X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=c1ad4659b5602ab2fb767edcdf586972ebc782e7;hb=eb5043c4c5932b46aa018e37ae42bd011405cd87;hp=ec2c59134b8a245e2107587a1e27aba62baa7e46;hpb=ecb334f98fca8ed9f27b6a7d027dea3bd4213023;p=jalview.git diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index ec2c591..c1ad465 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -27,8 +27,8 @@ 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 jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; import java.awt.Color; import java.beans.PropertyChangeListener; @@ -52,27 +52,18 @@ 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; - - /* - * feature types in ordering of rendering, where last means on top - */ protected String[] renderOrder; + Map featureOrder = null; + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); - protected AlignmentViewport av; - - /* - * map holds per feature type, {{min, max}, {min, max}} feature score - * values for positional and non-positional features respectively - */ - private Map minmax = new Hashtable(); + protected AlignViewportI av; @Override public AlignViewportI getViewport() @@ -200,6 +191,8 @@ public abstract class FeatureRendererModel implements renderOrder = neworder; } + protected Map minmax = new Hashtable(); + public Map getMinMax() { return minmax; @@ -295,8 +288,12 @@ public abstract class FeatureRendererModel implements continue; } - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) + // check if start/end are at res, and if not a contact feature, that res + // lies between start and end + if ((features[i].getBegin() == res || features[i].getEnd() == res) + || (!features[i].isContactFeature() + && (features[i].getBegin() < res) && (features[i] + .getEnd() >= res))) { tmp.add(features[i]); } @@ -449,7 +446,6 @@ 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) @@ -469,16 +465,13 @@ 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]); } } } @@ -502,15 +495,13 @@ 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]); } } } @@ -522,7 +513,7 @@ 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 @@ -540,22 +531,20 @@ 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 */ @Override - public Object getFeatureStyle(String featureType) + 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; } @@ -569,61 +558,32 @@ 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); } + /** + * Answers true if the feature type is currently selected to be displayed, + * else false + * + * @param type + * @return + */ protected boolean showFeatureOfType(String type) { - return av.getFeaturesDisplayed().isVisible(type); + return type == null ? false : av.getFeaturesDisplayed().isVisible(type); } @Override - public void setColour(String featureType, Object col) + 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))) - if (col instanceof FeatureColourI) - { - if (((FeatureColourI) col).isGraduatedColour()) - { - col = new GraduatedColor((FeatureColourI) col); - } - else - { - col = ((FeatureColourI) col).getColour(); - } - } - featureColours.put(featureType, col); + featureColours.put(featureType, col); } public void setTransparency(float value) @@ -636,8 +596,6 @@ 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. @@ -652,7 +610,7 @@ public abstract class FeatureRendererModel implements { if (featureOrder == null) { - featureOrder = new Hashtable(); + featureOrder = new Hashtable(); } featureOrder.put(type, new Float(position)); return position; @@ -670,14 +628,14 @@ 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; } @@ -710,7 +668,7 @@ public abstract class FeatureRendererModel implements * note visible feature ordering and colours before update */ List visibleFeatures = getDisplayedFeatureTypes(); - Map visibleColours = new HashMap( + Map visibleColours = new HashMap( getFeatureColours()); FeaturesDisplayedI av_featuresdisplayed = null; @@ -743,8 +701,7 @@ 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); @@ -869,9 +826,9 @@ public abstract class FeatureRendererModel implements { 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) @@ -913,19 +870,19 @@ 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, featureColours.get(col)); + String feature = features.next(); + fcols.put(feature, getFeatureStyle(feature)); } return fcols; }