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.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.wrapAlignment)
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258 if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
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259 ( (av.getStartSeq() > results[0]) ||
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260 (av.getEndSeq() < results[0])))
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262 setScrollValues(start, results[0]);
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267 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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268 if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
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270 vscroll.setValue(start / cwidth);
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279 * @return DOCUMENT ME!
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281 public OverviewPanel getOverviewPanel()
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283 return overviewPanel;
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289 * @param op DOCUMENT ME!
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291 public void setOverviewPanel(OverviewPanel op)
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293 overviewPanel = op;
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299 * @param b DOCUMENT ME!
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301 public void setAnnotationVisible(boolean b)
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303 if (!av.wrapAlignment)
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305 annotationSpaceFillerHolder.setVisible(b);
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306 annotationScroller.setVisible(b);
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314 * @param wrap DOCUMENT ME!
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316 public void setWrapAlignment(boolean wrap)
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319 scalePanelHolder.setVisible(!wrap);
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320 hscroll.setVisible(!wrap);
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321 idwidthAdjuster.setVisible(!wrap);
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325 annotationScroller.setVisible(false);
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326 annotationSpaceFillerHolder.setVisible(false);
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328 else if (av.showAnnotation)
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330 annotationScroller.setVisible(true);
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331 annotationSpaceFillerHolder.setVisible(true);
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334 idSpaceFillerPanel1.setVisible(!wrap);
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339 // return value is true if the scroll is valid
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340 public boolean scrollUp(boolean up)
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344 if (vscroll.getValue() < 1)
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350 vscroll.setValue(vscroll.getValue() - 1);
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354 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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360 vscroll.setValue(vscroll.getValue() + 1);
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371 * @param right DOCUMENT ME!
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373 * @return DOCUMENT ME!
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375 public boolean scrollRight(boolean right)
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379 if (hscroll.getValue() < 1)
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385 hscroll.setValue(hscroll.getValue() - 1);
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389 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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395 hscroll.setValue(hscroll.getValue() + 1);
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406 * @param x DOCUMENT ME!
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407 * @param y DOCUMENT ME!
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409 public void setScrollValues(int x, int y)
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411 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
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414 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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415 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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417 if (hextent > av.alignment.getWidth())
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419 hextent = av.alignment.getWidth();
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422 if (vextent > av.alignment.getHeight())
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424 vextent = av.alignment.getHeight();
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427 if ( (hextent + x) > av.getAlignment().getWidth())
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429 x = av.getAlignment().getWidth() - hextent;
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432 if ( (vextent + y) > av.getAlignment().getHeight())
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434 y = av.getAlignment().getHeight() - vextent;
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447 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
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448 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
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454 * @param evt DOCUMENT ME!
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456 public void adjustmentValueChanged(AdjustmentEvent evt)
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459 int oldX = av.getStartRes();
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460 int oldY = av.getStartSeq();
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462 if (evt.getSource() == hscroll)
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464 int x = hscroll.getValue();
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467 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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470 if (evt.getSource() == vscroll)
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472 int offy = vscroll.getValue();
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474 if (av.getWrapAlignment())
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476 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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477 seqCanvas.getWidth());
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478 av.setStartRes(vscroll.getValue() * rowSize);
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479 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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483 av.setStartSeq(offy);
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484 av.setEndSeq(offy +
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485 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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489 if (overviewPanel != null)
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491 overviewPanel.setBoxPosition();
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494 int xShift = av.getStartRes() - oldX;
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495 int yShift = av.getStartSeq() - oldY;
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497 if ( (xShift != 0 && yShift != 0) ||
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498 (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
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499 || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
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500 || av.getWrapAlignment()
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503 // Either no shift at all, or shift greater than visible amount
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508 idPanel.idCanvas.fastPaint(yShift);
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509 seqPanel.seqCanvas.fastPaint(xShift, yShift);
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511 scalePanel.repaint();
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513 if (av.getShowAnnotation())
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515 annotationPanel.fastPaint(xShift);
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523 * @param g DOCUMENT ME!
