1 package jalview.viewmodel.seqfeatures;
3 import jalview.api.AlignViewportI;
4 import jalview.api.FeaturesDisplayedI;
5 import jalview.datamodel.AlignmentI;
6 import jalview.datamodel.SequenceFeature;
7 import jalview.datamodel.SequenceI;
8 import jalview.renderer.seqfeatures.FeatureRenderer;
9 import jalview.schemes.GraduatedColor;
10 import jalview.viewmodel.AlignmentViewport;
12 import java.awt.Color;
13 import java.beans.PropertyChangeListener;
14 import java.beans.PropertyChangeSupport;
15 import java.util.ArrayList;
16 import java.util.Arrays;
17 import java.util.Hashtable;
18 import java.util.Iterator;
19 import java.util.List;
22 import java.util.concurrent.ConcurrentHashMap;
24 public abstract class FeatureRendererModel implements
25 jalview.api.FeatureRenderer
29 * global transparency for feature
31 protected float transparency = 1.0f;
33 protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
35 protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
37 protected Object currentColour;
39 protected String[] renderOrder;
41 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
44 protected AlignmentViewport av;
46 public AlignViewportI getViewport()
51 public FeatureRendererSettings getSettings()
53 return new FeatureRendererSettings(this);
56 public void transferSettings(FeatureRendererSettings fr)
58 this.renderOrder = fr.renderOrder;
59 this.featureGroups = fr.featureGroups;
60 this.featureColours = fr.featureColours;
61 this.transparency = fr.transparency;
62 this.featureOrder = fr.featureOrder;
66 * update from another feature renderer
71 public void transferSettings(jalview.api.FeatureRenderer _fr)
73 FeatureRenderer fr = (FeatureRenderer) _fr;
74 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
75 this.renderOrder = frs.renderOrder;
76 this.featureGroups = frs.featureGroups;
77 this.featureColours = frs.featureColours;
78 this.transparency = frs.transparency;
79 this.featureOrder = frs.featureOrder;
80 if (av != null && av != fr.getViewport())
82 // copy over the displayed feature settings
83 if (_fr.getFeaturesDisplayed() != null)
85 FeaturesDisplayedI fd = getFeaturesDisplayed();
88 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
95 java.util.Iterator<String> fdisp = _fr.getFeaturesDisplayed()
96 .getVisibleFeatures();
97 while (fdisp.hasNext())
99 fd.setVisible(fdisp.next());
107 public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
109 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
113 public void setVisible(String featureType)
115 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
118 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
120 if (!fdi.isRegistered(featureType))
122 pushFeatureType(Arrays.asList(new String[]
125 fdi.setVisible(featureType);
129 public void setAllVisible(List<String> featureTypes)
131 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
134 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
136 List<String> nft = new ArrayList<String>();
137 for (String featureType : featureTypes)
139 if (!fdi.isRegistered(featureType))
141 nft.add(featureType);
146 pushFeatureType(nft);
148 fdi.setAllVisible(featureTypes);
152 * push a set of new types onto the render order stack. Note - this is a
153 * direct mechanism rather than the one employed in updateRenderOrder
157 private void pushFeatureType(List<String> types)
160 int ts = types.size();
161 String neworder[] = new String[(renderOrder == null ? 0
162 : renderOrder.length) + ts];
163 types.toArray(neworder);
164 if (renderOrder != null)
166 System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
167 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
169 renderOrder = neworder;
172 protected Hashtable minmax = new Hashtable();
174 public Hashtable getMinMax()
180 * normalise a score against the max/min bounds for the feature type.
182 * @param sequenceFeature
183 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
186 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
188 float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
189 final byte[] r = new byte[]
193 if (r[0] != 0 || mm[0] < 0.0)
196 r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
200 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
206 boolean newFeatureAdded = false;
208 boolean findingFeatures = false;
210 protected boolean updateFeatures()
212 if (av.getFeaturesDisplayed() == null || renderOrder == null
216 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
221 // TODO: decide if we should check for the visible feature count first
226 * search the alignment for all new features, give them a colour and display
227 * them. Then fires a PropertyChangeEvent on the changeSupport object.
230 protected void findAllFeatures()
232 synchronized (firing)
234 if (firing.equals(Boolean.FALSE))
236 firing = Boolean.TRUE;
237 findAllFeatures(true); // add all new features as visible
238 changeSupport.firePropertyChange("changeSupport", null, null);
239 firing = Boolean.FALSE;
245 public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
247 ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
248 SequenceFeature[] features = sequence.getSequenceFeatures();
250 while (features == null && sequence.getDatasetSequence() != null)
252 sequence = sequence.getDatasetSequence();
253 features = sequence.getSequenceFeatures();
256 if (features != null)
258 for (int i = 0; i < features.length; i++)
260 if (!av.areFeaturesDisplayed()
261 || !av.getFeaturesDisplayed().isVisible(
262 features[i].getType()))
267 if (features[i].featureGroup != null
268 && featureGroups != null
269 && featureGroups.containsKey(features[i].featureGroup)
270 && !featureGroups.get(features[i].featureGroup)
276 if ((features[i].getBegin() <= res)
277 && (features[i].getEnd() >= res))
279 tmp.add(features[i]);
287 * Searches alignment for all features and updates colours
289 * @param newMadeVisible
290 * if true newly added feature types will be rendered immediatly
291 * TODO: check to see if this method should actually be proxied so
292 * repaint events can be propagated by the renderer code
295 public synchronized void findAllFeatures(boolean newMadeVisible)
297 newFeatureAdded = false;
301 newFeatureAdded = true;
305 findingFeatures = true;
306 if (av.getFeaturesDisplayed() == null)
308 av.setFeaturesDisplayed(new FeaturesDisplayed());
310 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
312 ArrayList<String> allfeatures = new ArrayList<String>();
313 ArrayList<String> oldfeatures = new ArrayList<String>();
314 if (renderOrder != null)
316 for (int i = 0; i < renderOrder.length; i++)
318 if (renderOrder[i] != null)
320 oldfeatures.add(renderOrder[i]);
326 minmax = new Hashtable();
328 AlignmentI alignment = av.getAlignment();
329 for (int i = 0; i < alignment.getHeight(); i++)
331 SequenceI asq = alignment.getSequenceAt(i);
332 SequenceFeature[] features = asq.getSequenceFeatures();
334 if (features == null)
340 while (index < features.length)
342 if (!featuresDisplayed.isRegistered(features[index].getType()))
344 String fgrp = features[index].getFeatureGroup();
347 Boolean groupDisplayed = featureGroups.get(fgrp);
348 if (groupDisplayed == null)
350 groupDisplayed = Boolean.valueOf(newMadeVisible);
351 featureGroups.put(fgrp, groupDisplayed);
353 if (!groupDisplayed.booleanValue())
359 if (!(features[index].begin == 0 && features[index].end == 0))
361 // If beginning and end are 0, the feature is for the whole sequence
362 // and we don't want to render the feature in the normal way
365 && !oldfeatures.contains(features[index].getType()))
367 // this is a new feature type on the alignment. Mark it for
369 featuresDisplayed.setVisible(features[index].getType());
370 setOrder(features[index].getType(), 0);
374 if (!allfeatures.contains(features[index].getType()))
376 allfeatures.add(features[index].getType());
378 if (features[index].score != Float.NaN)
380 int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
381 float[][] mm = (float[][]) minmax.get(features[index].getType());
386 minmax.put(features[index].getType(), mm);
388 if (mm[nonpos] == null)
390 mm[nonpos] = new float[]
391 { features[index].score, features[index].score };
396 if (mm[nonpos][0] > features[index].score)
398 mm[nonpos][0] = features[index].score;
400 if (mm[nonpos][1] < features[index].score)
402 mm[nonpos][1] = features[index].score;
409 updateRenderOrder(allfeatures);
410 findingFeatures = false;
413 protected Boolean firing = Boolean.FALSE;
416 * replaces the current renderOrder with the unordered features in
417 * allfeatures. The ordering of any types in both renderOrder and allfeatures
418 * is preserved, and all new feature types are rendered on top of the existing
419 * types, in the order given by getOrder or the order given in allFeatures.
420 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
421 * eliminate the float storage for computing/recalling the persistent ordering
422 * New Cability: updates min/max for colourscheme range if its dynamic
426 private void updateRenderOrder(List<String> allFeatures)
428 List<String> allfeatures = new ArrayList<String>(allFeatures);
429 String[] oldRender = renderOrder;
430 renderOrder = new String[allfeatures.size()];
431 Object mmrange, fc = null;
432 boolean initOrders = (featureOrder == null);
434 if (oldRender != null && oldRender.length > 0)
436 for (int j = 0; j < oldRender.length; j++)
438 if (oldRender[j] != null)
442 setOrder(oldRender[j], (1 - (1 + (float) j)
443 / oldRender.length));
445 if (allfeatures.contains(oldRender[j]))
447 renderOrder[opos++] = oldRender[j]; // existing features always
448 // appear below new features
449 allfeatures.remove(oldRender[j]);
452 mmrange = minmax.get(oldRender[j]);
455 fc = featureColours.get(oldRender[j]);
456 if (fc != null && fc instanceof GraduatedColor
457 && ((GraduatedColor) fc).isAutoScale())
459 ((GraduatedColor) fc).updateBounds(
460 ((float[][]) mmrange)[0][0],
461 ((float[][]) mmrange)[0][1]);
469 if (allfeatures.size() == 0)
471 // no new features - leave order unchanged.
474 int i = allfeatures.size() - 1;
476 boolean sort = false;
477 String[] newf = new String[allfeatures.size()];
478 float[] sortOrder = new float[allfeatures.size()];
479 for (String newfeat : allfeatures)
484 // update from new features minmax if necessary
485 mmrange = minmax.get(newf[i]);
488 fc = featureColours.get(newf[i]);
489 if (fc != null && fc instanceof GraduatedColor
490 && ((GraduatedColor) fc).isAutoScale())
492 ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
493 ((float[][]) mmrange)[0][1]);
497 if (initOrders || !featureOrder.containsKey(newf[i]))
499 int denom = initOrders ? allfeatures.size() : featureOrder.size();
500 // new unordered feature - compute persistent ordering at head of
501 // existing features.
502 setOrder(newf[i], i / (float) denom);
504 // set order from newly found feature from persisted ordering.
505 sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
508 // only sort if we need to
509 sort = sort || sortOrder[i] > sortOrder[i + 1];
513 if (iSize > 1 && sort)
515 jalview.util.QuickSort.sort(sortOrder, newf);
518 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
522 * get a feature style object for the given type string. Creates a
523 * java.awt.Color for a featureType with no existing colourscheme. TODO:
524 * replace return type with object implementing standard abstract colour/style
528 * @return java.awt.Color or GraduatedColor
530 public Object getFeatureStyle(String featureType)
532 Object fc = featureColours.get(featureType);
535 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
536 Color col = ucs.createColourFromName(featureType);
537 featureColours.put(featureType, fc = col);
543 * return a nominal colour for this feature
546 * @return standard color, or maximum colour for graduated colourscheme
548 public Color getColour(String featureType)
550 Object fc = getFeatureStyle(featureType);
552 if (fc instanceof Color)
558 if (fc instanceof GraduatedColor)
560 return ((GraduatedColor) fc).getMaxColor();
563 throw new Error("Implementation Error: Unrecognised render object "
564 + fc.getClass() + " for features of type " + featureType);
568 * calculate the render colour for a specific feature using current feature
572 * @return render colour for the given feature
574 public Color getColour(SequenceFeature feature)
576 Object fc = getFeatureStyle(feature.getType());
577 if (fc instanceof Color)
583 if (fc instanceof GraduatedColor)
585 return ((GraduatedColor) fc).findColor(feature);
588 throw new Error("Implementation Error: Unrecognised render object "
589 + fc.getClass() + " for features of type " + feature.getType());
592 protected boolean showFeature(SequenceFeature sequenceFeature)
594 Object fc = getFeatureStyle(sequenceFeature.type);
595 if (fc instanceof GraduatedColor)
597 return ((GraduatedColor) fc).isColored(sequenceFeature);
605 protected boolean showFeatureOfType(String type)
607 return av.getFeaturesDisplayed().isVisible(type);
610 public void setColour(String featureType, Object col)
613 // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
614 // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
615 // Object c = featureColours.get(featureType);
616 // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
617 // !((GraduatedColor)c).getMaxColor().equals(_col)))
619 featureColours.put(featureType, col);
623 public void setTransparency(float value)
625 transparency = value;
628 public float getTransparency()
633 Map featureOrder = null;
636 * analogous to colour - store a normalized ordering for all feature types in
637 * this rendering context.
640 * Feature type string
642 * normalized priority - 0 means always appears on top, 1 means
645 public float setOrder(String type, float position)
647 if (featureOrder == null)
649 featureOrder = new Hashtable();
651 featureOrder.put(type, new Float(position));
656 * get the global priority (0 (top) to 1 (bottom))
659 * @return [0,1] or -1 for a type without a priority
661 public float getOrder(String type)
663 if (featureOrder != null)
665 if (featureOrder.containsKey(type))
667 return ((Float) featureOrder.get(type)).floatValue();
674 public Map<String, Object> getFeatureColours()
676 return new ConcurrentHashMap<String, Object>(featureColours);
680 * Replace current ordering with new ordering
683 * { String(Type), Colour(Type), Boolean(Displayed) }
685 public void setFeaturePriority(Object[][] data)
687 setFeaturePriority(data, true);
693 * { String(Type), Colour(Type), Boolean(Displayed) }
695 * when true current featureDisplay list will be cleared
697 public void setFeaturePriority(Object[][] data, boolean visibleNew)
699 FeaturesDisplayedI av_featuresdisplayed = null;
702 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
704 av.getFeaturesDisplayed().clear();
708 av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
713 av_featuresdisplayed = av.getFeaturesDisplayed();
719 // The feature table will display high priority
720 // features at the top, but theses are the ones
721 // we need to render last, so invert the data
722 renderOrder = new String[data.length];
726 for (int i = 0; i < data.length; i++)
728 String type = data[i][0].toString();
729 setColour(type, data[i][1]); // todo : typesafety - feature color
731 if (((Boolean) data[i][2]).booleanValue())
733 av_featuresdisplayed.setVisible(type);
736 renderOrder[data.length - i - 1] = type;
744 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
746 public void addPropertyChangeListener(PropertyChangeListener listener)
748 changeSupport.addPropertyChangeListener(listener);
753 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
755 public void removePropertyChangeListener(PropertyChangeListener listener)
757 changeSupport.removePropertyChangeListener(listener);
760 public Set getAllFeatureColours()
762 return featureColours.keySet();
765 public void clearRenderOrder()
770 public boolean hasRenderOrder()
772 return renderOrder != null;
775 public List<String> getRenderOrder()
777 if (renderOrder == null)
779 return Arrays.asList(new String[]
782 return Arrays.asList(renderOrder);
785 public int getFeatureGroupsSize()
787 return featureGroups != null ? 0 : featureGroups.size();
791 public List<String> getFeatureGroups()
793 // conflict between applet and desktop - featureGroups returns the map in
794 // the desktop featureRenderer
795 return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
796 .asList(featureGroups.keySet().toArray(new String[0]));
799 public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
801 if (featureGroups == null)
803 // then an exception happens next..
805 if (featureGroups.containsKey(group))
807 return featureGroups.get(group).booleanValue();
809 if (newGroupsVisible)
811 featureGroups.put(group, new Boolean(true));
818 * get visible or invisible groups
821 * true to return visible groups, false to return hidden ones.
822 * @return list of groups
825 public List getGroups(boolean visible)
827 if (featureGroups != null)
829 ArrayList gp = new ArrayList();
831 for (Object grp : featureGroups.keySet())
833 Boolean state = featureGroups.get(grp);
834 if (state.booleanValue() == visible)
845 public void setGroupVisibility(String group, boolean visible)
847 featureGroups.put(group, new Boolean(visible));
851 public void setGroupVisibility(List<String> toset, boolean visible)
853 if (toset != null && toset.size() > 0 && featureGroups != null)
855 boolean rdrw = false;
856 for (String gst : toset)
858 Boolean st = featureGroups.get(gst);
859 featureGroups.put(gst, new Boolean(visible));
862 rdrw = rdrw || (visible != st.booleanValue());
867 // set local flag indicating redraw needed ?
873 public Hashtable getDisplayedFeatureCols()
875 Hashtable fcols = new Hashtable();
876 if (getViewport().getFeaturesDisplayed() == null)
880 Iterator<String> en = getViewport().getFeaturesDisplayed()
881 .getVisibleFeatures();
884 String col = en.next();
885 fcols.put(col, getColour(col));
891 public FeaturesDisplayedI getFeaturesDisplayed()
893 return av.getFeaturesDisplayed();
897 public String[] getDisplayedFeatureTypes()
900 typ = getRenderOrder().toArray(new String[0]);
901 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
902 if (feature_disp != null)
904 synchronized (feature_disp)
906 for (int i = 0; i < typ.length; i++)
908 if (!feature_disp.isVisible(typ[i]))
919 public String[] getDisplayedFeatureGroups()
922 ArrayList<String> _gps = new ArrayList<String>();
923 Iterator en = getFeatureGroups().iterator();
925 boolean valid = false;
928 String gp = (String) en.next();
929 if (checkGroupVisibility(gp, false))
940 gps = new String[_gps.size()];