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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62 * Creates a new AnnotationPanel object.
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64 * @param ap DOCUMENT ME!
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66 public AnnotationPanel(AlignmentPanel ap)
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68 ToolTipManager.sharedInstance().registerComponent(this);
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69 ToolTipManager.sharedInstance().setInitialDelay(0);
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70 ToolTipManager.sharedInstance().setDismissDelay(10000);
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73 this.setLayout(null);
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74 addMouseListener(this);
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75 addMouseMotionListener(this);
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76 ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
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79 public AnnotationPanel(AlignViewport av)
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88 * @param evt DOCUMENT ME!
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90 public void adjustmentValueChanged(AdjustmentEvent evt)
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92 ap.alabels.setScrollOffset(-evt.getValue());
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98 public int adjustPanelHeight()
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100 // setHeight of panels
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102 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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107 for (int i = 0; i < aa.length; i++)
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109 if (!aa[i].visible)
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118 aa[i].height += av.charHeight;
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121 if (aa[i].hasIcons)
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123 aa[i].height += 16;
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128 aa[i].height += aa[i].graphHeight;
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131 if (aa[i].height == 0)
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136 height += aa[i].height;
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144 this.setPreferredSize(new Dimension(1, height));
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154 * @param evt DOCUMENT ME!
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156 public void actionPerformed(ActionEvent evt)
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158 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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159 Annotation[] anot = aa[activeRow].annotations;
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161 if (evt.getActionCommand().equals(REMOVE))
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163 for (int i = 0; i < av.getColumnSelection().size(); i++)
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165 anot[av.getColumnSelection().columnAt(i)] = null;
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168 else if (evt.getActionCommand().equals(LABEL))
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170 String label = JOptionPane.showInputDialog(this, "Enter Label ",
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171 "Enter label", JOptionPane.QUESTION_MESSAGE);
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178 if ((label.length() > 0) && !aa[activeRow].hasText)
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180 aa[activeRow].hasText = true;
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183 for (int i = 0; i < av.getColumnSelection().size(); i++)
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185 int index = av.getColumnSelection().columnAt(i);
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187 if (anot[index] == null)
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189 anot[index] = new Annotation(label, "", ' ', 0);
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192 anot[index].displayCharacter = label;
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195 else if (evt.getActionCommand().equals(COLOUR))
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197 Color col = JColorChooser.showDialog(this,
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198 "Choose foreground colour", Color.black);
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200 for (int i = 0; i < av.getColumnSelection().size(); i++)
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202 int index = av.getColumnSelection().columnAt(i);
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204 if (anot[index] == null)
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206 anot[index] = new Annotation("", "", ' ', 0);
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209 anot[index].colour = col;
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212 else // HELIX OR SHEET
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215 String symbol = "\u03B1";
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217 if (evt.getActionCommand().equals(HELIX))
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221 else if (evt.getActionCommand().equals(SHEET))
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227 if (!aa[activeRow].hasIcons)
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229 aa[activeRow].hasIcons = true;
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232 String label = JOptionPane.showInputDialog("Enter a label for the structure?",
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240 if ((label.length() > 0) && !aa[activeRow].hasText)
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242 aa[activeRow].hasText = true;
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245 for (int i = 0; i < av.getColumnSelection().size(); i++)
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247 int index = av.getColumnSelection().columnAt(i);
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249 if (anot[index] == null)
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251 anot[index] = new Annotation(label, "", type, 0);
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254 anot[index].secondaryStructure = type;
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255 anot[index].displayCharacter = label;
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259 adjustPanelHeight();
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268 * @param evt DOCUMENT ME!
