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 if (overviewPanel != null)
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121 overviewPanel.updateOverviewImage();
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124 alignFrame.updateEditMenuBar();
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132 public void fontChanged()
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134 // set idCanvas bufferedImage to null
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135 // to prevent drawing old image
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136 FontMetrics fm = getFontMetrics(av.getFont());
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138 scalePanelHolder.setPreferredSize(new Dimension(10,
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139 av.charHeight + fm.getDescent()));
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140 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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141 av.charHeight + fm.getDescent()));
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143 idPanel.idCanvas.gg = null;
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144 seqPanel.seqCanvas.img = null;
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145 annotationPanel.adjustPanelHeight();
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147 Dimension d = calculateIdWidth();
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148 d.setSize(d.width + 4, d.height);
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149 idPanel.idCanvas.setPreferredSize(d);
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150 hscrollFillerPanel.setPreferredSize(d);
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152 if (overviewPanel != null)
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154 overviewPanel.setBoxPosition();
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163 * @return DOCUMENT ME!
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165 public Dimension calculateIdWidth()
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167 Container c = new Container();
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169 FontMetrics fm = c.getFontMetrics(
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170 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
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172 AlignmentI al = av.getAlignment();
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178 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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180 SequenceI s = al.getSequenceAt(i);
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182 id = s.getDisplayId(av.getShowJVSuffix());
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184 if (fm.stringWidth(id) > idWidth)
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186 idWidth = fm.stringWidth(id);
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192 // Also check annotation label widths
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195 if (al.getAlignmentAnnotation() != null)
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197 fm = c.getFontMetrics(alabels.getFont());
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199 while (i < al.getAlignmentAnnotation().length)
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201 String label = al.getAlignmentAnnotation()[i].label;
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203 if (fm.stringWidth(label) > idWidth)
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205 idWidth = fm.stringWidth(label);
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212 return new Dimension(idWidth, 12);
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218 * @param results DOCUMENT ME!
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220 public void highlightSearchResults(SearchResults results)
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222 seqPanel.seqCanvas.highlightSearchResults(results);
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224 // do we need to scroll the panel?
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225 if (results != null)
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227 SequenceI seq = results.getResultSequence(0);
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228 int seqIndex = av.alignment.findIndex(seq);
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229 int start = seq.findIndex(results.getResultStart(0)) - 1;
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230 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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232 if (!av.wrapAlignment)
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234 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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235 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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237 setScrollValues(start, seqIndex);
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242 scrollToWrappedVisible(start);
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246 paintAlignment(true);
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249 void scrollToWrappedVisible(int res)
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251 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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253 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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255 vscroll.setValue(res / cwidth);
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256 av.startRes = vscroll.getValue() * cwidth;
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263 * @return DOCUMENT ME!
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265 public OverviewPanel getOverviewPanel()
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267 return overviewPanel;
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273 * @param op DOCUMENT ME!
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275 public void setOverviewPanel(OverviewPanel op)
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277 overviewPanel = op;
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283 * @param b DOCUMENT ME!
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285 public void setAnnotationVisible(boolean b)
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287 if (!av.wrapAlignment)
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289 annotationSpaceFillerHolder.setVisible(b);
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290 annotationScroller.setVisible(b);
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295 public void adjustAnnotationHeight()
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297 if (alignFrame.getHeight() == 0)
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299 System.out.println("NEEDS FIXING");
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302 int height = annotationPanel.adjustPanelHeight() +
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303 hscroll.getPreferredSize().height;
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305 if (height > alignFrame.getHeight() / 2)
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307 height = alignFrame.getHeight() / 2;
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310 hscroll.addNotify();
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312 annotationScroller.setPreferredSize(
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313 new Dimension(annotationScroller.getWidth(),
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314 height + hscroll.getHeight()));
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317 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
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318 annotationSpaceFillerHolder.getWidth(),
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327 * @param wrap DOCUMENT ME!
