unused/appletgui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
   4  * \r
   5  * This file is part of Jalview.\r
   6  * \r
   7  * Jalview is free software: you can redistribute it and/or\r
   8  * modify it under the terms of the GNU General Public License \r
   9  * as published by the Free Software Foundation, either version 3\r
  10  * of the License, or (at your option) any later version.\r
  11  *  \r
  12  * Jalview is distributed in the hope that it will be useful, but \r
  13  * WITHOUT ANY WARRANTY; without even the implied warranty \r
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  15  * PURPOSE.  See the GNU General Public License for more details.\r
  16  * \r
  17  * You should have received a copy of the GNU General Public License\r
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.\r
  20  */\r
  21 package jalview.appletgui;\r
  22 \r
  23 import jalview.datamodel.SearchResults;\r
  24 import jalview.datamodel.SequenceFeature;\r
  25 import jalview.datamodel.SequenceI;\r
  26 import jalview.io.FeaturesFile;\r
  27 import jalview.schemes.AnnotationColourGradient;\r
  28 import jalview.schemes.GraduatedColor;\r
  29 import jalview.schemes.UserColourScheme;\r
  30 import jalview.util.MessageManager;\r
  31 import jalview.viewmodel.AlignmentViewport;\r
  32 \r
  33 import java.awt.BorderLayout;\r
  34 import javax.swing.JButton;\r
  35 import java.awt.Color;\r
  36 import java.awt.Dimension;\r
  37 import java.awt.Font;\r
  38 import java.awt.Graphics;\r
  39 import java.awt.GridLayout;\r
  40 import javax.swing.JLabel;\r
  41 import javax.swing.JPanel;\r
  42 import javax.swing.JScrollPane;\r
  43 import javax.swing.JTextArea;\r
  44 import javax.swing.JTextField;\r
  45 import java.awt.event.ActionEvent;\r
  46 import java.awt.event.ActionListener;\r
  47 import java.util.Hashtable;\r
  48 \r
  49 /**\r
  50  * DOCUMENT ME!\r
  51  * \r
  52  * @author $author$\r
  53  * @version $Revision$\r
  54  */\r
  55 public class FeatureRenderer extends\r
  56         jalview.renderer.seqfeatures.FeatureRenderer\r
  57 {\r
  58 \r
  59   // Holds web links for feature groups and feature types\r
  60   // in the form label|link\r
  61   Hashtable featureLinks = null;\r
  62 \r
  63   /**\r
  64    * Creates a new FeatureRenderer object.\r
  65    * \r
  66    * @param av\r
  67    *          DOCUMENT ME!\r
  68    */\r
  69   public FeatureRenderer(AlignmentViewport av)\r
  70   {\r
  71     super();\r
  72     this.av = av;\r
  73 \r
  74     setTransparencyAvailable(!System.getProperty("java.version")\r
  75             .startsWith("1.1"));\r
  76   }\r
  77 \r
  78   static String lastFeatureAdded;\r
  79 \r
  80   static String lastFeatureGroupAdded;\r
  81 \r
  82   static String lastDescriptionAdded;\r
  83 \r
  84   int featureIndex = 0;\r
  85 \r
  86   boolean deleteFeature = false;\r
  87 \r
  88   FeatureColourPanel colourPanel;\r
  89 \r
  90   class FeatureColourPanel extends JPanel\r
  91   {\r
  92     String label = "";\r
  93 \r
  94     private Color maxCol;\r
  95 \r
  96     private boolean isColourByLabel, isGcol;\r
  97 \r
  98     /**\r
  99      * render a feature style in the amend feature dialog box\r
 100      */\r
 101     public void updateColor(Object newcol)\r
 102     {\r
 103 \r
 104       Color bg, col = null;\r
 105       GraduatedColor gcol = null;\r
 106       String vlabel = "";\r
 107       if (newcol instanceof Color)\r
 108       {\r
 109         isGcol = false;\r
 110         col = (Color) newcol;\r
 111         gcol = null;\r
 112       }\r
 113       else if (newcol instanceof GraduatedColor)\r
 114       {\r
 115         isGcol = true;\r
 116         gcol = (GraduatedColor) newcol;\r
 117         col = null;\r
 118       }\r
 119       else\r
 120       {\r
 121         throw new Error(\r
 122                 MessageManager\r
 123                         .getString("error.invalid_colour_for_mycheckbox"));\r
 124       }\r
 125       if (col != null)\r
 126       {\r
 127         setBackground(bg = col);\r
 128       }\r
 129       else\r
 130       {\r
 131         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
 132         {\r
 133           vlabel += " "\r
 134                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"\r
 135                           : "(<)");\r
 136         }\r
 137         if (isColourByLabel = gcol.isColourByLabel())\r
 138         {\r
 139           setBackground(bg = Color.white);\r
 140           vlabel += " (by Label)";\r
 141         }\r
 142         else\r
 143         {\r
 144           setBackground(bg = gcol.getMinColor());\r
 145           maxCol = gcol.getMaxColor();\r
 146         }\r
 147       }\r
 148       label = vlabel;\r
 149       setBackground(bg);\r
 150       repaint();\r
 151     }\r
 152 \r
 153     FeatureColourPanel()\r
 154     {\r
 155       super(null);\r
 156     }\r
 157 \r
 158     public void paint(Graphics g)\r
 159     {\r
 160       Dimension d = getSize();\r
 161       if (isGcol)\r
 162       {\r
 163         if (isColourByLabel)\r
 164         {\r
 165           g.setColor(Color.white);\r
 166           g.fillRect(d.width / 2, 0, d.width / 2, d.height);\r
 167           g.setColor(Color.black);\r
 168           Font f = new Font("Verdana", Font.PLAIN, 10);\r
 169           g.setFont(f);\r
 170           g.drawString(MessageManager.getString("label.label"), 0, 0);\r
 171         }\r
 172         else\r
 173         {\r
 174           g.setColor(maxCol);\r
 175           g.fillRect(d.width / 2, 0, d.width / 2, d.height);\r
 176 \r
 177         }\r
 178       }\r
 179     }\r
 180 \r
 181   }\r
 182 \r
 183   boolean amendFeatures(final SequenceI[] sequences,\r
 184           final SequenceFeature[] features, boolean newFeatures,\r
 185           final AlignmentPanel ap)\r
 186   {\r
 187     JPanel bigPanel = new JPanel(new BorderLayout());\r
 188     final JTextField name = new JTextField(16);\r
 189     final JTextField source = new JTextField(16);\r
 190     final JTextArea description = new JTextArea(3, 35);\r
 191     final JTextField start = new JTextField(8);\r
 192     final JTextField end = new JTextField(8);\r
 193     final Choice overlaps;\r
 194     JButton deleteButton = new JButton("Delete");\r
 195     deleteFeature = false;\r
 196 \r
 197     colourPanel = new FeatureColourPanel();\r
 198     colourPanel.setSize(110, 15);\r
 199     final FeatureRenderer fr = this;\r
 200 \r
 201     JPanel panel = new JPanel(new GridLayout(3, 1));\r
 202 \r
 203     featureIndex = 0; // feature to be amended.\r
 204     JPanel tmp;\r
 205 \r
 206     // /////////////////////////////////////\r
 207     // /MULTIPLE FEATURES AT SELECTED RESIDUE\r
 208     if (!newFeatures && features.length > 1)\r
 209     {\r
 210       panel = new JPanel(new GridLayout(4, 1));\r
 211       tmp = new JPanel();\r
 212       tmp.add(new JLabel("Select Feature: "));\r
 213       overlaps = new Choice();\r
 214       for (int i = 0; i < features.length; i++)\r
 215       {\r
 216         String item = features[i].getType() + "/" + features[i].getBegin()\r
 217                 + "-" + features[i].getEnd();\r
 218 \r
 219         if (features[i].getFeatureGroup() != null)\r
 220         {\r
 221           item += " (" + features[i].getFeatureGroup() + ")";\r
 222         }\r
 223 \r
 224         overlaps.addItem(item);\r
 225       }\r
 226 \r
 227       tmp.add(overlaps);\r
 228 \r
 229       overlaps.addItemListener(new java.awt.event.ItemListener()\r
 230       {\r
 231         public void itemStateChanged(java.awt.event.ItemEvent e)\r
 232         {\r
 233           int index = overlaps.getSelectedIndex();\r
 234           if (index != -1)\r
 235           {\r
 236             featureIndex = index;\r
 237             name.setText(features[index].getType());\r
 238             description.setText(features[index].getDescription());\r
 239             source.setText(features[index].getFeatureGroup());\r
 240             start.setText(features[index].getBegin() + "");\r
 241             end.setText(features[index].getEnd() + "");\r
 242 \r
 243             SearchResults highlight = new SearchResults();\r
