src/jalview/gui/AnnotationRowFilter.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.gui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.GraphLine;
  25 import jalview.datamodel.SequenceGroup;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.event.FocusAdapter;
  30 import java.awt.event.FocusEvent;
  31 import java.awt.event.MouseAdapter;
  32 import java.awt.event.MouseEvent;
  33 import java.util.Vector;
  34
  35 import javax.swing.JButton;
  36 import javax.swing.JCheckBox;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JPanel;
  40 import javax.swing.JSlider;
  41 import javax.swing.JTextField;
  42 import javax.swing.event.ChangeEvent;
  43 import javax.swing.event.ChangeListener;
  44
  45 @SuppressWarnings("serial")
  46 public abstract class AnnotationRowFilter extends JPanel
  47 {
  48   protected AlignViewport av;
  49
  50   protected AlignmentPanel ap;
  51
  52   protected int[] annmap;
  53
  54   protected boolean enableSeqAss = false;
  55
  56   private AlignmentAnnotation currentAnnotation;
  57
  58   protected boolean adjusting = false;
  59
  60   protected JCheckBox currentColours = new JCheckBox();
  61
  62   protected JPanel minColour = new JPanel();
  63
  64   protected JPanel maxColour = new JPanel();
  65
  66   protected JCheckBox seqAssociated = new JCheckBox();
  67
  68   protected JCheckBox thresholdIsMin = new JCheckBox();
  69
  70   protected JSlider slider = new JSlider();
  71
  72   protected JTextField thresholdValue = new JTextField(20);
  73
  74   protected JInternalFrame frame;
  75
  76   protected JButton ok = new JButton();
  77
  78   protected JButton cancel = new JButton();
  79
  80   /**
  81    * enabled if the user is dragging the slider - try to keep updates to a
  82    * minimun
  83    */
  84   protected boolean sliderDragging = false;
  85
  86   protected void addSliderChangeListener()
  87   {
  88
  89     slider.addChangeListener(new ChangeListener()
  90     {
  91       @Override
  92       public void stateChanged(ChangeEvent evt)
  93       {
  94         if (!adjusting)
  95         {
  96           thresholdValue.setText((slider.getValue() / 1000f) + "");
  97           valueChanged(!sliderDragging);
  98         }
  99       }
 100     });
 101   }
 102
 103   protected void addSliderMouseListeners()
 104   {
 105
 106     slider.addMouseListener(new MouseAdapter()
 107     {
 108       @Override
 109       public void mousePressed(MouseEvent e)
 110       {
 111         sliderDragging = true;
 112         super.mousePressed(e);
 113       }
 114
 115       @Override
 116       public void mouseDragged(MouseEvent e)
 117       {
 118         sliderDragging = true;
 119         super.mouseDragged(e);
 120       }
 121
 122       @Override
 123       public void mouseReleased(MouseEvent evt)
 124       {
 125         if (sliderDragging)
 126         {
 127           sliderDragging = false;
 128           valueChanged(true);
 129         }
 130         ap.paintAlignment(true);
 131       }
 132     });
 133   }
 134
 135   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 136   {
 137     this.av = av;
 138     this.ap = ap;
 139     thresholdValue.addFocusListener(new FocusAdapter()
 140     {
 141       @Override
 142       public void focusLost(FocusEvent e)
 143       {
 144         thresholdValue_actionPerformed();
 145       }
 146     });
 147   }
 148
 149   public AnnotationRowFilter()
 150   {
 151
 152   }
 153
 154   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
 155   {
 156     Vector<String> list = new Vector<String>();
 157     int index = 1;
 158     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 159     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 160     {
 161       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 162       {
 163         if (isSeqAssociated)
 164         {
 165           continue;
 166         }
 167       }
 168       else
 169       {
 170         enableSeqAss = true;
 171       }
 172       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 173       // add associated sequence ID if available
 174       if (!isSeqAssociated
 175               && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
 176       {
 177         label = label
 178                 + "_"
 179                 + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
 180                         .getName();
 181       }
 182       // make label unique
 183       if (!list.contains(label))
 184       {
 185         anmap[list.size()] = i;
 186         list.add(label);
 187       }
 188       else
 189       {
 190         if (!isSeqAssociated)
 191         {
 192           anmap[list.size()] = i;
 193           list.add(label + "_" + (index++));
 194         }
 195       }
 196     }
 197     this.annmap = new int[list.size()];
 198     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 199     return list;
 200   }
 201
 202   protected int getSelectedThresholdItem(int indexValue)
 203   {
 204     int selectedThresholdItem = -1;
 205     if (indexValue == 1)
 206     {
 207       selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
 208     }
 209     else if (indexValue == 2)
 210     {
 211       selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
 212     }
 213     return selectedThresholdItem;
 214   }
 215
 216   public void modelChanged()
 217   {
 218     seqAssociated.setEnabled(enableSeqAss);
 219   }
 220
 221   public void ok_actionPerformed()
 222   {
