--- /dev/null
+package jalview.viewmodel.seqfeatures;
+
+import jalview.api.AlignViewportI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.GraduatedColor;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+import java.util.concurrent.ConcurrentHashMap;
+
+public abstract class FeatureRendererModel implements
+ jalview.api.FeatureRenderer
+{
+
+ /**
+ * global transparency for feature
+ */
+ protected float transparency = 1.0f;
+
+ protected Map<String, Object> featureColours = new ConcurrentHashMap<String, Object>();
+
+ protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
+
+ protected Object currentColour;
+
+ protected String[] renderOrder;
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ protected AlignmentViewport av;
+
+ public AlignViewportI getViewport()
+ {
+ return av;
+ }
+
+ public FeatureRendererSettings getSettings()
+ {
+ return new FeatureRendererSettings(this);
+ }
+
+ public void transferSettings(FeatureRendererSettings fr)
+ {
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
+ }
+
+ /**
+ * update from another feature renderer
+ *
+ * @param fr
+ * settings to copy
+ */
+ public void transferSettings(jalview.api.FeatureRenderer _fr)
+ {
+ FeatureRenderer fr = (FeatureRenderer) _fr;
+ FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+ this.renderOrder = frs.renderOrder;
+ this.featureGroups = frs.featureGroups;
+ this.featureColours = frs.featureColours;
+ this.transparency = frs.transparency;
+ this.featureOrder = frs.featureOrder;
+ if (av != null && av != fr.getViewport())
+ {
+ // copy over the displayed feature settings
+ if (_fr.getFeaturesDisplayed() != null)
+ {
+ FeaturesDisplayedI fd = getFeaturesDisplayed();
+ if (fd == null)
+ {
+ setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
+ }
+ else
+ {
+ synchronized (fd)
+ {
+ fd.clear();
+ java.util.Iterator<String> fdisp = _fr.getFeaturesDisplayed()
+ .getVisibleFeatures();
+ while (fdisp.hasNext())
+ {
+ fd.setVisible(fdisp.next());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
+ {
+ av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
+ }
+
+ @Override
+ public void setVisible(String featureType)
+ {
+ FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
+ if (fdi == null)
+ {
+ av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ }
+ if (!fdi.isRegistered(featureType))
+ {
+ pushFeatureType(Arrays.asList(new String[]
+ { featureType }));
+ }
+ fdi.setVisible(featureType);
+ }
+
+ @Override
+ public void setAllVisible(List<String> featureTypes)
+ {
+ FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
+ if (fdi == null)
+ {
+ av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
+ }
+ List<String> nft = new ArrayList<String>();
+ for (String featureType : featureTypes)
+ {
+ if (!fdi.isRegistered(featureType))
+ {
+ nft.add(featureType);
+ }
+ }
+ if (nft.size() > 0)
+ {
+ pushFeatureType(nft);
+ }
+ fdi.setAllVisible(featureTypes);
+ }
+
+ /**
+ * push a set of new types onto the render order stack. Note - this is a
+ * direct mechanism rather than the one employed in updateRenderOrder
+ *
+ * @param types
+ */
+ private void pushFeatureType(List<String> types)
+ {
+
+ int ts = types.size();
+ String neworder[] = new String[(renderOrder == null ? 0
+ : renderOrder.length) + ts];
+ types.toArray(neworder);
+ if (renderOrder != null)
+ {
+ System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+ System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
+ }
+ renderOrder = neworder;
+ }
+
+ protected Hashtable minmax = new Hashtable();
+
+ public Hashtable getMinMax()
+ {
+ return minmax;
+ }
+
+ /**
+ * normalise a score against the max/min bounds for the feature type.
+ *
+ * @param sequenceFeature
+ * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
+ * (0-255) value.
