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<>();
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<>();
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<>();
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,
301 * include features unless their feature group is not displayed, or
302 * they are hidden (have no colour) based on a filter or colour threshold
304 for (SequenceFeature sf : features)
306 if (!featureGroupNotShown(sf) && getColour(sf) != null)
315 * Searches alignment for all features and updates colours
317 * @param newMadeVisible
318 * if true newly added feature types will be rendered immediately
319 * TODO: check to see if this method should actually be proxied so
320 * repaint events can be propagated by the renderer code
323 public synchronized void findAllFeatures(boolean newMadeVisible)
325 newFeatureAdded = false;
329 newFeatureAdded = true;
333 findingFeatures = true;
334 if (av.getFeaturesDisplayed() == null)
336 av.setFeaturesDisplayed(new FeaturesDisplayed());
338 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
340 Set<String> oldfeatures = new HashSet<>();
341 if (renderOrder != null)
343 for (int i = 0; i < renderOrder.length; i++)
345 if (renderOrder[i] != null)
347 oldfeatures.add(renderOrder[i]);
352 AlignmentI alignment = av.getAlignment();
353 List<String> allfeatures = new ArrayList<>();
355 for (int i = 0; i < alignment.getHeight(); i++)
357 SequenceI asq = alignment.getSequenceAt(i);
358 for (String group : asq.getFeatures().getFeatureGroups(true))
360 boolean groupDisplayed = true;
363 if (featureGroups.containsKey(group))
365 groupDisplayed = featureGroups.get(group);
369 groupDisplayed = newMadeVisible;
370 featureGroups.put(group, groupDisplayed);
375 Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
377 for (String type : types)
379 if (!allfeatures.contains(type)) // or use HashSet and no test?
381 allfeatures.add(type);
383 updateMinMax(asq, type, true); // todo: for all features?
389 // uncomment to add new features in alphebetical order (but JAL-2575)
390 // Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
393 for (String type : allfeatures)
395 if (!oldfeatures.contains(type))
397 featuresDisplayed.setVisible(type);
403 updateRenderOrder(allfeatures);
404 findingFeatures = false;
408 * Updates the global (alignment) min and max values for a feature type from
409 * the score for a sequence, if the score is not NaN. Values are stored
410 * separately for positional and non-positional features.
416 protected void updateMinMax(SequenceI seq, String featureType,
419 float min = seq.getFeatures().getMinimumScore(featureType, positional);
420 if (Float.isNaN(min))
425 float max = seq.getFeatures().getMaximumScore(featureType, positional);
429 * { {positionalMin, positionalMax}, {nonPositionalMin, nonPositionalMax} }
433 minmax = new Hashtable<>();
435 synchronized (minmax)
437 float[][] mm = minmax.get(featureType);
438 int index = positional ? 0 : 1;
441 mm = new float[][] { null, null };
442 minmax.put(featureType, mm);
444 if (mm[index] == null)
446 mm[index] = new float[] { min, max };
450 mm[index][0] = Math.min(mm[index][0], min);
451 mm[index][1] = Math.max(mm[index][1], max);
455 protected Boolean firing = Boolean.FALSE;
458 * replaces the current renderOrder with the unordered features in
459 * allfeatures. The ordering of any types in both renderOrder and allfeatures
460 * is preserved, and all new feature types are rendered on top of the existing
461 * types, in the order given by getOrder or the order given in allFeatures.
462 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
463 * eliminate the float storage for computing/recalling the persistent ordering
464 * New Cability: updates min/max for colourscheme range if its dynamic
468 private void updateRenderOrder(List<String> allFeatures)
470 List<String> allfeatures = new ArrayList<>(allFeatures);
471 String[] oldRender = renderOrder;
472 renderOrder = new String[allfeatures.size()];
473 boolean initOrders = (featureOrder == null);
475 if (oldRender != null && oldRender.length > 0)
477 for (int j = 0; j < oldRender.length; j++)
479 if (oldRender[j] != null)
483 setOrder(oldRender[j],
484 (1 - (1 + (float) j) / oldRender.length));
486 if (allfeatures.contains(oldRender[j]))
488 renderOrder[opos++] = oldRender[j]; // existing features always
489 // appear below new features
490 allfeatures.remove(oldRender[j]);
493 float[][] mmrange = minmax.get(oldRender[j]);
496 FeatureColourI fc = featureColours.get(oldRender[j]);
497 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
498 && !fc.isColourByAttribute())
500 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
508 if (allfeatures.size() == 0)
510 // no new features - leave order unchanged.
