\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
renderOrder = fr.renderOrder;\r
featureGroups = fr.featureGroups;\r
featureColours = fr.featureColours;\r
+ transparency = fr.transparency;\r
}\r
\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
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
+ start, end, y1);\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
for (i = fstart; i <= fend; i++)\r
{\r
- s = seq.getSequence().charAt(i);\r
+ s = seq.getCharAt(i);\r
\r
if (jalview.util.Comparison.isGap(s))\r
{\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
{\r
void setTransparency(Graphics g, float value)\r
{\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, value));\r
+ /* Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, value));*/\r
}\r
}\r
\r