+ */
+ protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
+ {
+ float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+ final byte[] r = new byte[]
+ { 0, (byte) 255 };
+ if (mm != null)
+ {
+ if (r[0] != 0 || mm[0] < 0.0)
+ {
+ r[0] = 1;
+ r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ }
+ else
+ {
+ r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
+ }
+ }
+ return r;
+ }
+
+ boolean newFeatureAdded = false;
+
+ boolean findingFeatures = false;
+
+ protected boolean updateFeatures()
+ {
+ if (av.getFeaturesDisplayed() == null || renderOrder == null
+ || newFeatureAdded)
+ {
+ findAllFeatures();
+ if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
+ {
+ return false;
+ }
+ }
+ // TODO: decide if we should check for the visible feature count first
+ return true;
+ }
+
+ /**
+ * search the alignment for all new features, give them a colour and display
+ * them. Then fires a PropertyChangeEvent on the changeSupport object.
+ *
+ */
+ protected void findAllFeatures()
+ {
+ synchronized (firing)
+ {
+ if (firing.equals(Boolean.FALSE))
+ {
+ firing = Boolean.TRUE;
+ findAllFeatures(true); // add all new features as visible
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ firing = Boolean.FALSE;
+ }
+ }
+ }
+
+ @Override
+ public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (av.areFeaturesDisplayed()
+ || !av.getFeaturesDisplayed().isVisible(
+ features[i].getType()))
+ {
+ continue;
+ }
+
+ if (features[i].featureGroup != null
+ && featureGroups != null
+ && featureGroups.containsKey(features[i].featureGroup)
+ && !((Boolean) featureGroups.get(features[i].featureGroup))
+ .booleanValue())
+ continue;
+
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
+ {
+ tmp.add(features[i]);
+ }
+ }
+ }
+ return tmp;
+ }
+
+ /**
+ * Searches alignment for all features and updates colours
+ *
+ * @param newMadeVisible
+ * if true newly added feature types will be rendered immediatly
+ * TODO: check to see if this method should actually be proxied so
+ * repaint events can be propagated by the renderer code
+ */
+ @Override
+ public synchronized void findAllFeatures(boolean newMadeVisible)
+ {
+ newFeatureAdded = false;
+
+ if (findingFeatures)
+ {
+ newFeatureAdded = true;
+ return;
+ }
+
+ findingFeatures = true;
+ if (av.getFeaturesDisplayed() == null)
+ {
+ av.setFeaturesDisplayed(new FeaturesDisplayed());
+ }
+ FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
+
+ ArrayList<String> allfeatures = new ArrayList<String>();
+ ArrayList<String> oldfeatures = new ArrayList<String>();
+ if (renderOrder != null)
+ {
+ for (int i = 0; i < renderOrder.length; i++)
+ {
+ if (renderOrder[i] != null)
+ {
+ oldfeatures.add(renderOrder[i]);
+ }
+ }
+ }
+ if (minmax == null)
+ {
+ minmax = new Hashtable();
+ }
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ SequenceI asq = alignment.getSequenceAt(i);
+ SequenceI dasq = asq.getDatasetSequence();
+ SequenceFeature[] features = dasq != null ? dasq
+ .getSequenceFeatures() : asq.getSequenceFeatures();
+
+ if (features == null)
+ {
+ continue;
+ }
+
+ int index = 0;
+ while (index < features.length)
+ {
+ if (!featuresDisplayed.isRegistered(features[index].getType()))
+ {
+ String fgrp = features[index].getFeatureGroup();
+ if (fgrp != null)
+ {
+ Boolean groupDisplayed = featureGroups.get(fgrp);
+ if (groupDisplayed == null)
+ {
+ groupDisplayed = Boolean.valueOf(newMadeVisible);
+ featureGroups.put(fgrp, groupDisplayed);
+ }
+ if (!((Boolean) groupDisplayed).booleanValue())
+ {
+ index++;
+ continue;
+ }
+ }
+ if (!(features[index].begin == 0 && features[index].end == 0))
+ {
+ // If beginning and end are 0, the feature is for the whole sequence
+ // and we don't want to render the feature in the normal way
+
+ if (newMadeVisible
+ && !oldfeatures.contains(features[index].getType()))
+ {
+ // this is a new feature type on the alignment. Mark it for
+ // display.