513 int i = allfeatures.size() - 1;
515 boolean sort = false;
516 String[] newf = new String[allfeatures.size()];
517 float[] sortOrder = new float[allfeatures.size()];
518 for (String newfeat : allfeatures)
523 // update from new features minmax if necessary
524 float[][] mmrange = minmax.get(newf[i]);
527 FeatureColourI fc = featureColours.get(newf[i]);
528 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
529 && !fc.isColourByAttribute())
531 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
535 if (initOrders || !featureOrder.containsKey(newf[i]))
537 int denom = initOrders ? allfeatures.size() : featureOrder.size();
538 // new unordered feature - compute persistent ordering at head of
539 // existing features.
540 setOrder(newf[i], i / (float) denom);
542 // set order from newly found feature from persisted ordering.
543 sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
546 // only sort if we need to
547 sort = sort || sortOrder[i] > sortOrder[i + 1];
551 if (iSize > 1 && sort)
553 jalview.util.QuickSort.sort(sortOrder, newf);
556 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
560 * get a feature style object for the given type string. Creates a
561 * java.awt.Color for a featureType with no existing colourscheme.
567 public FeatureColourI getFeatureStyle(String featureType)
569 FeatureColourI fc = featureColours.get(featureType);
572 Color col = ColorUtils.createColourFromName(featureType);
573 fc = new FeatureColour(col);
574 featureColours.put(featureType, fc);
580 public Color getColour(SequenceFeature feature)
582 FeatureColourI fc = getFeatureStyle(feature.getType());
583 return getColor(feature, fc);
587 * Answers true if the feature type is currently selected to be displayed,
593 protected boolean showFeatureOfType(String type)
595 return type == null ? false : (av.getFeaturesDisplayed() == null ? true
596 : av.getFeaturesDisplayed().isVisible(type));
600 public void setColour(String featureType, FeatureColourI col)
602 featureColours.put(featureType, col);
606 public void setTransparency(float value)
608 transparency = value;
612 public float getTransparency()
618 * analogous to colour - store a normalized ordering for all feature types in
619 * this rendering context.
622 * Feature type string
624 * normalized priority - 0 means always appears on top, 1 means
627 public float setOrder(String type, float position)
629 if (featureOrder == null)
631 featureOrder = new Hashtable<>();
633 featureOrder.put(type, new Float(position));
638 * get the global priority (0 (top) to 1 (bottom))
641 * @return [0,1] or -1 for a type without a priority
643 public float getOrder(String type)
645 if (featureOrder != null)
647 if (featureOrder.containsKey(type))
649 return featureOrder.get(type).floatValue();
656 public Map<String, FeatureColourI> getFeatureColours()
658 return featureColours;
662 * Replace current ordering with new ordering
665 * { String(Type), Colour(Type), Boolean(Displayed) }
666 * @return true if any visible features have been reordered, else false
668 public boolean setFeaturePriority(Object[][] data)
670 return setFeaturePriority(data, true);
674 * Sets the priority order for features, with the highest priority (displayed
675 * on top) at the start of the data array
678 * { String(Type), Colour(Type), Boolean(Displayed) }
680 * when true current featureDisplay list will be cleared
681 * @return true if any visible features have been reordered or recoloured,
682 * else false (i.e. no need to repaint)
684 public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
687 * note visible feature ordering and colours before update
689 List<String> visibleFeatures = getDisplayedFeatureTypes();
