2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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 java.beans.*;
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25 import java.awt.event.*;
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26 import java.awt.print.*;
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27 import javax.swing.*;
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29 import jalview.datamodel.*;
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30 import jalview.jbgui.*;
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31 import jalview.schemes.*;
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37 * @version $Revision$
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39 public class AlignmentPanel
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40 extends GAlignmentPanel implements AdjustmentListener, Printable
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42 public AlignViewport av;
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43 OverviewPanel overviewPanel;
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46 IdwidthAdjuster idwidthAdjuster;
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48 /** DOCUMENT ME!! */
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49 public AlignFrame alignFrame;
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50 ScalePanel scalePanel;
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51 AnnotationPanel annotationPanel;
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52 AnnotationLabels alabels;
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54 // this value is set false when selection area being dragged
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55 boolean fastPaint = true;
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60 * Creates a new AlignmentPanel object.
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62 * @param af DOCUMENT ME!
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63 * @param av DOCUMENT ME!
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65 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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69 seqPanel = new SeqPanel(av, this);
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70 idPanel = new IdPanel(av, this);
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72 scalePanel = new ScalePanel(av, this);
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74 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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75 idwidthAdjuster = new IdwidthAdjuster(this);
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76 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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78 annotationPanel = new AnnotationPanel(this);
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79 alabels = new AnnotationLabels(this);
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81 annotationScroller.setViewportView(annotationPanel);
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82 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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84 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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85 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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87 setScrollValues(0, 0);
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89 setAnnotationVisible(av.getShowAnnotation());
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91 hscroll.addAdjustmentListener(this);
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92 vscroll.addAdjustmentListener(this);
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94 final AlignmentPanel ap = this;
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95 av.addPropertyChangeListener(new PropertyChangeListener()
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97 public void propertyChange(PropertyChangeEvent evt)
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99 if (evt.getPropertyName().equals("alignment"))
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101 PaintRefresher.Refresh(ap,
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102 av.getSequenceSetId(),
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105 alignmentChanged();
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111 adjustAnnotationHeight();
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115 public void alignmentChanged()
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117 av.alignmentChanged(this);
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119 alignFrame.updateEditMenuBar();
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121 paintAlignment(true);
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128 public void fontChanged()
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130 // set idCanvas bufferedImage to null
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131 // to prevent drawing old image
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132 FontMetrics fm = getFontMetrics(av.getFont());
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134 scalePanelHolder.setPreferredSize(new Dimension(10,
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135 av.charHeight + fm.getDescent()));
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136 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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137 av.charHeight + fm.getDescent()));
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139 idPanel.idCanvas.gg = null;
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140 seqPanel.seqCanvas.img = null;
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141 annotationPanel.adjustPanelHeight();
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143 Dimension d = calculateIdWidth();
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144 d.setSize(d.width + 4, d.height);
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145 idPanel.idCanvas.setPreferredSize(d);
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146 hscrollFillerPanel.setPreferredSize(d);
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148 if (overviewPanel != null)
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150 overviewPanel.setBoxPosition();
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159 * @return DOCUMENT ME!
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161 public Dimension calculateIdWidth()
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163 Container c = new Container();
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165 FontMetrics fm = c.getFontMetrics(
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166 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
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168 AlignmentI al = av.getAlignment();
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174 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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176 SequenceI s = al.getSequenceAt(i);
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178 id = s.getDisplayId(av.getShowJVSuffix());
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180 if (fm.stringWidth(id) > idWidth)
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182 idWidth = fm.stringWidth(id);
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188 // Also check annotation label widths
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191 if (al.getAlignmentAnnotation() != null)
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193 fm = c.getFontMetrics(alabels.getFont());
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195 while (i < al.getAlignmentAnnotation().length)
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197 String label = al.getAlignmentAnnotation()[i].label;
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199 if (fm.stringWidth(label) > idWidth)
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201 idWidth = fm.stringWidth(label);
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208 return new Dimension(idWidth, 12);
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214 * @param results DOCUMENT ME!
