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());
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163 case KeyEvent.VK_DELETE:
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166 seqPanel.deleteGapAtCursor(evt.isControlDown());
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170 case KeyEvent.VK_BACK_SPACE:
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173 alignFrame.cut_actionPerformed(null);
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174 seqPanel.seqCanvas.repaint();
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178 case KeyEvent.VK_S:
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181 seqPanel.setCursorRow();
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184 case KeyEvent.VK_C:
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187 seqPanel.setCursorColumn();
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190 case KeyEvent.VK_P:
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193 seqPanel.setCursorPosition();
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197 case KeyEvent.VK_ENTER:
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198 case KeyEvent.VK_COMMA:
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201 seqPanel.setCursorRowAndColumn();
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205 case KeyEvent.VK_Q:
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208 seqPanel.setSelectionAreaAtCursor(true);
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211 case KeyEvent.VK_M:
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214 seqPanel.setSelectionAreaAtCursor(false);
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218 case KeyEvent.VK_F2:
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219 av.cursorMode = ! av.cursorMode;
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220 alignFrame.statusBar.setText("Keyboard editing mode is "+
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221 (av.cursorMode ? "on" : "off"));
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224 seqPanel.seqCanvas.cursorX = av.startRes;
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225 seqPanel.seqCanvas.cursorY = av.startSeq;
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227 seqPanel.seqCanvas.repaint();
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230 case KeyEvent.VK_F1:
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233 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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234 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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235 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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237 javax.help.HelpBroker hb = hs.createHelpBroker();
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238 hb.setCurrentID("home");
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239 hb.setDisplayed(true);
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241 catch (Exception ex)
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243 ex.printStackTrace();
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255 public void fontChanged()
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257 // set idCanvas bufferedImage to null
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258 // to prevent drawing old image
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259 FontMetrics fm = getFontMetrics(av.getFont());
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261 scalePanelHolder.setPreferredSize(new Dimension(10,
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262 av.charHeight + fm.getDescent()));
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263 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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264 av.charHeight + fm.getDescent()));
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266 idPanel.idCanvas.gg = null;
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267 seqPanel.seqCanvas.img = null;
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268 annotationPanel.adjustPanelHeight();
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270 Dimension d = calculateIdWidth();
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271 d.setSize(d.width + 4, d.height);
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272 idPanel.idCanvas.setPreferredSize(d);
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273 hscrollFillerPanel.setPreferredSize(d);
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275 if (av.getWrapAlignment())
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277 int max = av.alignment.getWidth() /
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278 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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279 vscroll.setMaximum(max);
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280 vscroll.setUnitIncrement(1);
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281 vscroll.setVisibleAmount(1);
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285 setScrollValues(av.getStartRes(), av.getStartSeq());
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288 if (overviewPanel != null)
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289 overviewPanel.setBoxPosition();
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297 * @return DOCUMENT ME!
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299 public Dimension calculateIdWidth()
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301 Container c = new Container();
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303 FontMetrics fm = c.getFontMetrics(av.font);
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304 AlignmentI al = av.getAlignment();
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310 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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312 SequenceI s = al.getSequenceAt(i);
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314 id = s.getDisplayId(av.getShowJVSuffix());
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316 if (fm.stringWidth(id) > idWidth)
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318 idWidth = fm.stringWidth(id);
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324 // Also check annotation label widths
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327 if (al.getAlignmentAnnotation() != null)
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329 fm = c.getFontMetrics(alabels.getFont());
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331 while (i < al.getAlignmentAnnotation().length)
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333 String label = al.getAlignmentAnnotation()[i].label;
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335 if (fm.stringWidth(label) > idWidth)
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337 idWidth = fm.stringWidth(label);
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344 return new Dimension(idWidth, 12);
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350 * @param results DOCUMENT ME!
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352 public void highlightSearchResults(SearchResults results)
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354 seqPanel.seqCanvas.highlightSearchResults(results);
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356 // do we need to scroll the panel?
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357 if (results != null)
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359 SequenceI seq = results.getResultSequence(0);
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360 int seqIndex = av.alignment.findIndex(seq);
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361 int start = seq.findIndex(results.getResultStart(0)) - 1;
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362 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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364 if(!av.wrapAlignment)
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366 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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367 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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369 setScrollValues(start, seqIndex);
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374 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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375 if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
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377 vscroll.setValue(start / cwidth);
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378 av.startRes = vscroll.getValue() * cwidth;
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387 * @return DOCUMENT ME!
