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 annotationPanel.adjustPanelHeight();
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96 annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
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97 getPreferredSize());
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98 annotationScroller.setPreferredSize(annotationPanel.
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99 getPreferredSize());
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100 setAnnotationVisible(av.getShowAnnotation());
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102 hscroll.addAdjustmentListener(this);
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103 vscroll.addAdjustmentListener(this);
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105 af.addKeyListener(new KeyAdapter()
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107 public void keyPressed(KeyEvent evt)
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110 && evt.getKeyCode()>=KeyEvent.VK_0
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111 && evt.getKeyCode()<=KeyEvent.VK_9)
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113 seqPanel.numberPressed(evt.getKeyChar());
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116 switch (evt.getKeyCode())
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118 case 27: // escape key
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119 av.setSelectionGroup(null);
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124 case KeyEvent.VK_DOWN:
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127 seqPanel.moveCursor(0,1);
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130 alignFrame.moveSelectedSequences(false);
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133 case KeyEvent.VK_UP:
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136 seqPanel.moveCursor(0,-1);
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139 alignFrame.moveSelectedSequences(true);
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142 case KeyEvent.VK_LEFT:
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145 seqPanel.moveCursor(-1,0);
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149 case KeyEvent.VK_RIGHT:
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152 seqPanel.moveCursor(1,0);
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156 case KeyEvent.VK_SPACE:
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159 seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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163 case KeyEvent.VK_DELETE:
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164 case KeyEvent.VK_BACK_SPACE:
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167 alignFrame.cut_actionPerformed(null);
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168 seqPanel.seqCanvas.repaint();
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171 seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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175 case KeyEvent.VK_S:
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178 seqPanel.setCursorRow();
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181 case KeyEvent.VK_C:
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184 seqPanel.setCursorColumn();
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187 case KeyEvent.VK_P:
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190 seqPanel.setCursorPosition();
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194 case KeyEvent.VK_ENTER:
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195 case KeyEvent.VK_COMMA:
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198 seqPanel.setCursorRowAndColumn();
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202 case KeyEvent.VK_Q:
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205 seqPanel.setSelectionAreaAtCursor(true);
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208 case KeyEvent.VK_M:
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211 seqPanel.setSelectionAreaAtCursor(false);
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215 case KeyEvent.VK_F2:
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216 av.cursorMode = ! av.cursorMode;
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217 alignFrame.statusBar.setText("Keyboard editing mode is "+
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218 (av.cursorMode ? "on" : "off"));
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221 seqPanel.seqCanvas.cursorX = av.startRes;
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222 seqPanel.seqCanvas.cursorY = av.startSeq;
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224 seqPanel.seqCanvas.repaint();
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227 case KeyEvent.VK_F1:
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230 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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231 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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232 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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234 javax.help.HelpBroker hb = hs.createHelpBroker();
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235 hb.setCurrentID("home");
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236 hb.setDisplayed(true);
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238 catch (Exception ex)
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240 ex.printStackTrace();
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252 public void fontChanged()
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254 // set idCanvas bufferedImage to null
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255 // to prevent drawing old image
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256 FontMetrics fm = getFontMetrics(av.getFont());
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258 scalePanelHolder.setPreferredSize(new Dimension(10,
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259 av.charHeight + fm.getDescent()));
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260 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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261 av.charHeight + fm.getDescent()));
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263 idPanel.idCanvas.gg = null;
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264 seqPanel.seqCanvas.img = null;
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265 annotationPanel.adjustPanelHeight();
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267 Dimension d = calculateIdWidth();
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268 d.setSize(d.width + 4, d.height);
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269 idPanel.idCanvas.setPreferredSize(d);
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270 hscrollFillerPanel.setPreferredSize(d);
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272 if (av.getWrapAlignment())
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274 int max = av.alignment.getWidth() /
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275 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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276 vscroll.setMaximum(max);
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277 vscroll.setUnitIncrement(1);
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278 vscroll.setVisibleAmount(1);
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282 setScrollValues(av.getStartRes(), av.getStartSeq());
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285 if (overviewPanel != null)
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286 overviewPanel.setBoxPosition();
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294 * @return DOCUMENT ME!
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296 public Dimension calculateIdWidth()
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298 Container c = new Container();
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300 FontMetrics fm = c.getFontMetrics(av.font);
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301 AlignmentI al = av.getAlignment();
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307 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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309 SequenceI s = al.getSequenceAt(i);
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311 id = s.getDisplayId(av.getShowJVSuffix());
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313 if (fm.stringWidth(id) > idWidth)
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315 idWidth = fm.stringWidth(id);
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321 // Also check annotation label widths
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324 if (al.getAlignmentAnnotation() != null)
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326 fm = c.getFontMetrics(alabels.getFont());
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328 while (i < al.getAlignmentAnnotation().length)
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330 String label = al.getAlignmentAnnotation()[i].label;
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332 if (fm.stringWidth(label) > idWidth)
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334 idWidth = fm.stringWidth(label);
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341 return new Dimension(idWidth, 12);
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347 * @param results DOCUMENT ME!
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349 public void highlightSearchResults(SearchResults results)
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351 seqPanel.seqCanvas.highlightSearchResults(results);
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353 // do we need to scroll the panel?
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354 if (results != null)
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356 SequenceI seq = results.getResultSequence(0);
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357 int seqIndex = av.alignment.findIndex(seq);
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358 int start = seq.findIndex(results.getResultStart(0)) - 1;
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359 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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361 if(!av.wrapAlignment)
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363 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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364 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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366 setScrollValues(start, seqIndex);
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371 scrollToWrappedVisible(start);
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376 void scrollToWrappedVisible(int res)
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378 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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379 if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
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381 vscroll.setValue(res / cwidth);
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382 av.startRes = vscroll.getValue() * cwidth;
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389 * @return DOCUMENT ME!
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391 public OverviewPanel getOverviewPanel()
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393 return overviewPanel;
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399 * @param op DOCUMENT ME!
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401 public void setOverviewPanel(OverviewPanel op)
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403 overviewPanel = op;
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409 * @param b DOCUMENT ME!
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411 public void setAnnotationVisible(boolean b)
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413 if (!av.wrapAlignment)
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415 annotationSpaceFillerHolder.setVisible(b);
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416 annotationScroller.setVisible(b);
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424 * @param wrap DOCUMENT ME!
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426 public void setWrapAlignment(boolean wrap)
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429 scalePanelHolder.setVisible(!wrap);
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430 hscroll.setVisible(!wrap);
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431 idwidthAdjuster.setVisible(!wrap);
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435 annotationScroller.setVisible(false);
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436 annotationSpaceFillerHolder.setVisible(false);
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438 else if (av.showAnnotation)
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440 annotationScroller.setVisible(true);
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441 annotationSpaceFillerHolder.setVisible(true);
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444 idSpaceFillerPanel1.setVisible(!wrap);
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449 // return value is true if the scroll is valid
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450 public boolean scrollUp(boolean up)
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454 if (vscroll.getValue() < 1)
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460 vscroll.setValue(vscroll.getValue() - 1);
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464 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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470 vscroll.setValue(vscroll.getValue() + 1);
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481 * @param right DOCUMENT ME!
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483 * @return DOCUMENT ME!
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485 public boolean scrollRight(boolean right)
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489 if (hscroll.getValue() < 1)
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495 hscroll.setValue(hscroll.getValue() - 1);
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499 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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505 hscroll.setValue(hscroll.getValue() + 1);
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516 * @param x DOCUMENT ME!
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517 * @param y DOCUMENT ME!
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519 public void setScrollValues(int x, int y)
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522 int width = av.alignment.getWidth();
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523 int height = av.alignment.getHeight();
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525 if(av.hasHiddenColumns)
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526 width = av.getColumnSelection().findColumnPosition(width);
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528 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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530 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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531 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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533 if (hextent > width)
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538 if (vextent > height)
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543 if ( (hextent + x) > width)
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545 x = width - hextent;
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548 if ( (vextent + y) > height)
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550 y = height - vextent;
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563 hscroll.setValues(x, hextent, 0, width);
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564 vscroll.setValues(y, vextent, 0, height);
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570 * @param evt DOCUMENT ME!
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572 public void adjustmentValueChanged(AdjustmentEvent evt)
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574 int oldX = av.getStartRes();
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575 int oldY = av.getStartSeq();
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577 if (evt.getSource() == hscroll)
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579 int x = hscroll.getValue();
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582 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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585 if (evt.getSource() == vscroll)
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587 int offy = vscroll.getValue();
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589 if (av.getWrapAlignment())
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591 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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592 seqCanvas.getWidth());
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593 av.setStartRes(vscroll.getValue() * rowSize);
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594 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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598 av.setStartSeq(offy);
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599 av.setEndSeq(offy +
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600 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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604 if (overviewPanel != null)
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606 overviewPanel.setBoxPosition();
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609 int scrollX = av.startRes - oldX;
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610 int scrollY = av.startSeq - oldY;
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612 if (av.getWrapAlignment() || !fastPaint)
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618 // Make sure we're not trying to draw a panel
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619 // larger than the visible window
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620 if(scrollX>av.endRes-av.startRes)
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621 scrollX = av.endRes-av.startRes;
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622 else if(scrollX<av.startRes-av.endRes)
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623 scrollX = av.startRes - av.endRes;
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625 if(scrollX!=0 || scrollY!=0)
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627 idPanel.idCanvas.fastPaint(scrollY);
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628 seqPanel.seqCanvas.fastPaint(scrollX,
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630 scalePanel.repaint();
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632 if (av.getShowAnnotation())
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634 annotationPanel.fastPaint(scrollX);
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643 * @param g DOCUMENT ME!
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645 public void paintComponent(Graphics g)
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649 Dimension d = idPanel.idCanvas.getPreferredSize();
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650 idPanelHolder.setPreferredSize(d);
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651 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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654 if (av.getWrapAlignment())
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656 int max = av.alignment.getWidth() /
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657 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
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660 vscroll.setMaximum(max);
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661 vscroll.setUnitIncrement(1);
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662 vscroll.setVisibleAmount(1);
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666 setScrollValues(av.getStartRes(), av.getStartSeq());
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669 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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670 && overviewPanel != null)
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671 overviewPanel.updateOverviewImage();
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678 * @param pg DOCUMENT ME!
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679 * @param pf DOCUMENT ME!
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680 * @param pi DOCUMENT ME!
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682 * @return DOCUMENT ME!
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684 * @throws PrinterException DOCUMENT ME!
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686 public int print(Graphics pg, PageFormat pf, int pi)
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687 throws PrinterException
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689 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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691 int pwidth = (int) pf.getImageableWidth();
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692 int pheight = (int) pf.getImageableHeight();
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694 if (av.getWrapAlignment())
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696 return printWrappedAlignment(pg, pwidth, pheight, pi);
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700 return printUnwrapped(pg, pwidth, pheight, pi);
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707 * @param pg DOCUMENT ME!
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708 * @param pwidth DOCUMENT ME!
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709 * @param pheight DOCUMENT ME!
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710 * @param pi DOCUMENT ME!
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712 * @return DOCUMENT ME!
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714 * @throws PrinterException DOCUMENT ME!
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716 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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717 throws PrinterException
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719 int idWidth = calculateIdWidth().width + 4;
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720 FontMetrics fm = getFontMetrics(av.getFont());
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721 int scaleHeight = av.charHeight + fm.getDescent();
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723 pg.setColor(Color.white);
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724 pg.fillRect(0, 0, pwidth, pheight);
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725 pg.setFont(av.getFont());
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727 ////////////////////////////////////
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728 /// How many sequences and residues can we fit on a printable page?
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729 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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731 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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734 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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736 /////////////////////////////
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737 /// Only print these sequences and residues on this page
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740 /////////////////////////////
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741 /// Only print these sequences and residues on this page
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744 /////////////////////////////
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745 /// Only print these sequences and residues on this page
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748 /////////////////////////////
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749 /// Only print these sequences and residues on this page
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751 startRes = (pi % pagesWide) * totalRes;
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752 endRes = (startRes + totalRes) - 1;
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754 if (endRes > (av.getAlignment().getWidth() - 1))
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756 endRes = av.getAlignment().getWidth() - 1;
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759 startSeq = (pi / pagesWide) * totalSeq;
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760 endSeq = startSeq + totalSeq;
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762 if (endSeq > av.getAlignment().getHeight())
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764 endSeq = av.getAlignment().getHeight();
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767 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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769 if (av.showAnnotation)
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771 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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774 pagesHigh /= pheight;
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776 if (pi >= (pagesWide * pagesHigh))
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778 return Printable.NO_SUCH_PAGE;
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782 pg.translate(idWidth, 0);
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783 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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784 pg.translate( -idWidth, scaleHeight);
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788 Color currentColor = null;
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789 Color currentTextColor = null;
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791 pg.setFont(new Font(av.getFont().getName(),
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793 av.getFont().getSize()));
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794 for (int i = startSeq; i < endSeq; i++)
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796 if ( (av.getSelectionGroup() != null) &&
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797 av.getSelectionGroup().sequences.contains(
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798 av.getAlignment().getSequenceAt(i)))
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800 currentColor = Color.gray;
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801 currentTextColor = Color.black;
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805 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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806 currentTextColor = Color.black;
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809 pg.setColor(currentColor);
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810 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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811 av.getCharHeight());
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813 pg.setColor(currentTextColor);
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815 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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816 ( av.getShowJVSuffix());
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818 pg.drawString(string, 0,
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819 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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820 (av.getCharHeight() / 5));
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823 pg.setFont(av.getFont());
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825 // draw main sequence panel
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826 pg.translate(idWidth, 0);
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827 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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829 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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831 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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832 alabels.drawComponent( (Graphics2D) pg, idWidth);
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833 pg.translate(idWidth+3, 0);
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834 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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838 return Printable.PAGE_EXISTS;
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844 * @param pg DOCUMENT ME!
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845 * @param pwidth DOCUMENT ME!
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846 * @param pheight DOCUMENT ME!
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847 * @param pi DOCUMENT ME!
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849 * @return DOCUMENT ME!
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851 * @throws PrinterException DOCUMENT ME!
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853 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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855 throws PrinterException
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858 int annotationHeight = 0;
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859 AnnotationLabels labels = null;
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860 if (av.showAnnotation)
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862 annotationHeight = annotationPanel.adjustPanelHeight();
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863 labels = new AnnotationLabels(av);
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866 int hgap = av.charHeight;
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867 if (av.scaleAboveWrapped)
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868 hgap += av.charHeight;
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870 int cHeight = av.getAlignment().getHeight() * av.charHeight
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872 + annotationHeight;
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874 int idWidth = calculateIdWidth().width + 4;
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876 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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879 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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881 pg.setColor(Color.white);
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882 pg.fillRect(0, 0, pwidth, pheight);
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883 pg.setFont(av.getFont());
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887 pg.setColor(Color.black);
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889 pg.translate(0, -pi * pheight);
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891 pg.setClip(0, pi * pheight, pwidth, pheight);
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894 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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895 av.getFont().getSize());
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896 pg.setFont(italic);
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900 for (int i = 0; i < av.alignment.getHeight(); i++)
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902 SequenceI s = av.alignment.getSequenceAt(i);
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903 String string = s.getDisplayId( av.getShowJVSuffix());
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905 pg.drawString(string, 0,
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906 ( (i * av.charHeight) + ypos + av.charHeight) -
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907 (av.charHeight / 5));
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909 if (labels != null)
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913 (av.getAlignment().getHeight() * av.charHeight));
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915 pg.setFont(av.getFont());
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916 labels.drawComponent(pg, idWidth);
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917 pg.setFont(italic);
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920 (av.getAlignment().getHeight() * av.charHeight));
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925 while (ypos < totalHeight);
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927 pg.translate(idWidth, 0);
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929 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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931 if ( (pi * pheight) < totalHeight)
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933 return Printable.PAGE_EXISTS;
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938 return Printable.NO_SUCH_PAGE;
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942 void makeAlignmentImage(int type, File file)
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944 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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945 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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947 if (idPanel.getWidth() == 0)
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949 width += calculateIdWidth().getWidth() + 4;
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952 if (av.getWrapAlignment())
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954 height = getWrappedHeight();
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955 width = seqPanel.getWidth() + idPanel.getWidth();
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957 else if (av.getShowAnnotation())
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959 height += annotationPanel.adjustPanelHeight() + 3;
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962 jalview.util.ImageMaker im;
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963 if(type==jalview.util.ImageMaker.PNG)
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964 im = new jalview.util.ImageMaker(this,
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965 jalview.util.ImageMaker.PNG,
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966 "Create PNG image from alignment",
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967 width, height, file, null);
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969 im = new jalview.util.ImageMaker(this,
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970 jalview.util.ImageMaker.EPS,
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971 "Create EPS file from alignment",
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972 width, height, file, alignFrame.getTitle() );
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976 if (av.getWrapAlignment())
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978 if(im.getGraphics()!=null)
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980 printWrappedAlignment(im.getGraphics(), width, height, 0);
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986 if(im.getGraphics()!=null)
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988 printUnwrapped(im.getGraphics(), width, height, 0);
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993 catch (OutOfMemoryError err)
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995 System.out.println("########################\n"
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996 + "OUT OF MEMORY " + file + "\n"
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997 + "########################");
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999 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1000 "Out of Memory Creating Image!!"
\r
1002 "\nSee help files for increasing Java Virtual Machine memory."
