src/jalview/appletgui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.api.FeatureColourI;
  24 import jalview.datamodel.SearchResults;
  25 import jalview.datamodel.SearchResultsI;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.io.FeaturesFile;
  29 import jalview.schemes.FeatureColour;
  30 import jalview.util.ColorUtils;
  31 import jalview.util.MessageManager;
  32 import jalview.viewmodel.AlignmentViewport;
  33
  34 import java.awt.BorderLayout;
  35 import java.awt.Button;
  36 import java.awt.Choice;
  37 import java.awt.Color;
  38 import java.awt.Dimension;
  39 import java.awt.FlowLayout;
  40 import java.awt.Font;
  41 import java.awt.Frame;
  42 import java.awt.Graphics;
  43 import java.awt.GridLayout;
  44 import java.awt.Label;
  45 import java.awt.Panel;
  46 import java.awt.ScrollPane;
  47 import java.awt.TextArea;
  48 import java.awt.TextField;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseAdapter;
  52 import java.awt.event.MouseEvent;
  53 import java.awt.event.TextEvent;
  54 import java.awt.event.TextListener;
  55 import java.util.Hashtable;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class FeatureRenderer extends
  64         jalview.renderer.seqfeatures.FeatureRenderer
  65 {
  66
  67   // Holds web links for feature groups and feature types
  68   // in the form label|link
  69   Hashtable featureLinks = null;
  70
  71   /**
  72    * Creates a new FeatureRenderer object.
  73    *
  74    * @param av
  75    */
  76   public FeatureRenderer(AlignmentViewport av)
  77   {
  78     super(av);
  79
  80   }
  81
  82   static String lastFeatureAdded;
  83
  84   static String lastFeatureGroupAdded;
  85
  86   static String lastDescriptionAdded;
  87
  88   int featureIndex = 0;
  89
  90   boolean deleteFeature = false;
  91
  92   FeatureColourPanel colourPanel;
  93
  94   class FeatureColourPanel extends Panel
  95   {
  96     String label = "";
  97
  98     private Color maxCol;
  99
 100     private boolean isColourByLabel, isGcol;
 101
 102     /**
 103      * render a feature style in the amend feature dialog box
 104      */
 105     public void updateColor(FeatureColourI newcol)
 106     {
 107       Color bg = null;
 108       String vlabel = "";
 109       if (newcol.isSimpleColour())
 110       {
 111         bg = newcol.getColour();
 112         setBackground(bg);
 113       }
 114       else
 115       {
 116         if (newcol.isAboveThreshold())
 117         {
 118           vlabel += " (>)";
 119         }
 120         else if (newcol.isBelowThreshold())
 121         {
 122           vlabel += " (<)";
 123         }
 124
 125         if (isColourByLabel = newcol.isColourByLabel())
 126         {
 127           setBackground(bg = Color.white);
 128           vlabel += " (by Label)";
 129         }
 130         else
 131         {
 132           setBackground(bg = newcol.getMinColour());
 133           maxCol = newcol.getMaxColour();
 134         }
 135       }
 136       label = vlabel;
 137       setBackground(bg);
 138       repaint();
 139     }
 140
 141     FeatureColourPanel()
 142     {
 143       super(null);
 144     }
 145
 146     @Override
 147     public void paint(Graphics g)
 148     {
 149       Dimension d = getSize();
 150       if (isGcol)
 151       {
 152         if (isColourByLabel)
 153         {
 154           g.setColor(Color.white);
 155           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 156           g.setColor(Color.black);
 157           Font f = new Font("Verdana", Font.PLAIN, 10);
 158           g.setFont(f);
 159           g.drawString(MessageManager.getString("label.label"), 0, 0);
 160         }
 161         else
 162         {
 163           g.setColor(maxCol);
 164           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 165
 166         }
 167       }
 168     }
 169
 170   }
 171
 172   /**
 173    * Shows a dialog allowing the user to create, or amend or delete, sequence
 174    * features.
 175    *
 176    * @param sequences
 177    * @param features
 178    * @param create
 179    * @param ap
 180    * @param featureType
 181    * @return
 182    */
 183   boolean amendFeatures(final SequenceI[] sequences,
 184           final SequenceFeature[] features, boolean create,
 185           final AlignmentPanel ap, String featureType)
 186   {
 187     final Panel bigPanel = new Panel(new BorderLayout());
 188     final TextField name = new TextField(16);
 189     final TextField group = new TextField(16);
 190     final TextArea description = new TextArea(3, 35);
 191     final TextField start = new TextField(8);
 192     final TextField end = new TextField(8);
 193     final Choice overlaps;
 194     Button deleteButton = new Button("Delete");
 195     deleteFeature = false;
 196
 197     name.addTextListener(new TextListener()
 198     {
 199       @Override
 200       public void textValueChanged(TextEvent e)
 201       {
 202         warnIfTypeHidden(ap.alignFrame, name.getText());
 203       }
 204     });
 205     group.addTextListener(new TextListener()
 206     {
 207       @Override
 208       public void textValueChanged(TextEvent e)
 209       {
 210         warnIfGroupHidden(ap.alignFrame, group.getText());
 211       }
 212     });
 213     colourPanel = new FeatureColourPanel();
 214     colourPanel.setSize(110, 15);
 215     final FeatureRenderer fr = this;
 216
 217     Panel panel = new Panel(new GridLayout(3, 1));
 218
 219     featureIndex = 0; // feature to be amended.