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329 public void setWrapAlignment(boolean wrap)
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332 scalePanelHolder.setVisible(!wrap);
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333 hscroll.setVisible(!wrap);
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334 idwidthAdjuster.setVisible(!wrap);
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338 annotationScroller.setVisible(false);
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339 annotationSpaceFillerHolder.setVisible(false);
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341 else if (av.showAnnotation)
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343 annotationScroller.setVisible(true);
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344 annotationSpaceFillerHolder.setVisible(true);
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347 idSpaceFillerPanel1.setVisible(!wrap);
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352 // return value is true if the scroll is valid
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353 public boolean scrollUp(boolean up)
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357 if (vscroll.getValue() < 1)
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363 vscroll.setValue(vscroll.getValue() - 1);
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367 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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373 vscroll.setValue(vscroll.getValue() + 1);
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384 * @param right DOCUMENT ME!
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386 * @return DOCUMENT ME!
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388 public boolean scrollRight(boolean right)
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392 if (hscroll.getValue() < 1)
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398 hscroll.setValue(hscroll.getValue() - 1);
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402 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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408 hscroll.setValue(hscroll.getValue() + 1);
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419 * @param x DOCUMENT ME!
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420 * @param y DOCUMENT ME!
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422 public void setScrollValues(int x, int y)
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425 int width = av.alignment.getWidth();
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426 int height = av.alignment.getHeight();
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428 if (av.hasHiddenColumns)
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430 width = av.getColumnSelection().findColumnPosition(width);
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433 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
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435 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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436 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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438 if (hextent > width)
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443 if (vextent > height)
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448 if ( (hextent + x) > width)
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450 x = width - hextent;
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453 if ( (vextent + y) > height)
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455 y = height - vextent;
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468 hscroll.setValues(x, hextent, 0, width);
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469 vscroll.setValues(y, vextent, 0, height);
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475 * @param evt DOCUMENT ME!
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477 public void adjustmentValueChanged(AdjustmentEvent evt)
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480 int oldX = av.getStartRes();
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481 int oldY = av.getStartSeq();
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483 if (evt.getSource() == hscroll)
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485 int x = hscroll.getValue();
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488 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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491 if (evt.getSource() == vscroll)
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493 int offy = vscroll.getValue();
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495 if (av.getWrapAlignment())
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499 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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500 seqCanvas.getWidth());
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501 av.setStartRes(offy * rowSize);
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502 av.setEndRes( (offy + 1) * rowSize);
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506 //This is only called if file loaded is a jar file that
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507 //was wrapped when saved and user has wrap alignment true
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508 //as preference setting
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509 SwingUtilities.invokeLater(new Runnable()
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513 setScrollValues(av.getStartRes(), av.getStartSeq());
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520 av.setStartSeq(offy);
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521 av.setEndSeq(offy +
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522 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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526 if (overviewPanel != null)
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528 overviewPanel.setBoxPosition();
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531 int scrollX = av.startRes - oldX;
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532 int scrollY = av.startSeq - oldY;
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534 if (av.getWrapAlignment() || !fastPaint)
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540 // Make sure we're not trying to draw a panel
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541 // larger than the visible window
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542 if (scrollX > av.endRes - av.startRes)
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544 scrollX = av.endRes - av.startRes;
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546 else if (scrollX < av.startRes - av.endRes)
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548 scrollX = av.startRes - av.endRes;
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551 if (scrollX != 0 || scrollY != 0)
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553 idPanel.idCanvas.fastPaint(scrollY);
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554 seqPanel.seqCanvas.fastPaint(scrollX,
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556 scalePanel.repaint();
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558 if (av.getShowAnnotation())
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560 annotationPanel.fastPaint(scrollX);
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566 public void paintAlignment(boolean updateOverview)
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572 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
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573 .sequenceColoursChanged(this);
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575 if (overviewPanel != null)
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577 overviewPanel.updateOverviewImage();
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585 * @param g DOCUMENT ME!
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587 public void paintComponent(Graphics g)
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591 Dimension d = idPanel.idCanvas.getPreferredSize();
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592 idPanelHolder.setPreferredSize(d);
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593 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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596 if (av.getWrapAlignment())
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598 int maxwidth = av.alignment.getWidth();
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600 if (av.hasHiddenColumns)
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602 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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605 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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606 seqCanvas.getWidth());
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607 if (canvasWidth > 0)
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609 int max = maxwidth /
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610 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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613 vscroll.setMaximum(max);
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614 vscroll.setUnitIncrement(1);
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615 vscroll.setVisibleAmount(1);
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620 setScrollValues(av.getStartRes(), av.getStartSeq());
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627 * @param pg DOCUMENT ME!
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628 * @param pf DOCUMENT ME!
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629 * @param pi DOCUMENT ME!
