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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.viewmodel.seqfeatures

File FeatureRendererModel.java

 

Coverage histogram

../../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

208
378
58
2
1,333
935
189
0.5
6.52
29
3.26

Classes

Class Line # Actions
FeatureRendererModel 57 374 188
0.820031382%
FeatureRendererModel.FeatureSettingsBean 63 4 1
1.0100%
 

Contributing tests

This file is covered by 94 tests. .

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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.viewmodel.seqfeatures;
22   
23    import java.awt.Color;
24    import java.beans.PropertyChangeListener;
25    import java.beans.PropertyChangeSupport;
26    import java.util.ArrayList;
27    import java.util.Arrays;
28    import java.util.Comparator;
29    import java.util.HashMap;
30    import java.util.HashSet;
31    import java.util.Hashtable;
32    import java.util.Iterator;
33    import java.util.List;
34    import java.util.Map;
35    import java.util.Set;
36    import java.util.concurrent.ConcurrentHashMap;
37   
38    import jalview.api.AlignViewportI;
39    import jalview.api.FeatureColourI;
40    import jalview.api.FeaturesDisplayedI;
41    import jalview.datamodel.AlignedCodonFrame;
42    import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
43    import jalview.datamodel.AlignmentI;
44    import jalview.datamodel.MappedFeatures;
45    import jalview.datamodel.SearchResultMatchI;
46    import jalview.datamodel.SearchResults;
47    import jalview.datamodel.SearchResultsI;
48    import jalview.datamodel.SequenceFeature;
49    import jalview.datamodel.SequenceI;
50    import jalview.datamodel.features.FeatureMatcherSetI;
51    import jalview.datamodel.features.SequenceFeatures;
52    import jalview.renderer.seqfeatures.FeatureRenderer;
53    import jalview.schemes.FeatureColour;
54    import jalview.util.ColorUtils;
55    import jalview.util.Platform;
56   
 
57    public abstract class FeatureRendererModel
58    implements jalview.api.FeatureRenderer
59    {
60    /*
61    * a data bean to hold one row of feature settings from the gui
62    */
 
63    public static class FeatureSettingsBean
64    {
65    public final String featureType;
66   
67    public final FeatureColourI featureColour;
68   
69    public final FeatureMatcherSetI filter;
70   
71    public final Boolean show;
72   
 
73  39 toggle public FeatureSettingsBean(String type, FeatureColourI colour,
74    FeatureMatcherSetI theFilter, Boolean isShown)
75    {
76  39 featureType = type;
77  39 featureColour = colour;
78  39 filter = theFilter;
79  39 show = isShown;
80    }
81    }
82   
83    /*
84    * global transparency for feature
85    */
86    protected float transparency = 1.0f;
87   
88    /*
89    * colour scheme for each feature type
90    */
91    protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<>();
92   
93    /*
94    * visibility flag for each feature group
95    */
96    protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<>();
97   
98    /*
99    * filters for each feature type
100    */
101    protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
102   
103    protected String[] renderOrder;
104   
105    Map<String, Float> featureOrder = null;
106   
107    protected AlignViewportI av;
108   
109    private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
110    this);
111   
 
112  318660 toggle @Override
113    public AlignViewportI getViewport()
114    {
115  318656 return av;
116    }
117   
 
118  2 toggle public FeatureRendererSettings getSettings()
119    {
120  2 return new FeatureRendererSettings(this);
121    }
122   
 
123  36 toggle public void transferSettings(FeatureRendererSettings fr)
124    {
125  36 this.renderOrder = fr.renderOrder;
126  36 this.featureGroups = fr.featureGroups;
127  36 this.featureColours = fr.featureColours;
128  36 this.transparency = fr.transparency;
129  36 this.featureOrder = fr.featureOrder;
130    }
131   
132    /**
133    * update from another feature renderer
134    *
135    * @param fr
136    * settings to copy
137    */
 
138  57 toggle public void transferSettings(jalview.api.FeatureRenderer _fr)
139    {
140  57 FeatureRenderer fr = (FeatureRenderer) _fr;
141  57 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
142  57 this.renderOrder = frs.renderOrder;
143  57 this.featureGroups = frs.featureGroups;
144  57 this.featureColours = frs.featureColours;
145  57 this.featureFilters = frs.featureFilters;
146  57 this.transparency = frs.transparency;
147  57 this.featureOrder = frs.featureOrder;
148  57 if (av != null && av != fr.getViewport())
149    {
150    // copy over the displayed feature settings
151  4 if (_fr.getFeaturesDisplayed() != null)
152    {
153  4 FeaturesDisplayedI fd = getFeaturesDisplayed();
154  4 if (fd == null)
155    {
156  4 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
157    }
158    else
159    {
160  0 synchronized (fd)
161    {
162  0 fd.clear();
163  0 for (String type : _fr.getFeaturesDisplayed()
164    .getVisibleFeatures())
165    {
166  0 fd.setVisible(type);
167    }
168    }
169    }
170    }
171    }
172    }
173   
 
