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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24 import java.awt.event.*;
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25 import java.awt.image.*;
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27 import javax.swing.*;
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34 * @version $Revision$
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36 public class AnnotationPanel extends JPanel implements MouseListener,
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37 MouseMotionListener, ActionListener, AdjustmentListener
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39 final String HELIX = "Helix";
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40 final String SHEET = "Sheet";
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41 final String LABEL = "Label";
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42 final String REMOVE = "Remove Annotation";
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43 final String COLOUR = "Colour";
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44 final Color HELIX_COLOUR = Color.red.darker();
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45 final Color SHEET_COLOUR = Color.green.darker().darker();
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47 /** DOCUMENT ME!! */
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51 BufferedImage image;
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55 boolean fastPaint = false;
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57 //Used For mouse Dragging and resizing graphs
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58 int graphStretch = -1;
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59 int graphStretchY = -1;
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60 int min; //used by mouseDragged to see if user
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61 int max; //used by mouseDragged to see if user
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62 boolean mouseDragging = false;
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64 boolean MAC = false;
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67 * Creates a new AnnotationPanel object.
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69 * @param ap DOCUMENT ME!
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71 public AnnotationPanel(AlignmentPanel ap)
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74 if(System.getProperty("os.name").startsWith("Mac"))
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77 ToolTipManager.sharedInstance().registerComponent(this);
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78 ToolTipManager.sharedInstance().setInitialDelay(0);
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79 ToolTipManager.sharedInstance().setDismissDelay(10000);
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82 this.setLayout(null);
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83 addMouseListener(this);
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84 addMouseMotionListener(this);
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85 ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
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88 public AnnotationPanel(AlignViewport av)
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97 * @param evt DOCUMENT ME!
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99 public void adjustmentValueChanged(AdjustmentEvent evt)
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101 ap.alabels.setScrollOffset(-evt.getValue());
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107 public int adjustPanelHeight()
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109 // setHeight of panels
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111 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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116 for (int i = 0; i < aa.length; i++)
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118 if (!aa[i].visible)
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127 aa[i].height += av.charHeight;
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130 if (aa[i].hasIcons)
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132 aa[i].height += 16;
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137 aa[i].height += aa[i].graphHeight;
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140 if (aa[i].height == 0)
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145 height += aa[i].height;
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153 this.setPreferredSize(new Dimension(1, height));
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163 * @param evt DOCUMENT ME!
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165 public void actionPerformed(ActionEvent evt)
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167 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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168 Annotation[] anot = aa[activeRow].annotations;
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170 if (evt.getActionCommand().equals(REMOVE))
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172 for (int i = 0; i < av.getColumnSelection().size(); i++)
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174 anot[av.getColumnSelection().columnAt(i)] = null;
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177 else if (evt.getActionCommand().equals(LABEL))
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179 String label = JOptionPane.showInputDialog(this, "Enter Label ",
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180 "Enter label", JOptionPane.QUESTION_MESSAGE);
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187 if ((label.length() > 0) && !aa[activeRow].hasText)
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189 aa[activeRow].hasText = true;
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192 for (int i = 0; i < av.getColumnSelection().size(); i++)
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194 int index = av.getColumnSelection().columnAt(i);
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196 if (anot[index] == null)
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198 anot[index] = new Annotation(label, "", ' ', 0);
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201 anot[index].displayCharacter = label;
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204 else if (evt.getActionCommand().equals(COLOUR))
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206 Color col = JColorChooser.showDialog(this,
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207 "Choose foreground colour", Color.black);
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209 for (int i = 0; i < av.getColumnSelection().size(); i++)
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211 int index = av.getColumnSelection().columnAt(i);
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213 if (anot[index] == null)
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215 anot[index] = new Annotation("", "", ' ', 0);
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218 anot[index].colour = col;
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221 else // HELIX OR SHEET
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224 String symbol = "\u03B1";
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226 if (evt.getActionCommand().equals(HELIX))
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230 else if (evt.getActionCommand().equals(SHEET))
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236 if (!aa[activeRow].hasIcons)
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238 aa[activeRow].hasIcons = true;
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241 String label = JOptionPane.showInputDialog("Enter a label for the structure?",
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249 if ((label.length() > 0) && !aa[activeRow].hasText)
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251 aa[activeRow].hasText = true;
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254 for (int i = 0; i < av.getColumnSelection().size(); i++)
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256 int index = av.getColumnSelection().columnAt(i);
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258 if (anot[index] == null)
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260 anot[index] = new Annotation(label, "", type, 0);
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263 anot[index].secondaryStructure = type;
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264 anot[index].displayCharacter = label;
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268 adjustPanelHeight();
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277 * @param evt DOCUMENT ME!
