2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.datamodel.*;
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23 import jalview.jbgui.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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29 import java.awt.print.*;
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33 import javax.swing.*;
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40 * @version $Revision$
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42 public class AlignmentPanel extends GAlignmentPanel
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43 implements AdjustmentListener, Printable
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45 public AlignViewport av;
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46 OverviewPanel overviewPanel;
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49 IdwidthAdjuster idwidthAdjuster;
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51 /** DOCUMENT ME!! */
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52 public AlignFrame alignFrame;
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53 ScalePanel scalePanel;
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54 AnnotationPanel annotationPanel;
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55 AnnotationLabels alabels;
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57 // this value is set false when selection area being dragged
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58 boolean fastPaint = true;
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63 * Creates a new AlignmentPanel object.
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65 * @param af DOCUMENT ME!
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66 * @param av DOCUMENT ME!
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68 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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72 seqPanel = new SeqPanel(av, this);
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73 idPanel = new IdPanel(av, this);
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75 scalePanel = new ScalePanel(av, this);
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77 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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78 idwidthAdjuster = new IdwidthAdjuster(this);
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79 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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81 annotationPanel = new AnnotationPanel(this);
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82 alabels = new AnnotationLabels(this);
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85 annotationScroller.setViewportView(annotationPanel);
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86 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
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90 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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91 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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93 setScrollValues(0, 0);
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95 adjustAnnotationHeight();
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97 setAnnotationVisible(av.getShowAnnotation());
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99 hscroll.addAdjustmentListener(this);
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100 vscroll.addAdjustmentListener(this);
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102 af.addKeyListener(new KeyAdapter()
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104 public void keyPressed(KeyEvent evt)
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107 && evt.getKeyCode()>=KeyEvent.VK_0
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108 && evt.getKeyCode()<=KeyEvent.VK_9)
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110 seqPanel.numberPressed(evt.getKeyChar());
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113 switch (evt.getKeyCode())
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115 case 27: // escape key
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116 alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
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120 case KeyEvent.VK_DOWN:
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123 seqPanel.moveCursor(0,1);
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126 alignFrame.moveSelectedSequences(false);
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129 case KeyEvent.VK_UP:
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132 seqPanel.moveCursor(0,-1);
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135 alignFrame.moveSelectedSequences(true);
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138 case KeyEvent.VK_LEFT:
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141 seqPanel.moveCursor(-1,0);
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145 case KeyEvent.VK_RIGHT:
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148 seqPanel.moveCursor(1,0);
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152 case KeyEvent.VK_SPACE:
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155 seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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159 case KeyEvent.VK_DELETE:
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160 case KeyEvent.VK_BACK_SPACE:
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163 alignFrame.cut_actionPerformed(null);
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166 seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
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170 case KeyEvent.VK_S:
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173 seqPanel.setCursorRow();
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176 case KeyEvent.VK_C:
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177 if(av.cursorMode && !evt.isControlDown())
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179 seqPanel.setCursorColumn();
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182 case KeyEvent.VK_P:
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185 seqPanel.setCursorPosition();
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189 case KeyEvent.VK_ENTER:
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190 case KeyEvent.VK_COMMA:
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193 seqPanel.setCursorRowAndColumn();
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197 case KeyEvent.VK_Q:
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200 seqPanel.setSelectionAreaAtCursor(true);
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203 case KeyEvent.VK_M:
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206 seqPanel.setSelectionAreaAtCursor(false);
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210 case KeyEvent.VK_F2:
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211 av.cursorMode = ! av.cursorMode;
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212 alignFrame.statusBar.setText("Keyboard editing mode is "+
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213 (av.cursorMode ? "on" : "off"));
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216 seqPanel.seqCanvas.cursorX = av.startRes;
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217 seqPanel.seqCanvas.cursorY = av.startSeq;
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219 seqPanel.seqCanvas.repaint();
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222 case KeyEvent.VK_F1:
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225 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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226 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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227 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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229 javax.help.HelpBroker hb = hs.createHelpBroker();
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230 hb.setCurrentID("home");
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231 hb.setDisplayed(true);
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233 catch (Exception ex)
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235 ex.printStackTrace();
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247 public void fontChanged()
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249 // set idCanvas bufferedImage to null
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250 // to prevent drawing old image
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251 FontMetrics fm = getFontMetrics(av.getFont());
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253 scalePanelHolder.setPreferredSize(new Dimension(10,
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254 av.charHeight + fm.getDescent()));
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255 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
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256 av.charHeight + fm.getDescent()));
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258 idPanel.idCanvas.gg = null;
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259 seqPanel.seqCanvas.img = null;
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260 annotationPanel.adjustPanelHeight();
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262 Dimension d = calculateIdWidth();
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263 d.setSize(d.width + 4, d.height);
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264 idPanel.idCanvas.setPreferredSize(d);
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265 hscrollFillerPanel.setPreferredSize(d);
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267 if (av.getWrapAlignment())
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269 int max = av.alignment.getWidth() /
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270 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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271 vscroll.setMaximum(max);
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272 vscroll.setUnitIncrement(1);
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273 vscroll.setVisibleAmount(1);
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277 setScrollValues(av.getStartRes(), av.getStartSeq());
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280 if (overviewPanel != null)
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281 overviewPanel.setBoxPosition();
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289 * @return DOCUMENT ME!
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291 public Dimension calculateIdWidth()
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293 Container c = new Container();
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295 FontMetrics fm = c.getFontMetrics(av.font);
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296 AlignmentI al = av.getAlignment();
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302 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
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304 SequenceI s = al.getSequenceAt(i);
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306 id = s.getDisplayId(av.getShowJVSuffix());
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308 if (fm.stringWidth(id) > idWidth)
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310 idWidth = fm.stringWidth(id);
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316 // Also check annotation label widths
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319 if (al.getAlignmentAnnotation() != null)
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321 fm = c.getFontMetrics(alabels.getFont());
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323 while (i < al.getAlignmentAnnotation().length)
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325 String label = al.getAlignmentAnnotation()[i].label;
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327 if (fm.stringWidth(label) > idWidth)
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329 idWidth = fm.stringWidth(label);
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336 return new Dimension(idWidth, 12);
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342 * @param results DOCUMENT ME!
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344 public void highlightSearchResults(SearchResults results)
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346 seqPanel.seqCanvas.highlightSearchResults(results);
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348 // do we need to scroll the panel?
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349 if (results != null)
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351 SequenceI seq = results.getResultSequence(0);
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352 int seqIndex = av.alignment.findIndex(seq);
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353 int start = seq.findIndex(results.getResultStart(0)) - 1;
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354 int end = seq.findIndex(results.getResultEnd(0)) - 1;
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356 if(!av.wrapAlignment)
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358 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
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359 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
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361 setScrollValues(start, seqIndex);
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366 scrollToWrappedVisible(start);
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371 void scrollToWrappedVisible(int res)
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373 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
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374 if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
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376 vscroll.setValue(res / cwidth);
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377 av.startRes = vscroll.getValue() * cwidth;
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384 * @return DOCUMENT ME!
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386 public OverviewPanel getOverviewPanel()
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388 return overviewPanel;
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394 * @param op DOCUMENT ME!
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396 public void setOverviewPanel(OverviewPanel op)
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398 overviewPanel = op;
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404 * @param b DOCUMENT ME!
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406 public void setAnnotationVisible(boolean b)
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408 if (!av.wrapAlignment)
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410 annotationSpaceFillerHolder.setVisible(b);
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411 annotationScroller.setVisible(b);
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416 public void adjustAnnotationHeight()
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418 javax.swing.SwingUtilities.invokeLater(new Runnable()
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422 while(alignFrame.getHeight()==0)
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427 int height = annotationPanel.adjustPanelHeight();
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429 if (height > alignFrame.getHeight() / 2)
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431 height = alignFrame.getHeight() / 2;
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434 annotationScroller.setPreferredSize(
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435 new Dimension(annotationScroller.getWidth(),
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438 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
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439 annotationSpaceFillerHolder.getWidth(),
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442 annotationPanel.repaint();
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450 * @param wrap DOCUMENT ME!
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452 public void setWrapAlignment(boolean wrap)
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455 scalePanelHolder.setVisible(!wrap);
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456 hscroll.setVisible(!wrap);
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457 idwidthAdjuster.setVisible(!wrap);
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461 annotationScroller.setVisible(false);
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462 annotationSpaceFillerHolder.setVisible(false);
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464 else if (av.showAnnotation)
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466 annotationScroller.setVisible(true);
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467 annotationSpaceFillerHolder.setVisible(true);
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470 idSpaceFillerPanel1.setVisible(!wrap);
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475 // return value is true if the scroll is valid
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476 public boolean scrollUp(boolean up)
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480 if (vscroll.getValue() < 1)
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486 vscroll.setValue(vscroll.getValue() - 1);
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490 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
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496 vscroll.setValue(vscroll.getValue() + 1);
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507 * @param right DOCUMENT ME!
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509 * @return DOCUMENT ME!
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511 public boolean scrollRight(boolean right)
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515 if (hscroll.getValue() < 1)
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521 hscroll.setValue(hscroll.getValue() - 1);
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525 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
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531 hscroll.setValue(hscroll.getValue() + 1);
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542 * @param x DOCUMENT ME!
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543 * @param y DOCUMENT ME!
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545 public void setScrollValues(int x, int y)
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548 int width = av.alignment.getWidth();
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549 int height = av.alignment.getHeight();
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551 if(av.hasHiddenColumns)
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552 width = av.getColumnSelection().findColumnPosition(width);
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554 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
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556 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
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557 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
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559 if (hextent > width)
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564 if (vextent > height)
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569 if ( (hextent + x) > width)
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571 x = width - hextent;
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574 if ( (vextent + y) > height)
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576 y = height - vextent;
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589 hscroll.setValues(x, hextent, 0, width);
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590 vscroll.setValues(y, vextent, 0, height);
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596 * @param evt DOCUMENT ME!
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598 public void adjustmentValueChanged(AdjustmentEvent evt)
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601 int oldX = av.getStartRes();
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602 int oldY = av.getStartSeq();
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604 if (evt.getSource() == hscroll)
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606 int x = hscroll.getValue();
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609 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
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612 if (evt.getSource() == vscroll)
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614 int offy = vscroll.getValue();
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616 if (av.getWrapAlignment())
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620 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
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621 seqCanvas.getWidth());
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622 av.setStartRes(offy * rowSize);
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623 av.setEndRes( (offy + 1) * rowSize);
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627 //This is only called if file loaded is a jar file that
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628 //was wrapped when saved and user has wrap alignment true
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629 //as preference setting
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630 SwingUtilities.invokeLater(new Runnable()
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634 setScrollValues(av.getStartRes(), av.getStartSeq());
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641 av.setStartSeq(offy);
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642 av.setEndSeq(offy +
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643 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
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647 if (overviewPanel != null)
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649 overviewPanel.setBoxPosition();
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652 int scrollX = av.startRes - oldX;
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653 int scrollY = av.startSeq - oldY;
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655 if (av.getWrapAlignment() || !fastPaint)
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661 // Make sure we're not trying to draw a panel
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662 // larger than the visible window
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663 if(scrollX>av.endRes-av.startRes)
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664 scrollX = av.endRes-av.startRes;
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665 else if(scrollX<av.startRes-av.endRes)
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666 scrollX = av.startRes - av.endRes;
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668 if(scrollX!=0 || scrollY!=0)
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670 idPanel.idCanvas.fastPaint(scrollY);
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671 seqPanel.seqCanvas.fastPaint(scrollX,
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673 scalePanel.repaint();
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675 if (av.getShowAnnotation())
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677 annotationPanel.fastPaint(scrollX);
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686 * @param g DOCUMENT ME!
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688 public void paintComponent(Graphics g)
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692 Dimension d = idPanel.idCanvas.getPreferredSize();
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693 idPanelHolder.setPreferredSize(d);
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694 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
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697 if (av.getWrapAlignment())
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699 int maxwidth = av.alignment.getWidth();
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701 if (av.hasHiddenColumns)
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702 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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704 int max = maxwidth /
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705 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +
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709 vscroll.setMaximum(max);
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710 vscroll.setUnitIncrement(1);
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711 vscroll.setVisibleAmount(1);
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715 setScrollValues(av.getStartRes(), av.getStartSeq());
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718 if( this.getVisibleRect().getBounds() == g.getClipBounds()
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719 && overviewPanel != null)
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720 overviewPanel.updateOverviewImage();
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727 * @param pg DOCUMENT ME!
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728 * @param pf DOCUMENT ME!
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729 * @param pi DOCUMENT ME!
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731 * @return DOCUMENT ME!
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733 * @throws PrinterException DOCUMENT ME!
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735 public int print(Graphics pg, PageFormat pf, int pi)
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736 throws PrinterException
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738 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
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740 int pwidth = (int) pf.getImageableWidth();
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741 int pheight = (int) pf.getImageableHeight();
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743 if (av.getWrapAlignment())
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745 return printWrappedAlignment(pg, pwidth, pheight, pi);
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749 return printUnwrapped(pg, pwidth, pheight, pi);
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756 * @param pg DOCUMENT ME!