174  4 toggle public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
175    {
176  4 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
177    }
178   
 
179  18 toggle @Override
180    public void setVisible(String featureType)
181    {
182  18 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
183  18 if (fdi == null)
184    {
185  5 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
186    }
187  18 if (!fdi.isRegistered(featureType))
188    {
189  17 pushFeatureType(Arrays.asList(new String[] { featureType }));
190    }
191  18 fdi.setVisible(featureType);
192    }
193   
 
194  1 toggle @Override
195    public void setAllVisible(List<String> featureTypes)
196    {
197  1 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
198  1 if (fdi == null)
199    {
200  1 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
201    }
202  1 List<String> nft = new ArrayList<>();
203  1 for (String featureType : featureTypes)
204    {
205  1 if (!fdi.isRegistered(featureType))
206    {
207  1 nft.add(featureType);
208    }
209    }
210  1 if (nft.size() > 0)
211    {
212  1 pushFeatureType(nft);
213    }
214  1 fdi.setAllVisible(featureTypes);
215    }
216   
217    /**
218    * push a set of new types onto the render order stack. Note - this is a
219    * direct mechanism rather than the one employed in updateRenderOrder
220    *
221    * @param types
222    */
 
223  18 toggle private void pushFeatureType(List<String> types)
224    {
225   
226  18 int ts = types.size();
227  18 String neworder[] = new String[(renderOrder == null ? 0
228    : renderOrder.length) + ts];
229  18 types.toArray(neworder);
230  18 if (renderOrder != null)
231    {
232  12 System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
233  12 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
234    }
235  18 renderOrder = neworder;
236    }
237   
238    protected Map<String, float[][]> minmax = new Hashtable<>();
239   
 
240  28 toggle public Map<String, float[][]> getMinMax()
241    {
242  28 return minmax;
243    }
244   
245    /**
246    * normalise a score against the max/min bounds for the feature type.
247    *
248    * @param sequenceFeature
249    * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
250    * (0-255) value.
251    */
 
252  0 toggle protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
253    {
254  0 float[] mm = minmax.get(sequenceFeature.type)[0];
255  0 final byte[] r = new byte[] { 0, (byte) 255 };
256  0 if (mm != null)
257    {
258  0 if (r[0] != 0 || mm[0] < 0.0)
259    {
260  0 r[0] = 1;
261  0 r[1] = (byte) ((int) 128.0
262    + 127.0 * (sequenceFeature.score / mm[1]));
263    }
264    else
265    {
266  0 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
267    }
268    }
269  0 return r;
270    }
271   
272    boolean newFeatureAdded = false;
273   
274    boolean findingFeatures = false;
275   
 
276  20838 toggle protected boolean updateFeatures()
277    {
278  20838 if (av.getFeaturesDisplayed() == null || renderOrder == null
279    || newFeatureAdded)
280    {
281  0 findAllFeatures();
282  0 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
283    {
284  0 return false;
285    }
286    }
287    // TODO: decide if we should check for the visible feature count first
288  20838 return true;
289    }
290   
291    /**
292    * search the alignment for all new features, give them a colour and display
293    * them. Then fires a PropertyChangeEvent on the changeSupport object.
294    *
295    */
 
296  19 toggle protected void findAllFeatures()
297    {
298  19 synchronized (firing)
299    {
300  19 if (firing.equals(Boolean.FALSE))
301    {
302  19 firing = Boolean.TRUE;
303  19 findAllFeatures(true); // add all new features as visible
304  19 notifyFeaturesChanged();
305  19 firing = Boolean.FALSE;
306    }
307    }
308    }
309   
 
310  86 toggle @Override
311    public void notifyFeaturesChanged()
312    {
313  86 changeSupport.firePropertyChange("changeSupport", null, null);
314    }
315   
 
316  18 toggle @Override
317    public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
318    int column)
319    {
320    /*
321    * include features at the position provided their feature type is
322    * displayed, and feature group is null or marked for display
323    */
324  18 List<SequenceFeature> result = new ArrayList<>();
325  18 if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
326    {
327  1 return result;
328    }
329   
330  17 Set<String> visibleFeatures = getFeaturesDisplayed()
331    .getVisibleFeatures();
332  17 String[] visibleTypes = visibleFeatures
333    .toArray(new String[visibleFeatures.size()]);
334  17 List<SequenceFeature> features = sequence.findFeatures(column, column,
335    visibleTypes);
336   
337    /*
338    * include features unless they are hidden (have no colour), based on
339    * feature group visibility, or a filter or colour threshold
340    */
341  17 for (SequenceFeature sf : features)
342    {
343  33 if (getColour(sf) != null)
344    {
345  23 result.add(sf);
346    }
347    }
348  17 return result;
349    }
350   
351    /**
352    * Searches alignment for all features and updates colours
353    *
354    * @param newMadeVisible
355    * if true newly added feature types will be rendered immediately
356    * TODO: check to see if this method should actually be proxied so
357    * repaint events can be propagated by the renderer code
358    */
 