+ featuresDisplayed.setVisible(features[index].getType());
+ setOrder(features[index].getType(), 0);
+ }
+ }
+ }
+ if (!allfeatures.contains(features[index].getType()))
+ {
+ allfeatures.add(features[index].getType());
+ }
+ if (features[index].score != Float.NaN)
+ {
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
+ float[][] mm = (float[][]) minmax.get(features[index].getType());
+ if (mm == null)
+ {
+ mm = new float[][]
+ { null, null };
+ minmax.put(features[index].getType(), mm);
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
+ {
+ mm[nonpos][0] = features[index].score;
+ }
+ if (mm[nonpos][1] < features[index].score)
+ {
+ mm[nonpos][1] = features[index].score;
+ }
+ }
+ }
+ index++;
+ }
+ }
+ updateRenderOrder(allfeatures);
+ findingFeatures = false;
+ }
+
+ protected Boolean firing = Boolean.FALSE;
+
+ /**
+ * replaces the current renderOrder with the unordered features in
+ * allfeatures. The ordering of any types in both renderOrder and allfeatures
+ * is preserved, and all new feature types are rendered on top of the existing
+ * types, in the order given by getOrder or the order given in allFeatures.
+ * Note. this operates directly on the featureOrder hash for efficiency. TODO:
+ * eliminate the float storage for computing/recalling the persistent ordering
+ * New Cability: updates min/max for colourscheme range if its dynamic
+ *
+ * @param allFeatures
+ */
+ private void updateRenderOrder(List<String> allFeatures)
+ {
+ List<String> allfeatures = new ArrayList<String>(allFeatures);
+ String[] oldRender = renderOrder;
+ renderOrder = new String[allfeatures.size()];
+ Object mmrange, fc = null;
+ boolean initOrders = (featureOrder == null);
+ int opos = 0;
+ if (oldRender != null && oldRender.length > 0)
+ {
+ for (int j = 0; j < oldRender.length; j++)
+ {
+ if (oldRender[j] != null)
+ {
+ if (initOrders)
+ {
+ setOrder(oldRender[j], (1 - (1 + (float) j)
+ / (float) oldRender.length));
+ }
+ if (allfeatures.contains(oldRender[j]))
+ {
+ renderOrder[opos++] = oldRender[j]; // existing features always
+ // appear below new features
+ allfeatures.remove(oldRender[j]);
+ if (minmax != null)
+ {
+ mmrange = minmax.get(oldRender[j]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(oldRender[j]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(
+ ((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ if (allfeatures.size() == 0)
+ {
+ // no new features - leave order unchanged.
+ return;
+ }
+ int i = allfeatures.size() - 1;
+ int iSize = i;
+ boolean sort = false;
+ String[] newf = new String[allfeatures.size()];
+ float[] sortOrder = new float[allfeatures.size()];
+ for (String newfeat : allfeatures)
+ {
+ newf[i] = newfeat;
+ if (minmax != null)
+ {
+ // update from new features minmax if necessary
+ mmrange = minmax.get(newf[i]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(newf[i]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ if (initOrders || !featureOrder.containsKey(newf[i]))
+ {
+ int denom = initOrders ? allfeatures.size() : featureOrder.size();
+ // new unordered feature - compute persistent ordering at head of
+ // existing features.
+ setOrder(newf[i], i / (float) denom);
+ }
+ // set order from newly found feature from persisted ordering.
+ sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+ if (i < iSize)
+ {
+ // only sort if we need to
+ sort = sort || sortOrder[i] > sortOrder[i + 1];
+ }
+ i--;
+ }
+ if (iSize > 1 && sort)
+ {
+ jalview.util.QuickSort.sort(sortOrder, newf);
+ }
+ sortOrder = null;
+ System.arraycopy(newf, 0, renderOrder, opos, newf.length);
+ }
+
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(String featureType)
+ {
+ Object fc = featureColours.get(featureType);
+ if (fc == null)
+ {
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
+ Color col = ucs.createColourFromName(featureType);
+ featureColours.put(featureType, fc = col);
+ }
+ return fc;
+ }
+
+ /**
+ * return a nominal colour for this feature
+ *
+ * @param featureType
+ * @return standard color, or maximum colour for graduated colourscheme
+ */
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
+ }
+
+ /**
+ * calculate the render colour for a specific feature using current feature
+ * settings.
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
+ }
+
+ protected boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ protected boolean showFeatureOfType(String type)
+ {
+ return av.getFeaturesDisplayed().isVisible(type);
+ }
+
+ public void setColour(String featureType, Object col)
+ {
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_col)))
+ {
+ featureColours.put(featureType, col);
+ }
+ }
+
+ public void setTransparency(float value)
+ {
+ transparency = value;
+ }
+
+ public float getTransparency()
+ {
+ return transparency;
+ }
+
+ Map featureOrder = null;
+
+ /**
+ * analogous to colour - store a normalized ordering for all feature types in
+ * this rendering context.
+ *
+ * @param type
+ * Feature type string
+ * @param position
+ * normalized priority - 0 means always appears on top, 1 means
+ * always last.
+ */
+ public float setOrder(String type, float position)
+ {
+ if (featureOrder == null)
+ {
+ featureOrder = new Hashtable();
+ }
+ featureOrder.put(type, new Float(position));
+ return position;
+ }
+
+ /**
+ * get the global priority (0 (top) to 1 (bottom))
+ *
+ * @param type
+ * @return [0,1] or -1 for a type without a priority
+ */
+ public float getOrder(String type)
+ {
+ if (featureOrder != null)
+ {
+ if (featureOrder.containsKey(type))
+ {
+ return ((Float) featureOrder.get(type)).floatValue();
+ }
+ }
+ return -1;
+ }
+
+ @Override
+ public Map getFeatureColours()
+ {
+ return new ConcurrentHashMap<>(featureColours);
+ }
+
+ /**
+ * Replace current ordering with new ordering
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
+ */
+ public void setFeaturePriority(Object[][] data)
+ {
+ setFeaturePriority(data, true);
+ }
+
+ /**
+ *
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
+ * @param visibleNew
+ * when true current featureDisplay list will be cleared
+ */
+ public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ {
+ FeaturesDisplayedI av_featuresdisplayed = null;
+ if (visibleNew)
+ {
+ if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
+ {
+ av.getFeaturesDisplayed().clear();
+ }
+ else
+ {
+ av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+ }
+ }
+ else
+ {
+ av_featuresdisplayed = av.getFeaturesDisplayed();
+ }
+ if (data == null)
+ {
+ return;
+ }
+ // The feature table will display high priority
+ // features at the top, but theses are the ones
+ // we need to render last, so invert the data
+ renderOrder = new String[data.length];
+
+ if (data.length > 0)
+ {
+ for (int i = 0; i < data.length; i++)
+ {
+ String type = data[i][0].toString();
+ setColour(type, data[i][1]); // todo : typesafety - feature color
+ // interface object
+ if (((Boolean) data[i][2]).booleanValue())
+ {
+ av_featuresdisplayed.setVisible(type);
+ }
+
+ renderOrder[data.length - i - 1] = type;
+ }
+ }
+
+ }
+
+ /**
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * @param listener
+ * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+ */
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ public Set getAllFeatureColours()
+ {
+ return featureColours.keySet();
+ }
+
+ public void clearRenderOrder()
+ {
+ renderOrder = null;
+ }
+
+ public boolean hasRenderOrder()
+ {
+ return renderOrder != null;
+ }
+
+ public List<String> getRenderOrder()
+ {
+ if (renderOrder == null)
+ {
+ return Arrays.asList(new String[]
+ {});
+ }
+ return Arrays.asList(renderOrder);
+ }
+
+ public int getFeatureGroupsSize()
+ {
+ return featureGroups != null ? 0 : featureGroups.size();
+ }
+
+ @Override
+ public List<String> getFeatureGroups()
+ {
+ // conflict between applet and desktop - featureGroups returns the map in
+ // the desktop featureRenderer
+ return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
+ .asList(featureGroups.keySet().toArray(new String[0]));
+ }
+
+ public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+ {
+ if (featureGroups == null)
+ {
+ // then an exception happens next..