690 Map<String, FeatureColourI> visibleColours = new HashMap<>(
691 getFeatureColours());
693 FeaturesDisplayedI av_featuresdisplayed = null;
696 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
698 av.getFeaturesDisplayed().clear();
702 av.setFeaturesDisplayed(
703 av_featuresdisplayed = new FeaturesDisplayed());
708 av_featuresdisplayed = av.getFeaturesDisplayed();
714 // The feature table will display high priority
715 // features at the top, but these are the ones
716 // we need to render last, so invert the data
717 renderOrder = new String[data.length];
721 for (int i = 0; i < data.length; i++)
723 String type = data[i][0].toString();
724 setColour(type, (FeatureColourI) data[i][1]);
725 if (((Boolean) data[i][2]).booleanValue())
727 av_featuresdisplayed.setVisible(type);
730 renderOrder[data.length - i - 1] = type;
735 * get the new visible ordering and return true if it has changed
736 * order or any colour has changed
738 List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
739 if (!visibleFeatures.equals(reorderedVisibleFeatures))
742 * the list of ordered visible features has changed
748 * return true if any feature colour has changed
750 for (String feature : visibleFeatures)
752 if (visibleColours.get(feature) != getFeatureStyle(feature))
762 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
764 public void addPropertyChangeListener(PropertyChangeListener listener)
766 changeSupport.addPropertyChangeListener(listener);
771 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
773 public void removePropertyChangeListener(PropertyChangeListener listener)
775 changeSupport.removePropertyChangeListener(listener);
778 public Set<String> getAllFeatureColours()
780 return featureColours.keySet();
783 public void clearRenderOrder()
788 public boolean hasRenderOrder()
790 return renderOrder != null;
794 * Returns feature types in ordering of rendering, where last means on top
796 public List<String> getRenderOrder()
798 if (renderOrder == null)
800 return Arrays.asList(new String[] {});
802 return Arrays.asList(renderOrder);
805 public int getFeatureGroupsSize()
807 return featureGroups != null ? 0 : featureGroups.size();
811 public List<String> getFeatureGroups()
813 // conflict between applet and desktop - featureGroups returns the map in
814 // the desktop featureRenderer
815 return (featureGroups == null) ? Arrays.asList(new String[0])
816 : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
819 public boolean checkGroupVisibility(String group,
820 boolean newGroupsVisible)
822 if (featureGroups == null)
824 // then an exception happens next..
826 if (featureGroups.containsKey(group))
828 return featureGroups.get(group).booleanValue();
830 if (newGroupsVisible)
832 featureGroups.put(group, new Boolean(true));
839 * get visible or invisible groups
842 * true to return visible groups, false to return hidden ones.
843 * @return list of groups
846 public List<String> getGroups(boolean visible)
848 if (featureGroups != null)
850 List<String> gp = new ArrayList<>();
852 for (String grp : featureGroups.keySet())
854 Boolean state = featureGroups.get(grp);
855 if (state.booleanValue() == visible)
866 public void setGroupVisibility(String group, boolean visible)
868 featureGroups.put(group, new Boolean(visible));
872 public void setGroupVisibility(List<String> toset, boolean visible)
874 if (toset != null && toset.size() > 0 && featureGroups != null)
876 boolean rdrw = false;
877 for (String gst : toset)
879 Boolean st = featureGroups.get(gst);
880 featureGroups.put(gst, new Boolean(visible));
883 rdrw = rdrw || (visible != st.booleanValue());
888 // set local flag indicating redraw needed ?
894 public Map<String, FeatureColourI> getDisplayedFeatureCols()
896 Map<String, FeatureColourI> fcols = new Hashtable<>();
897 if (getViewport().getFeaturesDisplayed() == null)
901 Set<String> features = getViewport().getFeaturesDisplayed()
902 .getVisibleFeatures();
903 for (String feature : features)
905 fcols.put(feature, getFeatureStyle(feature));
911 public FeaturesDisplayedI getFeaturesDisplayed()
913 return av.getFeaturesDisplayed();
917 * Returns a (possibly empty) list of visible feature types, in render order
921 public List<String> getDisplayedFeatureTypes()
923 List<String> typ = getRenderOrder();
924 List<String> displayed = new ArrayList<>();
925 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
926 if (feature_disp != null)
928 synchronized (feature_disp)
930 for (String type : typ)
932 if (feature_disp.isVisible(type))
943 public List<String> getDisplayedFeatureGroups()
945 List<String> _gps = new ArrayList<>();
946 for (String gp : getFeatureGroups())
948 if (checkGroupVisibility(gp, false))
957 * Answers true if the feature belongs to a feature group which is not
958 * currently displayed, else false
960 * @param sequenceFeature
963 protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
965 return featureGroups != null
966 && sequenceFeature.featureGroup != null
967 && sequenceFeature.featureGroup.length() != 0
968 && featureGroups.containsKey(sequenceFeature.featureGroup)
969 && !featureGroups.get(sequenceFeature.featureGroup)
977 public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
980 List<SequenceFeature> result = new ArrayList<>();
981 if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
987 * include features at the position provided their feature type is
988 * displayed, and feature group is null or the empty string
989 * or marked for display
991 Set<String> visibleFeatures = getFeaturesDisplayed()
992 .getVisibleFeatures();
993 String[] visibleTypes = visibleFeatures
994 .toArray(new String[visibleFeatures.size()]);
995 List<SequenceFeature> features = sequence.getFeatures().findFeatures(
996 resNo, resNo, visibleTypes);
998 for (SequenceFeature sf : features)
1000 if (!featureGroupNotShown(sf) && getColour(sf) != null)
1009 * Removes from the list of features any that duplicate the location of a
1010 * feature of the same type. Should be used only for features of the same,
1011 * simple, feature colour (which normally implies the same feature type). Does
1012 * not check visibility settings for feature type or feature group.
1016 public void filterFeaturesForDisplay(List<SequenceFeature> features)
1018 if (features.isEmpty())
1022 SequenceFeatures.sortFeatures(features, true);
1023 SequenceFeature lastFeature = null;
1025 Iterator<SequenceFeature> it = features.iterator();
1026 while (it.hasNext())
1028 SequenceFeature sf = it.next();
1031 * a feature is redundant for rendering purposes if it has the
1032 * same extent as another (so would just redraw the same colour);
1033 * (checking type and isContactFeature as a fail-safe here, although
1034 * currently they are guaranteed to match in this context)
1036 if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
1037 && sf.getEnd() == lastFeature.getEnd()
1038 && sf.isContactFeature() == lastFeature.isContactFeature()
1039 && sf.getType().equals(lastFeature.getType()))
1048 public Map<String, KeyedMatcherSetI> getFeatureFilters()
1050 return new HashMap<>(featureFilters);
1054 public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
1056 featureFilters = filters;
1060 public KeyedMatcherSetI getFeatureFilter(String featureType)
1062 return featureFilters.get(featureType);
1066 public void setFeatureFilter(String featureType, KeyedMatcherSetI filter)
1068 if (filter == null || filter.isEmpty())
1070 featureFilters.remove(featureType);
1074 featureFilters.put(featureType, filter);
1079 * Answers the colour for the feature, or null if the feature is excluded by
1080 * feature type or group visibility, by filters, or by colour threshold
1087 public Color getColor(SequenceFeature sf, FeatureColourI fc)
1090 * is the feature type displayed?
1092 if (!showFeatureOfType(sf.getType()))
1098 * is the feature group displayed?
1100 if (featureGroupNotShown(sf))
1106 * does the feature pass filters?
1108 if (!featureMatchesFilters(sf))
1113 return fc.getColor(sf);
1117 * Answers true if there no are filters defined for the feature type, or this
1118 * feature matches the filters. Answers false if the feature fails to match
1124 protected boolean featureMatchesFilters(SequenceFeature sf)
1126 KeyedMatcherSetI filter = featureFilters.get(sf.getType());
1127 return filter == null ? true : filter.matches(key -> sf
1128 .getValueAsString(key));