src/jalview/appletgui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.appletgui;
  20
  21 import jalview.datamodel.*;
  22 import java.awt.*;
  23 import java.util.*;
  24 import java.awt.event.*;
  25
  26
  27 public class FeatureSettings extends Panel implements ItemListener,
  28     MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
  29 {
  30   FeatureRenderer fr;
  31   AlignmentPanel ap;
  32   AlignViewport av;
  33   Frame frame;
  34   Panel groupPanel;
  35   Panel featurePanel = new Panel();
  36   ScrollPane scrollPane;
  37   boolean alignmentHasFeatures = false;
  38   Image linkImage;
  39   Scrollbar transparency ;
  40
  41   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
  42   {
  43     this.ap = ap;
  44     this.av = av;
  45     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
  46
  47     transparency = new Scrollbar(Scrollbar.HORIZONTAL,
  48      100 - (int)(fr.transparency*100), 1, 1, 100);
  49
  50     if(fr.transparencySetter!=null)
  51     {
  52       transparency.addAdjustmentListener(this);
  53     }
  54     else
  55       transparency.setEnabled(false);
  56
  57     java.net.URL url = getClass().getResource("/images/link.gif");
  58     if (url != null)
  59     {
  60       linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
  61     }
  62
  63
  64     if(av.featuresDisplayed==null)
  65       fr.findAllFeatures();
  66
  67     setTableData();
  68
  69     this.setLayout(new BorderLayout());
  70     scrollPane = new ScrollPane();
  71     scrollPane.add(featurePanel);
  72     if (alignmentHasFeatures)
  73       add(scrollPane, BorderLayout.CENTER);
  74
  75     Button invert = new Button("Invert Selection");
  76     invert.addActionListener(this);
  77
  78     Panel lowerPanel = new Panel(new GridLayout(2,1,5,10));
  79     lowerPanel.add(invert);
  80
  81     Panel tPanel = new Panel(new BorderLayout());
  82
  83     if(fr.transparencySetter!=null)
  84     {
  85       tPanel.add(transparency, BorderLayout.CENTER);
  86       tPanel.add(new Label("Transparency"), BorderLayout.EAST);
  87     }
  88     else
  89       tPanel.add(new Label("Transparency not available in this web browser"), BorderLayout.CENTER);
  90
  91     lowerPanel.add(tPanel, BorderLayout.SOUTH);
  92
  93     add(lowerPanel, BorderLayout.SOUTH);
  94
  95
  96
  97     if(groupPanel!=null)
  98     {
  99       groupPanel.setLayout(
 100           new GridLayout( fr.featureGroups.size() / 4 + 1, 4));
 101       groupPanel.validate();
 102
 103       add(groupPanel, BorderLayout.NORTH);
 104     }
 105     frame = new Frame();
 106     frame.add(this);
 107     int height = featurePanel.getComponentCount()*50 +60;
 108
 109
 110     height = Math.max(200, height);
 111     height = Math.min(400, height);
 112
 113     jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,
 114                                      height);
 115   }
 116
 117   public void paint(Graphics g)
 118   {
 119     g.setColor(Color.black);
 120     g.drawString("No Features added to this alignment!!", 10, 20);
 121     g.drawString("(Features can be added from searches or", 10, 40);
 122     g.drawString("from Jalview / GFF features files)", 10, 60);
 123   }
 124
 125   void setTableData()
 126   {
 127     alignmentHasFeatures = false;
 128
 129     if(fr.featureGroups==null)
 130       fr.featureGroups = new Hashtable();
 131
 132     Vector allFeatures = new Vector();
 133     Vector allGroups = new Vector();
 134     SequenceFeature[] tmpfeatures;
 135     String group;
 136
 137
 138     for (int i = 0; i < av.alignment.getHeight(); i++)
 139     {
 140       if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
 141         continue;
 142
 143       alignmentHasFeatures = true;
 144
 145       tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
 146       int index = 0;
 147       while (index < tmpfeatures.length)
 148       {
 149         if(tmpfeatures[index].getFeatureGroup()!=null)
 150         {
 151           group = tmpfeatures[index].featureGroup;
 152           if(!allGroups.contains(group))
 153            {
 154              allGroups.addElement(group);
 155
 156              boolean visible = true;
 157              if (fr.featureGroups.containsKey(group))
 158              {
 159                visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
 160              }
 161
 162              fr.featureGroups.put(group, new Boolean(visible));
 163
 164              if (groupPanel == null)
 165              {
 166                groupPanel = new Panel();
 167              }
 168
 169              Checkbox check =  new MyCheckbox(
 170                 group,
 171                 visible,
 172                 (fr.featureLinks!=null && fr.featureLinks.containsKey(group))
 173                  );
