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[] { featureType }));
124 fdi.setVisible(featureType);
128 public void setAllVisible(List<String> featureTypes)
130 FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
133 av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
135 List<String> nft = new ArrayList<String>();
136 for (String featureType : featureTypes)
138 if (!fdi.isRegistered(featureType))
140 nft.add(featureType);
145 pushFeatureType(nft);
147 fdi.setAllVisible(featureTypes);
151 * push a set of new types onto the render order stack. Note - this is a
152 * direct mechanism rather than the one employed in updateRenderOrder
156 private void pushFeatureType(List<String> types)
159 int ts = types.size();
160 String neworder[] = new String[(renderOrder == null ? 0
161 : renderOrder.length) + ts];
162 types.toArray(neworder);
163 if (renderOrder != null)
165 System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
166 System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
168 renderOrder = neworder;
171 protected Hashtable minmax = new Hashtable();
173 public Hashtable getMinMax()
179 * normalise a score against the max/min bounds for the feature type.
181 * @param sequenceFeature
182 * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
185 protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
187 float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
188 final byte[] r = new byte[] { 0, (byte) 255 };
191 if (r[0] != 0 || mm[0] < 0.0)
194 r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
198 r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
204 boolean newFeatureAdded = false;
206 boolean findingFeatures = false;
208 protected boolean updateFeatures()
210 if (av.getFeaturesDisplayed() == null || renderOrder == null
214 if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
219 // TODO: decide if we should check for the visible feature count first
224 * search the alignment for all new features, give them a colour and display
225 * them. Then fires a PropertyChangeEvent on the changeSupport object.
228 protected void findAllFeatures()
230 synchronized (firing)
232 if (firing.equals(Boolean.FALSE))
234 firing = Boolean.TRUE;
235 findAllFeatures(true); // add all new features as visible
236 changeSupport.firePropertyChange("changeSupport", null, null);
237 firing = Boolean.FALSE;
243 public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
245 ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
246 SequenceFeature[] features = sequence.getSequenceFeatures();
248 if (features != null)
250 for (int i = 0; i < features.length; i++)
252 if (!av.areFeaturesDisplayed()
253 || !av.getFeaturesDisplayed().isVisible(
254 features[i].getType()))
259 if (features[i].featureGroup != null
260 && featureGroups != null
261 && featureGroups.containsKey(features[i].featureGroup)
262 && !featureGroups.get(features[i].featureGroup)
268 if ((features[i].getBegin() <= res)
269 && (features[i].getEnd() >= res))
271 tmp.add(features[i]);
279 * Searches alignment for all features and updates colours
281 * @param newMadeVisible
282 * if true newly added feature types will be rendered immediatly
283 * TODO: check to see if this method should actually be proxied so
284 * repaint events can be propagated by the renderer code
287 public synchronized void findAllFeatures(boolean newMadeVisible)
289 newFeatureAdded = false;
293 newFeatureAdded = true;
297 findingFeatures = true;
298 if (av.getFeaturesDisplayed() == null)
300 av.setFeaturesDisplayed(new FeaturesDisplayed());
302 FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
304 ArrayList<String> allfeatures = new ArrayList<String>();
305 ArrayList<String> oldfeatures = new ArrayList<String>();
306 if (renderOrder != null)
308 for (int i = 0; i < renderOrder.length; i++)
310 if (renderOrder[i] != null)
312 oldfeatures.add(renderOrder[i]);
318 minmax = new Hashtable();
320 AlignmentI alignment = av.getAlignment();
321 for (int i = 0; i < alignment.getHeight(); i++)
323 SequenceI asq = alignment.getSequenceAt(i);
324 SequenceFeature[] features = asq.getSequenceFeatures();
326 if (features == null)
332 while (index < features.length)
334 if (!featuresDisplayed.isRegistered(features[index].getType()))
336 String fgrp = features[index].getFeatureGroup();
339 Boolean groupDisplayed = featureGroups.get(fgrp);
340 if (groupDisplayed == null)
342 groupDisplayed = Boolean.valueOf(newMadeVisible);
343 featureGroups.put(fgrp, groupDisplayed);
345 if (!groupDisplayed.booleanValue())
351 if (!(features[index].begin == 0 && features[index].end == 0))
353 // If beginning and end are 0, the feature is for the whole sequence
354 // and we don't want to render the feature in the normal way
357 && !oldfeatures.contains(features[index].getType()))
359 // this is a new feature type on the alignment. Mark it for
361 featuresDisplayed.setVisible(features[index].getType());
362 setOrder(features[index].getType(), 0);
366 if (!allfeatures.contains(features[index].getType()))
368 allfeatures.add(features[index].getType());
370 if (!Float.isNaN(features[index].score))
372 int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
373 float[][] mm = (float[][]) minmax.get(features[index].getType());
376 mm = new float[][] { null, null };
377 minmax.put(features[index].getType(), mm);
379 if (mm[nonpos] == null)
381 mm[nonpos] = new float[] { features[index].score,
382 features[index].score };
387 if (mm[nonpos][0] > features[index].score)
389 mm[nonpos][0] = features[index].score;
391 if (mm[nonpos][1] < features[index].score)
393 mm[nonpos][1] = features[index].score;
400 updateRenderOrder(allfeatures);
401 findingFeatures = false;
404 protected Boolean firing = Boolean.FALSE;
407 * replaces the current renderOrder with the unordered features in
408 * allfeatures. The ordering of any types in both renderOrder and allfeatures
409 * is preserved, and all new feature types are rendered on top of the existing
410 * types, in the order given by getOrder or the order given in allFeatures.