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631 * @return DOCUMENT ME!
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633 * @throws PrinterException DOCUMENT ME!
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635 public int print(Graphics pg, PageFormat pf, int pi)
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636 throws PrinterException
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638 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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640 int pwidth = (int) pf.getImageableWidth();
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641 int pheight = (int) pf.getImageableHeight();
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643 if (av.getWrapAlignment())
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645 return printWrappedAlignment(pg, pwidth, pheight, pi);
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649 return printUnwrapped(pg, pwidth, pheight, pi);
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656 * @param pg DOCUMENT ME!
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657 * @param pwidth DOCUMENT ME!
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658 * @param pheight DOCUMENT ME!
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659 * @param pi DOCUMENT ME!
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661 * @return DOCUMENT ME!
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663 * @throws PrinterException DOCUMENT ME!
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665 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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666 throws PrinterException
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668 int idWidth = getVisibleIdWidth();
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669 FontMetrics fm = getFontMetrics(av.getFont());
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670 int scaleHeight = av.charHeight + fm.getDescent();
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672 pg.setColor(Color.white);
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673 pg.fillRect(0, 0, pwidth, pheight);
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674 pg.setFont(av.getFont());
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676 ////////////////////////////////////
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677 /// How many sequences and residues can we fit on a printable page?
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678 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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680 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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683 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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685 /////////////////////////////
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686 /// Only print these sequences and residues on this page
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689 /////////////////////////////
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690 /// Only print these sequences and residues on this page
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693 /////////////////////////////
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694 /// Only print these sequences and residues on this page
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697 /////////////////////////////
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698 /// Only print these sequences and residues on this page
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700 startRes = (pi % pagesWide) * totalRes;
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701 endRes = (startRes + totalRes) - 1;
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703 if (endRes > (av.getAlignment().getWidth() - 1))
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705 endRes = av.getAlignment().getWidth() - 1;
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708 startSeq = (pi / pagesWide) * totalSeq;
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709 endSeq = startSeq + totalSeq;
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711 if (endSeq > av.getAlignment().getHeight())
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713 endSeq = av.getAlignment().getHeight();
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716 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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718 if (av.showAnnotation)
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720 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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723 pagesHigh /= pheight;
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725 if (pi >= (pagesWide * pagesHigh))
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727 return Printable.NO_SUCH_PAGE;
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731 pg.translate(idWidth, 0);
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732 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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733 pg.translate( -idWidth, scaleHeight);
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737 Color currentColor = null;
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738 Color currentTextColor = null;
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740 pg.setFont(idPanel.idCanvas.idfont);
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743 for (int i = startSeq; i < endSeq; i++)
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745 seq = av.getAlignment().getSequenceAt(i);
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746 if ( (av.getSelectionGroup() != null) &&
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747 av.getSelectionGroup().getSequences(null).contains(seq))
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749 currentColor = Color.gray;
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750 currentTextColor = Color.black;
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754 currentColor = av.getSequenceColour(seq);
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755 currentTextColor = Color.black;
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758 pg.setColor(currentColor);
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759 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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760 av.getCharHeight());
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762 pg.setColor(currentTextColor);
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765 if (av.rightAlignIds)
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767 fm = pg.getFontMetrics();
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768 xPos = idWidth - fm.stringWidth(
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769 seq.getDisplayId(av.getShowJVSuffix())
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773 pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
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775 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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776 (av.getCharHeight() / 5));
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779 pg.setFont(av.getFont());
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781 // draw main sequence panel
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782 pg.translate(idWidth, 0);
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783 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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785 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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787 pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
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788 alabels.drawComponent( (Graphics2D) pg, idWidth);
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789 pg.translate(idWidth + 3, 0);
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790 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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794 return Printable.PAGE_EXISTS;
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800 * @param pg DOCUMENT ME!
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801 * @param pwidth DOCUMENT ME!
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802 * @param pheight DOCUMENT ME!
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803 * @param pi DOCUMENT ME!
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805 * @return DOCUMENT ME!
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807 * @throws PrinterException DOCUMENT ME!
