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.renderer.seqfeatures.FeatureRenderer;
30 import jalview.schemes.FeatureColour;
31 import jalview.util.ColorUtils;
33 import java.awt.Color;
34 import java.beans.PropertyChangeListener;
35 import java.beans.PropertyChangeSupport;
36 import java.util.ArrayList;
37 import java.util.Arrays;
38 import java.util.Collections;
39 import java.util.HashMap;
40 import java.util.HashSet;
41 import java.util.Hashtable;
42 import java.util.List;
45 import java.util.concurrent.ConcurrentHashMap;
47 public abstract class FeatureRendererModel implements
48 jalview.api.FeatureRenderer
52 * global transparency for feature
54 protected float transparency = 1.0f;
56 protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<String, FeatureColourI>();
58 protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
60 protected String[] renderOrder;
62 Map<String, Float> featureOrder = null;
64 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
67 protected AlignViewportI av;
70 public AlignViewportI getViewport()
75 public FeatureRendererSettings getSettings()
77 return new FeatureRendererSettings(this);
80 public void transferSettings(FeatureRendererSettings fr)
82 this.renderOrder = fr.renderOrder;
83 this.featureGroups = fr.featureGroups;
84 this.featureColours = fr.featureColours;
85 this.transparency = fr.transparency;
86 this.featureOrder = fr.featureOrder;
90 * update from another feature renderer
95 public void transferSettings(jalview.api.FeatureRenderer _fr)
97 FeatureRenderer fr = (FeatureRenderer) _fr;
98 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
99 this.renderOrder = frs.renderOrder;
100 this.featureGroups = frs.featureGroups;
101 this.featureColours = frs.featureColours;
102 this.transparency = frs.transparency;
103 this.featureOrder = frs.featureOrder;
104 if (av != null && av != fr.getViewport())
106 // copy over the displayed feature settings
107 if (_fr.getFeaturesDisplayed() != null)
109 FeaturesDisplayedI fd = getFeaturesDisplayed();
112 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
119 for (String type : _fr.getFeaturesDisplayed()
120 .getVisibleFeatures())
130 public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
132 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
136 public void setVisible(String featureType)
138 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
141 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
143 if (!fdi.isRegistered(featureType))
145 pushFeatureType(Arrays.asList(new String[] { featureType }));
147 fdi.setVisible(featureType);
151 public void setAllVisible(List<String> featureTypes)
153 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
156 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
158 List<String> nft = new ArrayList<String>();
159 for (String featureType : featureTypes)
161 if (!fdi.isRegistered(featureType))
163 nft.add(featureType);
168 pushFeatureType(nft);
170 fdi.setAllVisible(featureTypes);
174 * push a set of new types onto the render order stack. Note - this is a
175 * direct mechanism rather than the one employed in updateRenderOrder
179 private void pushFeatureType(List<String> types)
182 int ts = types.size();
183 String neworder[] = new String[(renderOrder == null ? 0
184 : renderOrder.length) + ts];
185 types.toArray(neworder);
186 if (renderOrder != null)
188 System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
189 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
191 renderOrder = neworder;
194 protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
196 public Map<String, float[][]> getMinMax()
202 * normalise a score against the max/min bounds for the feature type.
204 * @param sequenceFeature
205 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
208 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
210 float[] mm = minmax.get(sequenceFeature.type)[0];
211 final byte[] r = new byte[] { 0, (byte) 255 };
214 if (r[0] != 0 || mm[0] < 0.0)
217 r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
221 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
227 boolean newFeatureAdded = false;
229 boolean findingFeatures = false;
231 protected boolean updateFeatures()
233 if (av.getFeaturesDisplayed() == null || renderOrder == null
237 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
242 // TODO: decide if we should check for the visible feature count first
247 * search the alignment for all new features, give them a colour and display
248 * them. Then fires a PropertyChangeEvent on the changeSupport object.
251 protected void findAllFeatures()
253 synchronized (firing)
255 if (firing.equals(Boolean.FALSE))
257 firing = Boolean.TRUE;
258 findAllFeatures(true); // add all new features as visible
259 changeSupport.firePropertyChange("changeSupport", null, null);
260 firing = Boolean.FALSE;
266 public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
268 List<SequenceFeature> result = new ArrayList<SequenceFeature>();
269 if (!av.areFeaturesDisplayed())
274 Set<String> visibleFeatures = getFeaturesDisplayed()
275 .getVisibleFeatures();
276 String[] visibleTypes = visibleFeatures
277 .toArray(new String[visibleFeatures.size()]);
280 * include features at the position provided their feature type is
281 * displayed, and feature group is null or marked for display
283 List<SequenceFeature> features = sequence.getFeatures().findFeatures(
284 res, res, visibleTypes);
286 for (SequenceFeature sf : features)
288 if (!featureGroupNotShown(sf))
297 * Searches alignment for all features and updates colours
299 * @param newMadeVisible
300 * if true newly added feature types will be rendered immediately
301 * TODO: check to see if this method should actually be proxied so
302 * repaint events can be propagated by the renderer code
305 public synchronized void findAllFeatures(boolean newMadeVisible)
307 newFeatureAdded = false;
311 newFeatureAdded = true;
315 findingFeatures = true;
316 if (av.getFeaturesDisplayed() == null)
318 av.setFeaturesDisplayed(new FeaturesDisplayed());
320 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
322 Set<String> oldfeatures = new HashSet<String>();
323 if (renderOrder != null)
325 for (int i = 0; i < renderOrder.length; i++)
327 if (renderOrder[i] != null)
329 oldfeatures.add(renderOrder[i]);
334 AlignmentI alignment = av.getAlignment();
335 List<String> allfeatures = new ArrayList<String>(); // or HashSet?
337 for (int i = 0; i < alignment.getHeight(); i++)
339 SequenceI asq = alignment.getSequenceAt(i);
340 for (String group : asq.getFeatures().getFeatureGroups(true))
343 * features in null group are always displayed; other groups
344 * keep their current visibility; new groups as 'newMadeVisible'
346 boolean groupDisplayed = true;
349 if (featureGroups.containsKey(group))
351 groupDisplayed = featureGroups.get(group);
355 groupDisplayed = newMadeVisible;
356 featureGroups.put(group, groupDisplayed);
361 Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
363 for (String type : types)
365 if (!allfeatures.contains(type)) // or use HashSet and no test?
367 allfeatures.add(type);
369 updateMinMax(asq, type, true); // todo: for all features?
376 * mark any new feature types as visible
378 Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
381 for (String type : allfeatures)
383 if (!oldfeatures.contains(type))
385 featuresDisplayed.setVisible(type);
391 updateRenderOrder(allfeatures);
392 findingFeatures = false;
396 * Updates the global (alignment) min and max values for a feature type from
397 * the score for a sequence, if the score is not NaN. Values are stored
398 * separately for positional and non-positional features.
404 protected void updateMinMax(SequenceI seq, String featureType,
407 float min = seq.getFeatures().getMinimumScore(featureType, positional);
408 if (Float.isNaN(min))
413 float max = seq.getFeatures().getMaximumScore(featureType, positional);
417 * { {positionalMin, positionalMax}, {nonPositionalMin, nonPositionalMax} }
421 minmax = new Hashtable<String, float[][]>();
423 synchronized (minmax)
425 float[][] mm = minmax.get(featureType);
426 int index = positional ? 0 : 1;
429 mm = new float[][] { null, null };
430 minmax.put(featureType, mm);
432 if (mm[index] == null)
434 mm[index] = new float[] { min, max };
438 mm[index][0] = Math.min(mm[index][0], min);
439 mm[index][1] = Math.max(mm[index][1], max);
443 protected Boolean firing = Boolean.FALSE;
446 * replaces the current renderOrder with the unordered features in
447 * allfeatures. The ordering of any types in both renderOrder and allfeatures
448 * is preserved, and all new feature types are rendered on top of the existing
449 * types, in the order given by getOrder or the order given in allFeatures.
450 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
451 * eliminate the float storage for computing/recalling the persistent ordering
452 * New Cability: updates min/max for colourscheme range if its dynamic
456 private void updateRenderOrder(List<String> allFeatures)
458 List<String> allfeatures = new ArrayList<String>(allFeatures);
459 String[] oldRender = renderOrder;
460 renderOrder = new String[allfeatures.size()];
461 boolean initOrders = (featureOrder == null);
463 if (oldRender != null && oldRender.length > 0)
465 for (int j = 0; j < oldRender.length; j++)
467 if (oldRender[j] != null)
471 setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
473 if (allfeatures.contains(oldRender[j]))
475 renderOrder[opos++] = oldRender[j]; // existing features always
476 // appear below new features
477 allfeatures.remove(oldRender[j]);
480 float[][] mmrange = minmax.get(oldRender[j]);
483 FeatureColourI fc = featureColours.get(oldRender[j]);
484 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
486 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
494 if (allfeatures.size() == 0)
496 // no new features - leave order unchanged.