411 * Note. this operates directly on the featureOrder hash for efficiency. TODO:
412 * eliminate the float storage for computing/recalling the persistent ordering
413 * New Cability: updates min/max for colourscheme range if its dynamic
417 private void updateRenderOrder(List<String> allFeatures)
419 List<String> allfeatures = new ArrayList<String>(allFeatures);
420 String[] oldRender = renderOrder;
421 renderOrder = new String[allfeatures.size()];
422 Object mmrange, fc = null;
423 boolean initOrders = (featureOrder == null);
425 if (oldRender != null && oldRender.length > 0)
427 for (int j = 0; j < oldRender.length; j++)
429 if (oldRender[j] != null)
433 setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
435 if (allfeatures.contains(oldRender[j]))
437 renderOrder[opos++] = oldRender[j]; // existing features always
438 // appear below new features
439 allfeatures.remove(oldRender[j]);
442 mmrange = minmax.get(oldRender[j]);
445 fc = featureColours.get(oldRender[j]);
446 if (fc != null && fc instanceof GraduatedColor
447 && ((GraduatedColor) fc).isAutoScale())
449 ((GraduatedColor) fc).updateBounds(
450 ((float[][]) mmrange)[0][0],
451 ((float[][]) mmrange)[0][1]);
459 if (allfeatures.size() == 0)
461 // no new features - leave order unchanged.
464 int i = allfeatures.size() - 1;
466 boolean sort = false;
467 String[] newf = new String[allfeatures.size()];
468 float[] sortOrder = new float[allfeatures.size()];
469 for (String newfeat : allfeatures)
474 // update from new features minmax if necessary
475 mmrange = minmax.get(newf[i]);
478 fc = featureColours.get(newf[i]);
479 if (fc != null && fc instanceof GraduatedColor
480 && ((GraduatedColor) fc).isAutoScale())
482 ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
483 ((float[][]) mmrange)[0][1]);
487 if (initOrders || !featureOrder.containsKey(newf[i]))
489 int denom = initOrders ? allfeatures.size() : featureOrder.size();
490 // new unordered feature - compute persistent ordering at head of
491 // existing features.
492 setOrder(newf[i], i / (float) denom);
494 // set order from newly found feature from persisted ordering.
495 sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
498 // only sort if we need to
499 sort = sort || sortOrder[i] > sortOrder[i + 1];
503 if (iSize > 1 && sort)
505 jalview.util.QuickSort.sort(sortOrder, newf);
508 System.arraycopy(newf, 0, renderOrder, opos, newf.length);
512 * get a feature style object for the given type string. Creates a
513 * java.awt.Color for a featureType with no existing colourscheme. TODO:
514 * replace return type with object implementing standard abstract colour/style
518 * @return java.awt.Color or GraduatedColor
520 public Object getFeatureStyle(String featureType)
522 Object fc = featureColours.get(featureType);
525 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
526 Color col = ucs.createColourFromName(featureType);
527 featureColours.put(featureType, fc = col);
533 * return a nominal colour for this feature
536 * @return standard color, or maximum colour for graduated colourscheme
538 public Color getColour(String featureType)
540 Object fc = getFeatureStyle(featureType);
542 if (fc instanceof Color)
548 if (fc instanceof GraduatedColor)
550 return ((GraduatedColor) fc).getMaxColor();
553 throw new Error("Implementation Error: Unrecognised render object "
554 + fc.getClass() + " for features of type " + featureType);
558 * calculate the render colour for a specific feature using current feature
562 * @return render colour for the given feature
564 public Color getColour(SequenceFeature feature)
566 Object fc = getFeatureStyle(feature.getType());
567 if (fc instanceof Color)
573 if (fc instanceof GraduatedColor)
575 return ((GraduatedColor) fc).findColor(feature);
578 throw new Error("Implementation Error: Unrecognised render object "
579 + fc.getClass() + " for features of type " + feature.getType());
582 protected boolean showFeature(SequenceFeature sequenceFeature)
584 Object fc = getFeatureStyle(sequenceFeature.type);
585 if (fc instanceof GraduatedColor)
587 return ((GraduatedColor) fc).isColored(sequenceFeature);
595 protected boolean showFeatureOfType(String type)
597 return av.getFeaturesDisplayed().isVisible(type);
600 public void setColour(String featureType, Object col)
603 // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
604 // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
605 // Object c = featureColours.get(featureType);
606 // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
607 // !((GraduatedColor)c).getMaxColor().equals(_col)))
609 featureColours.put(featureType, col);
613 public void setTransparency(float value)
615 transparency = value;
618 public float getTransparency()
623 Map featureOrder = null;
626 * analogous to colour - store a normalized ordering for all feature types in
627 * this rendering context.