 174
 175
 176              check.addMouseListener(this);
 177              check.setFont(new Font("Serif", Font.BOLD, 12));
 178              check.addItemListener(this);
 179              groupPanel.add(check);
 180            }
 181         }
 182
 183         if (!allFeatures.contains(tmpfeatures[index].getType()))
 184         {
 185             allFeatures.addElement(tmpfeatures[index].getType());
 186         }
 187          index ++;
 188       }
 189     }
 190
 191     resetTable(false);
 192   }
 193
 194  //This routine adds and removes checkboxes depending on
 195  //Group selection states
 196   void resetTable(boolean groupsChanged)
 197   {
 198     SequenceFeature [] tmpfeatures;
 199     String group=null, type;
 200     Vector visibleChecks = new Vector();
 201
 202      for (int i = 0; i < av.alignment.getHeight(); i++)
 203      {
 204          if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
 205            continue;
 206
 207          tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
 208          int index = 0;
 209          while (index < tmpfeatures.length)
 210          {
 211            group = tmpfeatures[index].featureGroup;
 212
 213            if (group==null || fr.featureGroups.get(group)==null ||
 214                ((Boolean) fr.featureGroups.get(group)).booleanValue())
 215            {
 216              type = tmpfeatures[index].getType();
 217              if(!visibleChecks.contains(type) )
 218              {
 219                visibleChecks.addElement(type);
 220              }
 221            }
 222            index++;
 223          }
 224      }
 225
 226        Component[] comps;
 227        int cSize = featurePanel.getComponentCount();
 228        Checkbox check;
 229        //This will remove any checkboxes which shouldn't be
 230        //visible
 231        for (int i = 0; i < cSize; i++)
 232        {
 233          comps = featurePanel.getComponents();
 234          check = (Checkbox) comps[i];
 235          if (!visibleChecks.contains(check.getLabel()))
 236          {
 237            featurePanel.remove(i);
 238            cSize --;
 239            i--;
 240          }
 241        }
 242
 243        if(fr.renderOrder!=null)
 244        {
 245          //First add the checks in the previous render order,
 246          //in case the window has been closed and reopened
 247          for(int ro=fr.renderOrder.length-1; ro>-1; ro--)
 248          {
 249               String item = fr.renderOrder[ro];
 250
 251               if(!visibleChecks.contains(item))
 252                 continue;
 253
 254               visibleChecks.removeElement(item);
 255
 256               addCheck(false, item);
 257          }
 258        }
 259
 260        // now add checkboxes which should be visible,
 261        // if they have not already been added
 262        Enumeration en = visibleChecks.elements();
 263
 264        while(en.hasMoreElements())
 265        {
 266          addCheck(groupsChanged, en.nextElement().toString());
 267        }
 268
 269
 270    featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5));
 271    featurePanel.validate();
 272
 273
 274    if(scrollPane!=null)
 275      scrollPane.validate();
 276
 277    itemStateChanged(null);
 278   }
 279
 280   void addCheck(boolean groupsChanged, String type)
 281   {
 282     boolean addCheck;
 283     Component [] comps = featurePanel.getComponents();
 284     Checkbox check;
 285     addCheck = true;
 286     for (int i = 0; i < featurePanel.getComponentCount(); i++)
 287     {
 288       check = (Checkbox) comps[i];
 289       if (check.getLabel().equals(type))
 290       {
 291         addCheck = false;
 292         break;
 293       }
 294     }
 295
 296     if (addCheck)
 297     {
 298       boolean selected = false;
 299       if (groupsChanged || av.featuresDisplayed.containsKey(type))
 300       {
 301         selected = true;
 302       }
 303
 304       check = new MyCheckbox(type,
 305                              selected,
 306           (fr.featureLinks!=null && fr.featureLinks.containsKey(type))
 307            );
 308
 309       check.addMouseListener(this);
 310       check.addMouseMotionListener(this);
 311       check.setBackground(fr.getColour(type));
 312       check.addItemListener(this);
 313       featurePanel.add(check);
 314     }
 315   }
 316
 317   public void actionPerformed(ActionEvent evt)
 318   {
 319     for(int i=0; i<featurePanel.getComponentCount(); i++)
 320     {
 321       Checkbox check = (Checkbox)featurePanel.getComponent(i);
 322       check.setState(!check.getState());
 323     }
 324     selectionChanged();
 325   }
 326
 327   public void itemStateChanged(ItemEvent evt)
 328   {
 329     if (evt != null)
 330     {
 331       //Is the source a top level featureGroup?
