X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=b299624969dbbdd7b35848b5c1797530e7a6d5f0;hb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;hp=8db907c2a9ccd252a6188153be7f6f3eb130ba19;hpb=8b9c85b131fbaa1b9b29c489b661089c0ea404bd;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 8db907c..b299624 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -21,12 +21,14 @@ package jalview.viewmodel.seqfeatures; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; 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.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; import jalview.viewmodel.AlignmentViewport; import java.awt.Color; @@ -50,19 +52,20 @@ public abstract class FeatureRendererModel implements */ protected float transparency = 1.0f; - protected Map featureColours = new ConcurrentHashMap(); + protected Map featureColours = new ConcurrentHashMap(); protected Map featureGroups = new ConcurrentHashMap(); - protected Object currentColour; - protected String[] renderOrder; + Map featureOrder = null; + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); protected AlignmentViewport av; + @Override public AlignViewportI getViewport() { return av; @@ -188,9 +191,9 @@ public abstract class FeatureRendererModel implements renderOrder = neworder; } - protected Hashtable minmax = new Hashtable(); + protected Map minmax = new Hashtable(); - public Hashtable getMinMax() + public Map getMinMax() { return minmax; } @@ -204,7 +207,7 @@ public abstract class FeatureRendererModel implements */ protected final byte[] normaliseScore(SequenceFeature sequenceFeature) { - float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0]; + float[] mm = minmax.get(sequenceFeature.type)[0]; final byte[] r = new byte[] { 0, (byte) 255 }; if (mm != null) { @@ -335,7 +338,7 @@ public abstract class FeatureRendererModel implements } if (minmax == null) { - minmax = new Hashtable(); + minmax = new Hashtable(); } AlignmentI alignment = av.getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) @@ -390,7 +393,7 @@ public abstract class FeatureRendererModel implements if (!Float.isNaN(features[index].score)) { int nonpos = features[index].getBegin() >= 1 ? 0 : 1; - float[][] mm = (float[][]) minmax.get(features[index].getType()); + float[][] mm = minmax.get(features[index].getType()); if (mm == null) { mm = new float[][] { null, null }; @@ -439,7 +442,6 @@ public abstract class FeatureRendererModel implements List allfeatures = new ArrayList(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) @@ -459,16 +461,13 @@ public abstract class FeatureRendererModel implements allfeatures.remove(oldRender[j]); if (minmax != null) { - mmrange = minmax.get(oldRender[j]); + float[][] mmrange = minmax.get(oldRender[j]); if (mmrange != null) { - fc = featureColours.get(oldRender[j]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) + FeatureColourI fc = featureColours.get(oldRender[j]); + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) { - ((GraduatedColor) fc).updateBounds( - ((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); + fc.updateBounds(mmrange[0][0], mmrange[0][1]); } } } @@ -492,15 +491,13 @@ public abstract class FeatureRendererModel implements if (minmax != null) { // update from new features minmax if necessary - mmrange = minmax.get(newf[i]); + float[][] mmrange = minmax.get(newf[i]); if (mmrange != null) { - fc = featureColours.get(newf[i]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) + FeatureColourI fc = featureColours.get(newf[i]); + if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()) { - ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); + fc.updateBounds(mmrange[0][0], mmrange[0][1]); } } } @@ -512,7 +509,7 @@ public abstract class FeatureRendererModel implements setOrder(newf[i], i / (float) denom); } // set order from newly found feature from persisted ordering. - sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); + sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue(); if (i < iSize) { // only sort if we need to @@ -530,51 +527,25 @@ public abstract class FeatureRendererModel implements /** * 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 + * java.awt.Color for a featureType with no existing colourscheme. * * @param featureType - * @return java.awt.Color or GraduatedColor + * @return */ - public Object getFeatureStyle(String featureType) + @Override + public FeatureColourI getFeatureStyle(String featureType) { - Object fc = featureColours.get(featureType); + FeatureColourI 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); + Color col = UserColourScheme.createColourFromName(featureType); + fc = new FeatureColour(col); + featureColours.put(featureType, fc); } 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. * @@ -583,33 +554,14 @@ public abstract class FeatureRendererModel implements */ 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()); + FeatureColourI fc = getFeatureStyle(feature.getType()); + return fc.getColor(feature); } protected boolean showFeature(SequenceFeature sequenceFeature) { - Object fc = getFeatureStyle(sequenceFeature.type); - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).isColored(sequenceFeature); - } - else - { - return true; - } + FeatureColourI fc = getFeatureStyle(sequenceFeature.type); + return fc.isColored(sequenceFeature); } protected boolean showFeatureOfType(String type) @@ -617,14 +569,9 @@ public abstract class FeatureRendererModel implements return av.getFeaturesDisplayed().isVisible(type); } - public void setColour(String featureType, Object col) + @Override + public void setColour(String featureType, FeatureColourI 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); } @@ -640,8 +587,6 @@ public abstract class FeatureRendererModel implements return transparency; } - Map featureOrder = null; - /** * analogous to colour - store a normalized ordering for all feature types in * this rendering context. @@ -656,7 +601,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable(); } featureOrder.put(type, new Float(position)); return position; @@ -674,14 +619,14 @@ public abstract class FeatureRendererModel implements { if (featureOrder.containsKey(type)) { - return ((Float) featureOrder.get(type)).floatValue(); + return featureOrder.get(type).floatValue(); } } return -1; } @Override - public Map getFeatureColours() + public Map getFeatureColours() { return featureColours; } @@ -736,8 +681,7 @@ public abstract class FeatureRendererModel implements 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 + setColour(type, (FeatureColourI) data[i][1]); if (((Boolean) data[i][2]).booleanValue()) { av_featuresdisplayed.setVisible(type); @@ -767,7 +711,7 @@ public abstract class FeatureRendererModel implements changeSupport.removePropertyChangeListener(listener); } - public Set getAllFeatureColours() + public Set getAllFeatureColours() { return featureColours.keySet(); } @@ -831,13 +775,13 @@ public abstract class FeatureRendererModel implements * @return list of groups */ @Override - public List getGroups(boolean visible) + public List getGroups(boolean visible) { if (featureGroups != null) { - ArrayList gp = new ArrayList(); + List gp = new ArrayList(); - for (Object grp : featureGroups.keySet()) + for (String grp : featureGroups.keySet()) { Boolean state = featureGroups.get(grp); if (state.booleanValue() == visible) @@ -879,19 +823,19 @@ public abstract class FeatureRendererModel implements } @Override - public Hashtable getDisplayedFeatureCols() + public Map getDisplayedFeatureCols() { - Hashtable fcols = new Hashtable(); + Map fcols = new Hashtable(); if (getViewport().getFeaturesDisplayed() == null) { return fcols; } - Iterator en = getViewport().getFeaturesDisplayed() + Iterator features = getViewport().getFeaturesDisplayed() .getVisibleFeatures(); - while (en.hasNext()) + while (features.hasNext()) { - String col = en.next(); - fcols.put(col, getColour(col)); + String feature = features.next(); + fcols.put(feature, getFeatureStyle(feature)); } return fcols; }