 244             highlight.addResult(sequences[0], features[index].getBegin(),\r
 245                     features[index].getEnd());\r
 246 \r
 247             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
 248 \r
 249           }\r
 250           Object col = getFeatureStyle(name.getText());\r
 251           if (col == null)\r
 252           {\r
 253             col = new UserColourScheme().createColourFromName(name\r
 254                     .getText());\r
 255           }\r
 256 \r
 257           colourPanel.updateColor(col);\r
 258         }\r
 259       });\r
 260 \r
 261       panel.add(tmp);\r
 262     }\r
 263     // ////////\r
 264     // ////////////////////////////////////\r
 265 \r
 266     tmp = new JPanel();\r
 267     panel.add(tmp);\r
 268     tmp.add(new JLabel("Name: ", JLabel.RIGHT));\r
 269     tmp.add(name);\r
 270 \r
 271     tmp = new JPanel();\r
 272     panel.add(tmp);\r
 273     tmp.add(new JLabel("Group: ", JLabel.RIGHT));\r
 274     tmp.add(source);\r
 275 \r
 276     tmp = new JPanel();\r
 277     panel.add(tmp);\r
 278     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));\r
 279     tmp.add(colourPanel);\r
 280 \r
 281     bigPanel.add(panel, BorderLayout.NORTH);\r
 282 \r
 283     panel = new JPanel();\r
 284     panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
 285     panel.add(new JScrollPane().add(description));\r
 286 \r
 287     if (!newFeatures)\r
 288     {\r
 289       bigPanel.add(panel, BorderLayout.SOUTH);\r
 290 \r
 291       panel = new JPanel();\r
 292       panel.add(new JLabel(" Start:", JLabel.RIGHT));\r
 293       panel.add(start);\r
 294       panel.add(new JLabel("  End:", JLabel.RIGHT));\r
 295       panel.add(end);\r
 296       bigPanel.add(panel, BorderLayout.CENTER);\r
 297     }\r
 298     else\r
 299     {\r
 300       bigPanel.add(panel, BorderLayout.CENTER);\r
 301     }\r
 302 \r
 303     if (lastFeatureAdded == null)\r
 304     {\r
 305       if (features[0].type != null)\r
 306       {\r
 307         lastFeatureAdded = features[0].type;\r
 308       }\r
 309       else\r
 310       {\r
 311         lastFeatureAdded = "feature_1";\r
 312       }\r
 313     }\r
 314 \r
 315     if (lastFeatureGroupAdded == null)\r
 316     {\r
 317       if (features[0].featureGroup != null)\r
 318       {\r
 319         lastFeatureGroupAdded = features[0].featureGroup;\r
 320       }\r
 321       else\r
 322       {\r
 323         lastFeatureAdded = "Jalview";\r
 324       }\r
 325     }\r
 326 \r
 327     String title = newFeatures ? MessageManager\r
 328             .getString("label.create_new_sequence_features")\r
 329             : MessageManager.formatMessage("label.amend_delete_features",\r
 330                     new String[]\r
 331                     { sequences[0].getName() });\r
 332 \r
 333     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,\r
 334             240);\r
 335 \r
 336     dialog.setMainPanel(bigPanel);\r
 337 \r
 338     if (newFeatures)\r
 339     {\r
 340       name.setText(lastFeatureAdded);\r
 341       source.setText(lastFeatureGroupAdded);\r
 342     }\r
 343     else\r
 344     {\r
 345       dialog.ok.setLabel(MessageManager.getString("label.amend"));\r
 346       dialog.buttonPanel.add(deleteButton, 1);\r
 347       deleteButton.addActionListener(new ActionListener()\r
 348       {\r
 349         public void actionPerformed(ActionEvent evt)\r
 350         {\r
 351           deleteFeature = true;\r
 352           dialog.setVisible(false);\r
 353         }\r
 354       });\r
 355       name.setText(features[0].getType());\r
 356       source.setText(features[0].getFeatureGroup());\r
 357     }\r
 358 \r
 359     start.setText(features[0].getBegin() + "");\r
 360     end.setText(features[0].getEnd() + "");\r
 361     description.setText(features[0].getDescription());\r
 362     Color col = getColour(name.getText());\r
 363     if (col == null)\r
 364     {\r
 365       col = new UserColourScheme()\r
 366               .createColourFromName(name.getText());\r
 367     }\r
