2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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24 import java.awt.event.*;
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25 import javax.swing.*;
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26 import javax.swing.event.*;
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28 import jalview.datamodel.*;
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29 import jalview.schemes.*;
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30 import java.awt.Dimension;
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32 public class AnnotationColourChooser
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35 JInternalFrame frame;
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38 ColourSchemeI oldcs;
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39 Hashtable oldgroupColours;
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40 jalview.datamodel.AlignmentAnnotation currentAnnotation;
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41 boolean adjusting = false;
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43 public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
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45 oldcs = av.getGlobalColourScheme();
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46 if (av.alignment.getGroups() != null)
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48 oldgroupColours = new Hashtable();
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49 Vector allGroups = ap.av.alignment.getGroups();
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51 for (int g = 0; g < allGroups.size(); g++)
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53 sg = (SequenceGroup) allGroups.get(g);
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56 oldgroupColours.put(sg, sg.cs);
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62 frame = new JInternalFrame();
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63 frame.setContentPane(this);
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64 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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65 Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
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68 slider.addChangeListener(new ChangeListener()
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70 public void stateChanged(ChangeEvent evt)
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74 thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
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79 slider.addMouseListener(new MouseAdapter()
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81 public void mouseReleased(MouseEvent evt)
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83 ap.paintAlignment(true);
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87 if (av.alignment.getAlignmentAnnotation() == null)
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92 if (oldcs instanceof AnnotationColourGradient)
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94 AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
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95 minColour.setBackground(acg.getMinColour());
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96 maxColour.setBackground(acg.getMaxColour());
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100 minColour.setBackground(Color.orange);
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101 maxColour.setBackground(Color.red);
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105 Vector list = new Vector();
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107 for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
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109 String label = av.alignment.getAlignmentAnnotation()[i].label;
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110 if (!list.contains(label))
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111 list.addElement(label);
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113 list.addElement(label+"_"+(index++));
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116 annotations = new JComboBox(list);
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118 threshold.addItem("No Threshold");
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119 threshold.addItem("Above Threshold");
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120 threshold.addItem("Below Threshold");
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126 catch (Exception ex)
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135 public AnnotationColourChooser()
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141 catch (Exception ex)
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143 ex.printStackTrace();
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147 private void jbInit()
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150 minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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151 minColour.setBorder(BorderFactory.createEtchedBorder());
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152 minColour.setPreferredSize(new Dimension(40, 20));
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153 minColour.setToolTipText("Minimum Colour");
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154 minColour.addMouseListener(new MouseAdapter()
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156 public void mousePressed(MouseEvent e)
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158 if (minColour.isEnabled())
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160 minColour_actionPerformed();
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164 maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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165 maxColour.setBorder(BorderFactory.createEtchedBorder());
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166 maxColour.setPreferredSize(new Dimension(40, 20));
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167 maxColour.setToolTipText("Maximum Colour");
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168 maxColour.addMouseListener(new MouseAdapter()
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170 public void mousePressed(MouseEvent e)
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172 if (maxColour.isEnabled())
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174 maxColour_actionPerformed();
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178 ok.setOpaque(false);
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180 ok.addActionListener(new ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 ok_actionPerformed(e);
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187 cancel.setOpaque(false);
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188 cancel.setText("Cancel");
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189 cancel.addActionListener(new ActionListener()
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191 public void actionPerformed(ActionEvent e)
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193 cancel_actionPerformed(e);
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196 this.setLayout(borderLayout1);
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197 jPanel2.setLayout(flowLayout1);
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198 annotations.addActionListener(new ActionListener()
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200 public void actionPerformed(ActionEvent e)
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202 annotations_actionPerformed(e);
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205 jPanel1.setBackground(Color.white);
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206 jPanel2.setBackground(Color.white);
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207 threshold.addActionListener(new ActionListener()
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209 public void actionPerformed(ActionEvent e)
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211 threshold_actionPerformed(e);
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214 jPanel3.setLayout(flowLayout2);
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215 thresholdValue.addActionListener(new ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 thresholdValue_actionPerformed(e);
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222 slider.setPaintLabels(false);
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223 slider.setPaintTicks(true);
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224 slider.setBackground(Color.white);
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225 slider.setEnabled(false);
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226 slider.setOpaque(false);
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227 slider.setPreferredSize(new Dimension(100, 32));
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228 thresholdValue.setEnabled(false);
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229 thresholdValue.setColumns(7);
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230 jPanel3.setBackground(Color.white);
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231 currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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232 currentColours.setOpaque(false);
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233 currentColours.setText("Use Original Colours");
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234 currentColours.addActionListener(new ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 currentColours_actionPerformed(e);
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241 thresholdIsMin.setBackground(Color.white);
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242 thresholdIsMin.setText("Threshold is Min/Max");
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243 thresholdIsMin.addActionListener(new ActionListener()
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245 public void actionPerformed(ActionEvent actionEvent)
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247 thresholdIsMin_actionPerformed(actionEvent);
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251 jPanel1.add(cancel);
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252 jPanel2.add(annotations);
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253 jPanel2.add(currentColours);
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254 jPanel2.add(minColour);
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255 jPanel2.add(maxColour);
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256 this.add(jPanel3, java.awt.BorderLayout.CENTER);
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257 jPanel3.add(threshold);
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258 jPanel3.add(slider);
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259 jPanel3.add(thresholdValue);
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260 jPanel3.add(thresholdIsMin);
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261 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
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262 this.add(jPanel2, java.awt.BorderLayout.NORTH);
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265 JComboBox annotations;
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266 JPanel minColour = new JPanel();
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267 JPanel maxColour = new JPanel();
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268 JButton ok = new JButton();
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269 JButton cancel = new JButton();
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270 JPanel jPanel1 = new JPanel();
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271 JPanel jPanel2 = new JPanel();
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272 BorderLayout borderLayout1 = new BorderLayout();
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273 JComboBox threshold = new JComboBox();
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274 FlowLayout flowLayout1 = new FlowLayout();
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275 JPanel jPanel3 = new JPanel();
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276 FlowLayout flowLayout2 = new FlowLayout();
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277 JSlider slider = new JSlider();
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278 JTextField thresholdValue = new JTextField(20);
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279 JCheckBox currentColours = new JCheckBox();
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280 JCheckBox thresholdIsMin = new JCheckBox();
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282 public void minColour_actionPerformed()
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284 Color col = JColorChooser.showDialog(this,
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285 "Select Colour for Minimum Value",
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286 minColour.getBackground());
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289 minColour.setBackground(col);
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291 minColour.repaint();
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295 public void maxColour_actionPerformed()
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297 Color col = JColorChooser.showDialog(this,
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298 "Select Colour for Maximum Value",
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299 maxColour.getBackground());
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302 maxColour.setBackground(col);
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304 maxColour.repaint();
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308 void changeColour()
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310 // Check if combobox is still adjusting
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317 currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
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319 int aboveThreshold = -1;
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320 if (threshold.getSelectedItem().equals("Above Threshold"))
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322 aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
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324 else if (threshold.getSelectedItem().equals("Below Threshold"))
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326 aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
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329 slider.setEnabled(true);
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330 thresholdValue.setEnabled(true);
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332 if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
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334 slider.setEnabled(false);
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335 thresholdValue.setEnabled(false);
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336 thresholdValue.setText("");
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338 else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
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339 currentAnnotation.threshold == null)
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341 currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
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342 ( (currentAnnotation.graphMax -
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343 currentAnnotation.graphMin) / 2f,
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348 if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
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351 float range = currentAnnotation.graphMax * 1000 -
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352 currentAnnotation.graphMin * 1000;
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354 slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
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355 slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
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356 slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
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357 thresholdValue.setText(currentAnnotation.threshold.value + "");
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358 slider.setMajorTickSpacing( (int) (range / 10f));
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359 slider.setEnabled(true);
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360 thresholdValue.setEnabled(true);
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364 AnnotationColourGradient acg = null;
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365 if (currentColours.isSelected())
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367 acg = new AnnotationColourGradient(
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369 av.getGlobalColourScheme(), aboveThreshold);
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374 new AnnotationColourGradient(
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376 minColour.getBackground(),
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377 maxColour.getBackground(),
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381 if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
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383 acg.predefinedColours = true;
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386 acg.thresholdIsMinMax = thresholdIsMin.isSelected();
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388 av.setGlobalColourScheme(acg);
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390 if (av.alignment.getGroups() != null)
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392 Vector allGroups = ap.av.alignment.getGroups();
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394 for (int g = 0; g < allGroups.size(); g++)
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396 sg = (SequenceGroup) allGroups.get(g);
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403 if (currentColours.isSelected())
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405 sg.cs = new AnnotationColourGradient(
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407 sg.cs, aboveThreshold);
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411 sg.cs = new AnnotationColourGradient(
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413 minColour.getBackground(),
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414 maxColour.getBackground(),
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421 ap.paintAlignment(false);
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424 public void ok_actionPerformed(ActionEvent e)
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429 frame.setClosed(true);
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431 catch (Exception ex)
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435 public void cancel_actionPerformed(ActionEvent e)
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440 frame.setClosed(true);
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442 catch (Exception ex)
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448 av.setGlobalColourScheme(oldcs);
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449 if (av.alignment.getGroups() != null)
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451 Vector allGroups = ap.av.alignment.getGroups();
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453 for (int g = 0; g < allGroups.size(); g++)
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455 sg = (SequenceGroup) allGroups.get(g);
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456 sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
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461 public void thresholdCheck_actionPerformed(ActionEvent e)
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466 public void annotations_actionPerformed(ActionEvent e)
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471 public void threshold_actionPerformed(ActionEvent e)
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476 public void thresholdValue_actionPerformed(ActionEvent e)
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480 float f = Float.parseFloat(thresholdValue.getText());
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481 slider.setValue( (int) (f * 1000));
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483 catch (NumberFormatException ex)
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487 public void valueChanged()
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489 if (currentColours.isSelected()
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490 && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
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495 currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
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496 ap.paintAlignment(false);
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499 public void currentColours_actionPerformed(ActionEvent e)
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501 if (currentColours.isSelected())
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506 maxColour.setEnabled(!currentColours.isSelected());
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507 minColour.setEnabled(!currentColours.isSelected());
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512 public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
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