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279 public void mousePressed(MouseEvent evt)
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284 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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288 for (int i = 0; i < aa.length; i++)
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292 height += aa[i].height;
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295 if (evt.getY() < height)
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297 if (aa[i].editable)
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301 else if(aa[i].graph>0)
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305 graphStretchY = evt.getY();
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312 if (SwingUtilities.isRightMouseButton(evt))
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314 if (av.getColumnSelection() == null)
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319 JPopupMenu pop = new JPopupMenu("Structure type");
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320 JMenuItem item = new JMenuItem(HELIX);
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321 item.addActionListener(this);
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323 item = new JMenuItem(SHEET);
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324 item.addActionListener(this);
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326 item = new JMenuItem(LABEL);
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327 item.addActionListener(this);
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329 item = new JMenuItem(COLOUR);
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330 item.addActionListener(this);
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332 item = new JMenuItem(REMOVE);
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333 item.addActionListener(this);
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335 pop.show(this, evt.getX(), evt.getY());
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345 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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350 if (av.getColumnSelection().contains(res))
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351 av.getColumnSelection().removeElement(res);
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354 av.getColumnSelection().addElement(res);
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355 SequenceGroup sg = new SequenceGroup();
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357 for (int i = 0; i < av.alignment.getSequences().size(); i++)
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359 sg.addSequence(av.alignment.getSequenceAt(i), false);
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362 sg.setStartRes(res);
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364 av.setSelectionGroup(sg);
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374 * @param evt DOCUMENT ME!
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376 public void mouseReleased(MouseEvent evt)
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379 graphStretchY = -1;
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380 mouseDragging = false;
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386 * @param evt DOCUMENT ME!
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388 public void mouseEntered(MouseEvent evt)
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391 ap.seqPanel.scrollCanvas(null);
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397 * @param evt DOCUMENT ME!
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399 public void mouseExited(MouseEvent evt)
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402 ap.seqPanel.scrollCanvas(evt);
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409 * @param evt DOCUMENT ME!
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411 public void mouseDragged(MouseEvent evt)
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413 if(graphStretch>-1)
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415 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
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416 if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)
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417 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;
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418 graphStretchY = evt.getY();
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419 adjustPanelHeight();
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424 mouseDragging = true;
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426 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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428 SequenceGroup sg = av.getSelectionGroup();
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442 if (!av.getColumnSelection().contains(res))
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444 av.getColumnSelection().addElement(res);
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447 if (res > sg.getStartRes())
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451 else if (res < sg.getStartRes())
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453 sg.setStartRes(res);
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456 for (int i = min; i <= max; i++)
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458 if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
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460 av.getColumnSelection().removeElement(i);
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464 av.getColumnSelection().addElement(i);
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477 * @param evt DOCUMENT ME!
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479 public void mouseMoved(MouseEvent evt)
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481 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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491 for (int i = 0; i < aa.length; i++)
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495 height += aa[i].height;
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498 if (evt.getY() < height)
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506 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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508 if(av.hasHiddenColumns)
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509 res = av.getColumnSelection().adjustForHiddenColumns(res);
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511 if (row > -1 && res<aa[row].annotations.length)
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513 if(aa[row].graphGroup>-1)
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515 StringBuffer tip = new StringBuffer("<html>");
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516 for (int gg = 0; gg < aa.length; gg++)
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518 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
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519 tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
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521 if(tip.length()!=6)
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523 tip.setLength(tip.length() - 4);
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524 this.setToolTipText(tip.toString() + "</html>");
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527 else if(aa[row].annotations[res] != null)
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528 this.setToolTipText(aa[row].annotations[res].description);
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530 if(aa[row].annotations[res]!=null)
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532 StringBuffer text = new StringBuffer("Sequence position " +
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534 aa[row].annotations[res].description);
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536 ap.alignFrame.statusBar.setText(text.toString());
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544 * @param evt DOCUMENT ME!