359  134 toggle @Override
360    public synchronized void findAllFeatures(boolean newMadeVisible)
361    {
362  134 newFeatureAdded = false;
363   
364  134 if (findingFeatures)
365    {
366  0 newFeatureAdded = true;
367  0 return;
368    }
369   
370  134 findingFeatures = true;
371  134 if (av.getFeaturesDisplayed() == null)
372    {
373  60 av.setFeaturesDisplayed(new FeaturesDisplayed());
374    }
375  134 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
376   
377  134 Set<String> oldfeatures = new HashSet<>();
378  134 if (renderOrder != null)
379    {
380  388 for (int i = 0; i < renderOrder.length; i++)
381    {
382  330 if (renderOrder[i] != null)
383    {
384  330 oldfeatures.add(renderOrder[i]);
385    }
386    }
387    }
388   
389  134 AlignmentI alignment = av.getAlignment();
390  134 List<String> allfeatures = new ArrayList<>();
391   
392  1086 for (int i = 0; i < alignment.getHeight(); i++)
393    {
394  952 SequenceI asq = alignment.getSequenceAt(i);
395  952 for (String group : asq.getFeatures().getFeatureGroups(true))
396    {
397  827 boolean groupDisplayed = true;
398  827 if (group != null)
399    {
400  805 if (featureGroups.containsKey(group))
401    {
402  723 groupDisplayed = featureGroups.get(group);
403    }
404    else
405    {
406  82 groupDisplayed = newMadeVisible;
407  82 featureGroups.put(group, groupDisplayed);
408    }
409    }
410  827 if (groupDisplayed)
411    {
412  826 Set<String> types = asq.getFeatures()
413    .getFeatureTypesForGroups(true, group);
414  826 for (String type : types)
415    {
416  2101 if (!allfeatures.contains(type)) // or use HashSet and no test?
417    {
418  373 allfeatures.add(type);
419    }
420  2101 updateMinMax(asq, type, true); // todo: for all features?
421    }
422    }
423    }
424    }
425   
426    // uncomment to add new features in alphebetical order (but JAL-2575)
427    // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
428  134 if (newMadeVisible)
429    {
430  132 for (String type : allfeatures)
431    {
432  363 if (!oldfeatures.contains(type))
433    {
434  135 featuresDisplayed.setVisible(type);
435  135 setOrder(type, 0);
436    }
437    }
438    }
439   
440  134 updateRenderOrder(allfeatures);
441  134 findingFeatures = false;
442    }
443   
444    /**
445    * Updates the global (alignment) min and max values for a feature type from
446    * the score for a sequence, if the score is not NaN. Values are stored
447    * separately for positional and non-positional features.
448    *
449    * @param seq
450    * @param featureType
451    * @param positional
452    */
 
453  2101 toggle protected void updateMinMax(SequenceI seq, String featureType,
454    boolean positional)
455    {
456  2101 float min = seq.getFeatures().getMinimumScore(featureType, positional);
457  2101 if (Float.isNaN(min))
458    {
459  26 return;
460    }
461   
462  2075 float max = seq.getFeatures().getMaximumScore(featureType, positional);
463   
464    /*
465    * stored values are
466    * { {positionalMin, positionalMax}, {nonPositionalMin, nonPositionalMax} }
467    */
468  2075 if (minmax == null)
469    {
470  0 minmax = new Hashtable<>();
471    }
472  2075 synchronized (minmax)
473    {
474  2075 float[][] mm = minmax.get(featureType);
475  2075 int index = positional ? 0 : 1;
476  2075 if (mm == null)
477    {
478  275 mm = new float[][] { null, null };
479  275 minmax.put(featureType, mm);
480    }
481  2075 if (mm[index] == null)
482    {
483  275 mm[index] = new float[] { min, max };
484    }
485    else
486    {
487  1800 mm[index][0] = Math.min(mm[index][0], min);
488  1800 mm[index][1] = Math.max(mm[index][1], max);
489    }
490    }
491    }
492   
493    protected Boolean firing = Boolean.FALSE;
494   
495    /**
496    * replaces the current renderOrder with the unordered features in
497    * allfeatures. The ordering of any types in both renderOrder and allfeatures
498    * is preserved, and all new feature types are rendered on top of the existing
499    * types, in the order given by getOrder or the order given in allFeatures.
500    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
501    * eliminate the float storage for computing/recalling the persistent ordering
502    * New Cability: updates min/max for colourscheme range if its dynamic
503    *
504    * @param allFeatures
505    */
 
506  134 toggle private void updateRenderOrder(List<String> allFeatures)
507    {
508  134 List<String> allfeatures = new ArrayList<>(allFeatures);
509  134 String[] oldRender = renderOrder;
510  134 renderOrder = new String[allfeatures.size()];
511  134 boolean initOrders = (featureOrder == null);
512  134 int opos = 0;
513  134 if (oldRender != null && oldRender.length > 0)
514    {
515  386 for (int j = 0; j < oldRender.length; j++)
516    {
517  330 if (oldRender[j] != null)
518    {
519  330 if (initOrders)
520    {
521  9 setOrder(oldRender[j],
522    (1 - (1 + (float) j) / oldRender.length));
523    }
524  330 if (allfeatures.contains(oldRender[j]))
525    {
526  238 renderOrder[opos++] = oldRender[j]; // existing features always
527    // appear below new features
528  238 allfeatures.remove(oldRender[j]);
529  238 if (minmax != null)
530    {
531  238 float[][] mmrange = minmax.get(oldRender[j]);
532  238 if (mmrange != null)
533    {
534  236 FeatureColourI fc = featureColours.get(oldRender[j]);
535  236 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
536    && !fc.isColourByAttribute())
537    {
538  0 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
539    }
540    }
541    }
542    }
543    }
544    }
545    }
546  134 if (allfeatures.size() == 0)
547    {
548    // no new features - leave order unchanged.
549  55 return;
550    }
551  79 int i = allfeatures.size() - 1;
552  79 int iSize = i;
553  79 boolean sort = false;
554  79 String[] newf = new String[allfeatures.size()];
555  79 float[] sortOrder = new float[allfeatures.size()];
556  79 for (String newfeat : allfeatures)
557    {
558  135 newf[i] = newfeat;
559  135 if (minmax != null)
560    {
561    // update from new features minmax if necessary
562  135 float[][] mmrange = minmax.get(newf[i]);
563  135 if (mmrange != null)
564    {
565  126 FeatureColourI fc = featureColours.get(newf[i]);
566  126 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
567    && !fc.isColourByAttribute())
568    {
569  0 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
570    }
571    }
572    }
573  135 if (initOrders || !featureOrder.containsKey(newf[i]))
574    {
575  0 int denom = initOrders ? allfeatures.size() : featureOrder.size();
576    // new unordered feature - compute persistent ordering at head of
577    // existing features.
578  0 setOrder(newf[i], i / (float) denom);
579    }
580    // set order from newly found feature from persisted ordering.
581  135 sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
582  135 if (i < iSize)
583    {
584    // only sort if we need to
585  56 sort = sort || sortOrder[i] > sortOrder[i + 1];
586    }
587  135 i--;
588    }
589  79 if (iSize > 1 && sort)
590    {
591  0 jalview.util.QuickSort.sort(sortOrder, newf);
592    }
593  79 sortOrder = null;
594  79 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
595    }
596   
597    /**
598    * get a feature style object for the given type string. Creates a
599    * java.awt.Color for a featureType with no existing colourscheme.
600    *
601    * @param featureType
602    * @return
603    */
 
604  15087 toggle @Override
605    public FeatureColourI getFeatureStyle(String featureType)
606    {
607  15087 FeatureColourI fc = featureColours.get(featureType);
608  15087 if (fc == null)
609    {
610  70 Color col = ColorUtils.createColourFromName(featureType);
611  70 fc = new FeatureColour(col);
612  70 featureColours.put(featureType, fc);
613    }
614  15087 return fc;
615    }
616   
 
617  8576 toggle @Override
618    public Color getColour(SequenceFeature feature)
619    {
620  8576 FeatureColourI fc = getFeatureStyle(feature.getType());
621  8576 return getColor(feature, fc);
622    }
623   
624    /**
625    * Answers true if the feature type is currently selected to be displayed,
626    * else false
627    *
628    * @param type
629    * @return
630    */
 
631  589591 toggle public boolean showFeatureOfType(String type)
632    {
633  589674 return type == null ? false
634  589661 : (av.getFeaturesDisplayed() == null ? true
635    : av.getFeaturesDisplayed().isVisible(type));
636    }
637   
 
638  100 toggle @Override
639    public void setColour(String featureType, FeatureColourI col)
640    {
641  100 featureColours.put(featureType, col);
642    }
643   
 
644  70 toggle @Override
645    public void setTransparency(float value)
646    {
647  70 transparency = value;
648    }
649   
 
650  22668 toggle @Override
651    public float getTransparency()
652    {
653  22668 return transparency;
654    }
655   
656    /**
657    * analogous to colour - store a normalized ordering for all feature types in
658    * this rendering context.
659    *
660    * @param type
661    * Feature type string
662    * @param position
663    * normalized priority - 0 means always appears on top, 1 means
664    * always last.
665    */
 