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809 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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811 throws PrinterException
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814 int annotationHeight = 0;
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815 AnnotationLabels labels = null;
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816 if (av.showAnnotation)
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818 annotationHeight = annotationPanel.adjustPanelHeight();
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819 labels = new AnnotationLabels(av);
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822 int hgap = av.charHeight;
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823 if (av.scaleAboveWrapped)
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825 hgap += av.charHeight;
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828 int cHeight = av.getAlignment().getHeight() * av.charHeight
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830 + annotationHeight;
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832 int idWidth = getVisibleIdWidth();
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834 int maxwidth = av.alignment.getWidth();
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835 if (av.hasHiddenColumns)
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837 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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840 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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843 int totalHeight = cHeight * (maxwidth / resWidth + 1);
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845 pg.setColor(Color.white);
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846 pg.fillRect(0, 0, pwidth, pheight);
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847 pg.setFont(av.getFont());
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851 pg.setColor(Color.black);
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853 pg.translate(0, -pi * pheight);
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855 pg.setClip(0, pi * pheight, pwidth, pheight);
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861 for (int i = 0; i < av.alignment.getHeight(); i++)
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863 pg.setFont(idPanel.idCanvas.idfont);
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864 SequenceI s = av.alignment.getSequenceAt(i);
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865 String string = s.getDisplayId(av.getShowJVSuffix());
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867 if (av.rightAlignIds)
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869 FontMetrics fm = pg.getFontMetrics();
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870 xPos = idWidth - fm.stringWidth(string) - 4;
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872 pg.drawString(string, xPos,
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873 ( (i * av.charHeight) + ypos + av.charHeight) -
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874 (av.charHeight / 5));
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876 if (labels != null)
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880 (av.getAlignment().getHeight() * av.charHeight));
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882 pg.setFont(av.getFont());
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883 labels.drawComponent(pg, idWidth);
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886 (av.getAlignment().getHeight() * av.charHeight));
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891 while (ypos < totalHeight);
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893 pg.translate(idWidth, 0);
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895 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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897 if ( (pi * pheight) < totalHeight)
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899 return Printable.PAGE_EXISTS;
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904 return Printable.NO_SUCH_PAGE;
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908 int getVisibleIdWidth()
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911 idPanel.getWidth() > 0 ? idPanel.getWidth() :
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912 calculateIdWidth().width + 4;
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915 void makeAlignmentImage(int type, File file)
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917 int maxwidth = av.alignment.getWidth();
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918 if (av.hasHiddenColumns)
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920 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
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923 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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924 int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
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926 if (av.getWrapAlignment())
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928 height = getWrappedHeight();
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929 if (System.getProperty("java.awt.headless") != null
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930 && System.getProperty("java.awt.headless").equals("true"))
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932 width = alignFrame.getWidth()
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933 - vscroll.getPreferredSize().width
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934 - alignFrame.getInsets().left
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935 - alignFrame.getInsets().right;
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939 width = seqPanel.getWidth() + getVisibleIdWidth();
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943 else if (av.getShowAnnotation())
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945 height += annotationPanel.adjustPanelHeight() + 3;
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951 jalview.util.ImageMaker im;
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952 if (type == jalview.util.ImageMaker.PNG)
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954 im = new jalview.util.ImageMaker(this,
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955 jalview.util.ImageMaker.PNG,
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956 "Create PNG image from alignment",
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957 width, height, file, null);
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961 im = new jalview.util.ImageMaker(this,
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962 jalview.util.ImageMaker.EPS,
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963 "Create EPS file from alignment",
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964 width, height, file,
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965 alignFrame.getTitle());
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968 if (av.getWrapAlignment())
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970 if (im.getGraphics() != null)
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972 printWrappedAlignment(im.getGraphics(), width, height, 0);
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978 if (im.getGraphics() != null)
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980 printUnwrapped(im.getGraphics(), width, height, 0);
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985 catch (OutOfMemoryError err)
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987 System.out.println("########################\n"
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988 + "OUT OF MEMORY " + file + "\n"
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989 + "########################");
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991 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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992 "Out of Memory Creating Image!!"
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994 "\nSee help files for increasing Java Virtual Machine memory."
