if(row.annotations[j]!=null)\r
{\r
comma = "";\r
- if (row.annotations[j].displayCharacter.length() > 0\r
- && !row.annotations[j].displayCharacter.equals(" "))\r
- {\r
- text.append(row.annotations[j].displayCharacter);\r
- comma = ",";\r
- }\r
if (row.annotations[j].secondaryStructure!=' ')\r
{\r
text.append(comma + row.annotations[j].secondaryStructure);\r
comma = ",";\r
}\r
+ if (row.annotations[j].displayCharacter.length() > 0 \r
+ && !row.annotations[j].displayCharacter.equals(" "))\r
+ {\r
+ text.append(comma + row.annotations[j].displayCharacter);\r
+ comma = ",";\r
+ }\r
if (row.annotations[j].value!=0f)\r
{\r
color = row.annotations[j].colour;\r
\r
if(refSeq!=null)\r
{\r
- annotation.createSequenceMapping(refSeq, refSeqIndex);\r
+ annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
refSeq.addAlignmentAnnotation(annotation);\r
}\r
\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