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757 * @param pwidth DOCUMENT ME!
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758 * @param pheight DOCUMENT ME!
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759 * @param pi DOCUMENT ME!
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761 * @return DOCUMENT ME!
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763 * @throws PrinterException DOCUMENT ME!
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765 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
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766 throws PrinterException
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768 int idWidth = calculateIdWidth().width + 4;
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769 FontMetrics fm = getFontMetrics(av.getFont());
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770 int scaleHeight = av.charHeight + fm.getDescent();
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772 pg.setColor(Color.white);
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773 pg.fillRect(0, 0, pwidth, pheight);
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774 pg.setFont(av.getFont());
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776 ////////////////////////////////////
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777 /// How many sequences and residues can we fit on a printable page?
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778 int totalRes = (pwidth - idWidth) / av.getCharWidth();
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780 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
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783 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
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785 /////////////////////////////
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786 /// Only print these sequences and residues on this page
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789 /////////////////////////////
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790 /// Only print these sequences and residues on this page
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793 /////////////////////////////
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794 /// Only print these sequences and residues on this page
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797 /////////////////////////////
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798 /// Only print these sequences and residues on this page
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800 startRes = (pi % pagesWide) * totalRes;
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801 endRes = (startRes + totalRes) - 1;
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803 if (endRes > (av.getAlignment().getWidth() - 1))
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805 endRes = av.getAlignment().getWidth() - 1;
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808 startSeq = (pi / pagesWide) * totalSeq;
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809 endSeq = startSeq + totalSeq;
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811 if (endSeq > av.getAlignment().getHeight())
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813 endSeq = av.getAlignment().getHeight();
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816 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
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818 if (av.showAnnotation)
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820 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
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823 pagesHigh /= pheight;
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825 if (pi >= (pagesWide * pagesHigh))
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827 return Printable.NO_SUCH_PAGE;
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831 pg.translate(idWidth, 0);
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832 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
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833 pg.translate( -idWidth, scaleHeight);
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837 Color currentColor = null;
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838 Color currentTextColor = null;
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840 pg.setFont(new Font(av.getFont().getName(),
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842 av.getFont().getSize()));
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843 for (int i = startSeq; i < endSeq; i++)
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845 if ( (av.getSelectionGroup() != null) &&
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846 av.getSelectionGroup().getSequences(false).contains(
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847 av.getAlignment().getSequenceAt(i)))
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849 currentColor = Color.gray;
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850 currentTextColor = Color.black;
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854 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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855 currentTextColor = Color.black;
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858 pg.setColor(currentColor);
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859 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
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860 av.getCharHeight());
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862 pg.setColor(currentTextColor);
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864 String string = av.getAlignment().getSequenceAt(i).getDisplayId
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865 ( av.getShowJVSuffix());
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867 pg.drawString(string, 0,
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868 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
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869 (av.getCharHeight() / 5));
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872 pg.setFont(av.getFont());
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874 // draw main sequence panel
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875 pg.translate(idWidth, 0);
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876 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
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878 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
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880 pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
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881 alabels.drawComponent( (Graphics2D) pg, idWidth);
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882 pg.translate(idWidth+3, 0);
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883 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
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887 return Printable.PAGE_EXISTS;
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893 * @param pg DOCUMENT ME!
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894 * @param pwidth DOCUMENT ME!
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895 * @param pheight DOCUMENT ME!
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896 * @param pi DOCUMENT ME!
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898 * @return DOCUMENT ME!
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900 * @throws PrinterException DOCUMENT ME!
