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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166 seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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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 scrollToWrappedVisible(start);
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379 void scrollToWrappedVisible(int res)
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381 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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382 if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
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384 vscroll.setValue(res / cwidth);
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385 av.startRes = vscroll.getValue() * cwidth;
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392 * @return DOCUMENT ME!
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394 public OverviewPanel getOverviewPanel()
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396 return overviewPanel;
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402 * @param op DOCUMENT ME!
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404 public void setOverviewPanel(OverviewPanel op)
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406 overviewPanel = op;
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412 * @param b DOCUMENT ME!
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414 public void setAnnotationVisible(boolean b)
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416 if (!av.wrapAlignment)
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418 annotationSpaceFillerHolder.setVisible(b);
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419 annotationScroller.setVisible(b);
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427 * @param wrap DOCUMENT ME!
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429 public void setWrapAlignment(boolean wrap)
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432 scalePanelHolder.setVisible(!wrap);
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433 hscroll.setVisible(!wrap);
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434 idwidthAdjuster.setVisible(!wrap);
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438 annotationScroller.setVisible(false);
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439 annotationSpaceFillerHolder.setVisible(false);
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441 else if (av.showAnnotation)
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443 annotationScroller.setVisible(true);
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444 annotationSpaceFillerHolder.setVisible(true);
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447 idSpaceFillerPanel1.setVisible(!wrap);
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452 // return value is true if the scroll is valid
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453 public boolean scrollUp(boolean up)
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457 if (vscroll.getValue() < 1)
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463 vscroll.setValue(vscroll.getValue() - 1);
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467 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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473 vscroll.setValue(vscroll.getValue() + 1);
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484 * @param right DOCUMENT ME!
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486 * @return DOCUMENT ME!
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488 public boolean scrollRight(boolean right)
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492 if (hscroll.getValue() < 1)
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498 hscroll.setValue(hscroll.getValue() - 1);
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502 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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508 hscroll.setValue(hscroll.getValue() + 1);
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519 * @param x DOCUMENT ME!
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520 * @param y DOCUMENT ME!
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522 public void setScrollValues(int x, int y)
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525 int width = av.alignment.getWidth();
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526 int height = av.alignment.getHeight();
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528 if(av.hasHiddenColumns)
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529 width = av.getColumnSelection().findColumnPosition(width);
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531 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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533 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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534 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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536 if (hextent > width)
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541 if (vextent > height)
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546 if ( (hextent + x) > width)
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548 x = width - hextent;
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551 if ( (vextent + y) > height)
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553 y = height - vextent;
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566 hscroll.setValues(x, hextent, 0, width);
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567 vscroll.setValues(y, vextent, 0, height);
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573 * @param evt DOCUMENT ME!
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575 public void adjustmentValueChanged(AdjustmentEvent evt)
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577 int oldX = av.getStartRes();
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578 int oldY = av.getStartSeq();
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580 if (evt.getSource() == hscroll)
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582 int x = hscroll.getValue();
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585 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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588 if (evt.getSource() == vscroll)
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590 int offy = vscroll.getValue();
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592 if (av.getWrapAlignment())
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594 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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595 seqCanvas.getWidth());
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596 av.setStartRes(vscroll.getValue() * rowSize);
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597 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
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601 av.setStartSeq(offy);
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602 av.setEndSeq(offy +
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603 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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607 if (overviewPanel != null)
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609 overviewPanel.setBoxPosition();
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612 int scrollX = av.startRes - oldX;
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613 int scrollY = av.startSeq - oldY;
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615 if (av.getWrapAlignment() || !fastPaint)
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621 // Make sure we're not trying to draw a panel
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622 // larger than the visible window
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623 if(scrollX>av.endRes-av.startRes)
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624 scrollX = av.endRes-av.startRes;
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625 else if(scrollX<av.startRes-av.endRes)
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626 scrollX = av.startRes - av.endRes;
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628 if(scrollX!=0 || scrollY!=0)
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630 idPanel.idCanvas.fastPaint(scrollY);
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631 seqPanel.seqCanvas.fastPaint(scrollX,
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633 scalePanel.repaint();
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635 if (av.getShowAnnotation())
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637 annotationPanel.fastPaint(scrollX);
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646 * @param g DOCUMENT ME!
