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.datamodel.SearchResults;
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24 import jalview.datamodel.SequenceFeature;
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25 import jalview.datamodel.SequenceI;
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26 import jalview.io.FeaturesFile;
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27 import jalview.schemes.AnnotationColourGradient;
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28 import jalview.schemes.GraduatedColor;
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29 import jalview.schemes.UserColourScheme;
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30 import jalview.util.MessageManager;
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31 import jalview.viewmodel.AlignmentViewport;
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33 import java.awt.BorderLayout;
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34 import javax.swing.JButton;
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35 import java.awt.Color;
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36 import java.awt.Dimension;
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37 import java.awt.Font;
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38 import java.awt.Graphics;
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39 import java.awt.GridLayout;
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40 import javax.swing.JLabel;
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41 import javax.swing.JPanel;
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42 import javax.swing.JScrollPane;
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43 import javax.swing.JTextArea;
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44 import javax.swing.JTextField;
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45 import java.awt.event.ActionEvent;
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46 import java.awt.event.ActionListener;
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47 import java.util.Hashtable;
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53 * @version $Revision$
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55 public class FeatureRenderer extends
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56 jalview.renderer.seqfeatures.FeatureRenderer
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59 // Holds web links for feature groups and feature types
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60 // in the form label|link
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61 Hashtable featureLinks = null;
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64 * Creates a new FeatureRenderer object.
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69 public FeatureRenderer(AlignmentViewport av)
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74 setTransparencyAvailable(!System.getProperty("java.version")
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75 .startsWith("1.1"));
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78 static String lastFeatureAdded;
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80 static String lastFeatureGroupAdded;
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82 static String lastDescriptionAdded;
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84 int featureIndex = 0;
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86 boolean deleteFeature = false;
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88 FeatureColourPanel colourPanel;
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90 class FeatureColourPanel extends JPanel
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94 private Color maxCol;
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96 private boolean isColourByLabel, isGcol;
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99 * render a feature style in the amend feature dialog box
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101 public void updateColor(Object newcol)
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104 Color bg, col = null;
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105 GraduatedColor gcol = null;
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106 String vlabel = "";
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107 if (newcol instanceof Color)
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110 col = (Color) newcol;
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113 else if (newcol instanceof GraduatedColor)
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116 gcol = (GraduatedColor) newcol;
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123 .getString("error.invalid_colour_for_mycheckbox"));
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127 setBackground(bg = col);
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131 if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
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134 + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
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137 if (isColourByLabel = gcol.isColourByLabel())
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139 setBackground(bg = Color.white);
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140 vlabel += " (by Label)";
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144 setBackground(bg = gcol.getMinColor());
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145 maxCol = gcol.getMaxColor();
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153 FeatureColourPanel()
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158 public void paint(Graphics g)
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160 Dimension d = getSize();
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163 if (isColourByLabel)
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165 g.setColor(Color.white);
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166 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
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167 g.setColor(Color.black);
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168 Font f = new Font("Verdana", Font.PLAIN, 10);
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170 g.drawString(MessageManager.getString("label.label"), 0, 0);
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174 g.setColor(maxCol);
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175 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
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183 boolean amendFeatures(final SequenceI[] sequences,
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184 final SequenceFeature[] features, boolean newFeatures,
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185 final AlignmentPanel ap)
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187 JPanel bigPanel = new JPanel(new BorderLayout());
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188 final JTextField name = new JTextField(16);
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189 final JTextField source = new JTextField(16);
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190 final JTextArea description = new JTextArea(3, 35);
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191 final JTextField start = new JTextField(8);
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192 final JTextField end = new JTextField(8);
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193 final Choice overlaps;
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194 JButton deleteButton = new JButton("Delete");
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195 deleteFeature = false;
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197 colourPanel = new FeatureColourPanel();
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198 colourPanel.setSize(110, 15);
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199 final FeatureRenderer fr = this;
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201 JPanel panel = new JPanel(new GridLayout(3, 1));
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203 featureIndex = 0; // feature to be amended.