 220     Panel tmp;
 221
 222     // /////////////////////////////////////
 223     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 224     if (!create && features.length > 1)
 225     {
 226       panel = new Panel(new GridLayout(4, 1));
 227       tmp = new Panel();
 228       tmp.add(new Label("Select Feature: "));
 229       overlaps = new Choice();
 230       for (int i = 0; i < features.length; i++)
 231       {
 232         String item = features[i].getType() + "/" + features[i].getBegin()
 233                 + "-" + features[i].getEnd();
 234
 235         if (features[i].getFeatureGroup() != null)
 236         {
 237           item += " (" + features[i].getFeatureGroup() + ")";
 238         }
 239
 240         overlaps.addItem(item);
 241       }
 242
 243       tmp.add(overlaps);
 244
 245       overlaps.addItemListener(new java.awt.event.ItemListener()
 246       {
 247         @Override
 248         public void itemStateChanged(java.awt.event.ItemEvent e)
 249         {
 250           int index = overlaps.getSelectedIndex();
 251           if (index != -1)
 252           {
 253             featureIndex = index;
 254             name.setText(features[index].getType());
 255             description.setText(features[index].getDescription());
 256             group.setText(features[index].getFeatureGroup());
 257             start.setText(features[index].getBegin() + "");
 258             end.setText(features[index].getEnd() + "");
 259
 260             SearchResultsI highlight = new SearchResults();
 261             highlight.addResult(sequences[0], features[index].getBegin(),
 262                     features[index].getEnd());
 263
 264             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 265
 266           }
 267           FeatureColourI col = getFeatureStyle(name.getText());
 268           if (col == null)
 269           {
 270             Color generatedColour = ColorUtils
 271                     .createColourFromName(name.getText());
 272             col = new FeatureColour(generatedColour);
 273           }
 274
 275           colourPanel.updateColor(col);
 276         }
 277       });
 278
 279       panel.add(tmp);
 280     }
 281     // ////////
 282     // ////////////////////////////////////
 283
 284     tmp = new Panel();
 285     panel.add(tmp);
 286     tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
 287     tmp.add(name);
 288
 289     tmp = new Panel();
 290     panel.add(tmp);
 291     tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
 292     tmp.add(group);
 293
 294     tmp = new Panel();
 295     panel.add(tmp);
 296     tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
 297     tmp.add(colourPanel);
 298
 299     bigPanel.add(panel, BorderLayout.NORTH);
 300
 301     panel = new Panel();
 302     panel.add(new Label(MessageManager.getString("label.description:"),
 303             Label.RIGHT));
 304     panel.add(new ScrollPane().add(description));
 305
 306     if (!create)
 307     {
 308       bigPanel.add(panel, BorderLayout.SOUTH);
 309
 310       panel = new Panel();
 311       panel.add(new Label(MessageManager.getString("label.start"),
 312               Label.RIGHT));
 313       panel.add(start);
 314       panel.add(new Label(MessageManager.getString("label.end"),
 315               Label.RIGHT));
 316       panel.add(end);
 317       bigPanel.add(panel, BorderLayout.CENTER);
 318     }
 319     else
 320     {
 321       bigPanel.add(panel, BorderLayout.CENTER);
 322     }
 323
 324     if (featureType != null)
 325     {
 326       lastFeatureAdded = featureType;
 327     }
 328     else
 329     {
 330       if (lastFeatureAdded == null)
 331       {
 332         if (features[0].type != null)
 333         {
 334           lastFeatureAdded = features[0].type;
 335         }
 336         else
 337         {
 338           lastFeatureAdded = "feature_1";
 339         }
 340       }
 341     }
 342
 343     if (lastFeatureGroupAdded == null)
 344     {
 345       if (features[0].featureGroup != null)
 346       {
 347         lastFeatureGroupAdded = features[0].featureGroup;
 348       }
 349       else
 350       {
 351         lastFeatureAdded = "Jalview";
 352       }
 353     }
 354
 355     String title = create ? MessageManager
 356             .getString("label.create_new_sequence_features")
 357             : MessageManager.formatMessage("label.amend_delete_features",
 358                     new String[] { sequences[0].getName() });
 359
 360     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 361             240);
 362
 363     dialog.setMainPanel(bigPanel);
 364
 365     if (create)
 366     {
 367       name.setText(lastFeatureAdded);
 368       group.setText(lastFeatureGroupAdded);
 369     }
 370     else
 371     {
 372       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 373       dialog.buttonPanel.add(deleteButton, 1);
 374       deleteButton.addActionListener(new ActionListener()
 375       {
 376         @Override
 377         public void actionPerformed(ActionEvent evt)
 378         {
 379           deleteFeature = true;
 380           dialog.setVisible(false);
 381         }
 382       });
 383       name.setText(features[0].getType());
 384       group.setText(features[0].getFeatureGroup());
 385     }
 386
 387     start.setText(features[0].getBegin() + "");
 388     end.setText(features[0].getEnd() + "");
 389     description.setText(features[0].getDescription());
 390     // lookup (or generate) the feature colour
 391     FeatureColourI fcol = getFeatureStyle(name.getText());
 392     // simply display the feature color in a box
 393     colourPanel.updateColor(fcol);
 394     dialog.setResizable(true);
 395     // TODO: render the graduated color in the box.