+ }
+ if (featureGroups.containsKey(group))
+ {
+ return ((Boolean) featureGroups.get(group)).booleanValue();
+ }
+ if (newGroupsVisible)
+ {
+ featureGroups.put(group, new Boolean(true));
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * get visible or invisible groups
+ *
+ * @param visible
+ * true to return visible groups, false to return hidden ones.
+ * @return list of groups
+ */
+ @Override
+ public List getGroups(boolean visible)
+ {
+ if (featureGroups != null)
+ {
+ ArrayList gp = new ArrayList();
+
+ for (Object grp : featureGroups.keySet())
+ {
+ Boolean state = (Boolean) featureGroups.get(grp);
+ if (state.booleanValue() == visible)
+ {
+ gp.add(grp);
+ }
+ }
+ return gp;
+ }
+ return null;
+ }
+
+ @Override
+ public void setGroupVisibility(String group, boolean visible)
+ {
+ featureGroups.put(group, new Boolean(visible));
+ }
+
+ @Override
+ public void setGroupVisibility(List<String> toset, boolean visible)
+ {
+ if (toset != null && toset.size() > 0 && featureGroups != null)
+ {
+ boolean rdrw = false;
+ for (String gst : toset)
+ {
+ Boolean st = featureGroups.get(gst);
+ featureGroups.put(gst, new Boolean(visible));
+ if (st != null)
+ {
+ rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
+ }
+ }
+ if (rdrw)
+ {
+ // set local flag indicating redraw needed ?
+ }
+ }
+ }
+
+ @Override
+ public Hashtable getDisplayedFeatureCols()
+ {
+ Hashtable fcols = new Hashtable();
+ if (getViewport().getFeaturesDisplayed() == null)
+ {
+ return fcols;
+ }
+ Iterator<String> en = getViewport().getFeaturesDisplayed()
+ .getVisibleFeatures();
+ while (en.hasNext())
+ {
+ String col = en.next();
+ fcols.put(col, getColour(col));
+ }
+ return fcols;
+ }
+
+ @Override
+ public FeaturesDisplayedI getFeaturesDisplayed()
+ {
+ return av.getFeaturesDisplayed();
+ }
+
+ @Override
+ public String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ typ = getRenderOrder().toArray(new String[0]);
+ FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
+ if (feature_disp != null)
+ {
+ synchronized (feature_disp)
+ {
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (feature_disp.isVisible(typ[i]))
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ }
+ return typ;
+ }
+
+ @Override
+ public String[] getDisplayedFeatureGroups()
+ {
+ String[] gps = null;
+ ArrayList<String> _gps = new ArrayList<String>();
+ Iterator en = getFeatureGroups().iterator();
+ int g = 0;
+ boolean valid = false;
+ while (en.hasNext())
+ {
+ String gp = (String) en.next();
+ if (checkGroupVisibility(gp, false))
+ {
+ valid = true;
+ _gps.add(gp);
+ }
+ if (!valid)
+ {
+ return null;
+ }
+ else
+ {
+ gps = new String[_gps.size()];
+ _gps.toArray(gps);
+ }
+ }
+ return gps;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff