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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86 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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87 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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89 setScrollValues(0, 0);
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91 setAnnotationVisible(av.getShowAnnotation());
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93 hscroll.addAdjustmentListener(this);
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94 vscroll.addAdjustmentListener(this);
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96 final AlignmentPanel ap = this;
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97 av.addPropertyChangeListener(new PropertyChangeListener()
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99 public void propertyChange(PropertyChangeEvent evt)
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101 if (evt.getPropertyName().equals("alignment"))
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103 PaintRefresher.Refresh(ap,
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104 av.getSequenceSetId(),
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107 alignmentChanged();
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112 adjustAnnotationHeight();
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116 public void alignmentChanged()
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118 av.alignmentChanged(this);
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120 if (overviewPanel != null)
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122 overviewPanel.updateOverviewImage();
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125 alignFrame.updateEditMenuBar();
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133 public void fontChanged()
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135 // set idCanvas bufferedImage to null
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136 // to prevent drawing old image
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137 FontMetrics fm = getFontMetrics(av.getFont());
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139 scalePanelHolder.setPreferredSize(new Dimension(10,
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140 av.charHeight + fm.getDescent()));
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141 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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142 av.charHeight + fm.getDescent()));
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144 idPanel.idCanvas.gg = null;
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145 seqPanel.seqCanvas.img = null;
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146 annotationPanel.adjustPanelHeight();
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148 Dimension d = calculateIdWidth();
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149 d.setSize(d.width + 4, d.height);
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150 idPanel.idCanvas.setPreferredSize(d);
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151 hscrollFillerPanel.setPreferredSize(d);
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153 if (overviewPanel != null)
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155 overviewPanel.setBoxPosition();
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164 * @return DOCUMENT ME!
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166 public Dimension calculateIdWidth()
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168 Container c = new Container();
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170 FontMetrics fm = c.getFontMetrics(
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171 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
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173 AlignmentI al = av.getAlignment();
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179 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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181 SequenceI s = al.getSequenceAt(i);
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183 id = s.getDisplayId(av.getShowJVSuffix());
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185 if (fm.stringWidth(id) > idWidth)
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187 idWidth = fm.stringWidth(id);
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193 // Also check annotation label widths
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196 if (al.getAlignmentAnnotation() != null)
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198 fm = c.getFontMetrics(alabels.getFont());
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200 while (i < al.getAlignmentAnnotation().length)
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202 String label = al.getAlignmentAnnotation()[i].label;
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204 if (fm.stringWidth(label) > idWidth)
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206 idWidth = fm.stringWidth(label);
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213 return new Dimension(idWidth, 12);
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219 * @param results DOCUMENT ME!
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221 public void highlightSearchResults(SearchResults results)
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223 seqPanel.seqCanvas.highlightSearchResults(results);
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225 // do we need to scroll the panel?
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226 if (results != null)
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228 SequenceI seq = results.getResultSequence(0);
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229 int seqIndex = av.alignment.findIndex(seq);
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230 int start = seq.findIndex(results.getResultStart(0)) - 1;
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231 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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233 if (!av.wrapAlignment)
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235 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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236 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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238 setScrollValues(start, seqIndex);
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243 scrollToWrappedVisible(start);
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248 void scrollToWrappedVisible(int res)
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250 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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252 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
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254 vscroll.setValue(res / cwidth);
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255 av.startRes = vscroll.getValue() * cwidth;
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262 * @return DOCUMENT ME!
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264 public OverviewPanel getOverviewPanel()
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266 return overviewPanel;
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272 * @param op DOCUMENT ME!
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274 public void setOverviewPanel(OverviewPanel op)
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276 overviewPanel = op;
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282 * @param b DOCUMENT ME!
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284 public void setAnnotationVisible(boolean b)
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286 if (!av.wrapAlignment)
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288 annotationSpaceFillerHolder.setVisible(b);
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289 annotationScroller.setVisible(b);
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294 public void adjustAnnotationHeight()
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296 if (alignFrame.getHeight() == 0)
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298 System.out.println("NEEDS FIXING");
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301 int height = annotationPanel.adjustPanelHeight();
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303 if (height > alignFrame.getHeight() / 2)
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305 height = alignFrame.getHeight() / 2;
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308 annotationScroller.setPreferredSize(
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309 new Dimension(annotationScroller.getWidth(),
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312 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
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313 annotationSpaceFillerHolder.getWidth(),
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322 * @param wrap DOCUMENT ME!
