\r
if(refSeq!=null)\r
{\r
- annotation.createSequenceMapping(refSeq, refSeqIndex);\r
+ annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
refSeq.addAlignmentAnnotation(annotation);\r
}\r
\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r
ss = token.charAt(0);\r
- displayChar = "";\r
+ if(displayChar.equals(token.substring(0,1)))\r
+ displayChar = "";\r
}\r
else if(desc.length()<1)\r
desc = token;\r
for(int j=0; j<annotations.length; j++)\r
{\r
if(annotations[j]!=null)\r
- annotations[j].colour = ucs.findColour("A");\r
+ annotations[j].colour = ucs.findColour('A');\r
}\r
}\r
}\r
if(st.hasMoreTokens())\r
{\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colour = ucs.findColour("A");\r
+ colour = ucs.findColour('A');\r
}\r
\r
annotation.setThreshold(new GraphLine(value, label, colour));\r