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648 public void paintComponent(Graphics g)
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652 Dimension d = idPanel.idCanvas.getPreferredSize();
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653 idPanelHolder.setPreferredSize(d);
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654 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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657 if (av.getWrapAlignment())
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659 int max = av.alignment.getWidth() /
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660 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
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663 vscroll.setMaximum(max);
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664 vscroll.setUnitIncrement(1);
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665 vscroll.setVisibleAmount(1);
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669 setScrollValues(av.getStartRes(), av.getStartSeq());
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672 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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673 && overviewPanel != null)
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674 overviewPanel.updateOverviewImage();
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681 * @param pg DOCUMENT ME!
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682 * @param pf DOCUMENT ME!
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683 * @param pi DOCUMENT ME!
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685 * @return DOCUMENT ME!
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687 * @throws PrinterException DOCUMENT ME!
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689 public int print(Graphics pg, PageFormat pf, int pi)
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690 throws PrinterException
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692 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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694 int pwidth = (int) pf.getImageableWidth();
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695 int pheight = (int) pf.getImageableHeight();
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697 if (av.getWrapAlignment())
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699 return printWrappedAlignment(pg, pwidth, pheight, pi);
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703 return printUnwrapped(pg, pwidth, pheight, pi);
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710 * @param pg DOCUMENT ME!
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711 * @param pwidth DOCUMENT ME!
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712 * @param pheight DOCUMENT ME!
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713 * @param pi DOCUMENT ME!
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715 * @return DOCUMENT ME!
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717 * @throws PrinterException DOCUMENT ME!
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719 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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720 throws PrinterException
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722 int idWidth = calculateIdWidth().width + 4;
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723 FontMetrics fm = getFontMetrics(av.getFont());
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724 int scaleHeight = av.charHeight + fm.getDescent();
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726 pg.setColor(Color.white);
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727 pg.fillRect(0, 0, pwidth, pheight);
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728 pg.setFont(av.getFont());
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730 ////////////////////////////////////
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731 /// How many sequences and residues can we fit on a printable page?
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732 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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734 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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737 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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739 /////////////////////////////
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740 /// Only print these sequences and residues on this page
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743 /////////////////////////////
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744 /// Only print these sequences and residues on this page
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747 /////////////////////////////
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748 /// Only print these sequences and residues on this page
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751 /////////////////////////////
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752 /// Only print these sequences and residues on this page
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754 startRes = (pi % pagesWide) * totalRes;
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755 endRes = (startRes + totalRes) - 1;
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757 if (endRes > (av.getAlignment().getWidth() - 1))
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759 endRes = av.getAlignment().getWidth() - 1;
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762 startSeq = (pi / pagesWide) * totalSeq;
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763 endSeq = startSeq + totalSeq;
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765 if (endSeq > av.getAlignment().getHeight())
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767 endSeq = av.getAlignment().getHeight();
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770 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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772 if (av.showAnnotation)
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774 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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777 pagesHigh /= pheight;
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779 if (pi >= (pagesWide * pagesHigh))
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781 return Printable.NO_SUCH_PAGE;
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785 pg.translate(idWidth, 0);
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786 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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787 pg.translate( -idWidth, scaleHeight);
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791 Color currentColor = null;
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792 Color currentTextColor = null;
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794 pg.setFont(new Font(av.getFont().getName(),
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796 av.getFont().getSize()));
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797 for (int i = startSeq; i < endSeq; i++)
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799 if ( (av.getSelectionGroup() != null) &&
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800 av.getSelectionGroup().sequences.contains(
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801 av.getAlignment().getSequenceAt(i)))
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803 currentColor = Color.gray;
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804 currentTextColor = Color.black;
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808 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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809 currentTextColor = Color.black;
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812 pg.setColor(currentColor);
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813 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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814 av.getCharHeight());
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816 pg.setColor(currentTextColor);
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818 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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819 ( av.getShowJVSuffix());
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821 pg.drawString(string, 0,
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822 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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823 (av.getCharHeight() / 5));
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826 pg.setFont(av.getFont());
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828 // draw main sequence panel
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829 pg.translate(idWidth, 0);
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830 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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832 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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834 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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835 alabels.drawComponent( (Graphics2D) pg, idWidth);
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836 pg.translate(idWidth+3, 0);
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837 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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841 return Printable.PAGE_EXISTS;
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847 * @param pg DOCUMENT ME!
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848 * @param pwidth DOCUMENT ME!