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525 public void paintComponent(Graphics g)
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529 Dimension d = idPanel.idCanvas.getPreferredSize();
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530 idPanelHolder.setPreferredSize(d);
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531 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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534 if (av.getWrapAlignment())
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536 int max = av.alignment.getWidth() /
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537 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
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538 vscroll.setMaximum(max);
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539 vscroll.setUnitIncrement(1);
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540 vscroll.setVisibleAmount(1);
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544 setScrollValues(av.getStartRes(), av.getStartSeq());
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548 if( this.getVisibleRect().getBounds() == g.getClipBounds() )
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550 if (overviewPanel != null)
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551 overviewPanel.updateOverviewImage();
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558 * @param pg DOCUMENT ME!
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559 * @param pf DOCUMENT ME!
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560 * @param pi DOCUMENT ME!
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562 * @return DOCUMENT ME!
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564 * @throws PrinterException DOCUMENT ME!
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566 public int print(Graphics pg, PageFormat pf, int pi)
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567 throws PrinterException
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569 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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571 int pwidth = (int) pf.getImageableWidth();
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572 int pheight = (int) pf.getImageableHeight();
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574 if (av.getWrapAlignment())
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576 return printWrappedAlignment(pg, pwidth, pheight, pi);
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580 return printUnwrapped(pg, pwidth, pheight, pi);
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587 * @param pg DOCUMENT ME!
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588 * @param pwidth DOCUMENT ME!
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589 * @param pheight DOCUMENT ME!
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590 * @param pi DOCUMENT ME!
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592 * @return DOCUMENT ME!
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594 * @throws PrinterException DOCUMENT ME!
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596 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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597 throws PrinterException
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599 int idWidth = calculateIdWidth().width + 4;
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600 FontMetrics fm = getFontMetrics(av.getFont());
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601 int scaleHeight = av.charHeight + fm.getDescent();
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603 pg.setColor(Color.white);
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604 pg.fillRect(0, 0, pwidth, pheight);
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605 pg.setFont(av.getFont());
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607 ////////////////////////////////////
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608 /// How many sequences and residues can we fit on a printable page?
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609 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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611 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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614 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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616 /////////////////////////////
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617 /// Only print these sequences and residues on this page
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620 /////////////////////////////
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621 /// Only print these sequences and residues on this page
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624 /////////////////////////////
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625 /// Only print these sequences and residues on this page
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628 /////////////////////////////
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629 /// Only print these sequences and residues on this page
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631 startRes = (pi % pagesWide) * totalRes;
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632 endRes = (startRes + totalRes) - 1;
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634 if (endRes > (av.getAlignment().getWidth() - 1))
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636 endRes = av.getAlignment().getWidth() - 1;
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639 startSeq = (pi / pagesWide) * totalSeq;
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640 endSeq = startSeq + totalSeq;
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642 if (endSeq > av.getAlignment().getHeight())
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644 endSeq = av.getAlignment().getHeight();
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647 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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649 if (av.showAnnotation)
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651 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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654 pagesHigh /= pheight;
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656 if (pi >= (pagesWide * pagesHigh))
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658 return Printable.NO_SUCH_PAGE;
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662 pg.translate(idWidth, 0);
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663 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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664 pg.translate( -idWidth, scaleHeight);
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668 Color currentColor = null;
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669 Color currentTextColor = null;
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671 pg.setFont(new Font(av.getFont().getName(),
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673 av.getFont().getSize()));
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674 for (int i = startSeq; i < endSeq; i++)
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676 if ( (av.getSelectionGroup() != null) &&
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677 av.getSelectionGroup().sequences.contains(
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678 av.getAlignment().getSequenceAt(i)))
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680 currentColor = Color.gray;
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681 currentTextColor = Color.black;
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685 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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686 currentTextColor = Color.black;
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689 pg.setColor(currentColor);
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690 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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691 av.getCharHeight());
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693 pg.setColor(currentTextColor);
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695 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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696 ( av.getShowJVSuffix());
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698 pg.drawString(string, 0,
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699 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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700 (av.getCharHeight() / 5));
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703 pg.setFont(av.getFont());
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705 // draw main sequence panel
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706 pg.translate(idWidth, 0);
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707 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
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708 startRes, startSeq, 0);
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710 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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712 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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713 alabels.drawComponent( (Graphics2D) pg, idWidth);
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714 pg.translate(idWidth+3, 0);
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715 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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719 return Printable.PAGE_EXISTS;
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725 * @param pg DOCUMENT ME!
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726 * @param pwidth DOCUMENT ME!
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727 * @param pheight DOCUMENT ME!
