refSeq = row.sequenceRef;\r
text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
}\r
- boolean hasGlyphs = false, hasLabels = false, hasValues = false, hasText = false;\r
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;\r
// lookahead to check what the annotation row object actually contains.\r
for (int j = 0; row.annotations != null\r
&& j < row.annotations.length\r
if (row.annotations[j] != null)\r
{\r
comma = "";\r
- if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')\r
+ if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... \r
{\r
\r
text.append(comma + row.annotations[j].secondaryStructure);\r
}\r
}\r
\r
- if (hasSymbols && (token.equals("H") || token.equals("E")))\r
+ if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))\r
{\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r