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216 public void highlightSearchResults(SearchResults results)
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218 seqPanel.seqCanvas.highlightSearchResults(results);
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220 // do we need to scroll the panel?
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221 if (results != null)
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223 SequenceI seq = results.getResultSequence(0);
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224 int seqIndex = av.alignment.findIndex(seq);
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225 int start = seq.findIndex(results.getResultStart(0)) - 1;
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226 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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228 if (!av.wrapAlignment)
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230 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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231 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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233 setScrollValues(start, seqIndex);
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238 scrollToWrappedVisible(start);
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242 paintAlignment(true);
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245 void scrollToWrappedVisible(int res)
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247 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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249 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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251 vscroll.setValue(res / cwidth);
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252 av.startRes = vscroll.getValue() * cwidth;
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259 * @return DOCUMENT ME!
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261 public OverviewPanel getOverviewPanel()
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263 return overviewPanel;
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269 * @param op DOCUMENT ME!
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271 public void setOverviewPanel(OverviewPanel op)
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273 overviewPanel = op;
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279 * @param b DOCUMENT ME!
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281 public void setAnnotationVisible(boolean b)
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283 if (!av.wrapAlignment)
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285 annotationSpaceFillerHolder.setVisible(b);
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286 annotationScroller.setVisible(b);
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291 public void adjustAnnotationHeight()
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293 if (alignFrame.getHeight() == 0)
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295 System.out.println("NEEDS FIXING");
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298 int height = annotationPanel.adjustPanelHeight();
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300 if (hscroll.isVisible())
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302 height += hscroll.getPreferredSize().height;
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304 if (height > alignFrame.getHeight() / 2)
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306 height = alignFrame.getHeight() / 2;
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309 hscroll.addNotify();
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311 annotationScroller.setPreferredSize(
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312 new Dimension(annotationScroller.getWidth(), height));
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315 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
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316 annotationSpaceFillerHolder.getWidth(),
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325 * @param wrap DOCUMENT ME!
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327 public void setWrapAlignment(boolean wrap)
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330 scalePanelHolder.setVisible(!wrap);
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331 hscroll.setVisible(!wrap);
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332 idwidthAdjuster.setVisible(!wrap);
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336 annotationScroller.setVisible(false);
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337 annotationSpaceFillerHolder.setVisible(false);
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339 else if (av.showAnnotation)
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341 annotationScroller.setVisible(true);
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342 annotationSpaceFillerHolder.setVisible(true);
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345 idSpaceFillerPanel1.setVisible(!wrap);
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350 // return value is true if the scroll is valid
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351 public boolean scrollUp(boolean up)
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355 if (vscroll.getValue() < 1)
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361 vscroll.setValue(vscroll.getValue() - 1);
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365 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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371 vscroll.setValue(vscroll.getValue() + 1);
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382 * @param right DOCUMENT ME!
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384 * @return DOCUMENT ME!
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386 public boolean scrollRight(boolean right)
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390 if (hscroll.getValue() < 1)
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396 hscroll.setValue(hscroll.getValue() - 1);
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400 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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406 hscroll.setValue(hscroll.getValue() + 1);
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417 * @param x DOCUMENT ME!
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418 * @param y DOCUMENT ME!
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420 public void setScrollValues(int x, int y)
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423 int width = av.alignment.getWidth();
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424 int height = av.alignment.getHeight();
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426 if (av.hasHiddenColumns)
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428 width = av.getColumnSelection().findColumnPosition(width);
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431 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
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433 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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434 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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436 if (hextent > width)
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441 if (vextent > height)
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446 if ( (hextent + x) > width)
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448 x = width - hextent;
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451 if ( (vextent + y) > height)
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453 y = height - vextent;
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466 hscroll.setValues(x, hextent, 0, width);
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467 vscroll.setValues(y, vextent, 0, height);
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473 * @param evt DOCUMENT ME!