499 int i = allfeatures.size() - 1;
501 boolean sort = false;
502 String[] newf = new String[allfeatures.size()];
503 float[] sortOrder = new float[allfeatures.size()];
504 for (String newfeat : allfeatures)
509 // update from new features minmax if necessary
510 float[][] mmrange = minmax.get(newf[i]);
513 FeatureColourI fc = featureColours.get(newf[i]);
514 if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
516 fc.updateBounds(mmrange[0][0], mmrange[0][1]);
520 if (initOrders || !featureOrder.containsKey(newf[i]))
522 int denom = initOrders ? allfeatures.size() : featureOrder.size();
523 // new unordered feature - compute persistent ordering at head of
524 // existing features.
525 setOrder(newf[i], i / (float) denom);
527 // set order from newly found feature from persisted ordering.
528 sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
531 // only sort if we need to
532 sort = sort || sortOrder[i] > sortOrder[i + 1];
536 if (iSize > 1 && sort)
538 jalview.util.QuickSort.sort(sortOrder, newf);
541 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
545 * get a feature style object for the given type string. Creates a
546 * java.awt.Color for a featureType with no existing colourscheme.
552 public FeatureColourI getFeatureStyle(String featureType)
554 FeatureColourI fc = featureColours.get(featureType);
557 Color col = ColorUtils.createColourFromName(featureType);
558 fc = new FeatureColour(col);
559 featureColours.put(featureType, fc);
565 * Returns the configured colour for a particular feature instance. This
566 * includes calculation of 'colour by label', or of a graduated score colour,
567 * if applicable. It does not take into account feature visibility or colour
573 public Color getColour(SequenceFeature feature)
575 FeatureColourI fc = getFeatureStyle(feature.getType());
576 return fc.getColor(feature);
580 * Answers true unless the feature has a graduated colour scheme and the
581 * feature value lies outside the current threshold for display
583 * @param sequenceFeature
586 protected boolean showFeature(SequenceFeature sequenceFeature)
588 FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
589 return fc.isColored(sequenceFeature);
593 * Answers true if the feature type is currently selected to be displayed,
599 protected boolean showFeatureOfType(String type)
601 return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
605 public void setColour(String featureType, FeatureColourI col)
607 featureColours.put(featureType, col);
611 public void setTransparency(float value)
613 transparency = value;
617 public float getTransparency()
623 * analogous to colour - store a normalized ordering for all feature types in
624 * this rendering context.
627 * Feature type string
629 * normalized priority - 0 means always appears on top, 1 means
632 public float setOrder(String type, float position)
634 if (featureOrder == null)
636 featureOrder = new Hashtable<String, Float>();
638 featureOrder.put(type, new Float(position));
643 * get the global priority (0 (top) to 1 (bottom))
646 * @return [0,1] or -1 for a type without a priority
648 public float getOrder(String type)
650 if (featureOrder != null)
652 if (featureOrder.containsKey(type))
654 return featureOrder.get(type).floatValue();
661 public Map<String, FeatureColourI> getFeatureColours()
663 return featureColours;
667 * Replace current ordering with new ordering
670 * { String(Type), Colour(Type), Boolean(Displayed) }
671 * @return true if any visible features have been reordered, else false
673 public boolean setFeaturePriority(Object[][] data)
675 return setFeaturePriority(data, true);
679 * Sets the priority order for features, with the highest priority (displayed
680 * on top) at the start of the data array
683 * { String(Type), Colour(Type), Boolean(Displayed) }
685 * when true current featureDisplay list will be cleared
686 * @return true if any visible features have been reordered or recoloured,
687 * else false (i.e. no need to repaint)
689 public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
692 * note visible feature ordering and colours before update
694 List<String> visibleFeatures = getDisplayedFeatureTypes();
695 Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
696 getFeatureColours());
698 FeaturesDisplayedI av_featuresdisplayed = null;
701 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
703 av.getFeaturesDisplayed().clear();
707 av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
712 av_featuresdisplayed = av.getFeaturesDisplayed();
718 // The feature table will display high priority
719 // features at the top, but these are the ones
720 // we need to render last, so invert the data
