FontMetrics fm;\r
int charOffset;\r
\r
+ Hashtable featureColours = new Hashtable();\r
+\r
+\r
// A higher level for grouping features of a\r
// particular type\r
Hashtable featureGroups = null;\r
\r
-\r
// This is actually an Integer held in the hashtable,\r
// Retrieved using the key feature type\r
Object currentColour;\r
\r
String [] renderOrder;\r
\r
+ boolean newFeatureAdded = false;\r
+\r
\r
/**\r
* Creates a new FeatureRenderer object.\r
public FeatureRenderer(AlignViewport av)\r
{\r
this.av = av;\r
- initColours();\r
}\r
\r
public void transferSettings(FeatureRenderer fr)\r
fm = g.getFontMetrics();\r
\r
\r
- if (av.featuresDisplayed == null || renderOrder==null)\r
+ if (av.featuresDisplayed == null\r
+ || renderOrder==null\r
+ || newFeatureAdded)\r
{\r
findAllFeatures();\r
if(av.featuresDisplayed.size()<1)\r
for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
{\r
type = renderOrder[renderIndex];\r
+\r
if(!av.featuresDisplayed.containsKey(type))\r
continue;\r
\r
\r
g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
\r
- if(offscreenRender)\r
+ if(offscreenRender || !av.validCharWidth)\r
continue;\r
\r
g.setColor(Color.white);\r
}\r
}\r
\r
- void findAllFeatures()\r
+ int count = 0;\r
+ synchronized public void featuresAdded()\r
{\r
- av.featuresDisplayed = new Hashtable();\r
+ newFeatureAdded = true;\r
+ findAllFeatures();\r
+ newFeatureAdded = false;\r
+ }\r
+\r
+ synchronized void findAllFeatures()\r
+ {\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
+\r
+ if(av.featuresDisplayed==null)\r
+ av.featuresDisplayed = new Hashtable();\r
+\r
+ av.featuresDisplayed.clear();\r
+\r
Vector allfeatures = new Vector();\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
{\r
if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
{\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer( getColour(features[index].getType()).getRGB()) );\r
- allfeatures.addElement(features[index].getType());\r
+ if(!(features[index].begin == 0 && features[index].end ==0))\r
+ {\r
+ // If beginning and end are 0, the feature is for the whole sequence\r
+ // and we don't want to render the feature in the normal way\r
+\r
+ if (getColour(features[index].getType()) == null)\r
+ {\r
+ featureColours.put(features[index].getType(),\r
+ ucs.createColourFromName(features[index].\r
+ getType()));\r
+ }\r
+\r
+ av.featuresDisplayed.put(features[index].getType(),\r
+ new Integer(getColour(features[index].\r
+ getType()).getRGB()));\r
+ allfeatures.addElement(features[index].getType());\r
+ }\r
}\r
index++;\r
}\r
\r
public Color getColour(String featureType)\r
{\r
- return (Color)featureColours.get(featureType);\r
+ Color colour = (Color)featureColours.get(featureType);\r
+ return colour;\r
}\r
\r
+\r
public void addNewFeature(String name, Color col, String group)\r
{\r
\r
\r
}\r
\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
- {\r
- featureColours.put("active site", new Color(255, 75, 0));\r
- featureColours.put("binding site", new Color(245, 85, 0));\r
- featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
- featureColours.put("chain", new Color(225, 105, 0));\r
- featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
- featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
- featureColours.put("cross-link", new Color(195, 135, 0));\r
- featureColours.put("disulfide bond", new Color(230,230,0));\r
- featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
- featureColours.put("domain", new Color(165, 165, 0));\r
- featureColours.put("glycosylation site", new Color(155, 175, 0));\r
- featureColours.put("helix", new Color(145, 185, 0));\r
- featureColours.put("initiator methionine", new Color(135, 195, 5));\r
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
- featureColours.put("modified residue", new Color(105, 225, 35));\r
- featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
- featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
- featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
- featureColours.put("peptide", new Color(55, 235, 85));\r
- featureColours.put("propeptide", new Color(45, 225, 95));\r
- featureColours.put("region of interest", new Color(35, 215, 105));\r
- featureColours.put("repeat", new Color(25, 205, 115));\r
- featureColours.put("selenocysteine", new Color(15, 195, 125));\r
- featureColours.put("sequence conflict", new Color(5, 185, 135));\r
- featureColours.put("sequence variant", new Color(0, 175, 145));\r
- featureColours.put("short sequence motif", new Color(0, 165, 155));\r
- featureColours.put("signal peptide", new Color(0, 155, 165));\r
- featureColours.put("site", new Color(0, 145, 175));\r
- featureColours.put("splice variant", new Color(0, 135, 185));\r
- featureColours.put("strand", new Color(0, 125, 195));\r
- featureColours.put("topological domain", new Color(0, 115, 205));\r
- featureColours.put("transit peptide", new Color(0, 105, 215));\r
- featureColours.put("transmembrane region", new Color(0, 95, 225));\r
- featureColours.put("turn", new Color(0, 85, 235));\r
- featureColours.put("unsure residue", new Color(0, 75, 245));\r
- featureColours.put("zinc finger region", new Color(0, 65, 255));\r
- }\r
+\r
+\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff