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.GraduatedColor;
32 import java.awt.Color;
33 import java.beans.PropertyChangeListener;
34 import java.beans.PropertyChangeSupport;
35 import java.util.ArrayList;
36 import java.util.Arrays;
37 import java.util.HashMap;
38 import java.util.Hashtable;
39 import java.util.Iterator;
40 import java.util.List;
43 import java.util.concurrent.ConcurrentHashMap;
45 public abstract class FeatureRendererModel implements
46 jalview.api.FeatureRenderer
50 * global transparency for feature
52 protected float transparency = 1.0f;
54 protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
56 protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
58 protected Object currentColour;
61 * feature types in ordering of rendering, where last means on top
63 protected String[] renderOrder;
65 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
68 protected AlignViewportI av;
71 * map holds per feature type, {{min, max}, {min, max}} feature score
72 * values for positional and non-positional features respectively
74 private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
77 public AlignViewportI getViewport()
82 public FeatureRendererSettings getSettings()
84 return new FeatureRendererSettings(this);
87 public void transferSettings(FeatureRendererSettings fr)
89 this.renderOrder = fr.renderOrder;
90 this.featureGroups = fr.featureGroups;
91 this.featureColours = fr.featureColours;
92 this.transparency = fr.transparency;
93 this.featureOrder = fr.featureOrder;
97 * update from another feature renderer
102 public void transferSettings(jalview.api.FeatureRenderer _fr)
104 FeatureRenderer fr = (FeatureRenderer) _fr;
105 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
106 this.renderOrder = frs.renderOrder;
107 this.featureGroups = frs.featureGroups;
108 this.featureColours = frs.featureColours;
109 this.transparency = frs.transparency;
110 this.featureOrder = frs.featureOrder;
111 if (av != null && av != fr.getViewport())
113 // copy over the displayed feature settings
114 if (_fr.getFeaturesDisplayed() != null)
116 FeaturesDisplayedI fd = getFeaturesDisplayed();
119 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
126 java.util.Iterator<String> fdisp = _fr.getFeaturesDisplayed()
127 .getVisibleFeatures();
128 while (fdisp.hasNext())
130 fd.setVisible(fdisp.next());
138 public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
140 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
144 public void setVisible(String featureType)
146 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
149 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
151 if (!fdi.isRegistered(featureType))
153 pushFeatureType(Arrays.asList(new String[] { featureType }));
155 fdi.setVisible(featureType);
159 public void setAllVisible(List<String> featureTypes)
161 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
164 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
166 List<String> nft = new ArrayList<String>();
167 for (String featureType : featureTypes)
169 if (!fdi.isRegistered(featureType))
171 nft.add(featureType);
176 pushFeatureType(nft);
178 fdi.setAllVisible(featureTypes);
182 * push a set of new types onto the render order stack. Note - this is a
183 * direct mechanism rather than the one employed in updateRenderOrder
187 private void pushFeatureType(List<String> types)
190 int ts = types.size();
191 String neworder[] = new String[(renderOrder == null ? 0
192 : renderOrder.length) + ts];
193 types.toArray(neworder);
194 if (renderOrder != null)
196 System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
197 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
199 renderOrder = neworder;
202 public Map<String, float[][]> getMinMax()
208 * normalise a score against the max/min bounds for the feature type.
210 * @param sequenceFeature
211 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
214 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
216 float[] mm = minmax.get(sequenceFeature.type)[0];
217 final byte[] r = new byte[] { 0, (byte) 255 };
220 if (r[0] != 0 || mm[0] < 0.0)
223 r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
227 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
233 boolean newFeatureAdded = false;
235 boolean findingFeatures = false;
237 protected boolean updateFeatures()
239 if (av.getFeaturesDisplayed() == null || renderOrder == null
243 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
248 // TODO: decide if we should check for the visible feature count first
253 * search the alignment for all new features, give them a colour and display
254 * them. Then fires a PropertyChangeEvent on the changeSupport object.
257 protected void findAllFeatures()
259 synchronized (firing)
261 if (firing.equals(Boolean.FALSE))
263 firing = Boolean.TRUE;
264 findAllFeatures(true); // add all new features as visible
265 changeSupport.firePropertyChange("changeSupport", null, null);
266 firing = Boolean.FALSE;
272 public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
274 ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
275 SequenceFeature[] features = sequence.getSequenceFeatures();
277 if (features != null)
279 for (int i = 0; i < features.length; i++)
281 if (!av.areFeaturesDisplayed()
282 || !av.getFeaturesDisplayed().isVisible(
283 features[i].getType()))
288 if (features[i].featureGroup != null
289 && featureGroups != null
290 && featureGroups.containsKey(features[i].featureGroup)
291 && !featureGroups.get(features[i].featureGroup)
297 if ((features[i].getBegin() <= res)
298 && (features[i].getEnd() >= res))
300 tmp.add(features[i]);
308 * Searches alignment for all features and updates colours
310 * @param newMadeVisible
311 * if true newly added feature types will be rendered immediatly
312 * TODO: check to see if this method should actually be proxied so
313 * repaint events can be propagated by the renderer code
316 public synchronized void findAllFeatures(boolean newMadeVisible)
318 newFeatureAdded = false;
322 newFeatureAdded = true;
326 findingFeatures = true;
327 if (av.getFeaturesDisplayed() == null)
329 av.setFeaturesDisplayed(new FeaturesDisplayed());
331 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
333 ArrayList<String> allfeatures = new ArrayList<String>();
334 ArrayList<String> oldfeatures = new ArrayList<String>();
335 if (renderOrder != null)
337 for (int i = 0; i < renderOrder.length; i++)
339 if (renderOrder[i] != null)
341 oldfeatures.add(renderOrder[i]);
347 minmax = new Hashtable<String, float[][]>();
349 AlignmentI alignment = av.getAlignment();
350 for (int i = 0; i < alignment.getHeight(); i++)
352 SequenceI asq = alignment.getSequenceAt(i);
353 SequenceFeature[] features = asq.getSequenceFeatures();
355 if (features == null)
361 while (index < features.length)
363 if (!featuresDisplayed.isRegistered(features[index].getType()))
365 String fgrp = features[index].getFeatureGroup();
368 Boolean groupDisplayed = featureGroups.get(fgrp);
369 if (groupDisplayed == null)
371 groupDisplayed = Boolean.valueOf(newMadeVisible);
372 featureGroups.put(fgrp, groupDisplayed);
374 if (!groupDisplayed.booleanValue())
380 if (!(features[index].begin == 0 && features[index].end == 0))
382 // If beginning and end are 0, the feature is for the whole sequence
383 // and we don't want to render the feature in the normal way
386 && !oldfeatures.contains(features[index].getType()))
388 // this is a new feature type on the alignment. Mark it for
390 featuresDisplayed.setVisible(features[index].getType());
391 setOrder(features[index].getType(), 0);
395 if (!allfeatures.contains(features[index].getType()))
397 allfeatures.add(features[index].getType());
399 if (!Float.isNaN(features[index].score))
401 int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
402 float[][] mm = minmax.get(features[index].getType());
405 mm = new float[][] { null, null };
406 minmax.put(features[index].getType(), mm);
408 if (mm[nonpos] == null)
410 mm[nonpos] = new float[] { features[index].score,
411 features[index].score };
416 if (mm[nonpos][0] > features[index].score)
418 mm[nonpos][0] = features[index].score;
420 if (mm[nonpos][1] < features[index].score)
422 mm[nonpos][1] = features[index].score;
429 updateRenderOrder(allfeatures);
430 findingFeatures = false;
433 protected Boolean firing = Boolean.FALSE;
436 * replaces the current renderOrder with the unordered features in
437 * allfeatures. The ordering of any types in both renderOrder and allfeatures
438 * is preserved, and all new feature types are rendered on top of the existing
439 * types, in the order given by getOrder or the order given in allFeatures.
440 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
441 * eliminate the float storage for computing/recalling the persistent ordering
442 * New Cability: updates min/max for colourscheme range if its dynamic
446 private void updateRenderOrder(List<String> allFeatures)
448 List<String> allfeatures = new ArrayList<String>(allFeatures);
449 String[] oldRender = renderOrder;
450 renderOrder = new String[allfeatures.size()];
451 Object mmrange, fc = null;
452 boolean initOrders = (featureOrder == null);
454 if (oldRender != null && oldRender.length > 0)
456 for (int j = 0; j < oldRender.length; j++)
458 if (oldRender[j] != null)
462 setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
464 if (allfeatures.contains(oldRender[j]))
466 renderOrder[opos++] = oldRender[j]; // existing features always
467 // appear below new features
468 allfeatures.remove(oldRender[j]);
471 mmrange = minmax.get(oldRender[j]);
474 fc = featureColours.get(oldRender[j]);
475 if (fc != null && fc instanceof GraduatedColor
476 && ((GraduatedColor) fc).isAutoScale())
478 ((GraduatedColor) fc).updateBounds(
479 ((float[][]) mmrange)[0][0],
480 ((float[][]) mmrange)[0][1]);
488 if (allfeatures.size() == 0)
490 // no new features - leave order unchanged.