\r
1003 , "Out of memory",
\r
1004 JOptionPane.WARNING_MESSAGE);
\r
1005 System.out.println("Create IMAGE: " + err);
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1009 catch (Exception ex)
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1011 ex.printStackTrace();
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1017 public void makeEPS(File epsFile)
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1019 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
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1025 public void makePNG(File pngFile)
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1027 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
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1030 public void makePNGImageMap(File imgMapFile, String imageName)
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1032 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1033 //////////////////////////////////////////////
\r
1034 int idWidth = calculateIdWidth().width + 4;
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1035 FontMetrics fm = getFontMetrics(av.getFont());
\r
1036 int scaleHeight = av.charHeight + fm.getDescent();
\r
1039 //////////////////////////////////
\r
1040 if (imgMapFile != null)
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1044 int s, sSize = av.alignment.getHeight(),
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1045 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
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1046 StringBuffer text = new StringBuffer();
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1047 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
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1048 out.println(jalview.io.HTMLOutput.getImageMapHTML());
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1049 out.println("<img src=\"" + imageName +
\r
1050 "\" border=\"0\" usemap=\"#Map\" >"
\r
1051 + "<map name=\"Map\">");
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1053 for (s = 0; s < sSize; s++)
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1055 sy = s * av.charHeight + scaleHeight;
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1057 SequenceI seq = av.alignment.getSequenceAt(s);
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1058 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
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1059 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1060 for(res =0; res<alwidth; res++)
\r
1062 text = new StringBuffer();
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1063 Object obj = null;
\r
1064 if(av.alignment.isNucleotide())
\r
1065 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
\r
1067 obj = ResidueProperties.aa2Triplet.get(
\r
1068 seq.getCharAt(res) + "");
\r
1073 String triplet = obj.toString();
\r
1074 int alIndex = seq.findPosition(res);
\r
1075 gSize = groups.length;
\r
1076 for (g = 0; g < gSize; g++)
\r
1078 if(text.length()<1)
\r
1080 text.append("<area shape=\"rect\" coords=\""
\r
1081 + (idWidth + res * av.charWidth) + ","
\r
1083 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1084 + (av.charHeight + sy) + "\""
\r
1085 + " onMouseOver=\"toolTip('"
\r
1086 + alIndex + " " + triplet );
\r
1089 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
1090 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1093 if (features != null)
\r
1095 if(text.length()<1)
\r
1097 text.append("<area shape=\"rect\" coords=\""
\r
1098 + (idWidth + res * av.charWidth) + ","
\r
1100 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1101 + (av.charHeight + sy) + "\""
\r
1102 + " onMouseOver=\"toolTip('"
\r
1103 + alIndex + " " + triplet );
\r
1105 fSize = features.length;
\r
1106 for (f = 0; f < fSize; f++)
\r
1109 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1110 (features[f].getEnd() >= seq.findPosition(res)))
\r
1112 if (features[f].getType().equals("disulfide bond"))
\r
1114 if (features[f].getBegin() == seq.findPosition(res)
\r
1115 || features[f].getEnd() == seq.findPosition(res))
\r
1117 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
1118 features[f].getEnd());
\r
1123 text.append("<br>");
\r
1124 text.append(features[f].getType());
\r
1125 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
1126 text.append(" " + features[f].getDescription());
\r
1128 if (features[f].getStatus() != null && features[f].getStatus().length()>0)
\r
1130 text.append(" (" + features[f].getStatus() + ")");
\r
1137 if(text.length()>1)
\r
1139 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1140 out.println(text.toString());
\r
1144 out.println("</map></body></html>");
\r
1148 catch (Exception ex)
\r
1150 ex.printStackTrace();
\r
1152 } ///////////END OF IMAGE MAP
\r
1156 int getWrappedHeight()
\r
1159 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1160 seqPanel.seqCanvas.getWidth());
\r
1162 int hgap = av.charHeight;
\r
1163 if (av.scaleAboveWrapped)
\r
1164 hgap += av.charHeight;
\r
1166 int annotationHeight = 0;
\r
1167 if (av.showAnnotation)
\r
1169 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1172 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1174 + annotationHeight;
\r
1176 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
\r
1184 * @author $author$
\r
1185 * @version $Revision$
\r
1191 * Creates a new Preview object.
\r
1193 * @param image DOCUMENT ME!
\r
1195 public Preview(Image image)
\r
1197 setResizable(true);
\r
1198 setSize(image.getWidth(this), image.getHeight(this));
\r
1200 getContentPane().setLayout(new BorderLayout());
\r
1201 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1210 * @author $author$
\r
1211 * @version $Revision$
\r
1213 class PreviewPanel
\r
1219 * Creates a new PreviewPanel object.
\r
1221 * @param image DOCUMENT ME!
\r
1223 public PreviewPanel(Image image)
\r
1225 this.image = image;
\r
1231 * @param g DOCUMENT ME!
\r
1233 public void paintComponent(Graphics g)
\r
1235 if (image != null)
\r
1237 g.drawImage(image, 0, 0, this);
\r
1241 System.out.println("DEBUG:image is null");
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