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324 public void setWrapAlignment(boolean wrap)
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327 scalePanelHolder.setVisible(!wrap);
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328 hscroll.setVisible(!wrap);
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329 idwidthAdjuster.setVisible(!wrap);
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333 annotationScroller.setVisible(false);
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334 annotationSpaceFillerHolder.setVisible(false);
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336 else if (av.showAnnotation)
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338 annotationScroller.setVisible(true);
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339 annotationSpaceFillerHolder.setVisible(true);
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342 idSpaceFillerPanel1.setVisible(!wrap);
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347 // return value is true if the scroll is valid
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348 public boolean scrollUp(boolean up)
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352 if (vscroll.getValue() < 1)
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358 vscroll.setValue(vscroll.getValue() - 1);
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362 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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368 vscroll.setValue(vscroll.getValue() + 1);
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379 * @param right DOCUMENT ME!
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381 * @return DOCUMENT ME!
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383 public boolean scrollRight(boolean right)
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387 if (hscroll.getValue() < 1)
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393 hscroll.setValue(hscroll.getValue() - 1);
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397 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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403 hscroll.setValue(hscroll.getValue() + 1);
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414 * @param x DOCUMENT ME!
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415 * @param y DOCUMENT ME!
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417 public void setScrollValues(int x, int y)
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420 int width = av.alignment.getWidth();
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421 int height = av.alignment.getHeight();
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423 if (av.hasHiddenColumns)
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425 width = av.getColumnSelection().findColumnPosition(width);
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428 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
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430 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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431 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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433 if (hextent > width)
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438 if (vextent > height)
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443 if ( (hextent + x) > width)
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445 x = width - hextent;
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448 if ( (vextent + y) > height)
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450 y = height - vextent;
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463 hscroll.setValues(x, hextent, 0, width);
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464 vscroll.setValues(y, vextent, 0, height);
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470 * @param evt DOCUMENT ME!
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472 public void adjustmentValueChanged(AdjustmentEvent evt)
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475 int oldX = av.getStartRes();
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476 int oldY = av.getStartSeq();
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478 if (evt.getSource() == hscroll)
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480 int x = hscroll.getValue();
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483 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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486 if (evt.getSource() == vscroll)
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488 int offy = vscroll.getValue();
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490 if (av.getWrapAlignment())
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494 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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495 seqCanvas.getWidth());
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496 av.setStartRes(offy * rowSize);
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497 av.setEndRes( (offy + 1) * rowSize);
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501 //This is only called if file loaded is a jar file that
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502 //was wrapped when saved and user has wrap alignment true
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503 //as preference setting
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504 SwingUtilities.invokeLater(new Runnable()
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508 setScrollValues(av.getStartRes(), av.getStartSeq());
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515 av.setStartSeq(offy);
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516 av.setEndSeq(offy +
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517 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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521 if (overviewPanel != null)
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523 overviewPanel.setBoxPosition();
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526 int scrollX = av.startRes - oldX;
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527 int scrollY = av.startSeq - oldY;
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529 if (av.getWrapAlignment() || !fastPaint)
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535 // Make sure we're not trying to draw a panel
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536 // larger than the visible window
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537 if (scrollX > av.endRes - av.startRes)
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539 scrollX = av.endRes - av.startRes;
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541 else if (scrollX < av.startRes - av.endRes)
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543 scrollX = av.startRes - av.endRes;
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546 if (scrollX != 0 || scrollY != 0)
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548 idPanel.idCanvas.fastPaint(scrollY);
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549 seqPanel.seqCanvas.fastPaint(scrollX,
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551 scalePanel.repaint();
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553 if (av.getShowAnnotation())
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555 annotationPanel.fastPaint(scrollX);
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564 * @param g DOCUMENT ME!
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566 public void paintComponent(Graphics g)
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570 Dimension d = idPanel.idCanvas.getPreferredSize();
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571 idPanelHolder.setPreferredSize(d);
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572 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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575 if (av.getWrapAlignment())
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577 int maxwidth = av.alignment.getWidth();
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579 if (av.hasHiddenColumns)
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581 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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584 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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585 seqCanvas.getWidth());
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586 if (canvasWidth > 0)
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588 int max = maxwidth /
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589 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
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592 vscroll.setMaximum(max);
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593 vscroll.setUnitIncrement(1);
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594 vscroll.setVisibleAmount(1);
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599 setScrollValues(av.getStartRes(), av.getStartSeq());
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602 if (this.getVisibleRect().getBounds() == g.getClipBounds()
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603 && overviewPanel != null)
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605 overviewPanel.updateOverviewImage();
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612 * @param pg DOCUMENT ME!
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613 * @param pf DOCUMENT ME!
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614 * @param pi DOCUMENT ME!
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616 * @return DOCUMENT ME!
