2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.jbgui.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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29 import java.awt.print.*;
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33 import javax.swing.*;
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40 * @version $Revision$
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42 public class AlignmentPanel extends GAlignmentPanel
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43 implements AdjustmentListener, Printable
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45 public AlignViewport av;
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46 OverviewPanel overviewPanel;
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49 IdwidthAdjuster idwidthAdjuster;
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51 /** DOCUMENT ME!! */
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52 public AlignFrame alignFrame;
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53 ScalePanel scalePanel;
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54 AnnotationPanel annotationPanel;
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55 AnnotationLabels alabels;
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57 // this value is set false when selection area being dragged
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58 boolean fastPaint = true;
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63 * Creates a new AlignmentPanel object.
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65 * @param af DOCUMENT ME!
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66 * @param av DOCUMENT ME!
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68 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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72 seqPanel = new SeqPanel(av, this);
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73 idPanel = new IdPanel(av, this);
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75 scalePanel = new ScalePanel(av, this);
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77 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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78 idwidthAdjuster = new IdwidthAdjuster(this);
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79 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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81 annotationPanel = new AnnotationPanel(this);
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82 alabels = new AnnotationLabels(this);
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85 annotationScroller.setViewportView(annotationPanel);
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86 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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90 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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91 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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93 setScrollValues(0, 0);
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95 adjustAnnotationHeight();
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97 setAnnotationVisible(av.getShowAnnotation());
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99 hscroll.addAdjustmentListener(this);
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100 vscroll.addAdjustmentListener(this);
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102 af.addKeyListener(new KeyAdapter()
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104 public void keyPressed(KeyEvent evt)
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107 && evt.getKeyCode()>=KeyEvent.VK_0
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108 && evt.getKeyCode()<=KeyEvent.VK_9)
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110 seqPanel.numberPressed(evt.getKeyChar());
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113 switch (evt.getKeyCode())
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115 case 27: // escape key
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116 alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
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120 case KeyEvent.VK_DOWN:
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123 seqPanel.moveCursor(0,1);
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126 alignFrame.moveSelectedSequences(false);
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129 case KeyEvent.VK_UP:
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132 seqPanel.moveCursor(0,-1);
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135 alignFrame.moveSelectedSequences(true);
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138 case KeyEvent.VK_LEFT:
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141 seqPanel.moveCursor(-1,0);
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145 case KeyEvent.VK_RIGHT:
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148 seqPanel.moveCursor(1,0);
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152 case KeyEvent.VK_SPACE:
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155 seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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159 case KeyEvent.VK_DELETE:
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160 case KeyEvent.VK_BACK_SPACE:
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163 alignFrame.cut_actionPerformed(null);
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166 seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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170 case KeyEvent.VK_S:
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173 seqPanel.setCursorRow();
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176 case KeyEvent.VK_C:
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177 if(av.cursorMode && !evt.isControlDown())
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179 seqPanel.setCursorColumn();
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182 case KeyEvent.VK_P:
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185 seqPanel.setCursorPosition();
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189 case KeyEvent.VK_ENTER:
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190 case KeyEvent.VK_COMMA:
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193 seqPanel.setCursorRowAndColumn();
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197 case KeyEvent.VK_Q:
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200 seqPanel.setSelectionAreaAtCursor(true);
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203 case KeyEvent.VK_M:
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206 seqPanel.setSelectionAreaAtCursor(false);
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210 case KeyEvent.VK_F2:
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211 av.cursorMode = ! av.cursorMode;
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212 alignFrame.statusBar.setText("Keyboard editing mode is "+
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213 (av.cursorMode ? "on" : "off"));
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216 seqPanel.seqCanvas.cursorX = av.startRes;
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217 seqPanel.seqCanvas.cursorY = av.startSeq;
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219 seqPanel.seqCanvas.repaint();
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222 case KeyEvent.VK_F1:
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225 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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226 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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227 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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229 javax.help.HelpBroker hb = hs.createHelpBroker();
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230 hb.setCurrentID("home");
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231 hb.setDisplayed(true);
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233 catch (Exception ex)
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235 ex.printStackTrace();
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238 case KeyEvent.VK_H:
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240 boolean toggleSeqs = !evt.isControlDown();
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241 boolean toggleCols = !evt.isShiftDown();
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243 boolean hide = false;
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245 SequenceGroup sg = av.getSelectionGroup();
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248 if(sg != null && sg.getSize(false) != av.alignment.getHeight())
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250 alignFrame.hideSelSequences_actionPerformed(null);
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254 alignFrame.showAllSeqs_actionPerformed(null);
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259 if(av.colSel.getSelected().size() > 0)
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261 alignFrame.hideSelColumns_actionPerformed(null);
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263 av.selectionGroup = sg;
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266 alignFrame.showAllColumns_actionPerformed(null);
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279 public void fontChanged()
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281 // set idCanvas bufferedImage to null
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282 // to prevent drawing old image
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283 FontMetrics fm = getFontMetrics(av.getFont());
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285 scalePanelHolder.setPreferredSize(new Dimension(10,
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286 av.charHeight + fm.getDescent()));
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287 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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288 av.charHeight + fm.getDescent()));
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290 idPanel.idCanvas.gg = null;
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291 seqPanel.seqCanvas.img = null;
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292 annotationPanel.adjustPanelHeight();
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294 Dimension d = calculateIdWidth();
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295 d.setSize(d.width + 4, d.height);
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296 idPanel.idCanvas.setPreferredSize(d);
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297 hscrollFillerPanel.setPreferredSize(d);
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299 if (av.getWrapAlignment())
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301 int max = av.alignment.getWidth() /
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302 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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303 vscroll.setMaximum(max);
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304 vscroll.setUnitIncrement(1);
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305 vscroll.setVisibleAmount(1);
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309 setScrollValues(av.getStartRes(), av.getStartSeq());
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312 if (overviewPanel != null)
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313 overviewPanel.setBoxPosition();
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321 * @return DOCUMENT ME!
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323 public Dimension calculateIdWidth()
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325 Container c = new Container();
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327 FontMetrics fm = c.getFontMetrics(av.font);
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328 AlignmentI al = av.getAlignment();
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334 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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336 SequenceI s = al.getSequenceAt(i);
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338 id = s.getDisplayId(av.getShowJVSuffix());
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340 if (fm.stringWidth(id) > idWidth)
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342 idWidth = fm.stringWidth(id);
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348 // Also check annotation label widths
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351 if (al.getAlignmentAnnotation() != null)
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353 fm = c.getFontMetrics(alabels.getFont());
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355 while (i < al.getAlignmentAnnotation().length)
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357 String label = al.getAlignmentAnnotation()[i].label;
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359 if (fm.stringWidth(label) > idWidth)
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361 idWidth = fm.stringWidth(label);
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368 return new Dimension(idWidth, 12);
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374 * @param results DOCUMENT ME!
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376 public void highlightSearchResults(SearchResults results)
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378 seqPanel.seqCanvas.highlightSearchResults(results);
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380 // do we need to scroll the panel?
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381 if (results != null)
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383 SequenceI seq = results.getResultSequence(0);
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384 int seqIndex = av.alignment.findIndex(seq);
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385 int start = seq.findIndex(results.getResultStart(0)) - 1;
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386 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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388 if(!av.wrapAlignment)
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390 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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391 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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393 setScrollValues(start, seqIndex);
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398 scrollToWrappedVisible(start);
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403 void scrollToWrappedVisible(int res)
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405 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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406 if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
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408 vscroll.setValue(res / cwidth);
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409 av.startRes = vscroll.getValue() * cwidth;
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416 * @return DOCUMENT ME!
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418 public OverviewPanel getOverviewPanel()
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420 return overviewPanel;
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426 * @param op DOCUMENT ME!
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428 public void setOverviewPanel(OverviewPanel op)
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430 overviewPanel = op;
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436 * @param b DOCUMENT ME!
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438 public void setAnnotationVisible(boolean b)
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440 if (!av.wrapAlignment)
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442 annotationSpaceFillerHolder.setVisible(b);
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443 annotationScroller.setVisible(b);
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448 public void adjustAnnotationHeight()
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450 javax.swing.SwingUtilities.invokeLater(new Runnable()
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454 while(alignFrame.getHeight()==0)
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459 int height = annotationPanel.adjustPanelHeight();
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461 if (height > alignFrame.getHeight() / 2)
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463 height = alignFrame.getHeight() / 2;
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466 annotationScroller.setPreferredSize(
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467 new Dimension(annotationScroller.getWidth(),
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470 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
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471 annotationSpaceFillerHolder.getWidth(),
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474 annotationPanel.repaint();
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482 * @param wrap DOCUMENT ME!
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484 public void setWrapAlignment(boolean wrap)
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487 scalePanelHolder.setVisible(!wrap);
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488 hscroll.setVisible(!wrap);
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489 idwidthAdjuster.setVisible(!wrap);
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493 annotationScroller.setVisible(false);
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494 annotationSpaceFillerHolder.setVisible(false);
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496 else if (av.showAnnotation)
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498 annotationScroller.setVisible(true);
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499 annotationSpaceFillerHolder.setVisible(true);
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502 idSpaceFillerPanel1.setVisible(!wrap);
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507 // return value is true if the scroll is valid
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508 public boolean scrollUp(boolean up)
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512 if (vscroll.getValue() < 1)
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518 vscroll.setValue(vscroll.getValue() - 1);
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522 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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528 vscroll.setValue(vscroll.getValue() + 1);
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539 * @param right DOCUMENT ME!
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541 * @return DOCUMENT ME!
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543 public boolean scrollRight(boolean right)
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547 if (hscroll.getValue() < 1)
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553 hscroll.setValue(hscroll.getValue() - 1);
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557 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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563 hscroll.setValue(hscroll.getValue() + 1);
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574 * @param x DOCUMENT ME!
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575 * @param y DOCUMENT ME!
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577 public void setScrollValues(int x, int y)
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580 int width = av.alignment.getWidth();
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581 int height = av.alignment.getHeight();
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583 if(av.hasHiddenColumns)
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584 width = av.getColumnSelection().findColumnPosition(width);
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586 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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588 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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589 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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591 if (hextent > width)
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596 if (vextent > height)
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601 if ( (hextent + x) > width)
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603 x = width - hextent;
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606 if ( (vextent + y) > height)
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608 y = height - vextent;
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621 hscroll.setValues(x, hextent, 0, width);
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622 vscroll.setValues(y, vextent, 0, height);
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628 * @param evt DOCUMENT ME!
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630 public void adjustmentValueChanged(AdjustmentEvent evt)
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633 int oldX = av.getStartRes();
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634 int oldY = av.getStartSeq();
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636 if (evt.getSource() == hscroll)
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638 int x = hscroll.getValue();
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641 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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644 if (evt.getSource() == vscroll)
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646 int offy = vscroll.getValue();
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648 if (av.getWrapAlignment())
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652 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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653 seqCanvas.getWidth());
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654 av.setStartRes(offy * rowSize);
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655 av.setEndRes( (offy + 1) * rowSize);
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659 //This is only called if file loaded is a jar file that
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660 //was wrapped when saved and user has wrap alignment true
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661 //as preference setting
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662 SwingUtilities.invokeLater(new Runnable()
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666 setScrollValues(av.getStartRes(), av.getStartSeq());
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673 av.setStartSeq(offy);
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674 av.setEndSeq(offy +
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675 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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679 if (overviewPanel != null)
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681 overviewPanel.setBoxPosition();
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684 int scrollX = av.startRes - oldX;
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685 int scrollY = av.startSeq - oldY;
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687 if (av.getWrapAlignment() || !fastPaint)
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693 // Make sure we're not trying to draw a panel
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694 // larger than the visible window
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695 if(scrollX>av.endRes-av.startRes)
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696 scrollX = av.endRes-av.startRes;
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697 else if(scrollX<av.startRes-av.endRes)
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698 scrollX = av.startRes - av.endRes;
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700 if(scrollX!=0 || scrollY!=0)
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702 idPanel.idCanvas.fastPaint(scrollY);
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703 seqPanel.seqCanvas.fastPaint(scrollX,
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705 scalePanel.repaint();
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707 if (av.getShowAnnotation())
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709 annotationPanel.fastPaint(scrollX);
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718 * @param g DOCUMENT ME!
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720 public void paintComponent(Graphics g)
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724 Dimension d = idPanel.idCanvas.getPreferredSize();
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725 idPanelHolder.setPreferredSize(d);
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726 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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729 if (av.getWrapAlignment())
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731 int maxwidth = av.alignment.getWidth();
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733 if (av.hasHiddenColumns)
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734 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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736 int max = maxwidth /
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737 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +
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741 vscroll.setMaximum(max);
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742 vscroll.setUnitIncrement(1);
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743 vscroll.setVisibleAmount(1);
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747 setScrollValues(av.getStartRes(), av.getStartSeq());
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750 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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751 && overviewPanel != null)
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752 overviewPanel.updateOverviewImage();
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759 * @param pg DOCUMENT ME!
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760 * @param pf DOCUMENT ME!
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761 * @param pi DOCUMENT ME!
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763 * @return DOCUMENT ME!
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765 * @throws PrinterException DOCUMENT ME!
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767 public int print(Graphics pg, PageFormat pf, int pi)
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768 throws PrinterException
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770 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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772 int pwidth = (int) pf.getImageableWidth();
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773 int pheight = (int) pf.getImageableHeight();
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775 if (av.getWrapAlignment())
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777 return printWrappedAlignment(pg, pwidth, pheight, pi);
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781 return printUnwrapped(pg, pwidth, pheight, pi);
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788 * @param pg DOCUMENT ME!
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789 * @param pwidth DOCUMENT ME!
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790 * @param pheight DOCUMENT ME!
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791 * @param pi DOCUMENT ME!
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793 * @return DOCUMENT ME!
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795 * @throws PrinterException DOCUMENT ME!
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797 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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798 throws PrinterException
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800 int idWidth = calculateIdWidth().width + 4;
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801 FontMetrics fm = getFontMetrics(av.getFont());
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802 int scaleHeight = av.charHeight + fm.getDescent();
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804 pg.setColor(Color.white);
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805 pg.fillRect(0, 0, pwidth, pheight);
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806 pg.setFont(av.getFont());
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808 ////////////////////////////////////
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809 /// How many sequences and residues can we fit on a printable page?
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810 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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812 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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815 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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817 /////////////////////////////
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818 /// Only print these sequences and residues on this page
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821 /////////////////////////////
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822 /// Only print these sequences and residues on this page
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825 /////////////////////////////
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826 /// Only print these sequences and residues on this page
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829 /////////////////////////////
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830 /// Only print these sequences and residues on this page
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832 startRes = (pi % pagesWide) * totalRes;
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833 endRes = (startRes + totalRes) - 1;
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835 if (endRes > (av.getAlignment().getWidth() - 1))
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837 endRes = av.getAlignment().getWidth() - 1;
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840 startSeq = (pi / pagesWide) * totalSeq;
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841 endSeq = startSeq + totalSeq;
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843 if (endSeq > av.getAlignment().getHeight())
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845 endSeq = av.getAlignment().getHeight();
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848 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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850 if (av.showAnnotation)
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852 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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855 pagesHigh /= pheight;
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857 if (pi >= (pagesWide * pagesHigh))
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859 return Printable.NO_SUCH_PAGE;
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863 pg.translate(idWidth, 0);
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864 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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865 pg.translate( -idWidth, scaleHeight);
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869 Color currentColor = null;
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870 Color currentTextColor = null;
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872 pg.setFont(new Font(av.getFont().getName(),
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874 av.getFont().getSize()));
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875 for (int i = startSeq; i < endSeq; i++)
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877 if ( (av.getSelectionGroup() != null) &&
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878 av.getSelectionGroup().getSequences(false).contains(
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879 av.getAlignment().getSequenceAt(i)))
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881 currentColor = Color.gray;
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882 currentTextColor = Color.black;
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886 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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887 currentTextColor = Color.black;
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890 pg.setColor(currentColor);
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891 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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892 av.getCharHeight());
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894 pg.setColor(currentTextColor);
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896 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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897 ( av.getShowJVSuffix());
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899 pg.drawString(string, 0,
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900 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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901 (av.getCharHeight() / 5));
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904 pg.setFont(av.getFont());
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906 // draw main sequence panel
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907 pg.translate(idWidth, 0);
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908 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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910 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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912 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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913 alabels.drawComponent( (Graphics2D) pg, idWidth);
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914 pg.translate(idWidth+3, 0);
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915 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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919 return Printable.PAGE_EXISTS;
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925 * @param pg DOCUMENT ME!
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926 * @param pwidth DOCUMENT ME!
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927 * @param pheight DOCUMENT ME!
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928 * @param pi DOCUMENT ME!
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930 * @return DOCUMENT ME!
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932 * @throws PrinterException DOCUMENT ME!
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934 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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936 throws PrinterException
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939 int annotationHeight = 0;
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940 AnnotationLabels labels = null;
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941 if (av.showAnnotation)
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943 annotationHeight = annotationPanel.adjustPanelHeight();
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944 labels = new AnnotationLabels(av);
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947 int hgap = av.charHeight;
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948 if (av.scaleAboveWrapped)
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949 hgap += av.charHeight;
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951 int cHeight = av.getAlignment().getHeight() * av.charHeight
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953 + annotationHeight;
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955 int idWidth = calculateIdWidth().width + 4;
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957 int maxwidth = av.alignment.getWidth();
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958 if (av.hasHiddenColumns)
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959 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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962 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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965 int totalHeight = cHeight * (maxwidth / resWidth + 1);
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967 pg.setColor(Color.white);
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968 pg.fillRect(0, 0, pwidth, pheight);
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969 pg.setFont(av.getFont());
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973 pg.setColor(Color.black);
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975 pg.translate(0, -pi * pheight);
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977 pg.setClip(0, pi * pheight, pwidth, pheight);
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980 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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981 av.getFont().getSize());
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982 pg.setFont(italic);
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986 for (int i = 0; i < av.alignment.getHeight(); i++)
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988 SequenceI s = av.alignment.getSequenceAt(i);
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989 String string = s.getDisplayId( av.getShowJVSuffix());
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991 pg.drawString(string, 0,
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992 ( (i * av.charHeight) + ypos + av.charHeight) -
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993 (av.charHeight / 5));
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995 if (labels != null)
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999 (av.getAlignment().getHeight() * av.charHeight));
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1001 pg.setFont(av.getFont());
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1002 labels.drawComponent(pg, idWidth);
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1003 pg.setFont(italic);
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1006 (av.getAlignment().getHeight() * av.charHeight));
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1011 while (ypos < totalHeight);
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1013 pg.translate(idWidth, 0);
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1015 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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1017 if ( (pi * pheight) < totalHeight)
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1019 return Printable.PAGE_EXISTS;
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1024 return Printable.NO_SUCH_PAGE;
\r
1028 void makeAlignmentImage(int type, File file)
\r
1030 int maxwidth = av.alignment.getWidth();
\r
1031 if (av.hasHiddenColumns)
\r
1032 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
\r
1034 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
\r
1035 int width = idPanel.getWidth() + (maxwidth * av.charWidth);
\r
1036 if (idPanel.getWidth() == 0)
\r
1038 width += calculateIdWidth().getWidth() + 4;
\r
1041 if (av.getWrapAlignment())
\r
1043 height = getWrappedHeight();
\r
1044 if (System.getProperty("java.awt.headless") != null
\r
1045 && System.getProperty("java.awt.headless").equals("true"))
\r
1047 width = alignFrame.getWidth() - 22;
\r
1050 width = seqPanel.getWidth() + idPanel.getWidth();
\r
1053 else if (av.getShowAnnotation())
\r
1055 height += annotationPanel.adjustPanelHeight() + 3;
\r
1058 jalview.util.ImageMaker im;
\r
1059 if(type==jalview.util.ImageMaker.PNG)
\r
1060 im = new jalview.util.ImageMaker(this,
\r
1061 jalview.util.ImageMaker.PNG,
\r
1062 "Create PNG image from alignment",
\r
1063 width, height, file, null);
\r
1065 im = new jalview.util.ImageMaker(this,
\r
1066 jalview.util.ImageMaker.EPS,
\r
1067 "Create EPS file from alignment",
\r
1068 width, height, file, alignFrame.getTitle() );
\r
1072 if (av.getWrapAlignment())
\r
1074 if(im.getGraphics()!=null)
\r
1076 printWrappedAlignment(im.getGraphics(), width, height, 0);
\r
1082 if(im.getGraphics()!=null)
\r
1084 printUnwrapped(im.getGraphics(), width, height, 0);
\r
1089 catch (OutOfMemoryError err)
\r
1091 System.out.println("########################\n"
\r
1092 + "OUT OF MEMORY " + file + "\n"
\r
1093 + "########################");
\r
1095 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1096 "Out of Memory Creating Image!!"
\r
1098 "\nSee help files for increasing Java Virtual Machine memory."