666  149 toggle public float setOrder(String type, float position)
667    {
668  149 if (featureOrder == null)
669    {
670  61 featureOrder = new Hashtable<>();
671    }
672  149 featureOrder.put(type, Float.valueOf(position));
673  149 return position;
674    }
675   
676    /**
677    * get the global priority (0 (top) to 1 (bottom))
678    *
679    * @param type
680    * @return [0,1] or -1 for a type without a priority
681    */
 
682  204 toggle public float getOrder(String type)
683    {
684  204 if (featureOrder != null)
685    {
686  204 if (featureOrder.containsKey(type))
687    {
688  204 return featureOrder.get(type).floatValue();
689    }
690    }
691  0 return -1;
692    }
693   
 
694  59 toggle @Override
695    public Map<String, FeatureColourI> getFeatureColours()
696    {
697  59 return featureColours;
698    }
699   
700    /**
701    * Replace current ordering with new ordering
702    *
703    * @param data
704    * an array of { Type, Colour, Filter, Boolean }
705    * @return true if any visible features have been reordered, else false
706    */
 
707  13 toggle public boolean setFeaturePriority(FeatureSettingsBean[] data)
708    {
709  13 return setFeaturePriority(data, true);
710    }
711   
712    /**
713    * Sets the priority order for features, with the highest priority (displayed
714    * on top) at the start of the data array
715    *
716    * @param data
717    * an array of { Type, Colour, Filter, Boolean }
718    * @param visibleNew
719    * when true current featureDisplay list will be cleared
720    * @return true if any visible features have been reordered or recoloured,
721    * else false (i.e. no need to repaint)
722    */
 
723  16 toggle public boolean setFeaturePriority(FeatureSettingsBean[] data,
724    boolean visibleNew)
725    {
726    /*
727    * note visible feature ordering and colours before update
728    */
729  16 List<String> visibleFeatures = getDisplayedFeatureTypes();
730  16 Map<String, FeatureColourI> visibleColours = new HashMap<>(
731    getFeatureColours());
732   
733  16 FeaturesDisplayedI av_featuresdisplayed = null;
734  16 if (visibleNew)
735    {
736  ? if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
737    {
738  12 av.getFeaturesDisplayed().clear();
739    }
740    else
741    {
742  1 av.setFeaturesDisplayed(
743    av_featuresdisplayed = new FeaturesDisplayed());
744    }
745    }
746    else
747    {
748  3 av_featuresdisplayed = av.getFeaturesDisplayed();
749    }
750  16 if (data == null)
751    {
752  0 return false;
753    }
754    // The feature table will display high priority
755    // features at the top, but these are the ones
756    // we need to render last, so invert the data
757  16 renderOrder = new String[data.length];
758   
759  16 if (data.length > 0)
760    {
761  57 for (int i = 0; i < data.length; i++)
762    {
763  41 String type = data[i].featureType;
764  41 setColour(type, data[i].featureColour);
765  41 if (data[i].show)
766    {
767  29 av_featuresdisplayed.setVisible(type);
768    }
769   
770  41 renderOrder[data.length - i - 1] = type;
771    }
772    }
773   
774    /*
775    * get the new visible ordering and return true if it has changed
776    * order or any colour has changed
777    */
778  16 List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
779  16 if (!visibleFeatures.equals(reorderedVisibleFeatures))
780    {
781    /*
782    * the list of ordered visible features has changed
783    */
784  11 return true;
785    }
786   
787    /*
788    * return true if any feature colour has changed
789    */
790  5 for (String feature : visibleFeatures)
791    {
792  17 if (visibleColours.get(feature) != getFeatureStyle(feature))
793    {
794  0 return true;
795    }
796    }
797  5 return false;
798    }
799   
800    /**
801    * @param listener
802    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
803    */
 
804  1 toggle public void addPropertyChangeListener(PropertyChangeListener listener)
805    {
806  1 changeSupport.addPropertyChangeListener(listener);
807    }
808   
809    /**
810    * @param listener
811    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
812    */
 
813  1 toggle public void removePropertyChangeListener(PropertyChangeListener listener)
814    {
815  1 changeSupport.removePropertyChangeListener(listener);
816    }
817   
 
818  1 toggle public Set<String> getAllFeatureColours()
819    {
820  1 return featureColours.keySet();
821    }
822   
 
823  16 toggle public void clearRenderOrder()
824    {
825  16 renderOrder = null;
826    }
827   
 
828  29478 toggle public boolean hasRenderOrder()
829    {
830  29478 return renderOrder != null;
831    }
832   
833    /**
834    * Returns feature types in ordering of rendering, where last means on top
835    */
 
836  259 toggle public List<String> getRenderOrder()
837    {
838  259 if (renderOrder == null)
839    {
840  40 return Arrays.asList(new String[] {});
841    }
842  219 return Arrays.asList(renderOrder);
843    }
844   
 
845  2 toggle public int getFeatureGroupsSize()
846    {
847  2 return featureGroups != null ? 0 : featureGroups.size();
848    }
849   
 
