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