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475 public void adjustmentValueChanged(AdjustmentEvent evt)
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478 int oldX = av.getStartRes();
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479 int oldY = av.getStartSeq();
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481 if (evt.getSource() == hscroll)
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483 int x = hscroll.getValue();
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486 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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489 if (evt.getSource() == vscroll)
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491 int offy = vscroll.getValue();
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493 if (av.getWrapAlignment())
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497 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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498 seqCanvas.getWidth());
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499 av.setStartRes(offy * rowSize);
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500 av.setEndRes( (offy + 1) * rowSize);
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504 //This is only called if file loaded is a jar file that
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505 //was wrapped when saved and user has wrap alignment true
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506 //as preference setting
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507 SwingUtilities.invokeLater(new Runnable()
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511 setScrollValues(av.getStartRes(), av.getStartSeq());
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518 av.setStartSeq(offy);
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519 av.setEndSeq(offy +
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520 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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524 if (overviewPanel != null)
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526 overviewPanel.setBoxPosition();
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529 int scrollX = av.startRes - oldX;
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530 int scrollY = av.startSeq - oldY;
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532 if (av.getWrapAlignment() || !fastPaint)
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538 // Make sure we're not trying to draw a panel
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539 // larger than the visible window
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540 if (scrollX > av.endRes - av.startRes)
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542 scrollX = av.endRes - av.startRes;
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544 else if (scrollX < av.startRes - av.endRes)
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546 scrollX = av.startRes - av.endRes;
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549 if (scrollX != 0 || scrollY != 0)
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551 idPanel.idCanvas.fastPaint(scrollY);
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552 seqPanel.seqCanvas.fastPaint(scrollX,
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554 scalePanel.repaint();
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556 if (av.getShowAnnotation())
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558 annotationPanel.fastPaint(scrollX);
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564 public void paintAlignment(boolean updateOverview)
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570 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
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571 .sequenceColoursChanged(this);
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573 if (overviewPanel != null)
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575 overviewPanel.updateOverviewImage();
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583 * @param g DOCUMENT ME!
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585 public void paintComponent(Graphics g)
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589 Dimension d = idPanel.idCanvas.getPreferredSize();
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590 idPanelHolder.setPreferredSize(d);
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591 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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594 if (av.getWrapAlignment())
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596 int maxwidth = av.alignment.getWidth();
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598 if (av.hasHiddenColumns)
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600 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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603 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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604 seqCanvas.getWidth());
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605 if (canvasWidth > 0)
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607 int max = maxwidth /
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608 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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611 vscroll.setMaximum(max);
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612 vscroll.setUnitIncrement(1);
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613 vscroll.setVisibleAmount(1);
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618 setScrollValues(av.getStartRes(), av.getStartSeq());
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625 * @param pg DOCUMENT ME!
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626 * @param pf DOCUMENT ME!
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627 * @param pi DOCUMENT ME!
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629 * @return DOCUMENT ME!
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631 * @throws PrinterException DOCUMENT ME!
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633 public int print(Graphics pg, PageFormat pf, int pi)
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634 throws PrinterException
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636 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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638 int pwidth = (int) pf.getImageableWidth();
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639 int pheight = (int) pf.getImageableHeight();
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641 if (av.getWrapAlignment())
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643 return printWrappedAlignment(pg, pwidth, pheight, pi);
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647 return printUnwrapped(pg, pwidth, pheight, pi);
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654 * @param pg DOCUMENT ME!
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655 * @param pwidth DOCUMENT ME!
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656 * @param pheight DOCUMENT ME!
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657 * @param pi DOCUMENT ME!
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659 * @return DOCUMENT ME!
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661 * @throws PrinterException DOCUMENT ME!
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663 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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664 throws PrinterException
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666 int idWidth = getVisibleIdWidth();
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667 FontMetrics fm = getFontMetrics(av.getFont());
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668 int scaleHeight = av.charHeight + fm.getDescent();
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670 pg.setColor(Color.white);
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671 pg.fillRect(0, 0, pwidth, pheight);
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672 pg.setFont(av.getFont());
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674 ////////////////////////////////////
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675 /// How many sequences and residues can we fit on a printable page?
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676 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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678 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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681 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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683 /////////////////////////////
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684 /// Only print these sequences and residues on this page
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687 /////////////////////////////
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688 /// Only print these sequences and residues on this page
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691 /////////////////////////////
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692 /// Only print these sequences and residues on this page
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695 /////////////////////////////
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696 /// Only print these sequences and residues on this page
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698 startRes = (pi % pagesWide) * totalRes;
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699 endRes = (startRes + totalRes) - 1;
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701 if (endRes > (av.getAlignment().getWidth() - 1))
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703 endRes = av.getAlignment().getWidth() - 1;
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706 startSeq = (pi / pagesWide) * totalSeq;
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707 endSeq = startSeq + totalSeq;
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709 if (endSeq > av.getAlignment().getHeight())
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711 endSeq = av.getAlignment().getHeight();
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714 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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716 if (av.showAnnotation)
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718 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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721 pagesHigh /= pheight;
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723 if (pi >= (pagesWide * pagesHigh))
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725 return Printable.NO_SUCH_PAGE;
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729 pg.translate(idWidth, 0);
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730 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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731 pg.translate( -idWidth, scaleHeight);
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735 Color currentColor = null;
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736 Color currentTextColor = null;
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738 pg.setFont(idPanel.idCanvas.idfont);
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741 for (int i = startSeq; i < endSeq; i++)
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743 seq = av.getAlignment().getSequenceAt(i);
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744 if ( (av.getSelectionGroup() != null) &&
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745 av.getSelectionGroup().getSequences(null).contains(seq))
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747 currentColor = Color.gray;
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748 currentTextColor = Color.black;
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752 currentColor = av.getSequenceColour(seq);
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753 currentTextColor = Color.black;
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756 pg.setColor(currentColor);
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757 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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758 av.getCharHeight());
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760 pg.setColor(currentTextColor);
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763 if (av.rightAlignIds)
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765 fm = pg.getFontMetrics();
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766 xPos = idWidth - fm.stringWidth(
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767 seq.getDisplayId(av.getShowJVSuffix())
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771 pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
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773 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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774 (av.getCharHeight() / 5));
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777 pg.setFont(av.getFont());
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779 // draw main sequence panel
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780 pg.translate(idWidth, 0);
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781 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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783 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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785 pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
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786 alabels.drawComponent( (Graphics2D) pg, idWidth);
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787 pg.translate(idWidth + 3, 0);
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788 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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792 return Printable.PAGE_EXISTS;
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798 * @param pg DOCUMENT ME!
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799 * @param pwidth DOCUMENT ME!
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800 * @param pheight DOCUMENT ME!
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801 * @param pi DOCUMENT ME!
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803 * @return DOCUMENT ME!
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805 * @throws PrinterException DOCUMENT ME!