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902 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
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904 throws PrinterException
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907 int annotationHeight = 0;
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908 AnnotationLabels labels = null;
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909 if (av.showAnnotation)
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911 annotationHeight = annotationPanel.adjustPanelHeight();
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912 labels = new AnnotationLabels(av);
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915 int hgap = av.charHeight;
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916 if (av.scaleAboveWrapped)
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917 hgap += av.charHeight;
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919 int cHeight = av.getAlignment().getHeight() * av.charHeight
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921 + annotationHeight;
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923 int idWidth = calculateIdWidth().width + 4;
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925 int maxwidth = av.alignment.getWidth();
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926 if (av.hasHiddenColumns)
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927 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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930 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
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933 int totalHeight = cHeight * (maxwidth / resWidth + 1);
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935 pg.setColor(Color.white);
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936 pg.fillRect(0, 0, pwidth, pheight);
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937 pg.setFont(av.getFont());
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941 pg.setColor(Color.black);
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943 pg.translate(0, -pi * pheight);
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945 pg.setClip(0, pi * pheight, pwidth, pheight);
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948 Font italic = new Font(av.getFont().getName(), Font.ITALIC,
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949 av.getFont().getSize());
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950 pg.setFont(italic);
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954 for (int i = 0; i < av.alignment.getHeight(); i++)
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956 SequenceI s = av.alignment.getSequenceAt(i);
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957 String string = s.getDisplayId( av.getShowJVSuffix());
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959 pg.drawString(string, 0,
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960 ( (i * av.charHeight) + ypos + av.charHeight) -
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961 (av.charHeight / 5));
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963 if (labels != null)
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967 (av.getAlignment().getHeight() * av.charHeight));
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969 pg.setFont(av.getFont());
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970 labels.drawComponent(pg, idWidth);
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971 pg.setFont(italic);
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974 (av.getAlignment().getHeight() * av.charHeight));
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979 while (ypos < totalHeight);
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981 pg.translate(idWidth, 0);
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983 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
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985 if ( (pi * pheight) < totalHeight)
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987 return Printable.PAGE_EXISTS;
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992 return Printable.NO_SUCH_PAGE;
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996 void makeAlignmentImage(int type, File file)
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998 int maxwidth = av.alignment.getWidth();
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999 if (av.hasHiddenColumns)
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1000 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
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1002 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
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1003 int width = idPanel.getWidth() + (maxwidth * av.charWidth);
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1004 if (idPanel.getWidth() == 0)
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1006 width += calculateIdWidth().getWidth() + 4;
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1009 if (av.getWrapAlignment())
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1011 height = getWrappedHeight();
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1012 if (System.getProperty("java.awt.headless") != null
\r
1013 && System.getProperty("java.awt.headless").equals("true"))
\r
1015 width = alignFrame.getWidth() - 22;
\r
1018 width = seqPanel.getWidth() + idPanel.getWidth();
\r
1021 else if (av.getShowAnnotation())
\r
1023 height += annotationPanel.adjustPanelHeight() + 3;
\r
1026 jalview.util.ImageMaker im;
\r
1027 if(type==jalview.util.ImageMaker.PNG)
\r
1028 im = new jalview.util.ImageMaker(this,
\r
1029 jalview.util.ImageMaker.PNG,
\r
1030 "Create PNG image from alignment",
\r
1031 width, height, file, null);
\r
1033 im = new jalview.util.ImageMaker(this,
\r
1034 jalview.util.ImageMaker.EPS,
\r
1035 "Create EPS file from alignment",
\r
1036 width, height, file, alignFrame.getTitle() );
\r
1040 if (av.getWrapAlignment())
\r
1042 if(im.getGraphics()!=null)
\r
1044 printWrappedAlignment(im.getGraphics(), width, height, 0);
\r
1050 if(im.getGraphics()!=null)
\r
1052 printUnwrapped(im.getGraphics(), width, height, 0);
\r
1057 catch (OutOfMemoryError err)
\r
1059 System.out.println("########################\n"
\r
1060 + "OUT OF MEMORY " + file + "\n"
\r
1061 + "########################");
\r
1063 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1064 "Out of Memory Creating Image!!"
\r
1066 "\nSee help files for increasing Java Virtual Machine memory."