850  168 toggle @Override
851    public List<String> getFeatureGroups()
852    {
853    // conflict between applet and desktop - featureGroups returns the map in
854    // the desktop featureRenderer
855  168 return (featureGroups == null) ? Arrays.asList(new String[0])
856    : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
857    }
858   
 
859  49 toggle public boolean checkGroupVisibility(String group,
860    boolean newGroupsVisible)
861    {
862  49 if (featureGroups == null)
863    {
864    // then an exception happens next..
865    }
866  49 if (featureGroups.containsKey(group))
867    {
868  49 return featureGroups.get(group).booleanValue();
869    }
870  0 if (newGroupsVisible)
871    {
872  0 featureGroups.put(group, Boolean.valueOf(true));
873  0 return true;
874    }
875  0 return false;
876    }
877   
878    /**
879    * get visible or invisible groups
880    *
881    * @param visible
882    * true to return visible groups, false to return hidden ones.
883    * @return list of groups
884    */
 
885  16 toggle @Override
886    public List<String> getGroups(boolean visible)
887    {
888  16 if (featureGroups != null)
889    {
890  16 List<String> gp = new ArrayList<>();
891   
892  16 for (String grp : featureGroups.keySet())
893    {
894  60 Boolean state = featureGroups.get(grp);
895  60 if (state.booleanValue() == visible)
896    {
897  0 gp.add(grp);
898    }
899    }
900  16 return gp;
901    }
902  0 return null;
903    }
904   
 
905  131 toggle @Override
906    public void setGroupVisibility(String group, boolean visible)
907    {
908  131 featureGroups.put(group, Boolean.valueOf(visible));
909    }
910   
 
911  0 toggle @Override
912    public void setGroupVisibility(List<String> toset, boolean visible)
913    {
914  0 if (toset != null && toset.size() > 0 && featureGroups != null)
915    {
916  0 boolean rdrw = false;
917  0 for (String gst : toset)
918    {
919  0 Boolean st = featureGroups.get(gst);
920  0 featureGroups.put(gst, Boolean.valueOf(visible));
921  0 if (st != null)
922    {
923  0 rdrw = rdrw || (visible != st.booleanValue());
924    }
925    }
926  0 if (rdrw)
927    {
928    // set local flag indicating redraw needed ?
929    }
930    }
931    }
932   
 
933  22 toggle @Override
934    public Map<String, FeatureColourI> getDisplayedFeatureCols()
935    {
936  22 Map<String, FeatureColourI> fcols = new Hashtable<>();
937  22 if (getViewport().getFeaturesDisplayed() == null)
938    {
939  5 return fcols;
940    }
941  17 Set<String> features = getViewport().getFeaturesDisplayed()
942    .getVisibleFeatures();
943  17 for (String feature : features)
944    {
945  26 fcols.put(feature, getFeatureStyle(feature));
946    }
947  17 return fcols;
948    }
949   
 
950  22942 toggle @Override
951    public FeaturesDisplayedI getFeaturesDisplayed()
952    {
953  22942 return av.getFeaturesDisplayed();
954    }
955   
956    /**
957    * Returns a (possibly empty) list of visible feature types, in render order
958    * (last is on top)
959    */
 
960  106 toggle @Override
961    public List<String> getDisplayedFeatureTypes()
962    {
963  106 List<String> typ = getRenderOrder();
964  106 List<String> displayed = new ArrayList<>();
965  106 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
966  106 if (feature_disp != null)
967    {
968  105 synchronized (feature_disp)
969    {
970  105 for (String type : typ)
971    {
972  303 if (feature_disp.isVisible(type))
973    {
974  285 displayed.add(type);
975    }
976    }
977    }
978    }
979  106 return displayed;
980    }
981   
 
982  10 toggle @Override
983    public List<String> getDisplayedFeatureGroups()
984    {
985  10 List<String> _gps = new ArrayList<>();
986  10 for (String gp : getFeatureGroups())
987    {
988  13 if (checkGroupVisibility(gp, false))
989    {
990  11 _gps.add(gp);
991    }
992    }
993  10 return _gps;
994    }
995   
996    /**
997    * Answers true if the feature belongs to a feature group which is not
998    * currently displayed, else false
999    *
1000    * @param sequenceFeature
1001    * @return
1002    */
 
1003  42075 toggle public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
1004    {
1005  42077 return featureGroups != null && sequenceFeature.featureGroup != null
1006    && sequenceFeature.featureGroup.length() != 0
1007    && featureGroups.containsKey(sequenceFeature.featureGroup)
1008    && !featureGroups.get(sequenceFeature.featureGroup)
1009    .booleanValue();
1010    }
1011   
1012    /**
1013    * {@inheritDoc}
1014    */
 