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546 public void mouseClicked(MouseEvent evt)
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553 * @param g DOCUMENT ME!
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555 public void paintComponent(Graphics g)
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557 g.setColor(Color.white);
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558 g.fillRect(0, 0, getWidth(), getHeight());
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562 || (getVisibleRect().width != g.getClipBounds().width)
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563 || (getVisibleRect().height != g.getClipBounds().height))
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565 g.drawImage(image, 0, 0, this);
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570 imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
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572 if (image == null || imgWidth != image.getWidth()
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573 || image.getHeight(this) != getHeight())
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575 image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
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576 BufferedImage.TYPE_INT_RGB);
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577 gg = (Graphics2D) image.getGraphics();
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580 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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581 RenderingHints.VALUE_ANTIALIAS_ON);
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583 gg.setFont(av.getFont());
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584 fm = gg.getFontMetrics();
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588 drawComponent(gg, av.startRes, av.endRes + 1);
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589 g.drawImage(image, 0, 0, this);
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595 * @param horizontal DOCUMENT ME!
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597 public void fastPaint(int horizontal)
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599 if ((horizontal == 0) || gg==null ||
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600 (av.alignment.getAlignmentAnnotation() == null) ||
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601 (av.alignment.getAlignmentAnnotation().length < 1))
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607 gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
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609 int sr = av.startRes;
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610 int er = av.endRes + 1;
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613 if (horizontal > 0) // scrollbar pulled right, image to the left
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615 transX = (er - sr - horizontal) * av.charWidth;
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616 sr = er - horizontal;
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618 else if (horizontal < 0)
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620 er = sr - horizontal;
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623 gg.translate(transX, 0);
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625 drawComponent(gg, sr, er);
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627 gg.translate(-transX, 0);
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638 * @param g DOCUMENT ME!
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639 * @param startRes DOCUMENT ME!
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640 * @param endRes DOCUMENT ME!
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642 public void drawComponent(Graphics g, int startRes, int endRes)
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646 g.setFont(av.getFont());
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649 fm = g.getFontMetrics();
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652 g.setColor(Color.white);
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653 g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
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655 if ( (av.alignment.getAlignmentAnnotation() == null) ||
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656 (av.alignment.getAlignmentAnnotation().length < 1))
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658 g.setColor(Color.white);
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659 g.fillRect(0, 0, getWidth(), getHeight());
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660 g.setColor(Color.black);
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661 if(av.validCharWidth)
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662 g.drawString("Alignment has no annotations", 20, 15);
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667 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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673 int iconOffset = av.charHeight / 2;
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674 boolean validRes = false;
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676 boolean [] graphGroupDrawn = new boolean[aa.length];
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680 for (int i = 0; i < aa.length; i++)
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682 AlignmentAnnotation row = aa[i];
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695 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
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698 // this is so that we draw the characters below the graph
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703 y -= av.charHeight;
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709 iconOffset = av.charHeight / 2;
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716 int column = startRes;
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718 while (column < endRes)
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720 if (av.hasHiddenColumns)
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722 column = av.getColumnSelection().adjustForHiddenColumns(column);
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723 if (column > row.annotations.length-1)
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729 if ((row.annotations.length <= column) ||
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730 (row.annotations[column] == null))
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739 x = (column - startRes) * av.charWidth;
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741 if (activeRow == i)
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743 g.setColor(Color.red);
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745 if (av.getColumnSelection() != null)
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747 for (int n = 0; n < av.getColumnSelection().size(); n++)
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749 int v = av.getColumnSelection().columnAt(n);
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753 g.fillRect((column - startRes) * av.charWidth, y,
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754 av.charWidth, row.height);
