2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.viewmodel.seqfeatures;
23 import jalview.api.AlignViewportI;
24 import jalview.api.FeatureColourI;
25 import jalview.api.FeaturesDisplayedI;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.SequenceFeature;
28 import jalview.datamodel.SequenceI;
29 import jalview.datamodel.features.SequenceFeatures;
30 import jalview.renderer.seqfeatures.FeatureRenderer;
31 import jalview.schemes.FeatureColour;
32 import jalview.util.ColorUtils;
33 import jalview.util.matcher.KeyedMatcherSetI;
35 import java.awt.Color;
36 import java.beans.PropertyChangeListener;
37 import java.beans.PropertyChangeSupport;
38 import java.util.ArrayList;
39 import java.util.Arrays;
40 import java.util.HashMap;
41 import java.util.HashSet;
42 import java.util.Hashtable;
43 import java.util.Iterator;
44 import java.util.List;
47 import java.util.concurrent.ConcurrentHashMap;
49 public abstract class FeatureRendererModel
50 implements jalview.api.FeatureRenderer
54 * global transparency for feature
56 protected float transparency = 1.0f;
59 * colour scheme for each feature type
61 protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<>();
64 * visibility flag for each feature group
66 protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<>();
69 * filters for each feature type
71 protected Map<String, KeyedMatcherSetI> featureFilters = new HashMap<>();
73 protected String[] renderOrder;
75 Map<String, Float> featureOrder = null;
77 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
80 protected AlignViewportI av;
83 public AlignViewportI getViewport()
88 public FeatureRendererSettings getSettings()
90 return new FeatureRendererSettings(this);
93 public void transferSettings(FeatureRendererSettings fr)
95 this.renderOrder = fr.renderOrder;
96 this.featureGroups = fr.featureGroups;
97 this.featureColours = fr.featureColours;
98 this.transparency = fr.transparency;
99 this.featureOrder = fr.featureOrder;
103 * update from another feature renderer
108 public void transferSettings(jalview.api.FeatureRenderer _fr)
110 FeatureRenderer fr = (FeatureRenderer) _fr;
111 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
112 this.renderOrder = frs.renderOrder;
113 this.featureGroups = frs.featureGroups;
114 this.featureColours = frs.featureColours;
115 this.featureFilters = frs.featureFilters;
116 this.transparency = frs.transparency;
117 this.featureOrder = frs.featureOrder;
118 if (av != null && av != fr.getViewport())
120 // copy over the displayed feature settings
121 if (_fr.getFeaturesDisplayed() != null)
123 FeaturesDisplayedI fd = getFeaturesDisplayed();
126 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
133 for (String type : _fr.getFeaturesDisplayed()
134 .getVisibleFeatures())
144 public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
146 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
150 public void setVisible(String featureType)
152 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
155 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
157 if (!fdi.isRegistered(featureType))
159 pushFeatureType(Arrays.asList(new String[] { featureType }));
161 fdi.setVisible(featureType);
165 public void setAllVisible(List<String> featureTypes)
167 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
170 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
172 List<String> nft = new ArrayList<String>();
173 for (String featureType : featureTypes)
175 if (!fdi.isRegistered(featureType))
177 nft.add(featureType);
182 pushFeatureType(nft);
184 fdi.setAllVisible(featureTypes);
188 * push a set of new types onto the render order stack. Note - this is a
189 * direct mechanism rather than the one employed in updateRenderOrder
193 private void pushFeatureType(List<String> types)
196 int ts = types.size();
197 String neworder[] = new String[(renderOrder == null ? 0
198 : renderOrder.length) + ts];
199 types.toArray(neworder);
200 if (renderOrder != null)
202 System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
203 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
205 renderOrder = neworder;
208 protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
210 public Map<String, float[][]> getMinMax()
216 * normalise a score against the max/min bounds for the feature type.
218 * @param sequenceFeature
219 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
222 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
224 float[] mm = minmax.get(sequenceFeature.type)[0];
225 final byte[] r = new byte[] { 0, (byte) 255 };
228 if (r[0] != 0 || mm[0] < 0.0)
231 r[1] = (byte) ((int) 128.0
232 + 127.0 * (sequenceFeature.score / mm[1]));
236 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
242 boolean newFeatureAdded = false;
244 boolean findingFeatures = false;
246 protected boolean updateFeatures()
248 if (av.getFeaturesDisplayed() == null || renderOrder == null
252 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
257 // TODO: decide if we should check for the visible feature count first
262 * search the alignment for all new features, give them a colour and display
263 * them. Then fires a PropertyChangeEvent on the changeSupport object.
266 protected void findAllFeatures()
268 synchronized (firing)
270 if (firing.equals(Boolean.FALSE))
272 firing = Boolean.TRUE;
273 findAllFeatures(true); // add all new features as visible
274 changeSupport.firePropertyChange("changeSupport", null, null);
275 firing = Boolean.FALSE;
281 public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
284 * include features at the position provided their feature type is
285 * displayed, and feature group is null or marked for display
287 List<SequenceFeature> result = new ArrayList<SequenceFeature>();
288 if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
293 Set<String> visibleFeatures = getFeaturesDisplayed()
294 .getVisibleFeatures();
295 String[] visibleTypes = visibleFeatures
296 .toArray(new String[visibleFeatures.size()]);
297 List<SequenceFeature> features = sequence.findFeatures(column, column,
300 for (SequenceFeature sf : features)
302 if (!featureGroupNotShown(sf))
311 * Searches alignment for all features and updates colours
313 * @param newMadeVisible
314 * if true newly added feature types will be rendered immediately
315 * TODO: check to see if this method should actually be proxied so
316 * repaint events can be propagated by the renderer code
319 public synchronized void findAllFeatures(boolean newMadeVisible)
321 newFeatureAdded = false;
325 newFeatureAdded = true;
329 findingFeatures = true;
330 if (av.getFeaturesDisplayed() == null)
332 av.setFeaturesDisplayed(new FeaturesDisplayed());
334 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
336 Set<String> oldfeatures = new HashSet<String>();
337 if (renderOrder != null)
339 for (int i = 0; i < renderOrder.length; i++)
341 if (renderOrder[i] != null)
343 oldfeatures.add(renderOrder[i]);
348 AlignmentI alignment = av.getAlignment();
349 List<String> allfeatures = new ArrayList<String>();
351 for (int i = 0; i < alignment.getHeight(); i++)
353 SequenceI asq = alignment.getSequenceAt(i);
354 for (String group : asq.getFeatures().getFeatureGroups(true))
356 boolean groupDisplayed = true;
359 if (featureGroups.containsKey(group))
361 groupDisplayed = featureGroups.get(group);
365 groupDisplayed = newMadeVisible;
366 featureGroups.put(group, groupDisplayed);
371 Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
373 for (String type : types)
375 if (!allfeatures.contains(type)) // or use HashSet and no test?
377 allfeatures.add(type);
379 updateMinMax(asq, type, true); // todo: for all features?
385 // uncomment to add new features in alphebetical order (but JAL-2575)
386 // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
389 for (String type : allfeatures)
391 if (!oldfeatures.contains(type))
393 featuresDisplayed.setVisible(type);
399 updateRenderOrder(allfeatures);
400 findingFeatures = false;
404 * Updates the global (alignment) min and max values for a feature type from
405 * the score for a sequence, if the score is not NaN. Values are stored
406 * separately for positional and non-positional features.
412 protected void updateMinMax(SequenceI seq, String featureType,
415 float min = seq.getFeatures().getMinimumScore(featureType, positional);
416 if (Float.isNaN(min))
421 float max = seq.getFeatures().getMaximumScore(featureType, positional);
425 * { {positionalMin, positionalMax}, {nonPositionalMin, nonPositionalMax} }
429 minmax = new Hashtable<String, float[][]>();
431 synchronized (minmax)
433 float[][] mm = minmax.get(featureType);
434 int index = positional ? 0 : 1;
437 mm = new float[][] { null, null };
438 minmax.put(featureType, mm);
440 if (mm[index] == null)
442 mm[index] = new float[] { min, max };
446 mm[index][0] = Math.min(mm[index][0], min);
447 mm[index][1] = Math.max(mm[index][1], max);
451 protected Boolean firing = Boolean.FALSE;
454 * replaces the current renderOrder with the unordered features in
455 * allfeatures. The ordering of any types in both renderOrder and allfeatures
456 * is preserved, and all new feature types are rendered on top of the existing
457 * types, in the order given by getOrder or the order given in allFeatures.
458 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
459 * eliminate the float storage for computing/recalling the persistent ordering
460 * New Cability: updates min/max for colourscheme range if its dynamic
464 private void updateRenderOrder(List<String> allFeatures)
466 List<String> allfeatures = new ArrayList<String>(allFeatures);
467 String[] oldRender = renderOrder;
468 renderOrder = new String[allfeatures.size()];
469 boolean initOrders = (featureOrder == null);
471 if (oldRender != null && oldRender.length > 0)
473 for (int j = 0; j < oldRender.length; j++)
475 if (oldRender[j] != null)
479 setOrder(oldRender[j],
480 (1 - (1 + (float) j) / oldRender.length));
482 if (allfeatures.contains(oldRender[j]))
484 renderOrder[opos++] = oldRender[j]; // existing features always
485 // appear below new features
486 allfeatures.remove(oldRender[j]);
489 float[][] mmrange = minmax.get(oldRender[j]);
492 FeatureColourI fc = featureColours.get(oldRender[j]);
493 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
495 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
503 if (allfeatures.size() == 0)
505 // no new features - leave order unchanged.
508 int i = allfeatures.size() - 1;
510 boolean sort = false;
511 String[] newf = new String[allfeatures.size()];
512 float[] sortOrder = new float[allfeatures.size()];
513 for (String newfeat : allfeatures)
518 // update from new features minmax if necessary
519 float[][] mmrange = minmax.get(newf[i]);
522 FeatureColourI fc = featureColours.get(newf[i]);
523 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
525 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
529 if (initOrders || !featureOrder.containsKey(newf[i]))
531 int denom = initOrders ? allfeatures.size() : featureOrder.size();
532 // new unordered feature - compute persistent ordering at head of
533 // existing features.
534 setOrder(newf[i], i / (float) denom);
536 // set order from newly found feature from persisted ordering.
537 sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
540 // only sort if we need to
541 sort = sort || sortOrder[i] > sortOrder[i + 1];
545 if (iSize > 1 && sort)
547 jalview.util.QuickSort.sort(sortOrder, newf);
550 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
554 * get a feature style object for the given type string. Creates a
555 * java.awt.Color for a featureType with no existing colourscheme.
561 public FeatureColourI getFeatureStyle(String featureType)
563 FeatureColourI fc = featureColours.get(featureType);
566 Color col = ColorUtils.createColourFromName(featureType);
567 fc = new FeatureColour(col);
568 featureColours.put(featureType, fc);
574 public Color getColour(SequenceFeature feature)
576 FeatureColourI fc = getFeatureStyle(feature.getType());
577 return getColor(feature, fc);
581 * Answers true if the feature type is currently selected to be displayed,
587 protected boolean showFeatureOfType(String type)
589 return type == null ? false : (av.getFeaturesDisplayed() == null ? true
590 : av.getFeaturesDisplayed().isVisible(type));
594 public void setColour(String featureType, FeatureColourI col)
596 featureColours.put(featureType, col);
600 public void setTransparency(float value)
602 transparency = value;
606 public float getTransparency()
612 * analogous to colour - store a normalized ordering for all feature types in
613 * this rendering context.