493 int i = allfeatures.size() - 1;
495 boolean sort = false;
496 String[] newf = new String[allfeatures.size()];
497 float[] sortOrder = new float[allfeatures.size()];
498 for (String newfeat : allfeatures)
503 // update from new features minmax if necessary
504 mmrange = minmax.get(newf[i]);
507 fc = featureColours.get(newf[i]);
508 if (fc != null && fc instanceof GraduatedColor
509 && ((GraduatedColor) fc).isAutoScale())
511 ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
512 ((float[][]) mmrange)[0][1]);
516 if (initOrders || !featureOrder.containsKey(newf[i]))
518 int denom = initOrders ? allfeatures.size() : featureOrder.size();
519 // new unordered feature - compute persistent ordering at head of
520 // existing features.
521 setOrder(newf[i], i / (float) denom);
523 // set order from newly found feature from persisted ordering.
524 sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
527 // only sort if we need to
528 sort = sort || sortOrder[i] > sortOrder[i + 1];
532 if (iSize > 1 && sort)
534 jalview.util.QuickSort.sort(sortOrder, newf);
537 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
541 * get a feature style object for the given type string. Creates a
542 * java.awt.Color for a featureType with no existing colourscheme. TODO:
543 * replace return type with object implementing standard abstract colour/style
547 * @return java.awt.Color or GraduatedColor
550 public Object getFeatureStyle(String featureType)
552 Object fc = featureColours.get(featureType);
555 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
556 Color col = ucs.createColourFromName(featureType);
557 featureColours.put(featureType, fc = col);
563 * calculate the render colour for a specific feature using current feature
567 * @return render colour for the given feature
569 public Color getColour(SequenceFeature feature)
571 Object fc = getFeatureStyle(feature.getType());
572 if (fc instanceof Color)
578 if (fc instanceof GraduatedColor)
580 return ((GraduatedColor) fc).findColor(feature);
583 throw new Error("Implementation Error: Unrecognised render object "
584 + fc.getClass() + " for features of type " + feature.getType());
587 protected boolean showFeature(SequenceFeature sequenceFeature)
589 Object fc = getFeatureStyle(sequenceFeature.type);
590 if (fc instanceof GraduatedColor)
592 return ((GraduatedColor) fc).isColored(sequenceFeature);
600 protected boolean showFeatureOfType(String type)
602 return av.getFeaturesDisplayed().isVisible(type);
606 public void setColour(String featureType, Object col)
609 // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
610 // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
611 // Object c = featureColours.get(featureType);
612 // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
613 // !((GraduatedColor)c).getMaxColor().equals(_col)))
614 if (col instanceof FeatureColourI)
616 if (((FeatureColourI) col).isGraduatedColour())
618 col = new GraduatedColor((FeatureColourI) col);
622 col = ((FeatureColourI) col).getColour();
625 featureColours.put(featureType, col);
628 public void setTransparency(float value)
630 transparency = value;
633 public float getTransparency()
638 Map featureOrder = null;
641 * analogous to colour - store a normalized ordering for all feature types in
642 * this rendering context.