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760 if (av.validCharWidth && validRes &&
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761 (row.annotations[column].displayCharacter.length() > 0))
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764 int charOffset = (av.charWidth -
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765 fm.charWidth(row.annotations[column].displayCharacter.charAt(
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767 g.setColor(row.annotations[column].colour);
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769 if (column == 0 || row.graph>0)
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771 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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772 y + iconOffset + 3);
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775 row.annotations[column - 1] == null
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776 ||(!row.annotations[column].displayCharacter.equals(
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777 row.annotations[column - 1].displayCharacter)
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779 (row.annotations[column].displayCharacter.length() <2 &&
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780 row.annotations[column].secondaryStructure==' ')))
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782 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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783 y + iconOffset + 3);
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790 (row.annotations[column].secondaryStructure != lastSS))
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795 g.setColor(HELIX_COLOUR);
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798 //Off by 1 offset when drawing rects and ovals
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799 //to offscreen image on the MAC
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800 g.fillRoundRect(lastSSX, y + 4 + iconOffset,
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801 x - lastSSX, 7, 8, 8);
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805 int sCol = (lastSSX / av.charWidth) + startRes;
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810 row.annotations[sCol-1]==null ||
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811 row.annotations[sCol-1].secondaryStructure!='H')
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813 g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
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814 x1 += av.charWidth/2;
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817 if(row.annotations[column]==null ||
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818 row.annotations[column].secondaryStructure!='H')
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820 g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
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821 x2 -= av.charWidth/2;
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824 g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
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828 g.setColor(SHEET_COLOUR);
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829 g.fillRect(lastSSX, y + 4 + iconOffset,
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830 x - lastSSX - 4, 7);
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831 g.fillPolygon(new int[] { x - 5, x - 5, x },
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834 y + iconOffset, y + 14 + iconOffset,
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842 g.setColor(Color.gray);
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843 g.fillRect(lastSSX, y + 6 + iconOffset,
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851 lastSS = row.annotations[column].secondaryStructure;
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872 g.setColor(HELIX_COLOUR);
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875 //Off by 1 offset when drawing rects and ovals
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876 //to offscreen image on the MAC
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877 g.fillRoundRect(lastSSX, y + 4 + iconOffset,
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878 x - lastSSX, 7, 8, 8);
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883 int sCol = (lastSSX / av.charWidth) + startRes;
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888 row.annotations[sCol-1]==null ||
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889 row.annotations[sCol-1].secondaryStructure!='H')
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891 g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
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892 x1 += av.charWidth/2;
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895 if(row.annotations[column]==null ||
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896 row.annotations[column].secondaryStructure!='H')
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898 g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
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899 x2 -= av.charWidth/2;
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902 g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
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907 g.setColor(SHEET_COLOUR);
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909 if (row.annotations[endRes] ==null
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910 || row.annotations[endRes].secondaryStructure != 'E')
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912 g.fillRect(lastSSX, y + 4 + iconOffset,
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913 x - lastSSX - 4, 7);
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914 g.fillPolygon(new int[]
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918 y + iconOffset, y + 14 + iconOffset,
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923 g.fillRect(lastSSX, y + 4 + iconOffset,
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930 g.setColor(Color.gray);
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931 if(!av.wrapAlignment || endRes==av.endRes)
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932 g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
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940 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
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942 if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
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944 float groupmax=-999999, groupmin=9999999;
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945 for(int gg=0; gg<aa.length; gg++)
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947 if(aa[gg].graphGroup!=row.graphGroup)
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951 aa[gg].visible = false;
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953 if(aa[gg].graphMax>groupmax)
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954 groupmax = aa[gg].graphMax;
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955 if(aa[gg].graphMin<groupmin)
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956 groupmin = aa[gg].graphMin;
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959 for (int gg = 0; gg < aa.length; gg++)