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618 * @throws PrinterException DOCUMENT ME!
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620 public int print(Graphics pg, PageFormat pf, int pi)
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621 throws PrinterException
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623 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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625 int pwidth = (int) pf.getImageableWidth();
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626 int pheight = (int) pf.getImageableHeight();
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628 if (av.getWrapAlignment())
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630 return printWrappedAlignment(pg, pwidth, pheight, pi);
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634 return printUnwrapped(pg, pwidth, pheight, pi);
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641 * @param pg DOCUMENT ME!
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642 * @param pwidth DOCUMENT ME!
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643 * @param pheight DOCUMENT ME!
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644 * @param pi DOCUMENT ME!
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646 * @return DOCUMENT ME!
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648 * @throws PrinterException DOCUMENT ME!
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650 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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651 throws PrinterException
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653 int idWidth = getVisibleIdWidth();
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654 FontMetrics fm = getFontMetrics(av.getFont());
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655 int scaleHeight = av.charHeight + fm.getDescent();
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657 pg.setColor(Color.white);
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658 pg.fillRect(0, 0, pwidth, pheight);
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659 pg.setFont(av.getFont());
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661 ////////////////////////////////////
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662 /// How many sequences and residues can we fit on a printable page?
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663 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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665 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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668 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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670 /////////////////////////////
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671 /// Only print these sequences and residues on this page
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674 /////////////////////////////
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675 /// Only print these sequences and residues on this page
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678 /////////////////////////////
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679 /// Only print these sequences and residues on this page
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682 /////////////////////////////
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683 /// Only print these sequences and residues on this page
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685 startRes = (pi % pagesWide) * totalRes;
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686 endRes = (startRes + totalRes) - 1;
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688 if (endRes > (av.getAlignment().getWidth() - 1))
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690 endRes = av.getAlignment().getWidth() - 1;
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693 startSeq = (pi / pagesWide) * totalSeq;
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694 endSeq = startSeq + totalSeq;
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696 if (endSeq > av.getAlignment().getHeight())
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698 endSeq = av.getAlignment().getHeight();
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701 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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703 if (av.showAnnotation)
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705 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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708 pagesHigh /= pheight;
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710 if (pi >= (pagesWide * pagesHigh))
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712 return Printable.NO_SUCH_PAGE;
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716 pg.translate(idWidth, 0);
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717 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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718 pg.translate( -idWidth, scaleHeight);
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722 Color currentColor = null;
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723 Color currentTextColor = null;
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725 pg.setFont(idPanel.idCanvas.idfont);
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728 for (int i = startSeq; i < endSeq; i++)
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730 seq = av.getAlignment().getSequenceAt(i);
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731 if ( (av.getSelectionGroup() != null) &&
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732 av.getSelectionGroup().getSequences(null).contains(seq))
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734 currentColor = Color.gray;
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735 currentTextColor = Color.black;
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739 currentColor = av.getSequenceColour(seq);
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740 currentTextColor = Color.black;
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743 pg.setColor(currentColor);
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744 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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745 av.getCharHeight());
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747 pg.setColor(currentTextColor);
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750 if (av.rightAlignIds)
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752 fm = pg.getFontMetrics();
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753 xPos = idWidth - fm.stringWidth(
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754 seq.getDisplayId(av.getShowJVSuffix())
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758 pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
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760 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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761 (av.getCharHeight() / 5));
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764 pg.setFont(av.getFont());
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766 // draw main sequence panel
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767 pg.translate(idWidth, 0);
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768 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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770 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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772 pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
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773 alabels.drawComponent( (Graphics2D) pg, idWidth);
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774 pg.translate(idWidth + 3, 0);
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775 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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779 return Printable.PAGE_EXISTS;
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785 * @param pg DOCUMENT ME!
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786 * @param pwidth DOCUMENT ME!
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787 * @param pheight DOCUMENT ME!
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788 * @param pi DOCUMENT ME!
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790 * @return DOCUMENT ME!
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792 * @throws PrinterException DOCUMENT ME!
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794 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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796 throws PrinterException
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799 int annotationHeight = 0;
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800 AnnotationLabels labels = null;
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801 if (av.showAnnotation)
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803 annotationHeight = annotationPanel.adjustPanelHeight();
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804 labels = new AnnotationLabels(av);
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807 int hgap = av.charHeight;
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808 if (av.scaleAboveWrapped)
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810 hgap += av.charHeight;
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813 int cHeight = av.getAlignment().getHeight() * av.charHeight
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815 + annotationHeight;
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817 int idWidth = getVisibleIdWidth();
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819 int maxwidth = av.alignment.getWidth();
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820 if (av.hasHiddenColumns)
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822 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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825 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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828 int totalHeight = cHeight * (maxwidth / resWidth + 1);
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830 pg.setColor(Color.white);
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831 pg.fillRect(0, 0, pwidth, pheight);
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832 pg.setFont(av.getFont());
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836 pg.setColor(Color.black);
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838 pg.translate(0, -pi * pheight);
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840 pg.setClip(0, pi * pheight, pwidth, pheight);
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846 for (int i = 0; i < av.alignment.getHeight(); i++)
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848 pg.setFont(idPanel.idCanvas.idfont);
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849 SequenceI s = av.alignment.getSequenceAt(i);
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850 String string = s.getDisplayId(av.getShowJVSuffix());
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852 if (av.rightAlignIds)
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854 FontMetrics fm = pg.getFontMetrics();
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855 xPos = idWidth - fm.stringWidth(string) - 4;
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857 pg.drawString(string, xPos,
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858 ( (i * av.charHeight) + ypos + av.charHeight) -
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859 (av.charHeight / 5));
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861 if (labels != null)
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865 (av.getAlignment().getHeight() * av.charHeight));
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867 pg.setFont(av.getFont());
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868 labels.drawComponent(pg, idWidth);
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871 (av.getAlignment().getHeight() * av.charHeight));
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876 while (ypos < totalHeight);
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878 pg.translate(idWidth, 0);
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880 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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882 if ( (pi * pheight) < totalHeight)
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884 return Printable.PAGE_EXISTS;
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889 return Printable.NO_SUCH_PAGE;
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893 int getVisibleIdWidth()
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896 idPanel.getWidth() > 0 ? idPanel.getWidth() :
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897 calculateIdWidth().width + 4;
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900 void makeAlignmentImage(int type, File file)
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902 int maxwidth = av.alignment.getWidth();
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903 if (av.hasHiddenColumns)
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905 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
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908 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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909 int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
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911 if (av.getWrapAlignment())
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913 height = getWrappedHeight();
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914 if (System.getProperty("java.awt.headless") != null
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915 && System.getProperty("java.awt.headless").equals("true"))
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917 width = alignFrame.getWidth()
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918 - vscroll.getPreferredSize().width
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919 - alignFrame.getInsets().left
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920 - alignFrame.getInsets().right;
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924 width = seqPanel.getWidth() + getVisibleIdWidth();
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928 else if (av.getShowAnnotation())
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930 height += annotationPanel.adjustPanelHeight() + 3;
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936 jalview.util.ImageMaker im;
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937 if (type == jalview.util.ImageMaker.PNG)
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939 im = new jalview.util.ImageMaker(this,
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940 jalview.util.ImageMaker.PNG,
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941 "Create PNG image from alignment",
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942 width, height, file, null);
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946 im = new jalview.util.ImageMaker(this,
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947 jalview.util.ImageMaker.EPS,
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948 "Create EPS file from alignment",
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949 width, height, file,
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950 alignFrame.getTitle());
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953 if (av.getWrapAlignment())
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955 if (im.getGraphics() != null)
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957 printWrappedAlignment(im.getGraphics(), width, height, 0);
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963 if (im.getGraphics() != null)
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965 printUnwrapped(im.getGraphics(), width, height, 0);
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970 catch (OutOfMemoryError err)
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972 System.out.println("########################\n"
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973 + "OUT OF MEMORY " + file + "\n"
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974 + "########################");
\r
976 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
977 "Out of Memory Creating Image!!"
\r
979 "\nSee help files for increasing Java Virtual Machine memory."
\r
981 JOptionPane.WARNING_MESSAGE);
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982 System.out.println("Create IMAGE: " + err);
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986 catch (Exception ex)
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988 ex.printStackTrace();
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995 public void makeEPS(File epsFile)
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997 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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1003 public void makePNG(File pngFile)
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1005 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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1008 public void makePNGImageMap(File imgMapFile, String imageName)
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1010 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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1011 //////////////////////////////////////////////
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1012 int idWidth = getVisibleIdWidth();
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1013 FontMetrics fm = getFontMetrics(av.getFont());
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1014 int scaleHeight = av.charHeight + fm.getDescent();
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1017 //////////////////////////////////
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1018 if (imgMapFile != null)
\r
1022 int s, sSize = av.alignment.getHeight(),
\r
1023 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1024 StringBuffer text = new StringBuffer();
\r
1025 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1026 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1027 out.println("<img src=\"" + imageName +
\r
1028 "\" border=\"0\" usemap=\"#Map\" >"
\r
1029 + "<map name=\"Map\">");
\r
1031 for (s = 0; s < sSize; s++)
\r
1033 sy = s * av.charHeight + scaleHeight;
\r
1035 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1036 SequenceFeature[] features = seq.getDatasetSequence().
