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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65 * Creates a new AnnotationPanel object.
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67 * @param ap DOCUMENT ME!
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69 public AnnotationPanel(AlignmentPanel ap)
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71 ToolTipManager.sharedInstance().registerComponent(this);
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72 ToolTipManager.sharedInstance().setInitialDelay(0);
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73 ToolTipManager.sharedInstance().setDismissDelay(10000);
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76 this.setLayout(null);
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77 addMouseListener(this);
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78 addMouseMotionListener(this);
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79 ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
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82 public AnnotationPanel(AlignViewport av)
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91 * @param evt DOCUMENT ME!
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93 public void adjustmentValueChanged(AdjustmentEvent evt)
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95 ap.alabels.setScrollOffset(-evt.getValue());
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101 public int adjustPanelHeight()
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103 // setHeight of panels
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105 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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110 for (int i = 0; i < aa.length; i++)
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112 if (!aa[i].visible)
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121 aa[i].height += av.charHeight;
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124 if (aa[i].hasIcons)
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126 aa[i].height += 16;
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131 aa[i].height += aa[i].graphHeight;
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134 if (aa[i].height == 0)
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139 height += aa[i].height;
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147 this.setPreferredSize(new Dimension(1, height));
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157 * @param evt DOCUMENT ME!
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159 public void actionPerformed(ActionEvent evt)
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161 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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162 Annotation[] anot = aa[activeRow].annotations;
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164 if (evt.getActionCommand().equals(REMOVE))
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166 for (int i = 0; i < av.getColumnSelection().size(); i++)
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168 anot[av.getColumnSelection().columnAt(i)] = null;
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171 else if (evt.getActionCommand().equals(LABEL))
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173 String label = JOptionPane.showInputDialog(this, "Enter Label ",
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174 "Enter label", JOptionPane.QUESTION_MESSAGE);
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181 if ((label.length() > 0) && !aa[activeRow].hasText)
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183 aa[activeRow].hasText = true;
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186 for (int i = 0; i < av.getColumnSelection().size(); i++)
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188 int index = av.getColumnSelection().columnAt(i);
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190 if (anot[index] == null)
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192 anot[index] = new Annotation(label, "", ' ', 0);
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195 anot[index].displayCharacter = label;
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198 else if (evt.getActionCommand().equals(COLOUR))
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200 Color col = JColorChooser.showDialog(this,
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201 "Choose foreground colour", Color.black);
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203 for (int i = 0; i < av.getColumnSelection().size(); i++)
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205 int index = av.getColumnSelection().columnAt(i);
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207 if (anot[index] == null)
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209 anot[index] = new Annotation("", "", ' ', 0);
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212 anot[index].colour = col;
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215 else // HELIX OR SHEET
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218 String symbol = "\u03B1";
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220 if (evt.getActionCommand().equals(HELIX))
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224 else if (evt.getActionCommand().equals(SHEET))
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230 if (!aa[activeRow].hasIcons)
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232 aa[activeRow].hasIcons = true;
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235 String label = JOptionPane.showInputDialog("Enter a label for the structure?",
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243 if ((label.length() > 0) && !aa[activeRow].hasText)
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245 aa[activeRow].hasText = true;
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248 for (int i = 0; i < av.getColumnSelection().size(); i++)
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250 int index = av.getColumnSelection().columnAt(i);
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252 if (anot[index] == null)
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254 anot[index] = new Annotation(label, "", type, 0);
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257 anot[index].secondaryStructure = type;
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258 anot[index].displayCharacter = label;
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262 adjustPanelHeight();
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271 * @param evt DOCUMENT ME!
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273 public void mousePressed(MouseEvent evt)
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278 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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282 for (int i = 0; i < aa.length; i++)
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286 height += aa[i].height;
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289 if (evt.getY() < height)
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291 if (aa[i].editable)
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295 else if(aa[i].graph>0)
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299 graphStretchY = evt.getY();
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306 if (SwingUtilities.isRightMouseButton(evt))
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308 if (av.getColumnSelection() == null)
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313 JPopupMenu pop = new JPopupMenu("Structure type");
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314 JMenuItem item = new JMenuItem(HELIX);
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315 item.addActionListener(this);
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317 item = new JMenuItem(SHEET);
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318 item.addActionListener(this);
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320 item = new JMenuItem(LABEL);
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321 item.addActionListener(this);
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323 item = new JMenuItem(COLOUR);
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324 item.addActionListener(this);
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326 item = new JMenuItem(REMOVE);
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327 item.addActionListener(this);
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329 pop.show(this, evt.getX(), evt.getY());
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339 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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344 if (av.getColumnSelection().contains(res))
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345 av.getColumnSelection().removeElement(res);
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348 av.getColumnSelection().addElement(res);
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349 SequenceGroup sg = new SequenceGroup();
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351 for (int i = 0; i < av.alignment.getSequences().size(); i++)
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353 sg.addSequence(av.alignment.getSequenceAt(i), false);
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356 sg.setStartRes(res);
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358 av.setSelectionGroup(sg);
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368 * @param evt DOCUMENT ME!
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370 public void mouseReleased(MouseEvent evt)
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373 graphStretchY = -1;
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374 mouseDragging = false;
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380 * @param evt DOCUMENT ME!
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382 public void mouseEntered(MouseEvent evt)
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385 ap.seqPanel.scrollCanvas(null);
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391 * @param evt DOCUMENT ME!
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393 public void mouseExited(MouseEvent evt)
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396 ap.seqPanel.scrollCanvas(evt);
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403 * @param evt DOCUMENT ME!
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405 public void mouseDragged(MouseEvent evt)
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407 if(graphStretch>-1)
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409 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
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410 if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)
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411 av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;
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412 graphStretchY = evt.getY();
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413 adjustPanelHeight();
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418 mouseDragging = true;
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420 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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422 SequenceGroup sg = av.getSelectionGroup();
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436 if (!av.getColumnSelection().contains(res))
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438 av.getColumnSelection().addElement(res);
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441 if (res > sg.getStartRes())
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445 else if (res < sg.getStartRes())
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447 sg.setStartRes(res);
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450 for (int i = min; i <= max; i++)
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452 if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
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454 av.getColumnSelection().removeElement(i);
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458 av.getColumnSelection().addElement(i);
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471 * @param evt DOCUMENT ME!
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473 public void mouseMoved(MouseEvent evt)
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475 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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485 for (int i = 0; i < aa.length; i++)
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489 height += aa[i].height;
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492 if (evt.getY() < height)
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500 int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
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502 if(av.hasHiddenColumns)
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503 res = av.getColumnSelection().adjustForHiddenColumns(res);
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505 if (row > -1 && res<aa[row].annotations.length)
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507 if(aa[row].graphGroup>-1)
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509 StringBuffer tip = new StringBuffer("<html>");
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510 for (int gg = 0; gg < aa.length; gg++)
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512 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
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513 tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );
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515 if(tip.length()!=6)
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517 tip.setLength(tip.length() - 4);
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518 this.setToolTipText(tip.toString() + "</html>");
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521 else if(aa[row].annotations[res] != null)
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522 this.setToolTipText(aa[row].annotations[res].description);
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524 if(aa[row].annotations[res]!=null)
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526 StringBuffer text = new StringBuffer("Sequence position " +
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528 aa[row].annotations[res].description);
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530 ap.alignFrame.statusBar.setText(text.toString());
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538 * @param evt DOCUMENT ME!
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540 public void mouseClicked(MouseEvent evt)
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547 * @param g DOCUMENT ME!
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549 public void paintComponent(Graphics g)
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551 g.setColor(Color.white);
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552 g.fillRect(0, 0, getWidth(), getHeight());
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556 || (getVisibleRect().width != g.getClipBounds().width)
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557 || (getVisibleRect().height != g.getClipBounds().height))
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559 g.drawImage(image, 0, 0, this);
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564 imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
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566 if (image == null || imgWidth != image.getWidth()
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567 || image.getHeight(this) != getHeight())
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569 image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
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570 BufferedImage.TYPE_INT_RGB);
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571 gg = (Graphics2D) image.getGraphics();
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574 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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575 RenderingHints.VALUE_ANTIALIAS_ON);
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577 gg.setFont(av.getFont());
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578 fm = gg.getFontMetrics();
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582 drawComponent(gg, av.startRes, av.endRes + 1);
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583 g.drawImage(image, 0, 0, this);
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589 * @param horizontal DOCUMENT ME!
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591 public void fastPaint(int horizontal)
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593 if ((horizontal == 0) || gg==null ||
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594 (av.alignment.getAlignmentAnnotation() == null) ||
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595 (av.alignment.getAlignmentAnnotation().length < 1))
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601 gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
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603 int sr = av.startRes;
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604 int er = av.endRes + 1;
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607 if (horizontal > 0) // scrollbar pulled right, image to the left
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609 transX = (er - sr - horizontal) * av.charWidth;
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610 sr = er - horizontal;
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612 else if (horizontal < 0)
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614 er = sr - horizontal;
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617 gg.translate(transX, 0);
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619 drawComponent(gg, sr, er);
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621 gg.translate(-transX, 0);
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632 * @param g DOCUMENT ME!
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633 * @param startRes DOCUMENT ME!
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634 * @param endRes DOCUMENT ME!
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636 public void drawComponent(Graphics g, int startRes, int endRes)
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640 g.setFont(av.getFont());
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643 fm = g.getFontMetrics();
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646 g.setColor(Color.white);
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647 g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
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649 if ( (av.alignment.getAlignmentAnnotation() == null) ||
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650 (av.alignment.getAlignmentAnnotation().length < 1))
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652 g.setColor(Color.white);
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653 g.fillRect(0, 0, getWidth(), getHeight());
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654 g.setColor(Color.black);
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655 if(av.validCharWidth)
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656 g.drawString("Alignment has no annotations", 20, 15);
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661 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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667 int iconOffset = av.charHeight / 2;
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668 boolean validRes = false;
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670 boolean [] graphGroupDrawn = new boolean[aa.length];
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674 for (int i = 0; i < aa.length; i++)
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676 AlignmentAnnotation row = aa[i];
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689 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
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692 // this is so that we draw the characters below the graph
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697 y -= av.charHeight;
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703 iconOffset = av.charHeight / 2;
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710 int column = startRes;
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712 while (column < endRes)
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714 if (av.hasHiddenColumns)
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716 column = av.getColumnSelection().adjustForHiddenColumns(column);
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717 if (column > row.annotations.length-1)
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723 if ((row.annotations.length <= column) ||
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724 (row.annotations[column] == null))
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733 x = (column - startRes) * av.charWidth;
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735 if (activeRow == i)
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737 g.setColor(Color.red);
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739 if (av.getColumnSelection() != null)
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741 for (int n = 0; n < av.getColumnSelection().size(); n++)
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743 int v = av.getColumnSelection().columnAt(n);
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747 g.fillRect((column - startRes) * av.charWidth, y,
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748 av.charWidth, row.height);
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754 if (av.validCharWidth && validRes &&
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755 (row.annotations[column].displayCharacter.length() > 0))
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758 int charOffset = (av.charWidth -
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759 fm.charWidth(row.annotations[column].displayCharacter.charAt(
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761 g.setColor(row.annotations[column].colour);
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763 if (column == 0 || row.graph>0)
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765 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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766 y + iconOffset + 3);
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769 row.annotations[column - 1] == null
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770 ||(!row.annotations[column].displayCharacter.equals(
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771 row.annotations[column - 1].displayCharacter)
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773 (row.annotations[column].displayCharacter.length() <2 &&
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774 row.annotations[column].secondaryStructure==' ')))
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776 g.drawString(row.annotations[column].displayCharacter, x+charOffset,
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777 y + iconOffset + 3);
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784 (row.annotations[column].secondaryStructure != lastSS))
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789 g.setColor(HELIX_COLOUR);
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790 int sCol = (lastSSX / av.charWidth) + startRes;
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794 if(row.annotations[sCol-1]==null ||
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795 row.annotations[sCol-1].secondaryStructure!='H')
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797 g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
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798 x1 += av.charWidth/2;
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801 if(row.annotations[column]==null ||
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802 row.annotations[column].secondaryStructure!='H')
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804 g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
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805 x2 -= av.charWidth/2;
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808 g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
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812 g.setColor(SHEET_COLOUR);
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813 g.fillRect(lastSSX, y + 4 + iconOffset,
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814 x - lastSSX - 4, 7);
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815 g.fillPolygon(new int[] { x - 5, x - 5, x },
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818 y + iconOffset, y + 14 + iconOffset,
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826 g.setColor(Color.gray);
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827 g.fillRect(lastSSX, y + 6 + iconOffset,
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835 lastSS = row.annotations[column].secondaryStructure;
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856 g.setColor(HELIX_COLOUR);
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858 int sCol = (lastSSX / av.charWidth) + startRes;
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862 if(row.annotations[sCol-1]==null ||
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863 row.annotations[sCol-1].secondaryStructure!='H')
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865 g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ;
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866 x1 += av.charWidth/2;
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869 if(row.annotations[column]==null ||
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870 row.annotations[column].secondaryStructure!='H')
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872 g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180);
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873 x2 -= av.charWidth/2;
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876 g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7);
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881 g.setColor(SHEET_COLOUR);
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883 if (row.annotations[endRes] ==null
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884 || row.annotations[endRes].secondaryStructure != 'E')
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886 g.fillRect(lastSSX, y + 4 + iconOffset,
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887 x - lastSSX - 4, 7);
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888 g.fillPolygon(new int[]
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892 y + iconOffset, y + 14 + iconOffset,
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897 g.fillRect(lastSSX, y + 4 + iconOffset,
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904 g.setColor(Color.gray);
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905 if(!av.wrapAlignment || endRes==av.endRes)
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906 g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
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914 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
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916 if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
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918 float groupmax=-999999, groupmin=9999999;
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919 for(int gg=0; gg<aa.length; gg++)
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921 if(aa[gg].graphGroup!=row.graphGroup)
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925 aa[gg].visible = false;
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927 if(aa[gg].graphMax>groupmax)
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928 groupmax = aa[gg].graphMax;
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929 if(aa[gg].graphMin<groupmin)
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930 groupmin = aa[gg].graphMin;
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933 for (int gg = 0; gg < aa.length; gg++)
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935 if (aa[gg].graphGroup == row.graphGroup)
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937 drawLineGraph(g, aa[gg], startRes, endRes, y,
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938 groupmin, groupmax,
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943 graphGroupDrawn[ row.graphGroup ] = true;
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946 drawLineGraph(g, row, startRes, endRes,
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947 y, row.graphMin, row.graphMax, row.graphHeight );
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949 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
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950 drawBarGraph(g, row, startRes, endRes,
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951 row.graphMin, row.graphMax, y);
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954 if (row.graph>0 && row.hasText)
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956 y += av.charHeight;
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966 public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
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967 int sRes, int eRes,
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969 float min, float max,
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972 if(sRes>aa.annotations.length)
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975 eRes = Math.min(eRes, aa.annotations.length);
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979 //Adjustment for fastpaint to left
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990 float range = max - min;
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994 y2 = (int)(y - (0-min / range)*graphHeight);
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996 g.setColor(Color.gray);
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997 g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
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999 eRes = Math.min(eRes, aa.annotations.length);
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1001 int column = sRes;
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1002 int aaMax = aa.annotations.length-1;
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1004 while( column < eRes )
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1006 if(av.hasHiddenColumns)
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1008 column = av.getColumnSelection().adjustForHiddenColumns(column);
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1009 if(column > aaMax)
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1015 if(aa.annotations[column]==null || aa.annotations[column-1]==null)
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1022 g.setColor(aa.annotations[column].colour);
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1023 y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
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1024 y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
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1025 g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
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1026 x += av.charWidth;
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1031 if(aa.threshold!=null)
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1033 g.setColor(aa.threshold.colour);
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1034 Graphics2D g2 = (Graphics2D)g;
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1035 g2.setStroke(new BasicStroke(1,
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1036 BasicStroke.CAP_SQUARE,
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1037 BasicStroke.JOIN_ROUND, 3f,
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1038 new float[] { 5f, 3f }, 0f));
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1040 y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
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1041 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
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1042 g2.setStroke(new BasicStroke());
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1046 public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
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1047 int sRes, int eRes,
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1048 float min, float max,
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1051 if(sRes>aa.annotations.length)
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1054 eRes = Math.min(eRes, aa.annotations.length);
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1058 float range = max - min;
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1063 y2 = (int)(y - (0-min / (range))*aa.graphHeight);
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1065 g.setColor(Color.gray);
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1067 g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
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1070 int column = sRes;
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1071 int aaMax = aa.annotations.length-1;
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1073 while( column < eRes )
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1075 if(av.hasHiddenColumns)
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1077 column = av.getColumnSelection().adjustForHiddenColumns(column);
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1078 if(column > aaMax)
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1084 if (aa.annotations[column] == null)
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1086 x += av.charWidth;
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1091 g.setColor(aa.annotations[column].colour);
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1092 y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
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1095 g.fillRect(x, y2, av.charWidth, y1-y2 );
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1097 g.fillRect(x, y1, av.charWidth, y2-y1 );
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1099 x += av.charWidth;
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1103 if(aa.threshold!=null)
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1105 g.setColor(aa.threshold.colour);
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1106 Graphics2D g2 = (Graphics2D)g;
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1107 g2.setStroke(new BasicStroke(1,
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1108 BasicStroke.CAP_SQUARE,
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1109 BasicStroke.JOIN_ROUND, 3f,
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1110 new float[] { 5f, 3f }, 0f));
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1112 y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
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1113 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
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1114 g2.setStroke(new BasicStroke());
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1118 // used by overview window
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1119 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
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1121 g.setColor(Color.white);
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1122 g.fillRect(0, 0, width, y);
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1123 g.setColor(new Color(0, 0, 180));
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1125 int x = 0, height;
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1127 for (int j = sRes; j < eRes; j++)
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1129 g.setColor(aa.annotations[j].colour);
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1131 height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
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1135 g.fillRect(x, y - height, av.charWidth, height);
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1136 x += av.charWidth;
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