+\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
{\r
AlignViewport av;\r
\r
+ Hashtable featureColours = new Hashtable();\r
\r
// A higher level for grouping features of a\r
// particular type\r
Hashtable featureGroups = null;\r
\r
+ // Holds web links for feature groups and feature types\r
+ // in the form label|link\r
+ Hashtable featureLinks = null;\r
+\r
+\r
// This is actually an Integer held in the hashtable,\r
// Retrieved using the key feature type\r
Object currentColour;\r
FontMetrics fm;\r
int charOffset;\r
\r
+ float transparency = 1f;\r
+\r
+ TransparencySetter transparencySetter = null;\r
+\r
/**\r
* Creates a new FeatureRenderer object.\r
*\r
public FeatureRenderer(AlignViewport av)\r
{\r
this.av = av;\r
- initColours();\r
+\r
+ if(!System.getProperty("java.version").startsWith("1.1"))\r
+ transparencySetter = new TransparencySetter();\r
+ }\r
+\r
+\r
+ public void transferSettings(FeatureRenderer fr)\r
+ {\r
+ renderOrder = fr.renderOrder;\r
+ featureGroups = fr.featureGroups;\r
+ featureColours = fr.featureColours;\r
+ transparency = fr.transparency;\r
}\r
\r
\r
public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
{\r
+ overview = true;\r
if(!av.showSequenceFeatures)\r
return initialCol;\r
\r
\r
currentColour = null;\r
\r
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1);\r
\r
if(currentColour==null)\r
return initialCol;\r
\r
currentColour = null;\r
\r
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);\r
\r
if(currentColour==null)\r
return initialCol;\r
int sfSize, sfindex, spos, epos;\r
\r
public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1, int width, int height)\r
+ int start, int end, int y1)\r
{\r
if ( seq.getSequenceFeatures() == null\r
|| seq.getSequenceFeatures().length==0)\r
return;\r
\r
+ if(transparencySetter!=null && g!=null)\r
+ {\r
+ transparencySetter.setTransparency(g, transparency);\r
+ }\r
\r
if (av.featuresDisplayed == null || renderOrder==null)\r
{\r
if (!sequenceFeatures[sfindex].type.equals(type))\r
continue;\r
\r
- if(sequenceFeatures[sfindex]==null)\r
- {\r
- }\r
- else if (featureGroups != null\r
+ if (featureGroups != null\r
&& sequenceFeatures[sfindex].featureGroup != null\r
&&\r
featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
\r
if (overview)\r
{\r
-\r
- if (sequenceFeatures[sfindex].begin - 1 <= start &&\r
- sequenceFeatures[sfindex].end + 1 >= start)\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r
{\r
currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
type);\r
seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
new Color( ( (Integer) av.featuresDisplayed.get(\r
sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
+ start, end, y1);\r
renderFeature(g, seq,\r
seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
new Color( ( (Integer) av.featuresDisplayed.get(\r
sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
+ start, end, y1);\r
\r
}\r
else\r
seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1, width, height);\r
-\r
+ start, end, y1);\r
\r
}\r
+ }\r
\r
+ if(transparencySetter!=null && g!=null)\r
+ {\r
+ transparencySetter.setTransparency(g, 1.0f);\r
}\r
}\r
\r
char s;\r
int i;\r
void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height)\r
+ int fstart, int fend, Color featureColour, int start, int end, int y1)\r
{\r
\r
if (((fstart <= end) && (fend >= start)))\r
\r
g.setColor(featureColour);\r
\r
- g.fillRect( (i - start) * width, y1, width, height);\r
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);\r
+\r
+ if(!av.validCharWidth)\r
+ continue;\r
\r
g.setColor(Color.white);\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
g.drawString(String.valueOf(s),\r
- charOffset + (width * (i - start)),\r
- (y1 + height) - height / 5); //pady = height / 5;\r
+ charOffset + (av.charWidth * (i - start)),\r
+ (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
\r
}\r
}\r
\r
void findAllFeatures()\r
{\r
+ jalview.schemes.UserColourScheme ucs = new\r
+ jalview.schemes.UserColourScheme();\r
+\r
av.featuresDisplayed = new Hashtable();\r
Vector allfeatures = new Vector();\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
if (!av.featuresDisplayed.containsKey(features[index].getType()))\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
+\r
av.featuresDisplayed.put(features[index].getType(),\r
new Integer( getColour(features[index].getType()).getRGB()) );\r
allfeatures.addElement(features[index].getType());\r
renderOrder[data.length - i - 1] = type;\r
}\r
}\r
+}\r
\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
+ class TransparencySetter\r
+ {\r
+ void setTransparency(Graphics g, float value)\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
+ //Graphics2D g2 = (Graphics2D) g;\r
+ // g2.setComposite(\r
+ // AlphaComposite.getInstance(\r
+ // AlphaComposite.SRC_OVER, value));\r
}\r
+ }\r
\r
-}\r
\r
\r
\r
git://source.jalview.org / jalview.git / blobdiff