630 * Feature type string
632 * normalized priority - 0 means always appears on top, 1 means
635 public float setOrder(String type, float position)
637 if (featureOrder == null)
639 featureOrder = new Hashtable();
641 featureOrder.put(type, new Float(position));
646 * get the global priority (0 (top) to 1 (bottom))
649 * @return [0,1] or -1 for a type without a priority
651 public float getOrder(String type)
653 if (featureOrder != null)
655 if (featureOrder.containsKey(type))
657 return ((Float) featureOrder.get(type)).floatValue();
664 public Map<String, Object> getFeatureColours()
666 return new ConcurrentHashMap<String, Object>(featureColours);
670 * Replace current ordering with new ordering
673 * { String(Type), Colour(Type), Boolean(Displayed) }
675 public void setFeaturePriority(Object[][] data)
677 setFeaturePriority(data, true);
683 * { String(Type), Colour(Type), Boolean(Displayed) }
685 * when true current featureDisplay list will be cleared
687 public void setFeaturePriority(Object[][] data, boolean visibleNew)
689 FeaturesDisplayedI av_featuresdisplayed = null;
692 if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
694 av.getFeaturesDisplayed().clear();
698 av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
703 av_featuresdisplayed = av.getFeaturesDisplayed();
709 // The feature table will display high priority
710 // features at the top, but theses are the ones
711 // we need to render last, so invert the data
712 renderOrder = new String[data.length];
716 for (int i = 0; i < data.length; i++)
718 String type = data[i][0].toString();
719 setColour(type, data[i][1]); // todo : typesafety - feature color
721 if (((Boolean) data[i][2]).booleanValue())
723 av_featuresdisplayed.setVisible(type);
726 renderOrder[data.length - i - 1] = type;
734 * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
736 public void addPropertyChangeListener(PropertyChangeListener listener)
738 changeSupport.addPropertyChangeListener(listener);
743 * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
745 public void removePropertyChangeListener(PropertyChangeListener listener)
747 changeSupport.removePropertyChangeListener(listener);
750 public Set getAllFeatureColours()
752 return featureColours.keySet();
755 public void clearRenderOrder()
760 public boolean hasRenderOrder()
762 return renderOrder != null;
765 public List<String> getRenderOrder()
767 if (renderOrder == null)
769 return Arrays.asList(new String[] {});
771 return Arrays.asList(renderOrder);
774 public int getFeatureGroupsSize()
776 return featureGroups != null ? 0 : featureGroups.size();
780 public List<String> getFeatureGroups()
782 // conflict between applet and desktop - featureGroups returns the map in
783 // the desktop featureRenderer
784 return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
785 .asList(featureGroups.keySet().toArray(new String[0]));
788 public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
790 if (featureGroups == null)
792 // then an exception happens next..
794 if (featureGroups.containsKey(group))
796 return featureGroups.get(group).booleanValue();
798 if (newGroupsVisible)
800 featureGroups.put(group, new Boolean(true));
807 * get visible or invisible groups
810 * true to return visible groups, false to return hidden ones.
811 * @return list of groups
814 public List getGroups(boolean visible)
816 if (featureGroups != null)
818 ArrayList gp = new ArrayList();
820 for (Object grp : featureGroups.keySet())
822 Boolean state = featureGroups.get(grp);
823 if (state.booleanValue() == visible)
834 public void setGroupVisibility(String group, boolean visible)
836 featureGroups.put(group, new Boolean(visible));
840 public void setGroupVisibility(List<String> toset, boolean visible)
842 if (toset != null && toset.size() > 0 && featureGroups != null)
844 boolean rdrw = false;
845 for (String gst : toset)
847 Boolean st = featureGroups.get(gst);
848 featureGroups.put(gst, new Boolean(visible));
851 rdrw = rdrw || (visible != st.booleanValue());
856 // set local flag indicating redraw needed ?
862 public Hashtable getDisplayedFeatureCols()
864 Hashtable fcols = new Hashtable();
865 if (getViewport().getFeaturesDisplayed() == null)
869 Iterator<String> en = getViewport().getFeaturesDisplayed()
870 .getVisibleFeatures();
873 String col = en.next();
874 fcols.put(col, getColour(col));
880 public FeaturesDisplayedI getFeaturesDisplayed()
882 return av.getFeaturesDisplayed();
886 public String[] getDisplayedFeatureTypes()
889 typ = getRenderOrder().toArray(new String[0]);
890 FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
891 if (feature_disp != null)
893 synchronized (feature_disp)
895 for (int i = 0; i < typ.length; i++)
897 if (!feature_disp.isVisible(typ[i]))
908 public String[] getDisplayedFeatureGroups()
911 ArrayList<String> _gps = new ArrayList<String>();
912 Iterator en = getFeatureGroups().iterator();
914 boolean valid = false;
917 String gp = (String) en.next();
918 if (checkGroupVisibility(gp, false))
929 gps = new String[_gps.size()];