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849 * @param pheight DOCUMENT ME!
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850 * @param pi DOCUMENT ME!
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852 * @return DOCUMENT ME!
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854 * @throws PrinterException DOCUMENT ME!
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856 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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858 throws PrinterException
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861 int annotationHeight = 0;
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862 AnnotationLabels labels = null;
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863 if (av.showAnnotation)
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865 annotationHeight = annotationPanel.adjustPanelHeight();
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866 labels = new AnnotationLabels(av);
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869 int hgap = av.charHeight;
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870 if (av.scaleAboveWrapped)
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871 hgap += av.charHeight;
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873 int cHeight = av.getAlignment().getHeight() * av.charHeight
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875 + annotationHeight;
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877 int idWidth = calculateIdWidth().width + 4;
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879 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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882 int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
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884 pg.setColor(Color.white);
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885 pg.fillRect(0, 0, pwidth, pheight);
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886 pg.setFont(av.getFont());
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890 pg.setColor(Color.black);
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892 pg.translate(0, -pi * pheight);
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894 pg.setClip(0, pi * pheight, pwidth, pheight);
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897 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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898 av.getFont().getSize());
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899 pg.setFont(italic);
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903 for (int i = 0; i < av.alignment.getHeight(); i++)
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905 SequenceI s = av.alignment.getSequenceAt(i);
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906 String string = s.getDisplayId( av.getShowJVSuffix());
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908 pg.drawString(string, 0,
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909 ( (i * av.charHeight) + ypos + av.charHeight) -
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910 (av.charHeight / 5));
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912 if (labels != null)
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916 (av.getAlignment().getHeight() * av.charHeight));
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918 pg.setFont(av.getFont());
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919 labels.drawComponent(pg, idWidth);
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920 pg.setFont(italic);
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923 (av.getAlignment().getHeight() * av.charHeight));
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928 while (ypos < totalHeight);
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930 pg.translate(idWidth, 0);
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932 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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934 if ( (pi * pheight) < totalHeight)
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936 return Printable.PAGE_EXISTS;
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941 return Printable.NO_SUCH_PAGE;
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945 void makeAlignmentImage(int type, File file)
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947 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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948 int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
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950 if (idPanel.getWidth() == 0)
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952 width += calculateIdWidth().getWidth() + 4;
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955 if (av.getWrapAlignment())
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957 height = getWrappedHeight();
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958 width = seqPanel.getWidth() + idPanel.getWidth();
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960 else if (av.getShowAnnotation())
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962 height += annotationPanel.adjustPanelHeight() + 3;
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965 jalview.util.ImageMaker im;
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966 if(type==jalview.util.ImageMaker.PNG)
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967 im = new jalview.util.ImageMaker(this,
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968 jalview.util.ImageMaker.PNG,
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969 "Create PNG image from alignment",
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970 width, height, file, null);
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972 im = new jalview.util.ImageMaker(this,
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973 jalview.util.ImageMaker.EPS,
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974 "Create EPS file from alignment",
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975 width, height, file, alignFrame.getTitle() );
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979 if (av.getWrapAlignment())
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981 if(im.getGraphics()!=null)
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983 printWrappedAlignment(im.getGraphics(), width, height, 0);
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989 if(im.getGraphics()!=null)
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991 printUnwrapped(im.getGraphics(), width, height, 0);
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996 catch (OutOfMemoryError err)
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998 System.out.println("########################\n"
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999 + "OUT OF MEMORY " + file + "\n"
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1000 + "########################");
\r
1002 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1003 "Out of Memory Creating Image!!"
\r
1005 "\nSee help files for increasing Java Virtual Machine memory."
\r
1006 , "Out of memory",
\r
1007 JOptionPane.WARNING_MESSAGE);
\r
1008 System.out.println("Create IMAGE: " + err);
\r
1012 catch (Exception ex)
\r
1014 ex.printStackTrace();
\r
1020 public void makeEPS(File epsFile)
\r
1022 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
\r
1028 public void makePNG(File pngFile)
\r
1030 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
\r
1033 public void makePNGImageMap(File imgMapFile, String imageName)
\r
1035 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1036 //////////////////////////////////////////////
\r
1037 int idWidth = calculateIdWidth().width + 4;
\r
1038 FontMetrics fm = getFontMetrics(av.getFont());
\r
1039 int scaleHeight = av.charHeight + fm.getDescent();
\r
1042 //////////////////////////////////
\r
1043 if (imgMapFile != null)
\r
1047 int s, sSize = av.alignment.getHeight(),
\r
1048 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1049 StringBuffer text = new StringBuffer();
\r
1050 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1051 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1052 out.println("<img src=\"" + imageName +
\r
1053 "\" border=\"0\" usemap=\"#Map\" >"
\r
1054 + "<map name=\"Map\">");
\r
1056 for (s = 0; s < sSize; s++)
\r
1058 sy = s * av.charHeight + scaleHeight;
\r
1060 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1061 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
\r
1062 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1063 for(res =0; res<alwidth; res++)
\r
1065 text = new StringBuffer();
\r
1066 Object obj = null;
\r
1067 if(av.alignment.isNucleotide())
\r
1068 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
\r
1070 obj = ResidueProperties.aa2Triplet.get(
\r
1071 seq.getCharAt(res) + "");
\r
1076 String triplet = obj.toString();
\r
1077 int alIndex = seq.findPosition(res);
\r
1078 gSize = groups.length;
\r
1079 for (g = 0; g < gSize; g++)
\r
1081 if(text.length()<1)
\r
1083 text.append("<area shape=\"rect\" coords=\""
\r
1084 + (idWidth + res * av.charWidth) + ","
\r
1086 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1087 + (av.charHeight + sy) + "\""
\r
1088 + " onMouseOver=\"toolTip('"
\r
1089 + alIndex + " " + triplet );
\r
1092 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
1093 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1096 if (features != null)
\r
1098 if(text.length()<1)
\r
1100 text.append("<area shape=\"rect\" coords=\""
\r
1101 + (idWidth + res * av.charWidth) + ","
\r
1103 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1104 + (av.charHeight + sy) + "\""
\r
1105 + " onMouseOver=\"toolTip('"
\r
1106 + alIndex + " " + triplet );
\r
1108 fSize = features.length;
\r
1109 for (f = 0; f < fSize; f++)
\r
1112 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1113 (features[f].getEnd() >= seq.findPosition(res)))
\r
1115 if (features[f].getType().equals("disulfide bond"))
\r
1117 if (features[f].getBegin() == seq.findPosition(res)
\r
1118 || features[f].getEnd() == seq.findPosition(res))
\r
1120 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
1121 features[f].getEnd());
\r
1126 text.append("<br>");
\r
1127 text.append(features[f].getType());
\r
1128 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
1129 text.append(" " + features[f].getDescription());
\r
1131 if (features[f].getStatus() != null && features[f].getStatus().length()>0)
\r
1133 text.append(" (" + features[f].getStatus() + ")");
\r
1140 if(text.length()>1)
\r
1142 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1143 out.println(text.toString());
\r
1147 out.println("</map></body></html>");
\r
1151 catch (Exception ex)
\r
1153 ex.printStackTrace();
\r
1155 } ///////////END OF IMAGE MAP
\r
1159 int getWrappedHeight()
\r
1162 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1163 seqPanel.seqCanvas.getWidth());
\r
1165 int hgap = av.charHeight;
\r
1166 if (av.scaleAboveWrapped)
\r
1167 hgap += av.charHeight;
\r
1169 int annotationHeight = 0;
\r
1170 if (av.showAnnotation)
\r
1172 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1175 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1177 + annotationHeight;
\r
1179 int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
\r
1187 * @author $author$
\r
1188 * @version $Revision$
\r
1194 * Creates a new Preview object.
\r
1196 * @param image DOCUMENT ME!
\r
1198 public Preview(Image image)
\r
1200 setResizable(true);
\r
1201 setSize(image.getWidth(this), image.getHeight(this));
\r
1203 getContentPane().setLayout(new BorderLayout());
\r
1204 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1213 * @author $author$
\r
1214 * @version $Revision$
\r
1216 class PreviewPanel
\r
1222 * Creates a new PreviewPanel object.
\r
1224 * @param image DOCUMENT ME!
\r
1226 public PreviewPanel(Image image)
\r
1228 this.image = image;
\r
1234 * @param g DOCUMENT ME!
\r
1236 public void paintComponent(Graphics g)
\r
1238 if (image != null)
\r
1240 g.drawImage(image, 0, 0, this);
\r
1244 System.out.println("DEBUG:image is null");
\r