\r
1037 getSequenceFeatures();
\r
1038 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1039 for (res = 0; res < alwidth; res++)
\r
1041 text = new StringBuffer();
\r
1042 Object obj = null;
\r
1043 if (av.alignment.isNucleotide())
\r
1045 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
\r
1050 obj = ResidueProperties.aa2Triplet.get(
\r
1051 seq.getCharAt(res) + "");
\r
1059 String triplet = obj.toString();
\r
1060 int alIndex = seq.findPosition(res);
\r
1061 gSize = groups.length;
\r
1062 for (g = 0; g < gSize; g++)
\r
1064 if (text.length() < 1)
\r
1066 text.append("<area shape=\"rect\" coords=\""
\r
1067 + (idWidth + res * av.charWidth) + ","
\r
1069 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1070 + (av.charHeight + sy) + "\""
\r
1071 + " onMouseOver=\"toolTip('"
\r
1072 + alIndex + " " + triplet);
\r
1075 if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
\r
1077 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1081 if (features != null)
\r
1083 if (text.length() < 1)
\r
1085 text.append("<area shape=\"rect\" coords=\""
\r
1086 + (idWidth + res * av.charWidth) + ","
\r
1088 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1089 + (av.charHeight + sy) + "\""
\r
1090 + " onMouseOver=\"toolTip('"
\r
1091 + alIndex + " " + triplet);
\r
1093 fSize = features.length;
\r
1094 for (f = 0; f < fSize; f++)
\r
1097 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1098 (features[f].getEnd() >= seq.findPosition(res)))
\r
1100 if (features[f].getType().equals("disulfide bond"))
\r
1102 if (features[f].getBegin() == seq.findPosition(res)
\r
1103 || features[f].getEnd() == seq.findPosition(res))
\r
1105 text.append("<br>disulfide bond " + features[f].getBegin() +
\r
1107 features[f].getEnd());
\r
1112 text.append("<br>");
\r
1113 text.append(features[f].getType());
\r
1114 if (features[f].getDescription() != null &&
\r
1116 getType().equals(features[f].getDescription()))
\r
1118 text.append(" " + features[f].getDescription());
\r
1121 if (features[f].getValue("status") != null)
\r
1123 text.append(" (" + features[f].getValue("status") + ")");
\r
1130 if (text.length() > 1)
\r
1132 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1133 out.println(text.toString());
\r
1137 out.println("</map></body></html>");
\r
1141 catch (Exception ex)
\r
1143 ex.printStackTrace();
\r
1145 } ///////////END OF IMAGE MAP
\r
1149 int getWrappedHeight()
\r
1151 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1153 if (System.getProperty("java.awt.headless") != null
\r
1154 && System.getProperty("java.awt.headless").equals("true"))
\r
1156 seqPanelWidth = alignFrame.getWidth()
\r
1157 - getVisibleIdWidth()
\r
1158 - vscroll.getPreferredSize().width
\r
1159 - alignFrame.getInsets().left
\r
1160 - alignFrame.getInsets().right;
\r
1163 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1167 int hgap = av.charHeight;
\r
1168 if (av.scaleAboveWrapped)
\r
1170 hgap += av.charHeight;
\r
1173 int annotationHeight = 0;
\r
1174 if (av.showAnnotation)
\r
1176 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1179 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1181 + annotationHeight;
\r
1183 int maxwidth = av.alignment.getWidth();
\r
1184 if (av.hasHiddenColumns)
\r
1186 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1189 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r
1197 * @author $author$
\r
1198 * @version $Revision$
\r
1204 * Creates a new Preview object.
\r
1206 * @param image DOCUMENT ME!
\r
1208 public Preview(Image image)
\r
1210 setResizable(true);
\r
1211 setSize(image.getWidth(this), image.getHeight(this));
\r
1213 getContentPane().setLayout(new BorderLayout());
\r
1214 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1223 * @author $author$
\r
1224 * @version $Revision$
\r
1226 class PreviewPanel
\r
1232 * Creates a new PreviewPanel object.
\r
1234 * @param image DOCUMENT ME!
\r
1236 public PreviewPanel(Image image)
\r
1238 this.image = image;
\r
1244 * @param g DOCUMENT ME!
\r
1246 public void paintComponent(Graphics g)
\r
1248 if (image != null)
\r
1250 g.drawImage(image, 0, 0, this);
\r
1254 System.out.println("DEBUG:image is null");
\r