 223     try
 224     {
 225       frame.setClosed(true);
 226     } catch (Exception ex)
 227     {
 228     }
 229   }
 230
 231   public void cancel_actionPerformed()
 232   {
 233     reset();
 234     ap.paintAlignment(true);
 235     try
 236     {
 237       frame.setClosed(true);
 238     } catch (Exception ex)
 239     {
 240     }
 241   }
 242
 243   public void thresholdCheck_actionPerformed()
 244   {
 245     updateView();
 246   }
 247
 248   public void annotations_actionPerformed()
 249   {
 250     updateView();
 251   }
 252
 253   public void threshold_actionPerformed()
 254   {
 255     updateView();
 256   }
 257
 258   public void thresholdValue_actionPerformed()
 259   {
 260     try
 261     {
 262       float f = Float.parseFloat(thresholdValue.getText());
 263       slider.setValue((int) (f * 1000));
 264       updateView();
 265     } catch (NumberFormatException ex)
 266     {
 267     }
 268   }
 269
 270   public void thresholdIsMin_actionPerformed()
 271   {
 272     updateView();
 273   }
 274
 275   protected void populateThresholdComboBox(JComboBox<String> threshold)
 276   {
 277     threshold.addItem(MessageManager
 278             .getString("label.threshold_feature_no_threshold"));
 279     threshold.addItem(MessageManager
 280             .getString("label.threshold_feature_above_threshold"));
 281     threshold.addItem(MessageManager
 282             .getString("label.threshold_feature_below_threshold"));
 283   }
 284
 285   protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
 286   {
 287     adjusting = true;
 288     String cursel = (String) annotations.getSelectedItem();
 289     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 290     annotations.removeAllItems();
 291     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 292     {
 293       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 294       {
 295         isvalid = true;
 296         cursel = anitem;
 297       }
 298       annotations.addItem(anitem);
 299     }
 300     adjusting = false;
 301     if (isvalid)
 302     {
 303       annotations.setSelectedItem(cursel);
 304     }
 305     else
 306     {
 307       if (annotations.getItemCount() > 0)
 308       {
 309         annotations.setSelectedIndex(0);
 310       }
 311     }
 312   }
 313
 314   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
 315           AlignmentAnnotation annotation)
 316   {
 317     if (annotation.sequenceRef == null || annotation.threshold == null)
 318     {
 319       return;
 320     }
 321
 322     float thr = annotation.threshold.value;
 323     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 324     {
 325       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 326       if (aa.label.equals(annotation.label)
 327               && (annotation.getCalcId() == null ? aa.getCalcId() == null
 328                       : annotation.getCalcId().equals(aa.getCalcId())))
 329       {
 330         if (aa.threshold == null)
 331         {
 332           aa.threshold = new GraphLine(annotation.threshold);
 333         }
 334         else
 335         {
 336           aa.threshold.value = thr;
 337         }
 338       }
 339     }
 340   }
 341
 342   protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
 343           int selectedThresholdOption)
 344   {
 345
 346     AnnotationColourGradient acg = null;
 347     if (currentColours.isSelected())
 348     {
 349       acg = new AnnotationColourGradient(currentAnn,
 350               av.getGlobalColourScheme(), selectedThresholdOption);
 351     }
 352     else
 353     {
 354       acg = new AnnotationColourGradient(currentAnn,
 355               minColour.getBackground(), maxColour.getBackground(),
 356               selectedThresholdOption);
 357     }
 358     acg.setSeqAssociated(seqAssociated.isSelected());
 359
 360     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 361     {
 362       acg.setPredefinedColours(true);
 363     }
 364
 365     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 366
 367     av.setGlobalColourScheme(acg);
 368
 369     if (av.getAlignment().getGroups() != null)
 370     {
 371
 372       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 373       {
 374         if (sg.cs == null)
 375         {
 376           continue;
 377         }
 378
 379         if (currentColours.isSelected())
 380         {
 381           sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
 382                   selectedThresholdOption);
 383           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 384                   .isSelected());
 385
 386         }
 387         else
 388         {
 389           sg.cs = new AnnotationColourGradient(currentAnn,
 390                   minColour.getBackground(), maxColour.getBackground(),
 391                   selectedThresholdOption);
 392           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 393                   .isSelected());
 394         }
 395
 396       }
 397     }
 398     return false;
 399   }
 400
 401   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 402   {
 403     return currentAnnotation;
 404   }
 405
 406   public void setCurrentAnnotation(
 407           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 408   {
 409     this.currentAnnotation = currentAnnotation;
 410   }
 411
 412   public abstract void valueChanged(boolean updateAllAnnotation);
 413
 414   public abstract void updateView();
 415
 416   public abstract void reset();
 417 }