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961 if (aa[gg].graphGroup == row.graphGroup)
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963 drawLineGraph(g, aa[gg], startRes, endRes, y,
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964 groupmin, groupmax,
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969 graphGroupDrawn[ row.graphGroup ] = true;
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972 drawLineGraph(g, row, startRes, endRes,
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973 y, row.graphMin, row.graphMax, row.graphHeight );
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975 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
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976 drawBarGraph(g, row, startRes, endRes,
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977 row.graphMin, row.graphMax, y);
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980 if (row.graph>0 && row.hasText)
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982 y += av.charHeight;
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992 public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
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993 int sRes, int eRes,
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995 float min, float max,
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998 if(sRes>aa.annotations.length)
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1004 //Adjustment for fastpaint to left
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1005 if(eRes<av.endRes)
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1008 eRes = Math.min(eRes, aa.annotations.length);
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1017 float range = max - min;
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1021 y2 = y - (int)((0-min / range)*graphHeight);
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1023 g.setColor(Color.gray);
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1024 g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
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1026 eRes = Math.min(eRes, aa.annotations.length);
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1028 int column = sRes;
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1029 int aaMax = aa.annotations.length-1;
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1031 while( column < eRes )
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1033 if(av.hasHiddenColumns)
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1035 column = av.getColumnSelection().adjustForHiddenColumns(column);
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1036 if(column > aaMax)
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1042 if(aa.annotations[column]==null || aa.annotations[column-1]==null)
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1050 g.setColor(aa.annotations[column].colour);
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1051 y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
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1052 y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
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1054 g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
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1055 x += av.charWidth;
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1060 if(aa.threshold!=null)
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1062 g.setColor(aa.threshold.colour);
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1063 Graphics2D g2 = (Graphics2D)g;
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1064 g2.setStroke(new BasicStroke(1,
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1065 BasicStroke.CAP_SQUARE,
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1066 BasicStroke.JOIN_ROUND, 3f,
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1067 new float[] { 5f, 3f }, 0f));
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1069 y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
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1070 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
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1071 g2.setStroke(new BasicStroke());
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1075 public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
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1076 int sRes, int eRes,
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1077 float min, float max,
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1080 if(sRes>aa.annotations.length)
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1083 eRes = Math.min(eRes, aa.annotations.length);
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1087 float range = max - min;
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1092 y2 = y - (int)((0-min / (range))*aa.graphHeight);
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1094 g.setColor(Color.gray);
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1096 g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
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1099 int column = sRes;
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1100 int aaMax = aa.annotations.length-1;
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1102 while( column < eRes )
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1104 if(av.hasHiddenColumns)
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1106 column = av.getColumnSelection().adjustForHiddenColumns(column);
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1107 if(column > aaMax)
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1113 if (aa.annotations[column] == null)
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1115 x += av.charWidth;
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1120 g.setColor(aa.annotations[column].colour);
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1121 y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
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1124 g.fillRect(x, y2, av.charWidth, y1-y2 );
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1126 g.fillRect(x, y1, av.charWidth, y2-y1 );
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1128 x += av.charWidth;
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1132 if(aa.threshold!=null)
\r
1134 g.setColor(aa.threshold.colour);
\r
1135 Graphics2D g2 = (Graphics2D)g;
\r
1136 g2.setStroke(new BasicStroke(1,
\r
1137 BasicStroke.CAP_SQUARE,
\r
1138 BasicStroke.JOIN_ROUND, 3f,
\r
1139 new float[] { 5f, 3f }, 0f));
\r
1141 y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
\r
1142 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
\r
1143 g2.setStroke(new BasicStroke());
\r
1147 // used by overview window
\r
1148 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
\r
1150 g.setColor(Color.white);
\r
1151 g.fillRect(0, 0, width, y);
\r
1152 g.setColor(new Color(0, 0, 180));
\r
1154 int x = 0, height;
\r
1156 for (int j = sRes; j < eRes; j++)
\r
1158 g.setColor(aa.annotations[j].colour);
\r
1160 height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
\r
1164 g.fillRect(x, y - height, av.charWidth, height);
\r
1165 x += av.charWidth;
\r