645 * Feature type string
647 * normalized priority - 0 means always appears on top, 1 means
650 public float setOrder(String type, float position)
652 if (featureOrder == null)
654 featureOrder = new Hashtable();
656 featureOrder.put(type, new Float(position));
661 * get the global priority (0 (top) to 1 (bottom))
664 * @return [0,1] or -1 for a type without a priority
666 public float getOrder(String type)
668 if (featureOrder != null)
670 if (featureOrder.containsKey(type))
672 return ((Float) featureOrder.get(type)).floatValue();
679 public Map<String, Object> getFeatureColours()
681 return featureColours;
685 * Replace current ordering with new ordering
688 * { String(Type), Colour(Type), Boolean(Displayed) }
689 * @return true if any visible features have been reordered, else false
691 public boolean setFeaturePriority(Object[][] data)
693 return setFeaturePriority(data, true);
697 * Sets the priority order for features
700 * { String(Type), Colour(Type), Boolean(Displayed) }
702 * when true current featureDisplay list will be cleared
703 * @return true if any visible features have been reordered or recoloured,
704 * else false (i.e. no need to repaint)
706 public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
709 * note visible feature ordering and colours before update
711 List<String> visibleFeatures = getDisplayedFeatureTypes();
712 Map<String, Object> visibleColours = new HashMap<String, Object>(
713 getFeatureColours());
715 FeaturesDisplayedI av_featuresdisplayed = null;
718 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
720 av.getFeaturesDisplayed().clear();
724 av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
729 av_featuresdisplayed = av.getFeaturesDisplayed();
735 // The feature table will display high priority
736 // features at the top, but these are the ones
737 // we need to render last, so invert the data
738 renderOrder = new String[data.length];
742 for (int i = 0; i < data.length; i++)
744 String type = data[i][0].toString();
745 setColour(type, data[i][1]); // todo : typesafety - feature color
747 if (((Boolean) data[i][2]).booleanValue())
749 av_featuresdisplayed.setVisible(type);
752 renderOrder[data.length - i - 1] = type;
757 * get the new visible ordering and return true if it has changed
758 * order or any colour has changed
760 List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes();
761 if (!visibleFeatures.equals(reorderedVisibleFeatures))
764 * the list of ordered visible features has changed
770 * return true if any feature colour has changed
772 for (String feature : visibleFeatures)
774 if (visibleColours.get(feature) != getFeatureStyle(feature))
784 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
786 public void addPropertyChangeListener(PropertyChangeListener listener)
788 changeSupport.addPropertyChangeListener(listener);
793 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
795 public void removePropertyChangeListener(PropertyChangeListener listener)
797 changeSupport.removePropertyChangeListener(listener);
800 public Set<String> getAllFeatureColours()
802 return featureColours.keySet();
805 public void clearRenderOrder()
810 public boolean hasRenderOrder()
812 return renderOrder != null;
816 * Returns feature types in ordering of rendering, where last means on top
818 public List<String> getRenderOrder()
820 if (renderOrder == null)
822 return Arrays.asList(new String[] {});
824 return Arrays.asList(renderOrder);
827 public int getFeatureGroupsSize()
829 return featureGroups != null ? 0 : featureGroups.size();
833 public List<String> getFeatureGroups()
835 // conflict between applet and desktop - featureGroups returns the map in
836 // the desktop featureRenderer
837 return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
838 .asList(featureGroups.keySet().toArray(new String[0]));
841 public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
843 if (featureGroups == null)
845 // then an exception happens next..
847 if (featureGroups.containsKey(group))
849 return featureGroups.get(group).booleanValue();
851 if (newGroupsVisible)
853 featureGroups.put(group, new Boolean(true));
860 * get visible or invisible groups
863 * true to return visible groups, false to return hidden ones.
864 * @return list of groups
867 public List getGroups(boolean visible)
869 if (featureGroups != null)
871 ArrayList gp = new ArrayList();
873 for (Object grp : featureGroups.keySet())
875 Boolean state = featureGroups.get(grp);
876 if (state.booleanValue() == visible)
887 public void setGroupVisibility(String group, boolean visible)
889 featureGroups.put(group, new Boolean(visible));
893 public void setGroupVisibility(List<String> toset, boolean visible)
895 if (toset != null && toset.size() > 0 && featureGroups != null)
897 boolean rdrw = false;
898 for (String gst : toset)
900 Boolean st = featureGroups.get(gst);
901 featureGroups.put(gst, new Boolean(visible));
904 rdrw = rdrw || (visible != st.booleanValue());
909 // set local flag indicating redraw needed ?
915 public Hashtable getDisplayedFeatureCols()
917 Hashtable fcols = new Hashtable();
918 if (getViewport().getFeaturesDisplayed() == null)
922 Iterator<String> en = getViewport().getFeaturesDisplayed()
923 .getVisibleFeatures();
926 String col = en.next();
927 fcols.put(col, featureColours.get(col));
933 public FeaturesDisplayedI getFeaturesDisplayed()
935 return av.getFeaturesDisplayed();
939 * Returns a (possibly empty) list of visible feature types, in render order
943 public List<String> getDisplayedFeatureTypes()
945 List<String> typ = getRenderOrder();
946 List<String> displayed = new ArrayList<String>();
947 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
948 if (feature_disp != null)
950 synchronized (feature_disp)
952 for (String type : typ)
954 if (feature_disp.isVisible(type))
965 public List<String> getDisplayedFeatureGroups()
967 List<String> _gps = new ArrayList<String>();
968 boolean valid = false;
969 for (String gp : getFeatureGroups())
971 if (checkGroupVisibility(gp, false))
982 // gps = new String[_gps.size()];
983 // _gps.toArray(gps);