721 renderOrder = new String[data.length];
725 for (int i = 0; i < data.length; i++)
727 String type = data[i][0].toString();
728 setColour(type, (FeatureColourI) data[i][1]);
729 if (((Boolean) data[i][2]).booleanValue())
731 av_featuresdisplayed.setVisible(type);
734 renderOrder[data.length - i - 1] = type;
739 * get the new visible ordering and return true if it has changed
740 * order or any colour has changed
742 List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
743 if (!visibleFeatures.equals(reorderedVisibleFeatures))
746 * the list of ordered visible features has changed
752 * return true if any feature colour has changed
754 for (String feature : visibleFeatures)
756 if (visibleColours.get(feature) != getFeatureStyle(feature))
766 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
768 public void addPropertyChangeListener(PropertyChangeListener listener)
770 changeSupport.addPropertyChangeListener(listener);
775 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
777 public void removePropertyChangeListener(PropertyChangeListener listener)
779 changeSupport.removePropertyChangeListener(listener);
782 public Set<String> getAllFeatureColours()
784 return featureColours.keySet();
787 public void clearRenderOrder()
792 public boolean hasRenderOrder()
794 return renderOrder != null;
798 * Returns feature types in ordering of rendering, where last means on top
800 public List<String> getRenderOrder()
802 if (renderOrder == null)
804 return Arrays.asList(new String[] {});
806 return Arrays.asList(renderOrder);
809 public int getFeatureGroupsSize()
811 return featureGroups != null ? 0 : featureGroups.size();
815 public List<String> getFeatureGroups()
817 // conflict between applet and desktop - featureGroups returns the map in
818 // the desktop featureRenderer
819 return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
820 .asList(featureGroups.keySet().toArray(new String[0]));
823 public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
825 if (featureGroups == null)
827 // then an exception happens next..
829 if (featureGroups.containsKey(group))
831 return featureGroups.get(group).booleanValue();
833 if (newGroupsVisible)
835 featureGroups.put(group, new Boolean(true));
842 * get visible or invisible groups
845 * true to return visible groups, false to return hidden ones.
846 * @return list of groups
849 public List<String> getGroups(boolean visible)
851 if (featureGroups != null)
853 List<String> gp = new ArrayList<String>();
855 for (String grp : featureGroups.keySet())
857 Boolean state = featureGroups.get(grp);
858 if (state.booleanValue() == visible)
869 public void setGroupVisibility(String group, boolean visible)
871 featureGroups.put(group, new Boolean(visible));
875 public void setGroupVisibility(List<String> toset, boolean visible)
877 if (toset != null && toset.size() > 0 && featureGroups != null)
879 boolean rdrw = false;
880 for (String gst : toset)
882 Boolean st = featureGroups.get(gst);
883 featureGroups.put(gst, new Boolean(visible));
886 rdrw = rdrw || (visible != st.booleanValue());
891 // set local flag indicating redraw needed ?
897 public Map<String, FeatureColourI> getDisplayedFeatureCols()
899 Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
900 if (getViewport().getFeaturesDisplayed() == null)
904 Set<String> features = getViewport().getFeaturesDisplayed()
905 .getVisibleFeatures();
906 for (String feature : features)
908 fcols.put(feature, getFeatureStyle(feature));
914 public FeaturesDisplayedI getFeaturesDisplayed()
916 return av.getFeaturesDisplayed();
920 * Returns a (possibly empty) list of visible feature types, in render order
924 public List<String> getDisplayedFeatureTypes()
926 List<String> typ = getRenderOrder();
927 List<String> displayed = new ArrayList<String>();
928 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
929 if (feature_disp != null)
931 synchronized (feature_disp)
933 for (String type : typ)
935 if (feature_disp.isVisible(type))
946 public List<String> getDisplayedFeatureGroups()
948 List<String> _gps = new ArrayList<String>();
949 boolean valid = false;
950 for (String gp : getFeatureGroups())
952 if (checkGroupVisibility(gp, false))
963 // gps = new String[_gps.size()];
964 // _gps.toArray(gps);
971 * Answers true if the feature belongs to a feature group which is not
972 * currently displayed, else false
974 * @param sequenceFeature
977 protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
979 return featureGroups != null
980 && sequenceFeature.featureGroup != null
981 && sequenceFeature.featureGroup.length() != 0
982 && featureGroups.containsKey(sequenceFeature.featureGroup)
983 && !featureGroups.get(sequenceFeature.featureGroup)