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270 public void mousePressed(MouseEvent evt)
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275 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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279 for (int i = 0; i < aa.length; i++)
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283 height += aa[i].height;
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286 if (evt.getY() < height)
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288 if (aa[i].editable)
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292 else if(aa[i].graph>0)
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296 graphStretchY = evt.getY();
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303 if (SwingUtilities.isRightMouseButton(evt))
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305 if (av.getColumnSelection() == null)
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310 JPopupMenu pop = new JPopupMenu("Structure type");
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311 JMenuItem item = new JMenuItem(HELIX);
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312 item.addActionListener(this);
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314 item = new JMenuItem(SHEET);
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315 item.addActionListener(this);
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317 item = new JMenuItem(LABEL);
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318 item.addActionListener(this);
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320 item = new JMenuItem(COLOUR);
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321 item.addActionListener(this);
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323 item = new JMenuItem(REMOVE);
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324 item.addActionListener(this);
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326 pop.show(this, evt.getX(), evt.getY());
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336 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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338 if (evt.isShiftDown())
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340 /*int start = Integer.parseInt(activeRes.get(activeRes.size() -
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351 for (int n = start; n <= end; n++)
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353 addEditableColumn(n);
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358 if (av.getColumnSelection().contains(res))
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359 av.getColumnSelection().removeElement(res);
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361 av.getColumnSelection().addElement(res);
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371 * @param evt DOCUMENT ME!
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373 public void mouseReleased(MouseEvent evt)
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376 graphStretchY = -1;
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382 * @param evt DOCUMENT ME!
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384 public void mouseEntered(MouseEvent evt)
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391 * @param evt DOCUMENT ME!
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393 public void mouseExited(MouseEvent evt)
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400 * @param evt DOCUMENT ME!
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402 public void mouseDragged(MouseEvent evt)
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404 if(graphStretch>-1)
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406 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
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407 if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)
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408 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;
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409 graphStretchY = evt.getY();
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410 adjustPanelHeight();
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418 * @param evt DOCUMENT ME!
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420 public void mouseMoved(MouseEvent evt)
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422 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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432 for (int i = 0; i < aa.length; i++)
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436 height += aa[i].height;
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439 if (evt.getY() < height)
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447 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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449 if(av.hasHiddenColumns)
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450 res = av.getColumnSelection().adjustForHiddenColumns(res);
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452 if (row > -1 && res<aa[row].annotations.length)
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454 if(aa[row].graphGroup>-1)
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456 StringBuffer tip = new StringBuffer("<html>");
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457 for (int gg = 0; gg < aa.length; gg++)
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459 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
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460 tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
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462 if(tip.length()!=6)
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464 tip.setLength(tip.length() - 4);
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465 this.setToolTipText(tip.toString() + "</html>");
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468 else if(aa[row].annotations[res] != null)
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469 this.setToolTipText(aa[row].annotations[res].description);
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471 if(aa[row].annotations[res]!=null)
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473 StringBuffer text = new StringBuffer("Sequence position " +
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475 aa[row].annotations[res].description);
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477 ap.alignFrame.statusBar.setText(text.toString());
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485 * @param evt DOCUMENT ME!
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487 public void mouseClicked(MouseEvent evt)
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494 * @param g DOCUMENT ME!
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496 public void paintComponent(Graphics g)
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498 g.setColor(Color.white);
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499 g.fillRect(0, 0, getWidth(), getHeight());
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503 || (getVisibleRect().width != g.getClipBounds().width)
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504 || (getVisibleRect().height != g.getClipBounds().height))
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506 g.drawImage(image, 0, 0, this);
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511 imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
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513 if (image == null || imgWidth != image.getWidth()
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514 || image.getHeight(this) != getHeight())
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516 image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
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517 BufferedImage.TYPE_INT_RGB);
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518 gg = (Graphics2D) image.getGraphics();
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521 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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522 RenderingHints.VALUE_ANTIALIAS_ON);
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524 gg.setFont(av.getFont());
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525 fm = gg.getFontMetrics();
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529 drawComponent(gg, av.startRes, av.endRes + 1);
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530 g.drawImage(image, 0, 0, this);
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536 * @param horizontal DOCUMENT ME!
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538 public void fastPaint(int horizontal)
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540 if ((horizontal == 0) || gg==null ||
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541 (av.alignment.getAlignmentAnnotation() == null) ||
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542 (av.alignment.getAlignmentAnnotation().length < 1))
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548 gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
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550 int sr = av.startRes;
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551 int er = av.endRes + 1;
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554 if (horizontal > 0) // scrollbar pulled right, image to the left
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556 transX = (er - sr - horizontal) * av.charWidth;
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557 sr = er - horizontal;
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559 else if (horizontal < 0)
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561 er = sr - horizontal;
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564 gg.translate(transX, 0);
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566 drawComponent(gg, sr, er);
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568 gg.translate(-transX, 0);
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579 * @param g DOCUMENT ME!
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580 * @param startRes DOCUMENT ME!
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581 * @param endRes DOCUMENT ME!
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583 public void drawComponent(Graphics g, int startRes, int endRes)
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585 g.setFont(av.getFont());
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588 fm = g.getFontMetrics();
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591 g.setColor(Color.white);
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592 g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
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594 if ((av.alignment.getAlignmentAnnotation() == null) ||
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595 (av.alignment.getAlignmentAnnotation().length < 1))
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597 g.setColor(Color.white);
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598 g.fillRect(0, 0, getWidth(), getHeight());
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599 g.setColor(Color.black);
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600 g.drawString("Alignment has no annotations", 20, 15);
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605 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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609 char[] lastSS = new char[aa.length];
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610 int[] lastSSX = new int[aa.length];
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611 int iconOffset = av.charHeight / 2;
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612 boolean validRes = false;
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614 boolean [] graphGroupDrawn = new boolean[aa.length];
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618 for (int i = 0; i < aa.length; i++)
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620 AlignmentAnnotation row = aa[i];
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631 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
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634 // this is so that we draw the characters below the graph
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639 y -= av.charHeight;
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645 iconOffset = av.charHeight / 2;
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652 int column = startRes;
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653 int yPos = startRes;
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654 int aaMax = row.annotations.length-1;
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656 while (yPos < endRes)
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658 if (av.hasHiddenColumns)
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660 column = av.getColumnSelection().adjustForHiddenColumns(yPos);
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661 if (column > aaMax)
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669 if ((row.annotations.length <= column) ||
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670 (row.annotations[column] == null))
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679 x = (yPos - startRes) * av.charWidth;
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681 if (activeRow == i)
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683 g.setColor(Color.red);
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685 if (av.getColumnSelection() != null)
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687 for (int n = 0; n < av.getColumnSelection().size(); n++)
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689 int v = av.getColumnSelection().columnAt(n);
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693 g.fillRect((column - startRes) * av.charWidth, y,
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694 av.charWidth, row.height);
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701 (row.annotations[column].displayCharacter.length() > 0))
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704 int charOffset = (av.charWidth -
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705 fm.charWidth(row.annotations[column].displayCharacter.charAt(
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707 g.setColor(row.annotations[column].colour);
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709 if (column == 0 || row.graph>0)
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711 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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712 y + iconOffset + 3);
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714 else if (((row.annotations[column - 1] == null)
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716 (!row.annotations[column].displayCharacter.equals(
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717 row.annotations[column - 1].displayCharacter))))
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719 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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720 y + iconOffset + 3);
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727 (row.annotations[column].secondaryStructure != lastSS[i]))
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732 g.setColor(HELIX_COLOUR);
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733 g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
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734 x - lastSSX[i], 7, 8, 8);
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739 g.setColor(SHEET_COLOUR);
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740 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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741 x - lastSSX[i] - 4, 7);
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742 g.fillPolygon(new int[] { x - 4, x - 4, x },
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745 y + iconOffset, y + 14 + iconOffset,
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753 g.setColor(Color.gray);
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754 g.fillRect(lastSSX[i], y + 6 + iconOffset,
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755 x - lastSSX[i], 2);
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762 lastSS[i] = row.annotations[column].secondaryStructure;
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783 g.setColor(HELIX_COLOUR);
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784 g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
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785 x - lastSSX[i], 7, 8, 8);
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790 g.setColor(SHEET_COLOUR);
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792 if (row.annotations[endRes] !=null
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793 && row.annotations[endRes].secondaryStructure != 'E')
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795 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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796 x - lastSSX[i] - 4, 7);
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797 g.fillPolygon(new int[]
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801 y + iconOffset, y + 14 + iconOffset,
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806 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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807 x - lastSSX[i], 7);
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815 g.setColor(Color.gray);
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816 g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
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824 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
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826 if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
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828 float groupmax=-999999, groupmin=9999999;
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829 for(int gg=0; gg<aa.length; gg++)
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831 if(aa[gg].graphGroup!=row.graphGroup)
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835 aa[gg].visible = false;
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837 if(aa[gg].graphMax>groupmax)
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838 groupmax = aa[gg].graphMax;
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839 if(aa[gg].graphMin<groupmin)
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840 groupmin = aa[gg].graphMin;
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843 for (int gg = 0; gg < aa.length; gg++)
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845 if (aa[gg].graphGroup == row.graphGroup)
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847 drawLineGraph(g, aa[gg], startRes, endRes, y,
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848 groupmin, groupmax,
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853 graphGroupDrawn[ row.graphGroup ] = true;
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856 drawLineGraph(g, row, startRes, endRes,
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857 y, row.graphMin, row.graphMax, row.graphHeight );
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859 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
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860 drawBarGraph(g, row, startRes, endRes,
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861 row.graphMin, row.graphMax, y);
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864 if (row.graph>0 && row.hasText)
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866 y += av.charHeight;
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876 public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
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877 int sRes, int eRes,
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879 float min, float max,
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882 if(sRes>aa.annotations.length)
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885 eRes = Math.min(eRes, aa.annotations.length);
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889 //Adjustment for fastpaint to left
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900 float range = max - min;
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904 y2 = (int)(y - (0-min / range)*graphHeight);
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906 g.setColor(Color.gray);
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907 g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
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910 if(aa.threshold!=null)
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912 g.setColor(aa.threshold.colour);
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913 Graphics2D g2 = (Graphics2D)g;
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914 g2.setStroke(new BasicStroke(1,
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915 BasicStroke.CAP_SQUARE,
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916 BasicStroke.JOIN_ROUND, 3f,
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917 new float[] { 5f, 3f }, 0f));
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919 y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
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920 g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
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921 g2.setStroke(new BasicStroke());
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924 eRes = Math.min(eRes, aa.annotations.length);
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928 int aaMax = aa.annotations.length-1;
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930 while( yPos < eRes )
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932 if(av.hasHiddenColumns)
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934 column = av.getColumnSelection().adjustForHiddenColumns(yPos);
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945 if(aa.annotations[column]==null || aa.annotations[column-1]==null)
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951 g.setColor(aa.annotations[column].colour);
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952 y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
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953 y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
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954 g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
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959 public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
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960 int sRes, int eRes,
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961 float min, float max,
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964 if(sRes>aa.annotations.length)
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967 eRes = Math.min(eRes, aa.annotations.length);
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971 float range = max - min;
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973 if(aa.threshold!=null)
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975 g.setColor(aa.threshold.colour);
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976 Graphics2D g2 = (Graphics2D)g;
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977 g2.setStroke(new BasicStroke(1,
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978 BasicStroke.CAP_SQUARE,
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979 BasicStroke.JOIN_ROUND, 3f,
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980 new float[] { 5f, 3f }, 0f));
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982 y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
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983 g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
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984 g2.setStroke(new BasicStroke());
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990 y2 = (int)(y - (0-min / (range))*aa.graphHeight);
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992 g.setColor(Color.gray);
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994 g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
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999 int aaMax = aa.annotations.length-1;
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1001 while( yPos < eRes )
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1003 if(av.hasHiddenColumns)
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1005 column = av.getColumnSelection().adjustForHiddenColumns(yPos);
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1006 if(column > aaMax)
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1016 if (aa.annotations[column] == null)
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1018 x += av.charWidth;
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1023 g.setColor(aa.annotations[column].colour);
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1024 y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
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1027 g.fillRect(x, y2, av.charWidth, y1-y2 );
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1029 g.fillRect(x, y1, av.charWidth, y2-y1 );
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1031 x += av.charWidth;
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1036 // used by overview window
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1037 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
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1039 g.setColor(Color.white);
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1040 g.fillRect(0, 0, width, y);
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1041 g.setColor(new Color(0, 0, 180));
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1043 int x = 0, height;
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1045 for (int j = sRes; j < eRes; j++)
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1047 g.setColor(aa.annotations[j].colour);
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1049 height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
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1053 g.fillRect(x, y - height, av.charWidth, height);
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1054 x += av.charWidth;
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