\r
1067 , "Out of memory",
\r
1068 JOptionPane.WARNING_MESSAGE);
\r
1069 System.out.println("Create IMAGE: " + err);
\r
1073 catch (Exception ex)
\r
1075 ex.printStackTrace();
\r
1081 public void makeEPS(File epsFile)
\r
1083 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
\r
1089 public void makePNG(File pngFile)
\r
1091 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
\r
1094 public void makePNGImageMap(File imgMapFile, String imageName)
\r
1096 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1097 //////////////////////////////////////////////
\r
1098 int idWidth = calculateIdWidth().width + 4;
\r
1099 FontMetrics fm = getFontMetrics(av.getFont());
\r
1100 int scaleHeight = av.charHeight + fm.getDescent();
\r
1103 //////////////////////////////////
\r
1104 if (imgMapFile != null)
\r
1108 int s, sSize = av.alignment.getHeight(),
\r
1109 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1110 StringBuffer text = new StringBuffer();
\r
1111 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1112 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1113 out.println("<img src=\"" + imageName +
\r
1114 "\" border=\"0\" usemap=\"#Map\" >"
\r
1115 + "<map name=\"Map\">");
\r
1117 for (s = 0; s < sSize; s++)
\r
1119 sy = s * av.charHeight + scaleHeight;
\r
1121 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1122 SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
\r
1123 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1124 for(res =0; res<alwidth; res++)
\r
1126 text = new StringBuffer();
\r
1127 Object obj = null;
\r
1128 if(av.alignment.isNucleotide())
\r
1129 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
\r
1131 obj = ResidueProperties.aa2Triplet.get(
\r
1132 seq.getCharAt(res) + "");
\r
1137 String triplet = obj.toString();
\r
1138 int alIndex = seq.findPosition(res);
\r
1139 gSize = groups.length;
\r
1140 for (g = 0; g < gSize; g++)
\r
1142 if(text.length()<1)
\r
1144 text.append("<area shape=\"rect\" coords=\""
\r
1145 + (idWidth + res * av.charWidth) + ","
\r
1147 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1148 + (av.charHeight + sy) + "\""
\r
1149 + " onMouseOver=\"toolTip('"
\r
1150 + alIndex + " " + triplet );
\r
1153 if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
\r
1154 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1157 if (features != null)
\r
1159 if(text.length()<1)
\r
1161 text.append("<area shape=\"rect\" coords=\""
\r
1162 + (idWidth + res * av.charWidth) + ","
\r
1164 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1165 + (av.charHeight + sy) + "\""
\r
1166 + " onMouseOver=\"toolTip('"
\r
1167 + alIndex + " " + triplet );
\r
1169 fSize = features.length;
\r
1170 for (f = 0; f < fSize; f++)
\r
1173 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1174 (features[f].getEnd() >= seq.findPosition(res)))
\r
1176 if (features[f].getType().equals("disulfide bond"))
\r
1178 if (features[f].getBegin() == seq.findPosition(res)
\r
1179 || features[f].getEnd() == seq.findPosition(res))
\r
1181 text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
1182 features[f].getEnd());
\r
1187 text.append("<br>");
\r
1188 text.append(features[f].getType());
\r
1189 if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
1190 text.append(" " + features[f].getDescription());
\r
1192 if (features[f].getValue("status") != null )
\r
1194 text.append(" (" + features[f].getValue("status") + ")");
\r
1201 if(text.length()>1)
\r
1203 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1204 out.println(text.toString());
\r
1208 out.println("</map></body></html>");
\r
1212 catch (Exception ex)
\r
1214 ex.printStackTrace();
\r
1216 } ///////////END OF IMAGE MAP
\r
1220 int getWrappedHeight()
\r
1222 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1224 //If headless, seqPanel will have 0 width
\r
1225 if (System.getProperty("java.awt.headless") != null
\r
1226 && System.getProperty("java.awt.headless").equals("true"))
\r
1228 int idWidth = calculateIdWidth().width + 4;
\r
1229 seqPanelWidth = alignFrame.getWidth() - idWidth;
\r
1232 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1236 int hgap = av.charHeight;
\r
1237 if (av.scaleAboveWrapped)
\r
1238 hgap += av.charHeight;
\r
1240 int annotationHeight = 0;
\r
1241 if (av.showAnnotation)
\r
1243 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1246 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1248 + annotationHeight;
\r
1250 int maxwidth = av.alignment.getWidth();
\r
1251 if (av.hasHiddenColumns)
\r
1252 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1255 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r
1263 * @author $author$
\r
1264 * @version $Revision$
\r
1270 * Creates a new Preview object.
\r
1272 * @param image DOCUMENT ME!
\r
1274 public Preview(Image image)
\r
1276 setResizable(true);
\r
1277 setSize(image.getWidth(this), image.getHeight(this));
\r
1279 getContentPane().setLayout(new BorderLayout());
\r
1280 getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);
\r
1289 * @author $author$
\r
1290 * @version $Revision$
\r
1292 class PreviewPanel
\r
1298 * Creates a new PreviewPanel object.
\r
1300 * @param image DOCUMENT ME!
\r
1302 public PreviewPanel(Image image)
\r
1304 this.image = image;
\r
1310 * @param g DOCUMENT ME!
\r
1312 public void paintComponent(Graphics g)
\r
1314 if (image != null)
\r
1316 g.drawImage(image, 0, 0, this);
\r
1320 System.out.println("DEBUG:image is null");
\r