 332       Checkbox source = (Checkbox) evt.getSource();
 333       if (fr.featureGroups.containsKey(source.getLabel()))
 334       {
 335         fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
 336         ap.seqPanel.seqCanvas.repaint();
 337         if (ap.overviewPanel != null)
 338           ap.overviewPanel.updateOverviewImage();
 339
 340         resetTable(true);
 341         return;
 342       }
 343     }
 344     selectionChanged();
 345   }
 346
 347   void selectionChanged()
 348   {
 349       Component[] comps = featurePanel.getComponents();
 350       int cSize = comps.length;
 351
 352       Object[][] tmp = new Object[cSize][3];
 353       int tmpSize = 0;
 354       for (int i = 0; i < cSize; i++)
 355       {
 356         Checkbox check = (Checkbox) comps[i];
 357         tmp[tmpSize][0] = check.getLabel();
 358         tmp[tmpSize][1] = fr.getColour(check.getLabel());
 359         tmp[tmpSize][2] = new Boolean(check.getState());
 360         tmpSize++;
 361       }
 362
 363       Object[][]data = new Object[tmpSize][3];
 364       System.arraycopy(tmp, 0, data,0, tmpSize);
 365
 366       fr.setFeaturePriority(data);
 367       ap.seqPanel.seqCanvas.repaint();
 368       if (ap.overviewPanel != null)
 369         ap.overviewPanel.updateOverviewImage();
 370   }
 371
 372   MyCheckbox selectedCheck;
 373   boolean dragging = false;
 374
 375   public void mousePressed(MouseEvent evt)
 376   {
 377
 378     selectedCheck = (MyCheckbox)evt.getSource();
 379
 380     if(fr.featureLinks!=null
 381        && fr.featureLinks.containsKey(selectedCheck.getLabel() )
 382         )
 383       {
 384         if(evt.getX()>selectedCheck.stringWidth+20)
 385         {
 386           evt.consume();
 387         }
 388       }
 389
 390   }
 391
 392   public void mouseDragged(MouseEvent evt)
 393   {
 394     if(((Component)evt.getSource()).getParent()!=featurePanel)
 395       return;
 396       dragging = true;
 397   }
 398
 399   public void mouseReleased(MouseEvent evt)
 400   {
 401     if(((Component)evt.getSource()).getParent()!=featurePanel)
 402       return;
 403
 404     Component comp = null;
 405     Checkbox  target = null;
 406
 407     int height = evt.getY()+evt.getComponent().getLocation().y;
 408
 409     if(height > featurePanel.getSize().height)
 410      {
 411
 412        comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
 413      }
 414      else if(height < 0)
 415      {
 416        comp = featurePanel.getComponent(0);
 417      }
 418      else
 419      {
 420        comp = featurePanel.getComponentAt(evt.getX(),
 421                                   evt.getY() +
 422                                   evt.getComponent().getLocation().y);
 423      }
 424
 425     if(comp!=null && comp instanceof Checkbox)
 426       target = (Checkbox)comp;
 427
 428     if (   selectedCheck != null
 429         && target != null
 430         && selectedCheck != target)
 431     {
 432       int targetIndex = -1;
 433       for(int i=0; i<featurePanel.getComponentCount(); i++)
 434       {
 435           if(target==featurePanel.getComponent(i))
 436           { targetIndex = i; break; }
 437       }
 438
 439       featurePanel.remove(selectedCheck);
 440       featurePanel.add(selectedCheck, targetIndex);
 441       featurePanel.validate();
 442       itemStateChanged(null);
 443     }
 444   }
 445
 446   public void setUserColour(String feature, Color col)
 447   {
 448     fr.setColour(feature, col);
 449     featurePanel.removeAll();
 450     resetTable(false);
 451     ap.repaint();
 452   }
 453
 454   public void mouseEntered(MouseEvent evt){}
 455   public void mouseExited(MouseEvent evt){}
 456   public void mouseClicked(MouseEvent evt)
 457   {
 458     MyCheckbox check = (MyCheckbox) evt.getSource();
 459
 460     if (fr.featureLinks!=null
 461         && fr.featureLinks.containsKey(check.getLabel()))
 462     {
 463       if (evt.getX() > check.stringWidth + 20)
 464       {
 465         evt.consume();
 466         String link = fr.featureLinks.get(check.getLabel()).toString();
 467         ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
 468                               link.substring(0, link.indexOf("|")));
 469       }
 470     }
 471
 472     if(check.getParent()!=featurePanel)
 473       return;
 474
 475     if(evt.getClickCount()>1)
 476     {
 477        new UserDefinedColours(this, check.getLabel(),
 478                               fr.getColour(check.getLabel()));
 479     }
 480   }
 481   public void mouseMoved(MouseEvent evt){}
 482
 483   public void adjustmentValueChanged(AdjustmentEvent evt)
 484   {
 485     fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
 486     ap.seqPanel.seqCanvas.repaint();
 487
 488   }
 489
 490   class MyCheckbox extends Checkbox
 491   {
 492     public int stringWidth;
 493     boolean hasLink;
 494     public MyCheckbox(String label, boolean checked, boolean haslink)
 495     {
 496       super(label, checked);
 497
 498       FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
 499       stringWidth = fm.stringWidth(label);
 500       this.hasLink = haslink;
 501     }
 502
 503     public void paint(Graphics g)
 504     {
 505       if (hasLink)
 506         g.drawImage(linkImage, stringWidth + 25,(
 507         getSize().height-linkImage.getHeight(this))/2,
 508                     this);
 509     }
 510   }
 511 }
 512
 513