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807 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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809 throws PrinterException
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812 int annotationHeight = 0;
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813 AnnotationLabels labels = null;
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814 if (av.showAnnotation)
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816 annotationHeight = annotationPanel.adjustPanelHeight();
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817 labels = new AnnotationLabels(av);
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820 int hgap = av.charHeight;
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821 if (av.scaleAboveWrapped)
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823 hgap += av.charHeight;
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826 int cHeight = av.getAlignment().getHeight() * av.charHeight
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828 + annotationHeight;
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830 int idWidth = getVisibleIdWidth();
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832 int maxwidth = av.alignment.getWidth();
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833 if (av.hasHiddenColumns)
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835 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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838 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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841 int totalHeight = cHeight * (maxwidth / resWidth + 1);
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843 pg.setColor(Color.white);
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844 pg.fillRect(0, 0, pwidth, pheight);
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845 pg.setFont(av.getFont());
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849 pg.setColor(Color.black);
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851 pg.translate(0, -pi * pheight);
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853 pg.setClip(0, pi * pheight, pwidth, pheight);
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859 for (int i = 0; i < av.alignment.getHeight(); i++)
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861 pg.setFont(idPanel.idCanvas.idfont);
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862 SequenceI s = av.alignment.getSequenceAt(i);
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863 String string = s.getDisplayId(av.getShowJVSuffix());
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865 if (av.rightAlignIds)
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867 FontMetrics fm = pg.getFontMetrics();
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868 xPos = idWidth - fm.stringWidth(string) - 4;
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870 pg.drawString(string, xPos,
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871 ( (i * av.charHeight) + ypos + av.charHeight) -
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872 (av.charHeight / 5));
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874 if (labels != null)
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878 (av.getAlignment().getHeight() * av.charHeight));
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880 pg.setFont(av.getFont());
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881 labels.drawComponent(pg, idWidth);
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884 (av.getAlignment().getHeight() * av.charHeight));
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889 while (ypos < totalHeight);
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891 pg.translate(idWidth, 0);
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893 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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895 if ( (pi * pheight) < totalHeight)
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897 return Printable.PAGE_EXISTS;
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902 return Printable.NO_SUCH_PAGE;
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906 int getVisibleIdWidth()
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909 idPanel.getWidth() > 0 ? idPanel.getWidth() :
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910 calculateIdWidth().width + 4;
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913 void makeAlignmentImage(int type, File file)
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915 int maxwidth = av.alignment.getWidth();
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916 if (av.hasHiddenColumns)
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918 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
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921 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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922 int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
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924 if (av.getWrapAlignment())
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926 height = getWrappedHeight();
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927 if (System.getProperty("java.awt.headless") != null
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928 && System.getProperty("java.awt.headless").equals("true"))
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930 width = alignFrame.getWidth()
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931 - vscroll.getPreferredSize().width
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932 - alignFrame.getInsets().left
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933 - alignFrame.getInsets().right;
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937 width = seqPanel.getWidth() + getVisibleIdWidth();
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941 else if (av.getShowAnnotation())
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943 height += annotationPanel.adjustPanelHeight() + 3;
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949 jalview.util.ImageMaker im;
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950 if (type == jalview.util.ImageMaker.PNG)
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952 im = new jalview.util.ImageMaker(this,
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953 jalview.util.ImageMaker.PNG,
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954 "Create PNG image from alignment",
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955 width, height, file, null);
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959 im = new jalview.util.ImageMaker(this,
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960 jalview.util.ImageMaker.EPS,
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961 "Create EPS file from alignment",
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962 width, height, file,
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963 alignFrame.getTitle());
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966 if (av.getWrapAlignment())
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968 if (im.getGraphics() != null)
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970 printWrappedAlignment(im.getGraphics(), width, height, 0);
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976 if (im.getGraphics() != null)
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978 printUnwrapped(im.getGraphics(), width, height, 0);
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983 catch (OutOfMemoryError err)
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985 System.out.println("########################\n"
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986 + "OUT OF MEMORY " + file + "\n"
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987 + "########################");
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989 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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990 "Out of Memory Creating Image!!"
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992 "\nSee help files for increasing Java Virtual Machine memory."
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994 JOptionPane.WARNING_MESSAGE);
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995 System.out.println("Create IMAGE: " + err);
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999 catch (Exception ex)
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1001 ex.printStackTrace();
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1008 public void makeEPS(File epsFile)
\r
1010 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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1016 public void makePNG(File pngFile)
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1018 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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1021 public void makePNGImageMap(File imgMapFile, String imageName)
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1023 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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1024 //////////////////////////////////////////////
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1025 int idWidth = getVisibleIdWidth();
\r
1026 FontMetrics fm = getFontMetrics(av.getFont());
\r
1027 int scaleHeight = av.charHeight + fm.getDescent();
\r
1030 //////////////////////////////////
\r
1031 if (imgMapFile != null)
\r
1035 int s, sSize = av.alignment.getHeight(),
\r
1036 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1037 StringBuffer text = new StringBuffer();
\r
1038 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1039 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1040 out.println("<img src=\"" + imageName +
\r
1041 "\" border=\"0\" usemap=\"#Map\" >"
\r
1042 + "<map name=\"Map\">");
\r
1044 for (s = 0; s < sSize; s++)
\r
1046 sy = s * av.charHeight + scaleHeight;
\r
1048 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1049 SequenceFeature[] features = seq.getDatasetSequence().
