);
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315 annotationSpaceFillerHolder.setVisible(false);
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317 else if (av.showAnnotation)
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319 annotationScroller.setVisible(true);
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320 annotationSpaceFillerHolder.setVisible(true);
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323 idSpaceFillerPanel1.setVisible(!wrap);
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328 // return value is true if the scroll is valid
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329 public boolean scrollUp(boolean up)
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333 if (vscroll.getValue() < 1)
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339 vscroll.setValue(vscroll.getValue() - 1);
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343 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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349 vscroll.setValue(vscroll.getValue() + 1);
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360 * @param right DOCUMENT ME!
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362 * @return DOCUMENT ME!
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364 public boolean scrollRight(boolean right)
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368 if (hscroll.getValue() < 1)
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374 hscroll.setValue(hscroll.getValue() - 1);
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378 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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384 hscroll.setValue(hscroll.getValue() + 1);
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395 * @param x DOCUMENT ME!
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396 * @param y DOCUMENT ME!
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398 public void setScrollValues(int x, int y)
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400 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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403 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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404 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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406 if (hextent > av.alignment.getWidth())
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408 hextent = av.alignment.getWidth();
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411 if (vextent > av.alignment.getHeight())
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413 vextent = av.alignment.getHeight();
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416 if ( (hextent + x) > av.getAlignment().getWidth())
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418 x = av.getAlignment().getWidth() - hextent;
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421 if ( (vextent + y) > av.getAlignment().getHeight())
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423 y = av.getAlignment().getHeight() - vextent;
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436 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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437 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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443 * @param evt DOCUMENT ME!
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445 public void adjustmentValueChanged(AdjustmentEvent evt)
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448 int oldX = av.getStartRes();
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449 int oldY = av.getStartSeq();
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451 if (evt.getSource() == hscroll)
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453 int x = hscroll.getValue();
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456 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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459 if (evt.getSource() == vscroll)
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461 int offy = vscroll.getValue();
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463 if (av.getWrapAlignment())
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465 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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466 seqCanvas.getWidth());
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467 av.setStartRes(vscroll.getValue() * rowSize);
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468 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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472 av.setStartSeq(offy);
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473 av.setEndSeq(offy +
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474 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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478 if (overviewPanel != null)
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480 overviewPanel.setBoxPosition();
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483 int xShift = av.getStartRes() - oldX;
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484 int yShift = av.getStartSeq() - oldY;
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486 if ( (xShift != 0 && yShift != 0) ||
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487 (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
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488 || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
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489 || av.getWrapAlignment()
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492 // Either no shift at all, or shift greater than visible amount
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497 idPanel.idCanvas.fastPaint(yShift);
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498 seqPanel.seqCanvas.fastPaint(xShift, yShift);
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500 scalePanel.repaint();
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502 if (av.getShowAnnotation())
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504 annotationPanel.fastPaint(xShift);
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512 * @param g DOCUMENT ME!
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514 public void paintComponent(Graphics g)
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518 Dimension d = idPanel.idCanvas.getPreferredSize();
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519 idPanelHolder.setPreferredSize(d);
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520 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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523 if (av.getWrapAlignment())
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525 int max = av.alignment.getWidth() /
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526 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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527 vscroll.setMaximum(max);
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528 vscroll.setUnitIncrement(1);
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529 vscroll.setVisibleAmount(1);
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533 setScrollValues(av.getStartRes(), av.getStartSeq());
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540 * @param pg DOCUMENT ME!
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541 * @param pf DOCUMENT ME!
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542 * @param pi DOCUMENT ME!
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544 * @return DOCUMENT ME!
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546 * @throws PrinterException DOCUMENT ME!
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548 public int print(Graphics pg, PageFormat pf, int pi)
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549 throws PrinterException
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551 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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553 int pwidth = (int) pf.getImageableWidth();
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554 int pheight = (int) pf.getImageableHeight();
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556 if (av.getWrapAlignment())
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558 return printWrappedAlignment(pg, pwidth, pheight, pi);
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562 return printUnwrapped(pg, pwidth, pheight, pi);
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569 * @param pg DOCUMENT ME!
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570 * @param pwidth DOCUMENT ME!
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571 * @param pheight DOCUMENT ME!
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572 * @param pi DOCUMENT ME!
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574 * @return DOCUMENT ME!
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576 * @throws PrinterException DOCUMENT ME!
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578 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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579 throws PrinterException
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581 int idWidth = calculateIdWidth().width + 4;
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582 FontMetrics fm = getFontMetrics(av.getFont());
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583 int scaleHeight = av.charHeight + fm.getDescent();
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585 pg.setColor(Color.white);
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586 pg.fillRect(0, 0, pwidth, pheight);
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587 pg.setFont(av.getFont());
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589 ////////////////////////////////////
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590 /// How many sequences and residues can we fit on a printable page?