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728 * @param pi DOCUMENT ME!
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730 * @return DOCUMENT ME!
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732 * @throws PrinterException DOCUMENT ME!
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734 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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736 throws PrinterException
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739 int annotationHeight = 0;
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740 AnnotationLabels labels = null;
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741 if (av.showAnnotation)
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743 annotationHeight = annotationPanel.adjustPanelHeight();
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744 labels = new AnnotationLabels(av);
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747 int hgap = av.charHeight;
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748 if (av.scaleAboveWrapped)
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749 hgap += av.charHeight;
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751 int cHeight = av.getAlignment().getHeight() * av.charHeight
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753 + annotationHeight;
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755 int idWidth = calculateIdWidth().width + 4;
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757 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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760 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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762 pg.setColor(Color.white);
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763 pg.fillRect(0, 0, pwidth, pheight);
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764 pg.setFont(av.getFont());
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768 pg.setColor(Color.black);
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770 pg.translate(0, -pi * pheight);
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772 pg.setClip(0, pi * pheight, pwidth, pheight);
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775 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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776 av.getFont().getSize());
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777 pg.setFont(italic);
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781 for (int i = 0; i < av.alignment.getHeight(); i++)
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783 SequenceI s = av.alignment.getSequenceAt(i);
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784 String string = s.getDisplayId( av.getShowJVSuffix());
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786 pg.drawString(string, 0,
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787 ( (i * av.charHeight) + ypos + av.charHeight) -
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788 (av.charHeight / 5));
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790 if (labels != null)
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794 (av.getAlignment().getHeight() * av.charHeight));
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796 pg.setFont(av.getFont());
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797 labels.drawComponent(pg, idWidth);
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798 pg.setFont(italic);
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801 (av.getAlignment().getHeight() * av.charHeight));
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806 while (ypos < totalHeight);
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808 pg.translate(idWidth, 0);
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810 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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812 if ( (pi * pheight) < totalHeight)
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814 return Printable.PAGE_EXISTS;
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819 return Printable.NO_SUCH_PAGE;
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823 void makeAlignmentImage(int type, File file)
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825 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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826 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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828 if (idPanel.getWidth() == 0)
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830 width += calculateIdWidth().getWidth() + 4;
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833 if (av.getWrapAlignment())
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835 height = getWrappedHeight();
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836 width = seqPanel.getWidth() + idPanel.getWidth();
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838 else if (av.getShowAnnotation())
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840 height += annotationPanel.adjustPanelHeight() + 3;
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843 jalview.util.ImageMaker im;
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844 if(type==jalview.util.ImageMaker.PNG)
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845 im = new jalview.util.ImageMaker(this,
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846 jalview.util.ImageMaker.PNG,
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847 "Create PNG image from alignment",
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848 width, height, file, null);
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850 im = new jalview.util.ImageMaker(this,
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851 jalview.util.ImageMaker.EPS,
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852 "Create EPS file from alignment",
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853 width, height, file, alignFrame.getTitle() );
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857 if (av.getWrapAlignment())
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859 if(im.getGraphics()!=null)
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861 printWrappedAlignment(im.getGraphics(), width, height, 0);
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867 if(im.getGraphics()!=null)
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869 printUnwrapped(im.getGraphics(), width, height, 0);
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874 catch (OutOfMemoryError err)
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876 System.out.println("########################\n"
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877 + "OUT OF MEMORY " + file + "\n"
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878 + "########################");
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880 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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881 "Out of Memory Creating Image!!"
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883 "\nSee help files for increasing Java Virtual Machine memory."