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996 JOptionPane.WARNING_MESSAGE);
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997 System.out.println("Create IMAGE: " + err);
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1001 catch (Exception ex)
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1003 ex.printStackTrace();
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1010 public void makeEPS(File epsFile)
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1012 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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1018 public void makePNG(File pngFile)
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1020 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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1023 public void makePNGImageMap(File imgMapFile, String imageName)
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1025 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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1026 //////////////////////////////////////////////
\r
1027 int idWidth = getVisibleIdWidth();
\r
1028 FontMetrics fm = getFontMetrics(av.getFont());
\r
1029 int scaleHeight = av.charHeight + fm.getDescent();
\r
1032 //////////////////////////////////
\r
1033 if (imgMapFile != null)
\r
1037 int s, sSize = av.alignment.getHeight(),
\r
1038 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1039 StringBuffer text = new StringBuffer();
\r
1040 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1041 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1042 out.println("<img src=\"" + imageName +
\r
1043 "\" border=\"0\" usemap=\"#Map\" >"
\r
1044 + "<map name=\"Map\">");
\r
1046 for (s = 0; s < sSize; s++)
\r
1048 sy = s * av.charHeight + scaleHeight;
\r
1050 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1051 SequenceFeature[] features = seq.getDatasetSequence().
\r
1052 getSequenceFeatures();
\r
1053 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1054 for (res = 0; res < alwidth; res++)
\r
1056 text = new StringBuffer();
\r
1057 Object obj = null;
\r
1058 if (av.alignment.isNucleotide())
\r
1060 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
\r
1065 obj = ResidueProperties.aa2Triplet.get(
\r
1066 seq.getCharAt(res) + "");
\r
1074 String triplet = obj.toString();
\r
1075 int alIndex = seq.findPosition(res);
\r
1076 gSize = groups.length;
\r
1077 for (g = 0; g < gSize; g++)
\r
1079 if (text.length() < 1)
\r
1081 text.append("<area shape=\"rect\" coords=\""
\r
1082 + (idWidth + res * av.charWidth) + ","
\r
1084 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1085 + (av.charHeight + sy) + "\""
\r
1086 + " onMouseOver=\"toolTip('"
\r
1087 + alIndex + " " + triplet);
\r
1090 if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
\r
1092 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1096 if (features != null)
\r
1098 if (text.length() < 1)
\r
1100 text.append("<area shape=\"rect\" coords=\""
\r
1101 + (idWidth + res * av.charWidth) + ","
\r
1103 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1104 + (av.charHeight + sy) + "\""
\r
1105 + " onMouseOver=\"toolTip('"
\r
1106 + alIndex + " " + triplet);
\r
1108 fSize = features.length;
\r
1109 for (f = 0; f < fSize; f++)
\r
1112 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1113 (features[f].getEnd() >= seq.findPosition(res)))
\r
1115 if (features[f].getType().equals("disulfide bond"))
\r
1117 if (features[f].getBegin() == seq.findPosition(res)
\r
1118 || features[f].getEnd() == seq.findPosition(res))
\r
1120 text.append("<br>disulfide bond " + features[f].getBegin() +
\r
1122 features[f].getEnd());
\r
1127 text.append("<br>");
\r
1128 text.append(features[f].getType());
\r
1129 if (features[f].getDescription() != null &&
\r
1131 getType().equals(features[f].getDescription()))
\r
1133 text.append(" " + features[f].getDescription());
\r
1136 if (features[f].getValue("status") != null)
\r
1138 text.append(" (" + features[f].getValue("status") + ")");
\r
1145 if (text.length() > 1)
\r
1147 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1148 out.println(text.toString());
\r
1152 out.println("</map></body></html>");
\r
1156 catch (Exception ex)
\r
1158 ex.printStackTrace();
\r
1160 } ///////////END OF IMAGE MAP
\r
1164 int getWrappedHeight()
\r
1166 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1168 if (System.getProperty("java.awt.headless") != null
\r
1169 && System.getProperty("java.awt.headless").equals("true"))
\r
1171 seqPanelWidth = alignFrame.getWidth()
\r
1172 - getVisibleIdWidth()
\r
1173 - vscroll.getPreferredSize().width
\r
1174 - alignFrame.getInsets().left
\r
1175 - alignFrame.getInsets().right;
\r
1178 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1182 int hgap = av.charHeight;
\r
1183 if (av.scaleAboveWrapped)
\r
1185 hgap += av.charHeight;
\r
1188 int annotationHeight = 0;
\r
1189 if (av.showAnnotation)
\r
1191 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1194 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1196 + annotationHeight;
\r
1198 int maxwidth = av.alignment.getWidth();
\r
1199 if (av.hasHiddenColumns)
\r
1201 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1204 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r