1015  62 toggle @Override
1016    public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
1017    int fromResNo, int toResNo)
1018    {
1019  62 List<SequenceFeature> result = new ArrayList<>();
1020  62 if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
1021    {
1022  0 return result;
1023    }
1024   
1025    /*
1026    * include features at the position provided their feature type is
1027    * displayed, and feature group is null or the empty string
1028    * or marked for display
1029    */
1030  62 List<String> visibleFeatures = getDisplayedFeatureTypes();
1031  62 String[] visibleTypes = visibleFeatures
1032    .toArray(new String[visibleFeatures.size()]);
1033  62 List<SequenceFeature> features = sequence.getFeatures()
1034    .findFeatures(fromResNo, toResNo, visibleTypes);
1035   
1036  62 for (SequenceFeature sf : features)
1037    {
1038  73 if (!featureGroupNotShown(sf) && getColour(sf) != null)
1039    {
1040  73 result.add(sf);
1041    }
1042    }
1043  62 return result;
1044    }
1045   
1046    /**
1047    * Removes from the list of features any whose group is not shown, or that are
1048    * visible and duplicate the location of a visible feature of the same type.
1049    * Should be used only for features of the same, simple, feature colour (which
1050    * normally implies the same feature type). No filtering is done if
1051    * transparency, or any feature filters, are in force.
1052    *
1053    * @param features
1054    */
 
1055  1153 toggle public void filterFeaturesForDisplay(List<SequenceFeature> features)
1056    {
1057    /*
1058    * fudge: JalviewJS's IntervalStore lacks the sort method called :-(
1059    */
1060  1153 if (Platform.isJS())
1061    {
1062  0 return;
1063    }
1064   
1065    /*
1066    * don't remove 'redundant' features if
1067    * - transparency is applied (feature count affects depth of feature colour)
1068    * - filters are applied (not all features may be displayable)
1069    */
1070  1153 if (features.isEmpty() || transparency != 1f
1071    || !featureFilters.isEmpty())
1072    {
1073  2 return;
1074    }
1075   
1076  1151 SequenceFeatures.sortFeatures(features, true);
1077  1151 SequenceFeature lastFeature = null;
1078   
1079  1151 Iterator<SequenceFeature> it = features.iterator();
1080  13689 while (it.hasNext())
1081    {
1082  12538 SequenceFeature sf = it.next();
1083  12538 if (featureGroupNotShown(sf))
1084    {
1085  2 it.remove();
1086  2 continue;
1087    }
1088   
1089    /*
1090    * a feature is redundant for rendering purposes if it has the
1091    * same extent as another (so would just redraw the same colour);
1092    * (checking type and isContactFeature as a fail-safe here, although
1093    * currently they are guaranteed to match in this context)
1094    */
1095  12536 if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
1096    && sf.getEnd() == lastFeature.getEnd()
1097    && sf.isContactFeature() == lastFeature.isContactFeature()
1098    && sf.getType().equals(lastFeature.getType()))
1099    {
1100  3 it.remove();
1101    }
1102  12536 lastFeature = sf;
1103    }
1104    }
1105   
 
1106  15 toggle @Override
1107    public Map<String, FeatureMatcherSetI> getFeatureFilters()
1108    {
1109  15 return featureFilters;
1110    }
1111   
 
1112  0 toggle @Override
1113    public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters)
1114    {
1115  0 featureFilters = filters;
1116    }
1117   
 
1118  212 toggle @Override
1119    public FeatureMatcherSetI getFeatureFilter(String featureType)
1120    {
1121  212 return featureFilters.get(featureType);
1122    }
1123   
 
1124  23 toggle @Override
1125    public void setFeatureFilter(String featureType,
1126    FeatureMatcherSetI filter)
1127    {
1128  23 if (filter == null || filter.isEmpty())
1129    {
1130  0 featureFilters.remove(featureType);
1131    }
1132    else
1133    {
1134  23 featureFilters.put(featureType, filter);
1135    }
1136    }
1137   
1138    /**
1139    * Answers the colour for the feature, or null if the feature is excluded by
1140    * feature group visibility, by filters, or by colour threshold settings. This
1141    * method does not take feature type visibility into account.
1142    *
1143    * @param sf
1144    * @param fc
1145    * @return
1146    */
 
1147  21521 toggle public Color getColor(SequenceFeature sf, FeatureColourI fc)
1148    {
1149    /*
1150    * is the feature group displayed?
1151    */
1152  21521 if (featureGroupNotShown(sf))
1153    {
1154  8 return null;
1155    }
1156   
1157    /*
1158    * does the feature pass filters?
1159    */
1160  21512 if (!featureMatchesFilters(sf))
1161    {
1162  6 return null;
1163    }
1164   
1165  21507 return fc.getColor(sf);
1166    }
1167   
1168    /**
1169    * Answers true if there no are filters defined for the feature type, or this
1170    * feature matches the filters. Answers false if the feature fails to match
1171    * filters.
1172    *
1173    * @param sf
1174    * @return
1175    */
 