616 * Feature type string
618 * normalized priority - 0 means always appears on top, 1 means
621 public float setOrder(String type, float position)
623 if (featureOrder == null)
625 featureOrder = new Hashtable<String, Float>();
627 featureOrder.put(type, new Float(position));
632 * get the global priority (0 (top) to 1 (bottom))
635 * @return [0,1] or -1 for a type without a priority
637 public float getOrder(String type)
639 if (featureOrder != null)
641 if (featureOrder.containsKey(type))
643 return featureOrder.get(type).floatValue();
650 public Map<String, FeatureColourI> getFeatureColours()
652 return featureColours;
656 * Replace current ordering with new ordering
659 * { String(Type), Colour(Type), Boolean(Displayed) }
660 * @return true if any visible features have been reordered, else false
662 public boolean setFeaturePriority(Object[][] data)
664 return setFeaturePriority(data, true);
668 * Sets the priority order for features, with the highest priority (displayed
669 * on top) at the start of the data array
672 * { String(Type), Colour(Type), Boolean(Displayed) }
674 * when true current featureDisplay list will be cleared
675 * @return true if any visible features have been reordered or recoloured,
676 * else false (i.e. no need to repaint)
678 public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
681 * note visible feature ordering and colours before update
683 List<String> visibleFeatures = getDisplayedFeatureTypes();
684 Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
685 getFeatureColours());
687 FeaturesDisplayedI av_featuresdisplayed = null;
690 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
692 av.getFeaturesDisplayed().clear();
696 av.setFeaturesDisplayed(
697 av_featuresdisplayed = new FeaturesDisplayed());
702 av_featuresdisplayed = av.getFeaturesDisplayed();
708 // The feature table will display high priority
709 // features at the top, but these are the ones
710 // we need to render last, so invert the data
711 renderOrder = new String[data.length];
715 for (int i = 0; i < data.length; i++)
717 String type = data[i][0].toString();
718 setColour(type, (FeatureColourI) data[i][1]);
719 if (((Boolean) data[i][2]).booleanValue())
721 av_featuresdisplayed.setVisible(type);
724 renderOrder[data.length - i - 1] = type;
729 * get the new visible ordering and return true if it has changed
730 * order or any colour has changed
732 List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
733 if (!visibleFeatures.equals(reorderedVisibleFeatures))
736 * the list of ordered visible features has changed
742 * return true if any feature colour has changed
744 for (String feature : visibleFeatures)
746 if (visibleColours.get(feature) != getFeatureStyle(feature))
756 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
758 public void addPropertyChangeListener(PropertyChangeListener listener)
760 changeSupport.addPropertyChangeListener(listener);
765 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
767 public void removePropertyChangeListener(PropertyChangeListener listener)
769 changeSupport.removePropertyChangeListener(listener);
772 public Set<String> getAllFeatureColours()
774 return featureColours.keySet();
777 public void clearRenderOrder()
782 public boolean hasRenderOrder()
784 return renderOrder != null;
788 * Returns feature types in ordering of rendering, where last means on top
790 public List<String> getRenderOrder()
792 if (renderOrder == null)
794 return Arrays.asList(new String[] {});
796 return Arrays.asList(renderOrder);
799 public int getFeatureGroupsSize()
801 return featureGroups != null ? 0 : featureGroups.size();
805 public List<String> getFeatureGroups()
807 // conflict between applet and desktop - featureGroups returns the map in
808 // the desktop featureRenderer
809 return (featureGroups == null) ? Arrays.asList(new String[0])
810 : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
813 public boolean checkGroupVisibility(String group,
814 boolean newGroupsVisible)
816 if (featureGroups == null)
818 // then an exception happens next..
820 if (featureGroups.containsKey(group))
822 return featureGroups.get(group).booleanValue();
824 if (newGroupsVisible)
826 featureGroups.put(group, new Boolean(true));
833 * get visible or invisible groups
836 * true to return visible groups, false to return hidden ones.
837 * @return list of groups
840 public List<String> getGroups(boolean visible)
842 if (featureGroups != null)
844 List<String> gp = new ArrayList<String>();
846 for (String grp : featureGroups.keySet())
848 Boolean state = featureGroups.get(grp);
849 if (state.booleanValue() == visible)
860 public void setGroupVisibility(String group, boolean visible)
862 featureGroups.put(group, new Boolean(visible));
866 public void setGroupVisibility(List<String> toset, boolean visible)
868 if (toset != null && toset.size() > 0 && featureGroups != null)
870 boolean rdrw = false;
871 for (String gst : toset)
873 Boolean st = featureGroups.get(gst);
874 featureGroups.put(gst, new Boolean(visible));
877 rdrw = rdrw || (visible != st.booleanValue());
882 // set local flag indicating redraw needed ?
888 public Map<String, FeatureColourI> getDisplayedFeatureCols()
890 Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
891 if (getViewport().getFeaturesDisplayed() == null)
895 Set<String> features = getViewport().getFeaturesDisplayed()
896 .getVisibleFeatures();
897 for (String feature : features)
899 fcols.put(feature, getFeatureStyle(feature));
905 public FeaturesDisplayedI getFeaturesDisplayed()
907 return av.getFeaturesDisplayed();
911 * Returns a (possibly empty) list of visible feature types, in render order
915 public List<String> getDisplayedFeatureTypes()
917 List<String> typ = getRenderOrder();
918 List<String> displayed = new ArrayList<String>();
919 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
920 if (feature_disp != null)
922 synchronized (feature_disp)
924 for (String type : typ)
926 if (feature_disp.isVisible(type))
937 public List<String> getDisplayedFeatureGroups()
939 List<String> _gps = new ArrayList<String>();
940 for (String gp : getFeatureGroups())
942 if (checkGroupVisibility(gp, false))
951 * Answers true if the feature belongs to a feature group which is not
952 * currently displayed, else false
954 * @param sequenceFeature
957 protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
959 return featureGroups != null
960 && sequenceFeature.featureGroup != null
961 && sequenceFeature.featureGroup.length() != 0
962 && featureGroups.containsKey(sequenceFeature.featureGroup)
963 && !featureGroups.get(sequenceFeature.featureGroup)
971 public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
974 List<SequenceFeature> result = new ArrayList<SequenceFeature>();
975 if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
981 * include features at the position provided their feature type is
982 * displayed, and feature group is null or the empty string
983 * or marked for display
985 Set<String> visibleFeatures = getFeaturesDisplayed()
986 .getVisibleFeatures();
987 String[] visibleTypes = visibleFeatures
988 .toArray(new String[visibleFeatures.size()]);
989 List<SequenceFeature> features = sequence.getFeatures().findFeatures(
990 resNo, resNo, visibleTypes);
992 for (SequenceFeature sf : features)
994 if (!featureGroupNotShown(sf))
1003 * Removes from the list of features any that duplicate the location of a
1004 * feature of the same type. Should be used only for features of the same,
1005 * simple, feature colour (which normally implies the same feature type). Does
1006 * not check visibility settings for feature type or feature group.
1010 public void filterFeaturesForDisplay(List<SequenceFeature> features)
1012 if (features.isEmpty())
1016 SequenceFeatures.sortFeatures(features, true);
1017 SequenceFeature lastFeature = null;
1019 Iterator<SequenceFeature> it = features.iterator();
1020 while (it.hasNext())
1022 SequenceFeature sf = it.next();
1025 * a feature is redundant for rendering purposes if it has the
1026 * same extent as another (so would just redraw the same colour);
1027 * (checking type and isContactFeature as a fail-safe here, although
1028 * currently they are guaranteed to match in this context)
1030 if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
1031 && sf.getEnd() == lastFeature.getEnd()
1032 && sf.isContactFeature() == lastFeature.isContactFeature()
1033 && sf.getType().equals(lastFeature.getType()))
1042 public Map<String, KeyedMatcherSetI> getFeatureFilters()
1044 return new HashMap<>(featureFilters);
1048 public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
1050 featureFilters = filters;
1054 public KeyedMatcherSetI getFeatureFilter(String featureType)
1056 return featureFilters.get(featureType);
1060 public void setFeatureFilter(String featureType, KeyedMatcherSetI filter)
1062 if (filter == null || filter.isEmpty())
1064 featureFilters.remove(featureType);
1068 featureFilters.put(featureType, filter);
1073 * Answers the colour for the feature, or null if the feature is excluded by
1074 * feature type or group visibility, by filters, or by colour threshold
1081 public Color getColor(SequenceFeature sf, FeatureColourI fc)
1084 * is the feature type displayed?
1086 if (!showFeatureOfType(sf.getType()))
1092 * is the feature group displayed?
1094 if (featureGroupNotShown(sf))
1100 * does the feature pass filters?
1102 if (!featureMatchesFilters(sf))
1107 return fc.getColor(sf);
1111 * Answers true if there no are filters defined for the feature type, or this
1112 * feature matches the filters. Answers false if the feature fails to match
1118 protected boolean featureMatchesFilters(SequenceFeature sf)
1120 KeyedMatcherSetI filter = featureFilters.get(sf.getType());
1121 return filter == null ? true : filter.matches(key -> sf
1122 .getValueAsString(key));