2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.analysis.AlignmentUtils;
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24 import jalview.bin.JalviewLite;
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25 import jalview.datamodel.AlignmentAnnotation;
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26 import jalview.datamodel.Annotation;
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27 import jalview.datamodel.SequenceGroup;
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28 import jalview.datamodel.SequenceI;
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29 import jalview.util.MessageManager;
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30 import jalview.util.ParseHtmlBodyAndLinks;
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32 import java.awt.Color;
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33 import java.awt.Dimension;
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34 import java.awt.FlowLayout;
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35 import java.awt.FontMetrics;
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36 import java.awt.Graphics;
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37 import java.awt.Image;
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38 import java.awt.event.ActionEvent;
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39 import java.awt.event.ActionListener;
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40 import java.awt.event.InputEvent;
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41 import java.awt.event.ItemEvent;
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42 import java.awt.event.ItemListener;
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43 import java.awt.event.MouseEvent;
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44 import java.awt.event.MouseListener;
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45 import java.awt.event.MouseMotionListener;
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46 import java.util.Arrays;
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47 import java.util.Collections;
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48 import java.util.Vector;
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50 import javax.swing.JCheckBox;
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51 import javax.swing.JCheckBoxMenuItem;
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52 import javax.swing.JFrame;
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53 import javax.swing.JMenuItem;
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54 import javax.swing.JPanel;
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55 import javax.swing.JPopupMenu;
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57 public class AnnotationLabels extends JPanel implements ActionListener,
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58 MouseListener, MouseMotionListener
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62 boolean active = false;
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68 boolean resizing = false;
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72 static String ADDNEW = "Add New Row";
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74 static String EDITNAME = "Edit Label/Description";
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76 static String HIDE = "Hide This Row";
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78 static String SHOWALL = "Show All Hidden Rows";
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80 static String OUTPUT_TEXT = "Show Values In Textbox";
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82 static String COPYCONS_SEQ = "Copy Consensus Sequence";
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84 int scrollOffset = 0;
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86 int selectedRow = -1;
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90 private boolean hasHiddenRows;
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92 public AnnotationLabels(AlignmentPanel ap)
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99 * this retrieves the adjustable height glyph from resources. we don't use
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100 * it at the moment. java.net.URL url =
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101 * getClass().getResource("/images/idwidth.gif"); Image temp = null;
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103 * if (url != null) { temp =
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104 * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
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106 * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
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107 * mt.waitForID(0); } catch (Exception ex) { }
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109 * BufferedImage bi = new BufferedImage(temp.getHeight(this),
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110 * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
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111 * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
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112 * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
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114 addMouseListener(this);
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115 addMouseMotionListener(this);
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118 public AnnotationLabels(AlignViewport av)
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123 public void setScrollOffset(int y, boolean repaint)
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135 * @return -2 if no rows are visible at all, -1 if no visible rows were
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138 int getSelectedRow(int y)
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141 AlignmentAnnotation[] aa = ap.av.getAlignment()
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142 .getAlignmentAnnotation();
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149 for (int i = 0; i < aa.length; i++)
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152 if (!aa[i].visible)
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156 height += aa[i].height;
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167 public void actionPerformed(ActionEvent evt)
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169 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
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171 if (evt.getActionCommand().equals(ADDNEW))
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173 AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
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174 new Annotation[ap.av.getAlignment().getWidth()]);
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176 if (!editLabelDescription(newAnnotation))
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181 ap.av.getAlignment().addAnnotation(newAnnotation);
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182 ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
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184 else if (evt.getActionCommand().equals(EDITNAME))
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186 editLabelDescription(aa[selectedRow]);
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188 else if (evt.getActionCommand().equals(HIDE))
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190 aa[selectedRow].visible = false;
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192 else if (evt.getActionCommand().equals(SHOWALL))
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194 for (int i = 0; i < aa.length; i++)
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196 aa[i].visible = (aa[i].annotations == null) ? false : true;
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199 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
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201 CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
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203 JFrame frame = new JFrame();
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205 JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
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206 + " - " + aa[selectedRow].label, 500, 100);
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207 cap.setText(aa[selectedRow].toString());
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209 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
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211 SequenceI cons = av.getConsensusSeq();
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214 copy_annotseqtoclipboard(cons);
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222 * Adjust size and repaint
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224 protected void refresh()
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226 ap.annotationPanel.adjustPanelHeight();
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227 setSize(getSize().width, ap.annotationPanel.getSize().height);
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229 ap.paintAlignment(true);
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232 boolean editLabelDescription(AlignmentAnnotation annotation)
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234 JCheckBox padGaps = new JCheckBox("Fill Empty Gaps With \""
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235 + ap.av.getGapCharacter() + "\"", annotation.padGaps);
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237 EditNameDialog dialog = new EditNameDialog(annotation.label,
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238 annotation.description, " Annotation Label",
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239 "Annotation Description", ap.alignFrame,
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240 "Edit Annotation Name / Description", 500, 180, false);
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242 JPanel empty = new JPanel(new FlowLayout());
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243 empty.add(padGaps);
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247 dialog.setVisible(true);
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251 annotation.label = dialog.getName();
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252 annotation.description = dialog.getDescription();
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253 annotation.setPadGaps(padGaps.isSelected(), av.getGapCharacter());
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264 boolean resizePanel = false;
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266 public void mouseMoved(MouseEvent evt)
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268 resizePanel = evt.getY() < 10 && evt.getX() < 14;
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269 int row = getSelectedRow(evt.getY() + scrollOffset);
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273 ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
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274 av.getAlignment().getAlignmentAnnotation()[row]
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275 .getDescription(true),
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277 if (tooltip == null)
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279 tooltip = new Tooltip(phb.getNonHtmlContent(), this);
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283 tooltip.setTip(phb.getNonHtmlContent());
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286 else if (tooltip != null)
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288 tooltip.setTip("");
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293 * curent drag position
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295 MouseEvent dragEvent = null;
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298 * flag to indicate drag events should be ignored
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300 private boolean dragCancelled = false;
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303 * clear any drag events in progress
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305 public void cancelDrag()
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308 dragCancelled = true;
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311 public void mouseDragged(MouseEvent evt)
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322 Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
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323 .getSize(), f = ap.seqPanelHolder.getSize();
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324 int dif = evt.getY() - oldY;
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326 dif /= ap.av.getCharHeight();
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327 dif *= ap.av.getCharHeight();
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329 if ((d.height - dif) > 20 && (f.height + dif) > 20)
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331 ap.annotationPanel.setSize(d.width, d.height - dif);
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332 setSize(new Dimension(e.width, d.height - dif));
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333 ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
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335 ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
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337 ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
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338 av.calcPanelHeight());
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340 ap.seqPanelHolder.setPreferredSize(f);
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341 ap.setScrollValues(av.getStartRes(), av.getStartSeq());
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343 // ap.paintAlignment(true);
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351 if ((diff = 6 - evt.getY()) > 0)
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354 ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
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355 ap.adjustmentValueChanged(null);
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358 else if ((0 < (diff = 6
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359 - ap.annotationSpaceFillerHolder.getSize().height
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362 // nudge scroll down
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363 ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
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364 ap.adjustmentValueChanged(null);
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370 public void mouseClicked(MouseEvent evt)
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374 public void mouseReleased(MouseEvent evt)
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376 if (!resizePanel && !dragCancelled)
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378 int start = selectedRow;
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380 int end = getSelectedRow(evt.getY() + scrollOffset);
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382 if (start > -1 && start != end)
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384 // Swap these annotations
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385 AlignmentAnnotation startAA = ap.av.getAlignment()
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386 .getAlignmentAnnotation()[start];
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389 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
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391 AlignmentAnnotation endAA = ap.av.getAlignment()
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392 .getAlignmentAnnotation()[end];
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394 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
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395 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
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398 resizePanel = false;
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400 dragCancelled = false;
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402 ap.annotationPanel.repaint();
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405 public void mouseEntered(MouseEvent evt)
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407 if (evt.getY() < 10 && evt.getX() < 14)
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409 resizePanel = true;
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414 public void mouseExited(MouseEvent evt)
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416 dragCancelled = false;
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418 if (dragEvent == null)
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420 resizePanel = false;
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432 public void mousePressed(MouseEvent evt)
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439 dragCancelled = false;
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440 // todo: move below to mouseClicked ?
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441 selectedRow = getSelectedRow(evt.getY() + scrollOffset);
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443 AlignmentAnnotation[] aa = ap.av.getAlignment()
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444 .getAlignmentAnnotation();
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446 // DETECT RIGHT MOUSE BUTTON IN AWT
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447 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
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450 JPopupMenu popup = new JPopupMenu(
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451 MessageManager.getString("label.annotations"));
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453 JMenuItem item = new JMenuItem(ADDNEW);
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454 item.addActionListener(this);
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456 if (selectedRow < 0)
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458 // this never happens at moment: - see comment on JAL-563
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461 item = new JMenuItem(SHOWALL);
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462 item.addActionListener(this);
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466 popup.show(this, evt.getX(), evt.getY());
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469 // add the rest if there are actually rows to show
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470 item = new JMenuItem(EDITNAME);
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471 item.addActionListener(this);
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473 item = new JMenuItem(HIDE);
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474 item.addActionListener(this);
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478 * Hide all <label>:
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480 if (selectedRow < aa.length)
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482 if (aa[selectedRow].sequenceRef != null)
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484 final String label = aa[selectedRow].label;
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485 JMenuItem hideType = new JMenuItem(
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486 MessageManager.getString("label.hide_all") + " " + label);
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487 hideType.addActionListener(new ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 AlignmentUtils.showOrHideSequenceAnnotations(
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493 ap.av.getAlignment(), Collections.singleton(label),
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494 null, false, false);
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498 popup.add(hideType);
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504 item = new JMenuItem(SHOWALL);
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505 item.addActionListener(this);
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509 item = new JMenuItem(OUTPUT_TEXT);
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510 item.addActionListener(this);
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512 if (selectedRow < aa.length)
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514 if (aa[selectedRow].autoCalculated)
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516 if (aa[selectedRow].label.indexOf("Consensus") > -1)
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518 popup.addSeparator();
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519 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
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520 MessageManager.getString("label.ignore_gaps_consensus"),
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521 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
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522 .getIgnoreGapsConsensus() : ap.av
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523 .isIgnoreGapsConsensus());
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524 final AlignmentAnnotation aaa = aa[selectedRow];
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525 cbmi.addItemListener(new ItemListener()
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527 public void itemStateChanged(ItemEvent e)
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529 if (aaa.groupRef != null)
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531 // TODO: pass on reference to ap so the view can be updated.
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532 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
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536 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
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538 ap.paintAlignment(true);
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542 if (aaa.groupRef != null)
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544 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
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545 MessageManager.getString("label.show_group_histogram"),
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546 aa[selectedRow].groupRef.isShowConsensusHistogram());
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547 chist.addItemListener(new ItemListener()
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549 public void itemStateChanged(ItemEvent e)
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551 // TODO: pass on reference
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557 aaa.groupRef.setShowConsensusHistogram(chist.getState());
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559 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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563 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
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564 MessageManager.getString("label.show_group_logo"),
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565 aa[selectedRow].groupRef.isShowSequenceLogo());
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566 cprofl.addItemListener(new ItemListener()
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568 public void itemStateChanged(ItemEvent e)
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570 // TODO: pass on reference
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576 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
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578 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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583 final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(
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584 MessageManager.getString("label.normalise_group_logo"),
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585 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
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586 cprofn.addItemListener(new ItemListener()
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588 public void itemStateChanged(ItemEvent e)
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590 // TODO: pass on reference
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596 aaa.groupRef.setshowSequenceLogo(true);
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597 aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
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599 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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606 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
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607 MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
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608 chist.addItemListener(new ItemListener()
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610 public void itemStateChanged(ItemEvent e)
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612 // TODO: pass on reference
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618 av.setShowConsensusHistogram(chist.getState());
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619 ap.alignFrame.showConsensusHistogram.setState(chist
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620 .getState()); // TODO: implement
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621 // ap.updateGUI()/alignFrame.updateGUI
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624 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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628 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
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629 MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
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630 cprof.addItemListener(new ItemListener()
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632 public void itemStateChanged(ItemEvent e)
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634 // TODO: pass on reference
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640 av.setShowSequenceLogo(cprof.getState());
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641 ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
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643 // ap.updateGUI()/alignFrame.updateGUI
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647 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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651 final JCheckBoxMenuItem cprofn = new JCheckBoxMenuItem(
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652 MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
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653 cprofn.addItemListener(new ItemListener()
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655 public void itemStateChanged(ItemEvent e)
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657 // TODO: pass on reference
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663 av.setShowSequenceLogo(true);
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664 ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
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666 // ap.updateGUI()/alignFrame.updateGUI
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669 av.setNormaliseSequenceLogo(cprofn.getState());
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671 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
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677 item = new JMenuItem(COPYCONS_SEQ);
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678 item.addActionListener(this);
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683 popup.show(this, evt.getX(), evt.getY());
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687 // selection action.
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688 if (selectedRow > -1 && selectedRow < aa.length)
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690 if (aa[selectedRow].groupRef != null)
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692 if (evt.getClickCount() >= 2)
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694 // todo: make the ap scroll to the selection - not necessary, first
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695 // click highlights/scrolls, second selects
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696 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
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697 ap.av.setSelectionGroup(// new SequenceGroup(
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698 aa[selectedRow].groupRef); // );
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699 ap.av.sendSelection();
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700 ap.paintAlignment(false);
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701 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
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705 ap.seqPanel.ap.idPanel
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706 .highlightSearchResults(aa[selectedRow].groupRef
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707 .getSequences(null));
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711 else if (aa[selectedRow].sequenceRef != null)
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713 if (evt.getClickCount() == 1)
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715 ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
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716 .asList(new SequenceI[]
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717 { aa[selectedRow].sequenceRef }));
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719 else if (evt.getClickCount() >= 2)
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721 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
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722 SequenceGroup sg = ap.av.getSelectionGroup();
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725 // we make a copy rather than edit the current selection if no modifiers pressed
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726 // see Enhancement JAL-1557
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727 if (!(evt.isControlDown() || evt.isShiftDown()))
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729 sg = new SequenceGroup(sg);
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731 sg.addSequence(aa[selectedRow].sequenceRef, false);
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733 if (evt.isControlDown())
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735 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
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737 // notionally, we should also add intermediate sequences from last added sequence ?
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738 sg.addSequence(aa[selectedRow].sequenceRef, true);
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742 sg = new SequenceGroup();
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744 sg.setEndRes(ap.av.getAlignment().getWidth()-1);
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745 sg.addSequence(aa[selectedRow].sequenceRef, false);
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747 ap.av.setSelectionGroup(sg);
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748 ap.paintAlignment(false);
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749 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
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750 ap.av.sendSelection();
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765 protected void copy_annotseqtoclipboard(SequenceI sq)
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767 if (sq == null || sq.getLength() < 1)
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771 AlignFrame.copiedSequences = new StringBuffer();
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772 AlignFrame.copiedSequences.append(sq.getName() + "\t"
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773 + sq.getStart() + "\t" + sq.getEnd() + "\t"
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774 + sq.getSequenceAsString() + "\n");
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775 if (av.hasHiddenColumns())
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777 AlignFrame.copiedHiddenColumns = new Vector();
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778 for (int[] region : av.getColumnSelection().getHiddenColumns())
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780 AlignFrame.copiedHiddenColumns
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781 .addElement(new int[]
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782 { region[0], region[1] });
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787 public void update(Graphics g)
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792 public void paint(Graphics g)
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794 int w = getSize().width;
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795 int h = getSize().height;
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796 if (image == null || w != image.getWidth(this)
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797 || h != image.getHeight(this))
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799 image = createImage(w, ap.annotationPanel.getSize().height);
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802 drawComponent(image.getGraphics(), w);
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803 g.drawImage(image, 0, 0, this);
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806 public void drawComponent(Graphics g, int width)
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808 g.setFont(av.getFont());
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809 FontMetrics fm = g.getFontMetrics(av.getFont());
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810 g.setColor(Color.white);
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811 g.fillRect(0, 0, getSize().width, getSize().height);
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813 g.translate(0, -scrollOffset);
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814 g.setColor(Color.black);
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816 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
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817 int y = 0, fy = g.getFont().getSize();
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822 hasHiddenRows = false;
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823 for (int i = 0; i < aa.length; i++)
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825 if (!aa[i].visible)
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827 hasHiddenRows = true;
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831 x = width - fm.stringWidth(aa[i].label) - 3;
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834 offset = -(aa[i].height - fy) / 2;
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836 g.drawString(aa[i].label, x, y + offset);
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839 g.translate(0, +scrollOffset);
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842 g.setColor(Color.red);
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844 g.drawLine(2, 8, 5, 2);
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845 g.drawLine(5, 2, 8, 8);
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847 else if (!dragCancelled && dragEvent != null && aa != null)
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849 g.setColor(Color.lightGray);
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850 g.drawString(aa[selectedRow].label, dragEvent.getX(),
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854 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
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856 g.setColor(Color.black);
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857 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
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858 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
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