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.Enumeration;
18 import java.util.Hashtable;
19 import java.util.Iterator;
20 import java.util.List;
23 import java.util.Vector;
24 import java.util.concurrent.ConcurrentHashMap;
26 public abstract class FeatureRendererModel implements
27 jalview.api.FeatureRenderer
31 * global transparency for feature
33 protected float transparency = 1.0f;
35 protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
37 protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
39 protected Object currentColour;
41 protected String[] renderOrder;
43 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
46 protected AlignmentViewport av;
48 public AlignViewportI getViewport()
53 public FeatureRendererSettings getSettings()
55 return new FeatureRendererSettings(this);
58 public void transferSettings(FeatureRendererSettings fr)
60 this.renderOrder = fr.renderOrder;
61 this.featureGroups = fr.featureGroups;
62 this.featureColours = fr.featureColours;
63 this.transparency = fr.transparency;
64 this.featureOrder = fr.featureOrder;
68 * update from another feature renderer
73 public void transferSettings(jalview.api.FeatureRenderer _fr)
75 FeatureRenderer fr = (FeatureRenderer) _fr;
76 FeatureRendererSettings frs = new FeatureRendererSettings(fr);
77 this.renderOrder = frs.renderOrder;
78 this.featureGroups = frs.featureGroups;
79 this.featureColours = frs.featureColours;
80 this.transparency = frs.transparency;
81 this.featureOrder = frs.featureOrder;
82 if (av != null && av != fr.getViewport())
84 // copy over the displayed feature settings
85 if (_fr.getFeaturesDisplayed() != null)
87 FeaturesDisplayedI fd = getFeaturesDisplayed();
90 setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
97 java.util.Iterator<String> fdisp = _fr.getFeaturesDisplayed()
98 .getVisibleFeatures();
99 while (fdisp.hasNext())
101 fd.setVisible(fdisp.next());
109 public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
111 av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
115 public void setVisible(String featureType)
117 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
120 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
122 if (!fdi.isRegistered(featureType))
124 pushFeatureType(Arrays.asList(new String[]
127 fdi.setVisible(featureType);
131 public void setAllVisible(List<String> featureTypes)
133 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
136 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
138 List<String> nft = new ArrayList<String>();
139 for (String featureType : featureTypes)
141 if (!fdi.isRegistered(featureType))
143 nft.add(featureType);
148 pushFeatureType(nft);
150 fdi.setAllVisible(featureTypes);
154 * push a set of new types onto the render order stack. Note - this is a
155 * direct mechanism rather than the one employed in updateRenderOrder
159 private void pushFeatureType(List<String> types)
162 int ts = types.size();
163 String neworder[] = new String[(renderOrder == null ? 0
164 : renderOrder.length) + ts];
165 types.toArray(neworder);
166 if (renderOrder != null)
168 System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
169 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
171 renderOrder = neworder;
174 protected Hashtable minmax = new Hashtable();
176 public Hashtable getMinMax()
182 * normalise a score against the max/min bounds for the feature type.
184 * @param sequenceFeature
185 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
188 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
190 float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
191 final byte[] r = new byte[]
195 if (r[0] != 0 || mm[0] < 0.0)
198 r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
202 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
208 boolean newFeatureAdded = false;
210 boolean findingFeatures = false;
212 protected boolean updateFeatures()
214 if (av.getFeaturesDisplayed() == null || renderOrder == null
218 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
223 // TODO: decide if we should check for the visible feature count first
228 * search the alignment for all new features, give them a colour and display
229 * them. Then fires a PropertyChangeEvent on the changeSupport object.
