SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
Graphics graphics;\r
+ float transparency = 1.0f;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed;\r
\r
/**\r
* Creates a new FeatureRenderer object.\r
public FeatureRenderer(AlignViewport av)\r
{\r
this.av = av;\r
+ initColours();\r
}\r
\r
/**\r
* @param width DOCUMENT ME!\r
* @param height DOCUMENT ME!\r
*/\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ public void drawSequence(Graphics g1, SequenceI seq, SequenceGroup[] sg,\r
int start, int end, int x1, int y1, int width, int height)\r
{\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
+\r
+ if(seq.getSequenceFeatures()==null)\r
+ return;\r
+\r
+ Enumeration e = null, e2;\r
+ String type;\r
+ if(featuresDisplayed!=null)\r
+ e = featuresDisplayed.elements();\r
+ else\r
+ e = seq.getSequenceFeatures().elements();\r
+\r
+ Graphics2D g = (Graphics2D)g1;\r
+ g.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER,transparency));\r
\r
while (e.hasMoreElements())\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ SequenceFeature sf=null;\r
+ if(featuresDisplayed!=null)\r
+ {\r
+ e2 = seq.getSequenceFeatures().elements();\r
+ type = e.nextElement().toString();\r
+ while(e2.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if(sf.getType().equals(type))\r
+ break;\r
+ else\r
+ sf = null;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sf = (SequenceFeature) e.nextElement();\r
+ type = sf.getType();\r
+ }\r
+\r
+ if(sf==null)\r
+ continue;\r
\r
- if (sf.getStart() > seq.getEnd())\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
{\r
continue;\r
}\r
\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fstart = seq.findIndex(sf.getBegin()) - 1;\r
int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
if (((fstart <= end) && (fend >= start)))\r
\r
if (fstart == fend)\r
{\r
- g.setColor(Color.red);\r
+ g.setColor(getColour(type));\r
g.fillRoundRect((fstart - start) * width, y1, width,\r
height, 4, 4);\r
g.setColor(Color.white);\r
continue;\r
}\r
\r
- g.setColor(Color.blue);\r
+ g.setColor(getColour(type));\r
g.fillRect((i - start) * width, y1, width, height);\r
\r
g.setColor(Color.white);\r
}\r
}\r
}\r
+ g.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER,1.0f));\r
+\r
}\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\r
+ }\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setTransparency(float value)\r
+ {\r
+ transparency = value;\r
+ }\r
+\r
+ public float getTransparency()\r
+ {\r
+ return transparency;\r
+ }\r
+\r
+ public void setFeaturePriority(Object [][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ featuresDisplayed = new Vector();\r
+ for(int i=data.length-1; i>-1; i--)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color)data[i][1]);\r
+ if( ((Boolean)data[i][2]).booleanValue() )\r
+ featuresDisplayed.addElement(type);\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(185, 145, 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",\r
+ 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
git://source.jalview.org / jalview.git / blobdiff