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389 public OverviewPanel getOverviewPanel()
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391 return overviewPanel;
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397 * @param op DOCUMENT ME!
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399 public void setOverviewPanel(OverviewPanel op)
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401 overviewPanel = op;
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407 * @param b DOCUMENT ME!
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409 public void setAnnotationVisible(boolean b)
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411 if (!av.wrapAlignment)
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413 annotationSpaceFillerHolder.setVisible(b);
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414 annotationScroller.setVisible(b);
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422 * @param wrap DOCUMENT ME!
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424 public void setWrapAlignment(boolean wrap)
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427 scalePanelHolder.setVisible(!wrap);
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428 hscroll.setVisible(!wrap);
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429 idwidthAdjuster.setVisible(!wrap);
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433 annotationScroller.setVisible(false);
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434 annotationSpaceFillerHolder.setVisible(false);
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436 else if (av.showAnnotation)
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438 annotationScroller.setVisible(true);
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439 annotationSpaceFillerHolder.setVisible(true);
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442 idSpaceFillerPanel1.setVisible(!wrap);
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447 // return value is true if the scroll is valid
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448 public boolean scrollUp(boolean up)
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452 if (vscroll.getValue() < 1)
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458 vscroll.setValue(vscroll.getValue() - 1);
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462 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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468 vscroll.setValue(vscroll.getValue() + 1);
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479 * @param right DOCUMENT ME!
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481 * @return DOCUMENT ME!
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483 public boolean scrollRight(boolean right)
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487 if (hscroll.getValue() < 1)
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493 hscroll.setValue(hscroll.getValue() - 1);
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497 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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503 hscroll.setValue(hscroll.getValue() + 1);
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514 * @param x DOCUMENT ME!
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515 * @param y DOCUMENT ME!
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517 public void setScrollValues(int x, int y)
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520 int width = av.alignment.getWidth();
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521 int height = av.alignment.getHeight();
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523 if(av.hasHiddenColumns)
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524 width = av.getColumnSelection().findColumnPosition(width);
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526 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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528 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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529 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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531 if (hextent > width)
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536 if (vextent > height)
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541 if ( (hextent + x) > width)
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543 x = width - hextent;
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546 if ( (vextent + y) > height)
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548 y = height - vextent;
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561 hscroll.setValues(x, hextent, 0, width);
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562 vscroll.setValues(y, vextent, 0, height);
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568 * @param evt DOCUMENT ME!
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570 public void adjustmentValueChanged(AdjustmentEvent evt)
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572 int oldX = av.getStartRes();
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573 int oldY = av.getStartSeq();
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575 if (evt.getSource() == hscroll)
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577 int x = hscroll.getValue();
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580 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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583 if (evt.getSource() == vscroll)
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585 int offy = vscroll.getValue();
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587 if (av.getWrapAlignment())
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589 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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590 seqCanvas.getWidth());
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591 av.setStartRes(vscroll.getValue() * rowSize);
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592 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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596 av.setStartSeq(offy);
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597 av.setEndSeq(offy +
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598 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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602 if (overviewPanel != null)
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604 overviewPanel.setBoxPosition();
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607 int scrollX = av.startRes - oldX;
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608 int scrollY = av.startSeq - oldY;
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610 if (av.getWrapAlignment() || !fastPaint)
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616 // Make sure we're not trying to draw a panel
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617 // larger than the visible window
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618 if(scrollX>av.endRes-av.startRes)
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619 scrollX = av.endRes-av.startRes;
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620 else if(scrollX<av.startRes-av.endRes)
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621 scrollX = av.startRes - av.endRes;
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623 if(scrollX!=0 || scrollY!=0)
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625 idPanel.idCanvas.fastPaint(scrollY);
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626 seqPanel.seqCanvas.fastPaint(scrollX,
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628 scalePanel.repaint();
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630 if (av.getShowAnnotation())
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632 annotationPanel.fastPaint(scrollX);
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641 * @param g DOCUMENT ME!
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643 public void paintComponent(Graphics g)
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647 Dimension d = idPanel.idCanvas.getPreferredSize();
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648 idPanelHolder.setPreferredSize(d);
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649 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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652 if (av.getWrapAlignment())
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654 int max = av.alignment.getWidth() /
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655 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
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658 vscroll.setMaximum(max);
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659 vscroll.setUnitIncrement(1);
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660 vscroll.setVisibleAmount(1);
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664 setScrollValues(av.getStartRes(), av.getStartSeq());
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667 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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668 && overviewPanel != null)
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669 overviewPanel.updateOverviewImage();
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676 * @param pg DOCUMENT ME!
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677 * @param pf DOCUMENT ME!
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678 * @param pi DOCUMENT ME!
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680 * @return DOCUMENT ME!
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682 * @throws PrinterException DOCUMENT ME!
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684 public int print(Graphics pg, PageFormat pf, int pi)
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685 throws PrinterException
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687 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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689 int pwidth = (int) pf.getImageableWidth();
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690 int pheight = (int) pf.getImageableHeight();
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692 if (av.getWrapAlignment())
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694 return printWrappedAlignment(pg, pwidth, pheight, pi);
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698 return printUnwrapped(pg, pwidth, pheight, pi);
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705 * @param pg DOCUMENT ME!
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706 * @param pwidth DOCUMENT ME!
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707 * @param pheight DOCUMENT ME!
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708 * @param pi DOCUMENT ME!
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710 * @return DOCUMENT ME!
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712 * @throws PrinterException DOCUMENT ME!
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714 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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715 throws PrinterException
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717 int idWidth = calculateIdWidth().width + 4;
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718 FontMetrics fm = getFontMetrics(av.getFont());
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719 int scaleHeight = av.charHeight + fm.getDescent();
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721 pg.setColor(Color.white);
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722 pg.fillRect(0, 0, pwidth, pheight);
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723 pg.setFont(av.getFont());
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725 ////////////////////////////////////
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726 /// How many sequences and residues can we fit on a printable page?
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727 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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729 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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732 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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734 /////////////////////////////
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735 /// Only print these sequences and residues on this page
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738 /////////////////////////////
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739 /// Only print these sequences and residues on this page
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742 /////////////////////////////
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743 /// Only print these sequences and residues on this page
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746 /////////////////////////////
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747 /// Only print these sequences and residues on this page
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749 startRes = (pi % pagesWide) * totalRes;
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750 endRes = (startRes + totalRes) - 1;
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752 if (endRes > (av.getAlignment().getWidth() - 1))
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754 endRes = av.getAlignment().getWidth() - 1;
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757 startSeq = (pi / pagesWide) * totalSeq;
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758 endSeq = startSeq + totalSeq;
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760 if (endSeq > av.getAlignment().getHeight())
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762 endSeq = av.getAlignment().getHeight();
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765 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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767 if (av.showAnnotation)
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769 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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772 pagesHigh /= pheight;
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774 if (pi >= (pagesWide * pagesHigh))
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776 return Printable.NO_SUCH_PAGE;
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780 pg.translate(idWidth, 0);
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781 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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782 pg.translate( -idWidth, scaleHeight);
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786 Color currentColor = null;
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787 Color currentTextColor = null;
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789 pg.setFont(new Font(av.getFont().getName(),
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791 av.getFont().getSize()));
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792 for (int i = startSeq; i < endSeq; i++)
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794 if ( (av.getSelectionGroup() != null) &&
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795 av.getSelectionGroup().sequences.contains(
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796 av.getAlignment().getSequenceAt(i)))
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798 currentColor = Color.gray;
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799 currentTextColor = Color.black;
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803 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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804 currentTextColor = Color.black;
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807 pg.setColor(currentColor);
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808 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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809 av.getCharHeight());
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811 pg.setColor(currentTextColor);
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813 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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814 ( av.getShowJVSuffix());
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816 pg.drawString(string, 0,
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817 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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818 (av.getCharHeight() / 5));
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821 pg.setFont(av.getFont());
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823 // draw main sequence panel
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824 pg.translate(idWidth, 0);
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825 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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827 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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829 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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830 alabels.drawComponent( (Graphics2D) pg, idWidth);
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831 pg.translate(idWidth+3, 0);
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832 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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836 return Printable.PAGE_EXISTS;
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842 * @param pg DOCUMENT ME!
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843 * @param pwidth DOCUMENT ME!
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844 * @param pheight DOCUMENT ME!
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845 * @param pi DOCUMENT ME!
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847 * @return DOCUMENT ME!
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849 * @throws PrinterException DOCUMENT ME!
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851 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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853 throws PrinterException
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856 int annotationHeight = 0;
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857 AnnotationLabels labels = null;
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858 if (av.showAnnotation)
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860 annotationHeight = annotationPanel.adjustPanelHeight();
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861 labels = new AnnotationLabels(av);
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864 int hgap = av.charHeight;
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865 if (av.scaleAboveWrapped)
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866 hgap += av.charHeight;
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868 int cHeight = av.getAlignment().getHeight() * av.charHeight
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870 + annotationHeight;
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872 int idWidth = calculateIdWidth().width + 4;
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874 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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877 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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879 pg.setColor(Color.white);
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880 pg.fillRect(0, 0, pwidth, pheight);
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881 pg.setFont(av.getFont());
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885 pg.setColor(Color.black);
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887 pg.translate(0, -pi * pheight);
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889 pg.setClip(0, pi * pheight, pwidth, pheight);
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892 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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893 av.getFont().getSize());
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894 pg.setFont(italic);
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898 for (int i = 0; i < av.alignment.getHeight(); i++)
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900 SequenceI s = av.alignment.getSequenceAt(i);
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901 String string = s.getDisplayId( av.getShowJVSuffix());
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903 pg.drawString(string, 0,
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904 ( (i * av.charHeight) + ypos + av.charHeight) -
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905 (av.charHeight / 5));
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907 if (labels != null)
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911 (av.getAlignment().getHeight() * av.charHeight));
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913 pg.setFont(av.getFont());
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914 labels.drawComponent(pg, idWidth);
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915 pg.setFont(italic);
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918 (av.getAlignment().getHeight() * av.charHeight));
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923 while (ypos < totalHeight);
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925 pg.translate(idWidth, 0);
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927 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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929 if ( (pi * pheight) < totalHeight)
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931 return Printable.PAGE_EXISTS;
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936 return Printable.NO_SUCH_PAGE;
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940 void makeAlignmentImage(int type, File file)
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942 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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943 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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945 if (idPanel.getWidth() == 0)
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947 width += calculateIdWidth().getWidth() + 4;
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950 if (av.getWrapAlignment())
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952 height = getWrappedHeight();
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953 width = seqPanel.getWidth() + idPanel.getWidth();
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955 else if (av.getShowAnnotation())
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957 height += annotationPanel.adjustPanelHeight() + 3;
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960 jalview.util.ImageMaker im;
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961 if(type==jalview.util.ImageMaker.PNG)
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962 im = new jalview.util.ImageMaker(this,
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963 jalview.util.ImageMaker.PNG,
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964 "Create PNG image from alignment",
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965 width, height, file, null);
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967 im = new jalview.util.ImageMaker(this,
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968 jalview.util.ImageMaker.EPS,
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969 "Create EPS file from alignment",
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970 width, height, file, alignFrame.getTitle() );
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974 if (av.getWrapAlignment())
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976 if(im.getGraphics()!=null)
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978 printWrappedAlignment(im.getGraphics(), width, height, 0);
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984 if(im.getGraphics()!=null)
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986 printUnwrapped(im.getGraphics(), width, height, 0);
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991 catch (OutOfMemoryError err)
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993 System.out.println("########################\n"
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994 + "OUT OF MEMORY " + file + "\n"
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995 + "########################");
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997 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
998 "Out of Memory Creating Image!!"
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1000 "\nSee help files for increasing Java Virtual Machine memory."