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591 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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593 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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596 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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598 /////////////////////////////
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599 /// Only print these sequences and residues on this page
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602 /////////////////////////////
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603 /// Only print these sequences and residues on this page
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606 /////////////////////////////
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607 /// Only print these sequences and residues on this page
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610 /////////////////////////////
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611 /// Only print these sequences and residues on this page
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613 startRes = (pi % pagesWide) * totalRes;
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614 endRes = (startRes + totalRes) - 1;
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616 if (endRes > (av.getAlignment().getWidth() - 1))
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618 endRes = av.getAlignment().getWidth() - 1;
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621 startSeq = (pi / pagesWide) * totalSeq;
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622 endSeq = startSeq + totalSeq;
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624 if (endSeq > av.getAlignment().getHeight())
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626 endSeq = av.getAlignment().getHeight();
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629 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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631 if (av.showAnnotation)
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633 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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636 pagesHigh /= pheight;
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638 if (pi >= (pagesWide * pagesHigh))
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640 return Printable.NO_SUCH_PAGE;
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644 pg.translate(idWidth, 0);
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645 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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646 pg.translate( -idWidth, scaleHeight);
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650 Color currentColor = null;
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651 Color currentTextColor = null;
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653 for (int i = startSeq; i < endSeq; i++)
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655 if ( (av.getSelectionGroup() != null) &&
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656 av.getSelectionGroup().sequences.contains(
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657 av.getAlignment().getSequenceAt(i)))
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659 currentColor = Color.gray;
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660 currentTextColor = Color.black;
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664 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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665 currentTextColor = Color.black;
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668 pg.setColor(currentColor);
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669 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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670 av.getCharHeight());
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672 pg.setColor(currentTextColor);
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674 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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675 (av.getShowDBPrefix(), av.getShowJVSuffix());
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677 pg.drawString(string, 0,
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678 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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679 (av.getCharHeight() / 5));
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682 // draw main sequence panel
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683 pg.translate(idWidth, 0);
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684 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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685 startRes, startSeq, 0);
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687 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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689 pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);
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690 alabels.drawComponent( (Graphics2D) pg, idWidth);
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691 pg.translate(idWidth, 0);
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692 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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696 return Printable.PAGE_EXISTS;
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702 * @param pg DOCUMENT ME!
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703 * @param pwidth DOCUMENT ME!
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704 * @param pheight DOCUMENT ME!
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705 * @param pi DOCUMENT ME!
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707 * @return DOCUMENT ME!
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709 * @throws PrinterException DOCUMENT ME!
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711 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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713 throws PrinterException
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716 int annotationHeight = 0;
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717 AnnotationLabels labels = null;
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718 if (av.showAnnotation)
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720 annotationHeight = annotationPanel.adjustPanelHeight();
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721 labels = new AnnotationLabels(av);
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724 int hgap = av.charHeight;
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725 if (av.scaleAboveWrapped)
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726 hgap += av.charHeight;
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728 int cHeight = av.getAlignment().getHeight() * av.charHeight
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730 + annotationHeight;
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732 int idWidth = calculateIdWidth().width + 4;
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734 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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737 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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739 pg.setColor(Color.white);
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740 pg.fillRect(0, 0, pwidth, pheight);
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741 pg.setFont(av.getFont());
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745 pg.setColor(Color.black);
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747 pg.translate(0, -pi * pheight);
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749 pg.setClip(0, pi * pheight, pwidth, pheight);
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752 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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753 av.getFont().getSize());
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754 pg.setFont(italic);
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758 for (int i = 0; i < av.alignment.getHeight(); i++)
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760 SequenceI s = av.alignment.getSequenceAt(i);
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761 String string = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
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763 pg.drawString(string, 0,
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764 ( (i * av.charHeight) + ypos + av.charHeight) -
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765 (av.charHeight / 5));
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767 if (labels != null)
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771 (av.getAlignment().getHeight() * av.charHeight));
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773 pg.setFont(av.getFont());
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774 labels.drawComponent(pg, idWidth);
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775 pg.setFont(italic);
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778 (av.getAlignment().getHeight() * av.charHeight));
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783 while (ypos < totalHeight);
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785 pg.translate(idWidth, 0);
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787 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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789 if ( (pi * pheight) < totalHeight)
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791 return Printable.PAGE_EXISTS;
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796 return Printable.NO_SUCH_PAGE;
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800 void makeAlignmentImage(int type, File file)
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802 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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803 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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805 if (av.getWrapAlignment())
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807 height = getWrappedHeight();
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808 width = seqPanel.getWidth() + idPanel.getWidth();
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810 else if (av.getShowAnnotation())
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812 height += annotationPanel.adjustPanelHeight() + 3;
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815 jalview.util.ImageMaker im;
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816 if(type==jalview.util.ImageMaker.PNG)
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817 im = new jalview.util.ImageMaker(this,
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818 jalview.util.ImageMaker.PNG,
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819 "Create PNG image from alignment",
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820 width, height, file, null);
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822 im = new jalview.util.ImageMaker(this,
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823 jalview.util.ImageMaker.EPS,
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824 "Create EPS file from alignment",
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825 width, height, file, alignFrame.getTitle() );
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829 if (av.getWrapAlignment())
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831 if(im.getGraphics()!=null)
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832 printWrappedAlignment(im.getGraphics(), width, height, 0);
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836 if(im.getGraphics()!=null)
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837 printUnwrapped(im.getGraphics(), width, height, 0);
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842 catch (OutOfMemoryError err)
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844 System.out.println("########################\n"
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845 + "OUT OF MEMORY " + file + "\n"
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846 + "########################");
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848 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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849 "Out of Memory Creating Image!!"