 368     Object fcol = getFeatureStyle(name.getText());\r
 369     // simply display the feature color in a box\r
 370     colourPanel.updateColor(fcol);\r
 371     dialog.setResizable(true);\r
 372     // TODO: render the graduated color in the box.\r
 373     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()\r
 374     {\r
 375       public void mousePressed(java.awt.event.MouseEvent evt)\r
 376       {\r
 377         if (!colourPanel.isGcol)\r
 378         {\r
 379           new UserDefinedColours(fr, ap.alignFrame);\r
 380         }\r
 381         else\r
 382         {\r
 383           FeatureColourChooser fcc = new FeatureColourChooser(\r
 384                   ap.alignFrame, name.getText());\r
 385           dialog.transferFocus();\r
 386         }\r
 387       }\r
 388     });\r
 389     dialog.setVisible(true);\r
 390 \r
 391     FeaturesFile ffile = new FeaturesFile();\r
 392 \r
 393     if (dialog.accept)\r
 394     {\r
 395       // This ensures that the last sequence\r
 396       // is refreshed and new features are rendered\r
 397       lastSeq = null;\r
 398       lastFeatureAdded = name.getText().trim();\r
 399       lastFeatureGroupAdded = source.getText().trim();\r
 400       lastDescriptionAdded = description.getText().replace('\n', ' ');\r
 401     }\r
 402 \r
 403     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)\r
 404     {\r
 405       lastFeatureGroupAdded = null;\r
 406     }\r
 407 \r
 408     if (!newFeatures)\r
 409     {\r
 410 \r
 411       SequenceFeature sf = features[featureIndex];\r
 412       if (dialog.accept)\r
 413       {\r
 414         sf.type = lastFeatureAdded;\r
 415         sf.featureGroup = lastFeatureGroupAdded;\r
 416         sf.description = lastDescriptionAdded;\r
 417         if (!colourPanel.isGcol)\r
 418         {\r
 419           // update colour - otherwise its already done.\r
 420           setColour(sf.type, colourPanel.getBackground());\r
 421         }\r
 422         try\r
 423         {\r
 424           sf.begin = Integer.parseInt(start.getText());\r
 425           sf.end = Integer.parseInt(end.getText());\r
 426         } catch (NumberFormatException ex)\r
 427         {\r
 428         }\r
 429 \r
 430         ffile.parseDescriptionHTML(sf, false);\r
 431         setVisible(lastFeatureAdded); // if user edited name then make sure new\r
 432                                       // type is visible\r
 433       }\r
 434       if (deleteFeature)\r
 435       {\r
 436         sequences[0].deleteFeature(sf);\r
 437       }\r
 438 \r
 439     }\r
 440     else\r
 441     {\r
 442       if (dialog.accept && name.getText().length() > 0)\r
 443       {\r
 444         for (int i = 0; i < sequences.length; i++)\r
 445         {\r
 446           features[i].type = lastFeatureAdded;\r
 447           features[i].featureGroup = lastFeatureGroupAdded;\r
 448           features[i].description = lastDescriptionAdded;\r
 449           sequences[i].addSequenceFeature(features[i]);\r
 450           ffile.parseDescriptionHTML(features[i], false);\r
 451         }\r
 452 \r
 453         Color newColour = colourPanel.getBackground();\r
 454         // setColour(lastFeatureAdded, fcol);\r
 455 \r
 456         if (lastFeatureGroupAdded != null)\r
 457         {\r
 458           setGroupVisibility(lastFeatureGroupAdded, true);\r
 459         }\r
 460         setColour(lastFeatureAdded, newColour); // was fcol\r
 461         setVisible(lastFeatureAdded);\r
 462         findAllFeatures(false); // different to original applet behaviour ?\r
 463         // findAllFeatures();\r
 464       }\r
 465       else\r
 466       {\r
 467         // no update to the alignment\r
 468         return false;\r
 469       }\r
 470     }\r
 471     // refresh the alignment and the feature settings dialog\r
 472     if (((AlignViewport) av).featureSettings != null)\r
 473     {\r
 474       ((AlignViewport) av).featureSettings.refreshTable();\r
 475     }\r
 476     // findAllFeatures();\r
 477 \r
 478     ap.paintAlignment(true);\r
 479 \r
 480     return true;\r
 481   }\r
 482 }\r