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885 JOptionPane.WARNING_MESSAGE);
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886 System.out.println("Create IMAGE: " + err);
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890 catch (Exception ex)
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892 ex.printStackTrace();
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898 public void makeEPS(File epsFile)
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900 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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906 public void makePNG(File pngFile)
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908 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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911 public void makePNGImageMap(File imgMapFile, String imageName)
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913 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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914 //////////////////////////////////////////////
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915 int idWidth = calculateIdWidth().width + 4;
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916 FontMetrics fm = getFontMetrics(av.getFont());
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917 int scaleHeight = av.charHeight + fm.getDescent();
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920 //////////////////////////////////
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921 if (imgMapFile != null)
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925 int s, sSize = av.alignment.getHeight(),
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926 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
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927 StringBuffer text = new StringBuffer();
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928 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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929 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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930 out.println("<img src=\"" + imageName +
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931 "\" border=\"0\" usemap=\"#Map\" >"
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932 + "<map name=\"Map\">");
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934 for (s = 0; s < sSize; s++)
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936 sy = s * av.charHeight + scaleHeight;
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938 SequenceI seq = av.alignment.getSequenceAt(s);
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939 java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
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940 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
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941 for(res =0; res<alwidth; res++)
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943 text = new StringBuffer();
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945 if(av.alignment.isNucleotide())
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946 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
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948 obj = ResidueProperties.aa2Triplet.get(
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949 seq.getCharAt(res) + "");
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954 String triplet = obj.toString();
\r
955 int alIndex = seq.findPosition(res);
\r
956 gSize = groups.length;
\r
957 for (g = 0; g < gSize; g++)
\r
959 if(text.length()<1)
\r
961 text.append("<area shape=\"rect\" coords=\""
\r
962 + (idWidth + res * av.charWidth) + ","
\r
964 + (idWidth + (res + 1) * av.charWidth) + ","
\r
965 + (av.charHeight + sy) + "\""
\r
966 + " onMouseOver=\"toolTip('"
\r
967 + alIndex + " " + triplet );
\r
970 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
971 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
974 if (features != null)
\r
976 if(text.length()<1)
\r
978 text.append("<area shape=\"rect\" coords=\""
\r
979 + (idWidth + res * av.charWidth) + ","
\r
981 + (idWidth + (res + 1) * av.charWidth) + ","
\r
982 + (av.charHeight + sy) + "\""
\r
983 + " onMouseOver=\"toolTip('"
\r
984 + alIndex + " " + triplet );
\r
986 fSize = features.size();
\r
987 for (f = 0; f < fSize; f++)
\r
989 SequenceFeature sf = (SequenceFeature) features.elementAt(f);
\r
991 if ( (sf.getBegin() <= seq.findPosition(res)) &&
\r
992 (sf.getEnd() >= seq.findPosition(res)))
\r
994 if (sf.getType().equals("disulfide bond"))
\r
996 if (sf.getBegin() == seq.findPosition(res)
\r
997 || sf.getEnd() == seq.findPosition(res))
\r
999 text.append("<br>disulfide bond " + sf.getBegin() + ":" +
\r
1005 text.append("<br>");
\r
1006 text.append(sf.getType());
\r
1007 if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
\r
1008 text.append(" " + sf.getDescription());
\r
1010 if (sf.getStatus() != null && sf.getStatus().length()>0)
\r
1012 text.append(" (" + sf.getStatus() + ")");
\r
1019 if(text.length()>1)
\r
1021 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1022 out.println(text.toString());
\r
1026 out.println("</map></body></html>");
\r
1030 catch (Exception ex)
\r
1032 ex.printStackTrace();
\r
1034 } ///////////END OF IMAGE MAP
\r
1038 int getWrappedHeight()
\r
1041 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1042 seqPanel.seqCanvas.getWidth());
\r
1044 int hgap = av.charHeight;
\r
1045 if (av.scaleAboveWrapped)
\r
1046 hgap += av.charHeight;
\r
1048 int annotationHeight = 0;
\r
1049 if (av.showAnnotation)
\r
1051 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1054 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1056 + annotationHeight;
\r
1058 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
\r
1066 * @author $author$
\r
1067 * @version $Revision$
\r
1073 * Creates a new Preview object.
\r
1075 * @param image DOCUMENT ME!
\r
1077 public Preview(Image image)
\r
1079 setResizable(true);
\r
1080 setSize(image.getWidth(this), image.getHeight(this));
\r
1082 getContentPane().setLayout(new BorderLayout());
\r
1083 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1092 * @author $author$
\r
1093 * @version $Revision$
\r
1095 class PreviewPanel
\r
1101 * Creates a new PreviewPanel object.
\r
1103 * @param image DOCUMENT ME!
\r
1105 public PreviewPanel(Image image)
\r
1107 this.image = image;
\r
1113 * @param g DOCUMENT ME!
\r
1115 public void paintComponent(Graphics g)
\r
1117 if (image != null)
\r
1119 g.drawImage(image, 0, 0, this);
\r
1123 System.out.println("DEBUG:image is null");
\r