1176  21551 toggle protected boolean featureMatchesFilters(SequenceFeature sf)
1177    {
1178  21551 FeatureMatcherSetI filter = featureFilters.get(sf.getType());
1179  21549 return filter == null ? true : filter.matches(sf);
1180    }
1181   
1182    /**
1183    * Answers true unless the specified group is set to hidden. Defaults to true
1184    * if group visibility is not set.
1185    *
1186    * @param group
1187    * @return
1188    */
 
1189  0 toggle public boolean isGroupVisible(String group)
1190    {
1191  0 if (!featureGroups.containsKey(group))
1192    {
1193  0 return true;
1194    }
1195  0 return featureGroups.get(group);
1196    }
1197   
1198    /**
1199    * Orders features in render precedence (last in order is last to render, so
1200    * displayed on top of other features)
1201    *
1202    * @param order
1203    */
 
1204  67 toggle public void orderFeatures(Comparator<String> order)
1205    {
1206  67 Arrays.sort(renderOrder, order);
1207    }
1208   
 
1209  2 toggle @Override
1210    public MappedFeatures findComplementFeaturesAtResidue(
1211    final SequenceI sequence, final int pos)
1212    {
1213  2 SequenceI ds = sequence.getDatasetSequence();
1214  2 if (ds == null)
1215    {
1216  0 ds = sequence;
1217    }
1218  2 final char residue = ds.getCharAt(pos - ds.getStart());
1219   
1220  2 List<SequenceFeature> found = new ArrayList<>();
1221  2 List<AlignedCodonFrame> mappings = this.av.getAlignment()
1222    .getCodonFrame(sequence);
1223   
1224    /*
1225    * fudge: if no mapping found, check the complementary alignment
1226    * todo: only store in one place? StructureSelectionManager?
1227    */
1228  2 if (mappings.isEmpty())
1229    {
1230  2 mappings = this.av.getCodingComplement().getAlignment()
1231    .getCodonFrame(sequence);
1232    }
1233   
1234    /*
1235    * todo: direct lookup of CDS for peptide and vice-versa; for now,
1236    * have to search through an unordered list of mappings for a candidate
1237    */
1238  2 SequenceToSequenceMapping mapping = null;
1239  2 SequenceI mapFrom = null;
1240   
1241  2 for (AlignedCodonFrame acf : mappings)
1242    {
1243  2 mapping = acf.getCoveringCodonMapping(ds);
1244  2 if (mapping == null)
1245    {
1246  0 continue;
1247    }
1248  2 SearchResultsI sr = new SearchResults();
1249  2 mapping.markMappedRegion(ds, pos, sr);
1250  2 for (SearchResultMatchI match : sr.getResults())
1251    {
1252  2 int fromRes = match.getStart();
1253  2 int toRes = match.getEnd();
1254  2 mapFrom = match.getSequence();
1255  2 List<SequenceFeature> fs = findFeaturesAtResidue(mapFrom, fromRes,
1256    toRes);
1257  2 for (SequenceFeature sf : fs)
1258    {
1259  3 if (!found.contains(sf))
1260    {
1261  3 found.add(sf);
1262    }
1263    }
1264    }
1265   
1266    /*
1267    * just take the first mapped features we find
1268    */
1269  2 if (!found.isEmpty())
1270    {
1271  2 break;
1272    }
1273    }
1274  2 if (found.isEmpty())
1275    {
1276  0 return null;
1277    }
1278   
1279    /*
1280    * sort by renderorder (inefficiently but ok for small scale);
1281    * NB this sorts 'on top' feature to end, for rendering
1282    */
1283  2 List<SequenceFeature> result = new ArrayList<>();
1284  2 final int toAdd = found.size();
1285  2 int added = 0;
1286  2 for (String type : renderOrder)
1287    {
1288  3 for (SequenceFeature sf : found)
1289    {
1290  4 if (type.equals(sf.getType()))
1291    {
1292  3 result.add(sf);
1293  3 added++;
1294    }
1295  4 if (added == toAdd)
1296    {
1297  2 break;
1298    }
1299    }
1300    }
1301   
1302  2 return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue,
1303    result);
1304    }
1305   
 
1306  46 toggle @Override
1307    public boolean isVisible(SequenceFeature feature)
1308    {
1309  46 if (feature == null)
1310    {
1311  1 return false;
1312    }
1313  45 if (getFeaturesDisplayed() == null
1314    || !getFeaturesDisplayed().isVisible(feature.getType()))
1315    {
1316  1 return false;
1317    }
1318  44 if (featureGroupNotShown(feature))
1319    {
1320  2 return false;
1321    }
1322  42 FeatureColourI fc = featureColours.get(feature.getType());
1323  42 if (fc != null && fc.isOutwithThreshold(feature))
1324    {
1325  4 return false;
1326    }
1327  38 if (!featureMatchesFilters(feature))
1328    {
1329  3 return false;
1330    }
1331  35 return true;
1332    }
1333    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.