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206 // /////////////////////////////////////
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207 // /MULTIPLE FEATURES AT SELECTED RESIDUE
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208 if (!newFeatures && features.length > 1)
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210 panel = new JPanel(new GridLayout(4, 1));
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211 tmp = new JPanel();
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212 tmp.add(new JLabel("Select Feature: "));
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213 overlaps = new Choice();
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214 for (int i = 0; i < features.length; i++)
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216 String item = features[i].getType() + "/" + features[i].getBegin()
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217 + "-" + features[i].getEnd();
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219 if (features[i].getFeatureGroup() != null)
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221 item += " (" + features[i].getFeatureGroup() + ")";
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224 overlaps.addItem(item);
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229 overlaps.addItemListener(new java.awt.event.ItemListener()
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231 public void itemStateChanged(java.awt.event.ItemEvent e)
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233 int index = overlaps.getSelectedIndex();
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236 featureIndex = index;
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237 name.setText(features[index].getType());
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238 description.setText(features[index].getDescription());
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239 source.setText(features[index].getFeatureGroup());
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240 start.setText(features[index].getBegin() + "");
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241 end.setText(features[index].getEnd() + "");
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243 SearchResults highlight = new SearchResults();
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244 highlight.addResult(sequences[0], features[index].getBegin(),
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245 features[index].getEnd());
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247 ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
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250 Object col = getFeatureStyle(name.getText());
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253 col = new UserColourScheme().createColourFromName(name
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257 colourPanel.updateColor(col);
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264 // ////////////////////////////////////
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266 tmp = new JPanel();
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268 tmp.add(new JLabel("Name: ", JLabel.RIGHT));
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271 tmp = new JPanel();
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273 tmp.add(new JLabel("Group: ", JLabel.RIGHT));
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276 tmp = new JPanel();
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278 tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
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279 tmp.add(colourPanel);
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281 bigPanel.add(panel, BorderLayout.NORTH);
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283 panel = new JPanel();
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284 panel.add(new JLabel("Description: ", JLabel.RIGHT));
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285 panel.add(new JScrollPane().add(description));
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289 bigPanel.add(panel, BorderLayout.SOUTH);
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291 panel = new JPanel();
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292 panel.add(new JLabel(" Start:", JLabel.RIGHT));
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294 panel.add(new JLabel(" End:", JLabel.RIGHT));
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296 bigPanel.add(panel, BorderLayout.CENTER);
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300 bigPanel.add(panel, BorderLayout.CENTER);
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303 if (lastFeatureAdded == null)
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305 if (features[0].type != null)
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307 lastFeatureAdded = features[0].type;
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311 lastFeatureAdded = "feature_1";
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315 if (lastFeatureGroupAdded == null)
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317 if (features[0].featureGroup != null)
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319 lastFeatureGroupAdded = features[0].featureGroup;
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323 lastFeatureAdded = "Jalview";
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327 String title = newFeatures ? MessageManager
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328 .getString("label.create_new_sequence_features")
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329 : MessageManager.formatMessage("label.amend_delete_features",
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331 { sequences[0].getName() });
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333 final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
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336 dialog.setMainPanel(bigPanel);
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340 name.setText(lastFeatureAdded);
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341 source.setText(lastFeatureGroupAdded);
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345 dialog.ok.setLabel(MessageManager.getString("label.amend"));
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346 dialog.buttonPanel.add(deleteButton, 1);
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347 deleteButton.addActionListener(new ActionListener()
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349 public void actionPerformed(ActionEvent evt)
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351 deleteFeature = true;
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352 dialog.setVisible(false);
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355 name.setText(features[0].getType());
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356 source.setText(features[0].getFeatureGroup());
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359 start.setText(features[0].getBegin() + "");
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360 end.setText(features[0].getEnd() + "");
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361 description.setText(features[0].getDescription());
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362 Color col = getColour(name.getText());
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365 col = new UserColourScheme()
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366 .createColourFromName(name.getText());
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368 Object fcol = getFeatureStyle(name.getText());
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369 // simply display the feature color in a box
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370 colourPanel.updateColor(fcol);
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371 dialog.setResizable(true);
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372 // TODO: render the graduated color in the box.
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373 colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
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375 public void mousePressed(java.awt.event.MouseEvent evt)
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377 if (!colourPanel.isGcol)
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379 new UserDefinedColours(fr, ap.alignFrame);
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383 FeatureColourChooser fcc = new FeatureColourChooser(
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384 ap.alignFrame, name.getText());
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385 dialog.transferFocus();
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389 dialog.setVisible(true);
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391 FeaturesFile ffile = new FeaturesFile();
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395 // This ensures that the last sequence
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396 // is refreshed and new features are rendered
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398 lastFeatureAdded = name.getText().trim();
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399 lastFeatureGroupAdded = source.getText().trim();
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400 lastDescriptionAdded = description.getText().replace('\n', ' ');
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403 if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
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405 lastFeatureGroupAdded = null;
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411 SequenceFeature sf = features[featureIndex];
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414 sf.type = lastFeatureAdded;
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415 sf.featureGroup = lastFeatureGroupAdded;
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416 sf.description = lastDescriptionAdded;
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417 if (!colourPanel.isGcol)
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419 // update colour - otherwise its already done.
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420 setColour(sf.type, colourPanel.getBackground());
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424 sf.begin = Integer.parseInt(start.getText());
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425 sf.end = Integer.parseInt(end.getText());
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426 } catch (NumberFormatException ex)
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430 ffile.parseDescriptionHTML(sf, false);
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431 setVisible(lastFeatureAdded); // if user edited name then make sure new
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436 sequences[0].deleteFeature(sf);
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442 if (dialog.accept && name.getText().length() > 0)
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444 for (int i = 0; i < sequences.length; i++)
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446 features[i].type = lastFeatureAdded;
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447 features[i].featureGroup = lastFeatureGroupAdded;
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448 features[i].description = lastDescriptionAdded;
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449 sequences[i].addSequenceFeature(features[i]);
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450 ffile.parseDescriptionHTML(features[i], false);
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453 Color newColour = colourPanel.getBackground();
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454 // setColour(lastFeatureAdded, fcol);
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456 if (lastFeatureGroupAdded != null)
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458 setGroupVisibility(lastFeatureGroupAdded, true);
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460 setColour(lastFeatureAdded, newColour); // was fcol
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461 setVisible(lastFeatureAdded);
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462 findAllFeatures(false); // different to original applet behaviour ?
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463 // findAllFeatures();
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467 // no update to the alignment
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471 // refresh the alignment and the feature settings dialog
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472 if (((AlignViewport) av).featureSettings != null)
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474 ((AlignViewport) av).featureSettings.refreshTable();
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476 // findAllFeatures();
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478 ap.paintAlignment(true);
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