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1001 , "Out of memory",
\r
1002 JOptionPane.WARNING_MESSAGE);
\r
1003 System.out.println("Create IMAGE: " + err);
\r
1007 catch (Exception ex)
\r
1009 ex.printStackTrace();
\r
1015 public void makeEPS(File epsFile)
\r
1017 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
\r
1023 public void makePNG(File pngFile)
\r
1025 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
\r
1028 public void makePNGImageMap(File imgMapFile, String imageName)
\r
1030 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1031 //////////////////////////////////////////////
\r
1032 int idWidth = calculateIdWidth().width + 4;
\r
1033 FontMetrics fm = getFontMetrics(av.getFont());
\r
1034 int scaleHeight = av.charHeight + fm.getDescent();
\r
1037 //////////////////////////////////
\r
1038 if (imgMapFile != null)
\r
1042 int s, sSize = av.alignment.getHeight(),
\r
1043 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1044 StringBuffer text = new StringBuffer();
\r
1045 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1046 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1047 out.println("<img src=\"" + imageName +
\r
1048 "\" border=\"0\" usemap=\"#Map\" >"
\r
1049 + "<map name=\"Map\">");
\r
1051 for (s = 0; s < sSize; s++)
\r
1053 sy = s * av.charHeight + scaleHeight;
\r
1055 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1056 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
\r
1057 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1058 for(res =0; res<alwidth; res++)
\r
1060 text = new StringBuffer();
\r
1061 Object obj = null;
\r
1062 if(av.alignment.isNucleotide())
\r
1063 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
\r
1065 obj = ResidueProperties.aa2Triplet.get(
\r
1066 seq.getCharAt(res) + "");
\r
1071 String triplet = obj.toString();
\r
1072 int alIndex = seq.findPosition(res);
\r
1073 gSize = groups.length;
\r
1074 for (g = 0; g < gSize; g++)
\r
1076 if(text.length()<1)
\r
1078 text.append("<area shape=\"rect\" coords=\""
\r
1079 + (idWidth + res * av.charWidth) + ","
\r
1081 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1082 + (av.charHeight + sy) + "\""
\r
1083 + " onMouseOver=\"toolTip('"
\r
1084 + alIndex + " " + triplet );
\r
1087 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
1088 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1091 if (features != null)
\r
1093 if(text.length()<1)
\r
1095 text.append("<area shape=\"rect\" coords=\""
\r
1096 + (idWidth + res * av.charWidth) + ","
\r
1098 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1099 + (av.charHeight + sy) + "\""
\r
1100 + " onMouseOver=\"toolTip('"
\r
1101 + alIndex + " " + triplet );
\r
1103 fSize = features.length;
\r
1104 for (f = 0; f < fSize; f++)
\r
1107 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1108 (features[f].getEnd() >= seq.findPosition(res)))
\r
1110 if (features[f].getType().equals("disulfide bond"))
\r
1112 if (features[f].getBegin() == seq.findPosition(res)
\r
1113 || features[f].getEnd() == seq.findPosition(res))
\r
1115 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
1116 features[f].getEnd());
\r
1121 text.append("<br>");
\r
1122 text.append(features[f].getType());
\r
1123 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
1124 text.append(" " + features[f].getDescription());
\r
1126 if (features[f].getStatus() != null && features[f].getStatus().length()>0)
\r
1128 text.append(" (" + features[f].getStatus() + ")");
\r
1135 if(text.length()>1)
\r
1137 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1138 out.println(text.toString());
\r
1142 out.println("</map></body></html>");
\r
1146 catch (Exception ex)
\r
1148 ex.printStackTrace();
\r
1150 } ///////////END OF IMAGE MAP
\r
1154 int getWrappedHeight()
\r
1157 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1158 seqPanel.seqCanvas.getWidth());
\r
1160 int hgap = av.charHeight;
\r
1161 if (av.scaleAboveWrapped)
\r
1162 hgap += av.charHeight;
\r
1164 int annotationHeight = 0;
\r
1165 if (av.showAnnotation)
\r
1167 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1170 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1172 + annotationHeight;
\r
1174 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
\r
1182 * @author $author$
\r
1183 * @version $Revision$
\r
1189 * Creates a new Preview object.
\r
1191 * @param image DOCUMENT ME!
\r
1193 public Preview(Image image)
\r
1195 setResizable(true);
\r
1196 setSize(image.getWidth(this), image.getHeight(this));
\r
1198 getContentPane().setLayout(new BorderLayout());
\r
1199 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1208 * @author $author$
\r
1209 * @version $Revision$
\r
1211 class PreviewPanel
\r
1217 * Creates a new PreviewPanel object.
\r
1219 * @param image DOCUMENT ME!
\r
1221 public PreviewPanel(Image image)
\r
1223 this.image = image;
\r
1229 * @param g DOCUMENT ME!
\r
1231 public void paintComponent(Graphics g)
\r
1233 if (image != null)
\r
1235 g.drawImage(image, 0, 0, this);
\r
1239 System.out.println("DEBUG:image is null");
\r