\r
1050 getSequenceFeatures();
\r
1051 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1052 for (res = 0; res < alwidth; res++)
\r
1054 text = new StringBuffer();
\r
1055 Object obj = null;
\r
1056 if (av.alignment.isNucleotide())
\r
1058 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
\r
1063 obj = ResidueProperties.aa2Triplet.get(
\r
1064 seq.getCharAt(res) + "");
\r
1072 String triplet = obj.toString();
\r
1073 int alIndex = seq.findPosition(res);
\r
1074 gSize = groups.length;
\r
1075 for (g = 0; g < gSize; g++)
\r
1077 if (text.length() < 1)
\r
1079 text.append("<area shape=\"rect\" coords=\""
\r
1080 + (idWidth + res * av.charWidth) + ","
\r
1082 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1083 + (av.charHeight + sy) + "\""
\r
1084 + " onMouseOver=\"toolTip('"
\r
1085 + alIndex + " " + triplet);
\r
1088 if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
\r
1090 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1094 if (features != null)
\r
1096 if (text.length() < 1)
\r
1098 text.append("<area shape=\"rect\" coords=\""
\r
1099 + (idWidth + res * av.charWidth) + ","
\r
1101 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1102 + (av.charHeight + sy) + "\""
\r
1103 + " onMouseOver=\"toolTip('"
\r
1104 + alIndex + " " + triplet);
\r
1106 fSize = features.length;
\r
1107 for (f = 0; f < fSize; f++)
\r
1110 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1111 (features[f].getEnd() >= seq.findPosition(res)))
\r
1113 if (features[f].getType().equals("disulfide bond"))
\r
1115 if (features[f].getBegin() == seq.findPosition(res)
\r
1116 || features[f].getEnd() == seq.findPosition(res))
\r
1118 text.append("<br>disulfide bond " + features[f].getBegin() +
\r
1120 features[f].getEnd());
\r
1125 text.append("<br>");
\r
1126 text.append(features[f].getType());
\r
1127 if (features[f].getDescription() != null &&
\r
1129 getType().equals(features[f].getDescription()))
\r
1131 text.append(" " + features[f].getDescription());
\r
1134 if (features[f].getValue("status") != null)
\r
1136 text.append(" (" + features[f].getValue("status") + ")");
\r
1143 if (text.length() > 1)
\r
1145 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1146 out.println(text.toString());
\r
1150 out.println("</map></body></html>");
\r
1154 catch (Exception ex)
\r
1156 ex.printStackTrace();
\r
1158 } ///////////END OF IMAGE MAP
\r
1162 int getWrappedHeight()
\r
1164 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1166 if (System.getProperty("java.awt.headless") != null
\r
1167 && System.getProperty("java.awt.headless").equals("true"))
\r
1169 seqPanelWidth = alignFrame.getWidth()
\r
1170 - getVisibleIdWidth()
\r
1171 - vscroll.getPreferredSize().width
\r
1172 - alignFrame.getInsets().left
\r
1173 - alignFrame.getInsets().right;
\r
1176 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1180 int hgap = av.charHeight;
\r
1181 if (av.scaleAboveWrapped)
\r
1183 hgap += av.charHeight;
\r
1186 int annotationHeight = 0;
\r
1187 if (av.showAnnotation)
\r
1189 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1192 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1194 + annotationHeight;
\r
1196 int maxwidth = av.alignment.getWidth();
\r
1197 if (av.hasHiddenColumns)
\r
1199 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1202 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r