 396     colourPanel.addMouseListener(new MouseAdapter()
 397     {
 398       @Override
 399       public void mousePressed(MouseEvent evt)
 400       {
 401         if (!colourPanel.isGcol)
 402         {
 403           new UserDefinedColours(fr, ap.alignFrame);
 404         }
 405         else
 406         {
 407           new FeatureColourChooser(ap.alignFrame, name.getText());
 408           dialog.transferFocus();
 409         }
 410       }
 411     });
 412     dialog.setVisible(true);
 413
 414     FeaturesFile ffile = new FeaturesFile();
 415
 416     if (dialog.accept)
 417     {
 418       lastFeatureAdded = name.getText().trim();
 419       lastFeatureGroupAdded = group.getText().trim();
 420       lastDescriptionAdded = description.getText().replace('\n', ' ');
 421     }
 422
 423     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 424     {
 425       lastFeatureGroupAdded = null;
 426     }
 427
 428     if (!create)
 429     {
 430
 431       SequenceFeature sf = features[featureIndex];
 432       if (dialog.accept)
 433       {
 434         boolean typeOrGroupChanged = (!lastFeatureAdded.equals(sf.type) || !lastFeatureGroupAdded
 435                 .equals(sf.featureGroup));
 436         sf.type = lastFeatureAdded;
 437         sf.featureGroup = lastFeatureGroupAdded;
 438         sf.description = lastDescriptionAdded;
 439         if (!colourPanel.isGcol)
 440         {
 441           // update colour - otherwise its already done.
 442           setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
 443         }
 444         try
 445         {
 446           sf.begin = Integer.parseInt(start.getText());
 447           sf.end = Integer.parseInt(end.getText());
 448         } catch (NumberFormatException ex)
 449         {
 450         }
 451
 452         ffile.parseDescriptionHTML(sf, false);
 453         if (typeOrGroupChanged)
 454         {
 455           featuresAdded();
 456         }
 457       }
 458       if (deleteFeature)
 459       {
 460         sequences[0].deleteFeature(sf);
 461         // ensure Feature Settings reflects removal of feature / group
 462         featuresAdded();
 463       }
 464
 465     }
 466     else
 467     {
 468       /*
 469        * adding feature(s)
 470        */
 471       if (dialog.accept && name.getText().length() > 0)
 472       {
 473         for (int i = 0; i < sequences.length; i++)
 474         {
 475           features[i].type = lastFeatureAdded;
 476           features[i].featureGroup = lastFeatureGroupAdded;
 477           features[i].description = lastDescriptionAdded;
 478           sequences[i].addSequenceFeature(features[i]);
 479           ffile.parseDescriptionHTML(features[i], false);
 480         }
 481
 482         Color newColour = colourPanel.getBackground();
 483         // setColour(lastFeatureAdded, fcol);
 484
 485         setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
 486         featuresAdded();
 487       }
 488       else
 489       {
 490         // no update to the alignment
 491         return false;
 492       }
 493     }
 494     // refresh the alignment and the feature settings dialog
 495     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 496     {
 497       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 498     }
 499     // findAllFeatures();
 500
 501     ap.paintAlignment(true);
 502
 503     return true;
 504   }
 505
 506   protected void warnIfGroupHidden(Frame frame, String group)
 507   {
 508     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 509     {
 510       String msg = MessageManager.formatMessage("label.warning_hidden",
 511               MessageManager.getString("label.group"), group);
 512       showWarning(frame, msg);
 513     }
 514   }
 515
 516   protected void warnIfTypeHidden(Frame frame, String type)
 517   {
 518     if (getRenderOrder().contains(type))
 519     {
 520       if (!showFeatureOfType(type))
 521       {
 522         String msg = MessageManager.formatMessage("label.warning_hidden",
 523                 MessageManager.getString("label.feature_type"), type);
 524         showWarning(frame, msg);
 525       }
 526     }
 527   }
 528
 529   /**
 530    * @param frame
 531    * @param msg
 532    */
 533   protected void showWarning(Frame frame, String msg)
 534   {
 535     JVDialog d = new JVDialog(frame, "", true, 350, 200);
 536     Panel mp = new Panel();
 537     d.ok.setLabel(MessageManager.getString("action.ok"));
 538     d.cancel.setVisible(false);
 539     mp.setLayout(new FlowLayout());
 540     mp.add(new Label(msg));
 541     d.setMainPanel(mp);
 542     d.setVisible(true);
 543   }
 544 }