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851 "\nSee help files for increasing Java Virtual Machine memory."
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853 JOptionPane.WARNING_MESSAGE);
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854 System.out.println("Create IMAGE: " + err);
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858 catch (Exception ex)
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860 ex.printStackTrace();
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866 public void makeEPS(File epsFile)
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868 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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874 public void makePNG(File pngFile)
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876 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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879 public void makePNGImageMap(File imgMapFile, String imageName)
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881 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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882 //////////////////////////////////////////////
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883 int idWidth = calculateIdWidth().width + 4;
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884 FontMetrics fm = getFontMetrics(av.getFont());
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885 int scaleHeight = av.charHeight + fm.getDescent();
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888 //////////////////////////////////
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889 if (imgMapFile != null)
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893 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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894 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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895 out.println("<img src=\"" + imageName +
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896 "\" border=\"0\" usemap=\"#Map\" >"
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897 + "<map name=\"Map\">");
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899 for (int s = 0; s < av.alignment.getHeight(); s++)
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901 SequenceI seq = av.alignment.getSequenceAt(s);
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902 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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903 for (int i = 0; i < groups.length; i++)
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905 int sy = s * av.charHeight + scaleHeight;
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906 for (int res = groups[i].getStartRes();
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907 res < groups[i].getEndRes() + 1; res++)
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909 int alIndex = seq.findPosition(res);
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910 Object obj = ResidueProperties.aa2Triplet.get(
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911 seq.getCharAt(res) + "");
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915 String triplet = obj.toString();
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918 "<area shape=\"rect\" coords=\""
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919 + (idWidth + res * av.charWidth) + ","
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921 + (idWidth + (res + 1) * av.charWidth) + ","
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922 + (av.charHeight + sy) + "\""
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923 + " onMouseOver=\"toolTip('"
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924 + alIndex + " " + triplet +
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925 "<br><em>" + groups[i].getName() +
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926 "</em>')\"; onMouseOut=\"toolTip()\"; "
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932 out.println("</map></body></html>");
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936 catch (Exception ex)
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938 ex.printStackTrace();
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940 } ///////////END OF IMAGE MAP
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944 int getWrappedHeight()
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947 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
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948 seqPanel.seqCanvas.getWidth());
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950 int hgap = av.charHeight;
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951 if (av.scaleAboveWrapped)
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952 hgap += av.charHeight;
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954 int annotationHeight = 0;
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955 if (av.showAnnotation)
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957 annotationHeight = annotationPanel.adjustPanelHeight();
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960 int cHeight = av.getAlignment().getHeight() * av.charHeight
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962 + annotationHeight;
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964 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
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973 * @version $Revision$
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979 * Creates a new Preview object.
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981 * @param image DOCUMENT ME!
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983 public Preview(Image image)
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985 setResizable(true);
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986 setSize(image.getWidth(this), image.getHeight(this));
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988 getContentPane().setLayout(new BorderLayout());
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989 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
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999 * @version $Revision$
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1001 class PreviewPanel
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1007 * Creates a new PreviewPanel object.
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1009 * @param image DOCUMENT ME!
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1011 public PreviewPanel(Image image)
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1013 this.image = image;
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1019 * @param g DOCUMENT ME!
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1021 public void paintComponent(Graphics g)
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1023 if (image != null)
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1025 g.drawImage(image, 0, 0, this);
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1029 System.out.println("DEBUG:image is null");
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