\r
1099 , "Out of memory",
\r
1100 JOptionPane.WARNING_MESSAGE);
\r
1101 System.out.println("Create IMAGE: " + err);
\r
1105 catch (Exception ex)
\r
1107 ex.printStackTrace();
\r
1113 public void makeEPS(File epsFile)
\r
1115 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
\r
1121 public void makePNG(File pngFile)
\r
1123 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
\r
1126 public void makePNGImageMap(File imgMapFile, String imageName)
\r
1128 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1129 //////////////////////////////////////////////
\r
1130 int idWidth = calculateIdWidth().width + 4;
\r
1131 FontMetrics fm = getFontMetrics(av.getFont());
\r
1132 int scaleHeight = av.charHeight + fm.getDescent();
\r
1135 //////////////////////////////////
\r
1136 if (imgMapFile != null)
\r
1140 int s, sSize = av.alignment.getHeight(),
\r
1141 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1142 StringBuffer text = new StringBuffer();
\r
1143 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1144 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1145 out.println("<img src=\"" + imageName +
\r
1146 "\" border=\"0\" usemap=\"#Map\" >"
\r
1147 + "<map name=\"Map\">");
\r
1149 for (s = 0; s < sSize; s++)
\r
1151 sy = s * av.charHeight + scaleHeight;
\r
1153 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1154 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
\r
1155 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1156 for(res =0; res<alwidth; res++)
\r
1158 text = new StringBuffer();
\r
1159 Object obj = null;
\r
1160 if(av.alignment.isNucleotide())
\r
1161 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
\r
1163 obj = ResidueProperties.aa2Triplet.get(
\r
1164 seq.getCharAt(res) + "");
\r
1169 String triplet = obj.toString();
\r
1170 int alIndex = seq.findPosition(res);
\r
1171 gSize = groups.length;
\r
1172 for (g = 0; g < gSize; g++)
\r
1174 if(text.length()<1)
\r
1176 text.append("<area shape=\"rect\" coords=\""
\r
1177 + (idWidth + res * av.charWidth) + ","
\r
1179 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1180 + (av.charHeight + sy) + "\""
\r
1181 + " onMouseOver=\"toolTip('"
\r
1182 + alIndex + " " + triplet );
\r
1185 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
1186 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1189 if (features != null)
\r
1191 if(text.length()<1)
\r
1193 text.append("<area shape=\"rect\" coords=\""
\r
1194 + (idWidth + res * av.charWidth) + ","
\r
1196 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1197 + (av.charHeight + sy) + "\""
\r
1198 + " onMouseOver=\"toolTip('"
\r
1199 + alIndex + " " + triplet );
\r
1201 fSize = features.length;
\r
1202 for (f = 0; f < fSize; f++)
\r
1205 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1206 (features[f].getEnd() >= seq.findPosition(res)))
\r
1208 if (features[f].getType().equals("disulfide bond"))
\r
1210 if (features[f].getBegin() == seq.findPosition(res)
\r
1211 || features[f].getEnd() == seq.findPosition(res))
\r
1213 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
1214 features[f].getEnd());
\r
1219 text.append("<br>");
\r
1220 text.append(features[f].getType());
\r
1221 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
1222 text.append(" " + features[f].getDescription());
\r
1224 if (features[f].getValue("status") != null )
\r
1226 text.append(" (" + features[f].getValue("status") + ")");
\r
1233 if(text.length()>1)
\r
1235 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1236 out.println(text.toString());
\r
1240 out.println("</map></body></html>");
\r
1244 catch (Exception ex)
\r
1246 ex.printStackTrace();
\r
1248 } ///////////END OF IMAGE MAP
\r
1252 int getWrappedHeight()
\r
1254 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1256 //If headless, seqPanel will have 0 width
\r
1257 if (System.getProperty("java.awt.headless") != null
\r
1258 && System.getProperty("java.awt.headless").equals("true"))
\r
1260 int idWidth = calculateIdWidth().width + 4;
\r
1261 seqPanelWidth = alignFrame.getWidth() - idWidth;
\r
1264 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1268 int hgap = av.charHeight;
\r
1269 if (av.scaleAboveWrapped)
\r
1270 hgap += av.charHeight;
\r
1272 int annotationHeight = 0;
\r
1273 if (av.showAnnotation)
\r
1275 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1278 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1280 + annotationHeight;
\r
1282 int maxwidth = av.alignment.getWidth();
\r
1283 if (av.hasHiddenColumns)
\r
1284 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1287 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r
1295 * @author $author$
\r
1296 * @version $Revision$
\r
1302 * Creates a new Preview object.
\r
1304 * @param image DOCUMENT ME!
\r
1306 public Preview(Image image)
\r
1308 setResizable(true);
\r
1309 setSize(image.getWidth(this), image.getHeight(this));
\r
1311 getContentPane().setLayout(new BorderLayout());
\r
1312 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1321 * @author $author$
\r
1322 * @version $Revision$
\r
1324 class PreviewPanel
\r
1330 * Creates a new PreviewPanel object.
\r
1332 * @param image DOCUMENT ME!
\r
1334 public PreviewPanel(Image image)
\r
1336 this.image = image;
\r
1342 * @param g DOCUMENT ME!
\r
1344 public void paintComponent(Graphics g)
\r
1346 if (image != null)
\r
1348 g.drawImage(image, 0, 0, this);
\r
1352 System.out.println("DEBUG:image is null");
\r