232 protected void findAllFeatures()
234 synchronized (firing)
236 if (firing.equals(Boolean.FALSE))
238 firing = Boolean.TRUE;
239 findAllFeatures(true); // add all new features as visible
240 changeSupport.firePropertyChange("changeSupport", null, null);
241 firing = Boolean.FALSE;
247 public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
249 ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
250 SequenceFeature[] features = sequence.getSequenceFeatures();
251 if (features != null)
253 for (int i = 0; i < features.length; i++)
255 if (av.areFeaturesDisplayed()
256 || !av.getFeaturesDisplayed().isVisible(
257 features[i].getType()))
262 if (features[i].featureGroup != null
263 && featureGroups != null
264 && featureGroups.containsKey(features[i].featureGroup)
265 && !((Boolean) featureGroups.get(features[i].featureGroup))
269 if ((features[i].getBegin() <= res)
270 && (features[i].getEnd() >= res))
272 tmp.add(features[i]);
280 * Searches alignment for all features and updates colours
282 * @param newMadeVisible
283 * if true newly added feature types will be rendered immediatly
284 * TODO: check to see if this method should actually be proxied so
285 * repaint events can be propagated by the renderer code
288 public synchronized void findAllFeatures(boolean newMadeVisible)
290 newFeatureAdded = false;
294 newFeatureAdded = true;
298 findingFeatures = true;
299 if (av.getFeaturesDisplayed() == null)
301 av.setFeaturesDisplayed(new FeaturesDisplayed());
303 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
305 ArrayList<String> allfeatures = new ArrayList<String>();
306 ArrayList<String> oldfeatures = new ArrayList<String>();
307 if (renderOrder != null)
309 for (int i = 0; i < renderOrder.length; i++)
311 if (renderOrder[i] != null)
313 oldfeatures.add(renderOrder[i]);
319 minmax = new Hashtable();
321 AlignmentI alignment = av.getAlignment();
322 for (int i = 0; i < alignment.getHeight(); i++)
324 SequenceI asq = alignment.getSequenceAt(i);
325 SequenceI dasq = asq.getDatasetSequence();
326 SequenceFeature[] features = dasq != null ? dasq
327 .getSequenceFeatures() : asq.getSequenceFeatures();
329 if (features == null)
335 while (index < features.length)
337 if (!featuresDisplayed.isRegistered(features[index].getType()))
339 String fgrp = features[index].getFeatureGroup();
342 Boolean groupDisplayed = featureGroups.get(fgrp);
343 if (groupDisplayed == null)
345 groupDisplayed = Boolean.valueOf(newMadeVisible);
346 featureGroups.put(fgrp, groupDisplayed);
348 if (!((Boolean) groupDisplayed).booleanValue())
354 if (!(features[index].begin == 0 && features[index].end == 0))
356 // If beginning and end are 0, the feature is for the whole sequence
357 // and we don't want to render the feature in the normal way
360 && !oldfeatures.contains(features[index].getType()))
362 // this is a new feature type on the alignment. Mark it for
364 featuresDisplayed.setVisible(features[index].getType());
365 setOrder(features[index].getType(), 0);
369 if (!allfeatures.contains(features[index].getType()))
371 allfeatures.add(features[index].getType());
373 if (features[index].score != Float.NaN)
375 int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
376 float[][] mm = (float[][]) minmax.get(features[index].getType());
381 minmax.put(features[index].getType(), mm);
383 if (mm[nonpos] == null)
385 mm[nonpos] = new float[]
386 { features[index].score, features[index].score };
391 if (mm[nonpos][0] > features[index].score)
393 mm[nonpos][0] = features[index].score;
395 if (mm[nonpos][1] < features[index].score)
397 mm[nonpos][1] = features[index].score;
404 updateRenderOrder(allfeatures);
405 findingFeatures = false;
408 protected Boolean firing = Boolean.FALSE;
411 * replaces the current renderOrder with the unordered features in
412 * allfeatures. The ordering of any types in both renderOrder and allfeatures
413 * is preserved, and all new feature types are rendered on top of the existing
414 * types, in the order given by getOrder or the order given in allFeatures.
415 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
416 * eliminate the float storage for computing/recalling the persistent ordering
417 * New Cability: updates min/max for colourscheme range if its dynamic
421 private void updateRenderOrder(List<String> allFeatures)
423 List<String> allfeatures = new ArrayList<String>(allFeatures);
424 String[] oldRender = renderOrder;
425 renderOrder = new String[allfeatures.size()];
426 Object mmrange, fc = null;
427 boolean initOrders = (featureOrder == null);
429 if (oldRender != null && oldRender.length > 0)
431 for (int j = 0; j < oldRender.length; j++)
433 if (oldRender[j] != null)
437 setOrder(oldRender[j], (1 - (1 + (float) j)
438 / (float) oldRender.length));
440 if (allfeatures.contains(oldRender[j]))
442 renderOrder[opos++] = oldRender[j]; // existing features always
443 // appear below new features
444 allfeatures.remove(oldRender[j]);
447 mmrange = minmax.get(oldRender[j]);
450 fc = featureColours.get(oldRender[j]);
451 if (fc != null && fc instanceof GraduatedColor
452 && ((GraduatedColor) fc).isAutoScale())
454 ((GraduatedColor) fc).updateBounds(
455 ((float[][]) mmrange)[0][0],
456 ((float[][]) mmrange)[0][1]);
464 if (allfeatures.size() == 0)
466 // no new features - leave order unchanged.
469 int i = allfeatures.size() - 1;
471 boolean sort = false;
472 String[] newf = new String[allfeatures.size()];
473 float[] sortOrder = new float[allfeatures.size()];
474 for (String newfeat : allfeatures)
479 // update from new features minmax if necessary
480 mmrange = minmax.get(newf[i]);
483 fc = featureColours.get(newf[i]);
484 if (fc != null && fc instanceof GraduatedColor
485 && ((GraduatedColor) fc).isAutoScale())
487 ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
488 ((float[][]) mmrange)[0][1]);
492 if (initOrders || !featureOrder.containsKey(newf[i]))
494 int denom = initOrders ? allfeatures.size() : featureOrder.size();
495 // new unordered feature - compute persistent ordering at head of
496 // existing features.
497 setOrder(newf[i], i / (float) denom);
499 // set order from newly found feature from persisted ordering.
500 sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
503 // only sort if we need to
504 sort = sort || sortOrder[i] > sortOrder[i + 1];
508 if (iSize > 1 && sort)
510 jalview.util.QuickSort.sort(sortOrder, newf);
513 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
517 * get a feature style object for the given type string. Creates a
518 * java.awt.Color for a featureType with no existing colourscheme. TODO:
519 * replace return type with object implementing standard abstract colour/style
523 * @return java.awt.Color or GraduatedColor
525 public Object getFeatureStyle(String featureType)
527 Object fc = featureColours.get(featureType);
530 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
531 Color col = ucs.createColourFromName(featureType);
532 featureColours.put(featureType, fc = col);
538 * return a nominal colour for this feature
541 * @return standard color, or maximum colour for graduated colourscheme
543 public Color getColour(String featureType)
545 Object fc = getFeatureStyle(featureType);
547 if (fc instanceof Color)
553 if (fc instanceof GraduatedColor)
555 return ((GraduatedColor) fc).getMaxColor();
558 throw new Error("Implementation Error: Unrecognised render object "
559 + fc.getClass() + " for features of type " + featureType);
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);
605 public void setColour(String featureType, Object col)
608 // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
609 // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
610 // Object c = featureColours.get(featureType);
611 // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
612 // !((GraduatedColor)c).getMaxColor().equals(_col)))
614 featureColours.put(featureType, col);
618 public void setTransparency(float value)
620 transparency = value;
623 public float getTransparency()
628 Map featureOrder = null;
631 * analogous to colour - store a normalized ordering for all feature types in
632 * this rendering context.
635 * Feature type string
637 * normalized priority - 0 means always appears on top, 1 means
640 public float setOrder(String type, float position)
642 if (featureOrder == null)
644 featureOrder = new Hashtable();
646 featureOrder.put(type, new Float(position));
651 * get the global priority (0 (top) to 1 (bottom))
654 * @return [0,1] or -1 for a type without a priority
656 public float getOrder(String type)
658 if (featureOrder != null)
660 if (featureOrder.containsKey(type))
662 return ((Float) featureOrder.get(type)).floatValue();
669 public Map getFeatureColours()
671 return new ConcurrentHashMap<>(featureColours);
675 * Replace current ordering with new ordering
678 * { String(Type), Colour(Type), Boolean(Displayed) }
680 public void setFeaturePriority(Object[][] data)
682 setFeaturePriority(data, true);
688 * { String(Type), Colour(Type), Boolean(Displayed) }
690 * when true current featureDisplay list will be cleared
692 public void setFeaturePriority(Object[][] data, boolean visibleNew)
694 FeaturesDisplayedI av_featuresdisplayed = null;
697 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
699 av.getFeaturesDisplayed().clear();
703 av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
708 av_featuresdisplayed = av.getFeaturesDisplayed();
714 // The feature table will display high priority
715 // features at the top, but theses 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, data[i][1]); // todo : typesafety - feature color
726 if (((Boolean) data[i][2]).booleanValue())
728 av_featuresdisplayed.setVisible(type);
731 renderOrder[data.length - i - 1] = type;
739 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
741 public void addPropertyChangeListener(PropertyChangeListener listener)
743 changeSupport.addPropertyChangeListener(listener);
748 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
750 public void removePropertyChangeListener(PropertyChangeListener listener)
752 changeSupport.removePropertyChangeListener(listener);
755 public Set getAllFeatureColours()
757 return featureColours.keySet();
760 public void clearRenderOrder()
765 public boolean hasRenderOrder()
767 return renderOrder != null;
770 public List<String> getRenderOrder()
772 if (renderOrder == null)
774 return Arrays.asList(new String[]
777 return Arrays.asList(renderOrder);
780 public int getFeatureGroupsSize()
782 return featureGroups != null ? 0 : featureGroups.size();
786 public List<String> getFeatureGroups()
788 // conflict between applet and desktop - featureGroups returns the map in
789 // the desktop featureRenderer
790 return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
791 .asList(featureGroups.keySet().toArray(new String[0]));
794 public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
796 if (featureGroups == null)
798 // then an exception happens next..
800 if (featureGroups.containsKey(group))
802 return ((Boolean) featureGroups.get(group)).booleanValue();
804 if (newGroupsVisible)
806 featureGroups.put(group, new Boolean(true));
813 * get visible or invisible groups
816 * true to return visible groups, false to return hidden ones.
817 * @return list of groups
820 public List getGroups(boolean visible)
822 if (featureGroups != null)
824 ArrayList gp = new ArrayList();
826 for (Object grp : featureGroups.keySet())
828 Boolean state = (Boolean) featureGroups.get(grp);
829 if (state.booleanValue() == visible)
840 public void setGroupVisibility(String group, boolean visible)
842 featureGroups.put(group, new Boolean(visible));
846 public void setGroupVisibility(List<String> toset, boolean visible)
848 if (toset != null && toset.size() > 0 && featureGroups != null)
850 boolean rdrw = false;
851 for (String gst : toset)
853 Boolean st = featureGroups.get(gst);
854 featureGroups.put(gst, new Boolean(visible));
857 rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
862 // set local flag indicating redraw needed ?
868 public Hashtable getDisplayedFeatureCols()
870 Hashtable fcols = new Hashtable();
871 if (getViewport().getFeaturesDisplayed() == null)
875 Iterator<String> en = getViewport().getFeaturesDisplayed()
876 .getVisibleFeatures();
879 String col = en.next();
880 fcols.put(col, getColour(col));
886 public FeaturesDisplayedI getFeaturesDisplayed()
888 return av.getFeaturesDisplayed();
892 public String[] getDisplayedFeatureTypes()
895 typ = getRenderOrder().toArray(new String[0]);
896 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
897 if (feature_disp != null)
899 synchronized (feature_disp)
901 for (int i = 0; i < typ.length; i++)
903 if (feature_disp.isVisible(typ[i]))
914 public String[] getDisplayedFeatureGroups()
917 ArrayList<String> _gps = new ArrayList<String>();
918 Iterator en = getFeatureGroups().iterator();
920 boolean valid = false;
923 String gp = (String) en.next();
924 if (checkGroupVisibility(gp, false))
935 gps = new String[_gps.size()];