\r
public class RNAStructReader {\r
\r
- private static Logger log = Logger.getLogger(RNAStructReader.class);\r
- \r
// Whitespace patterns\r
static String s = "[+\\s=]+";\r
static String bracket = "\\(|\\)|\\{|\\}|\\[|\\]";\r
assert (sline != null \r
&& Pattern.matches(AlifoldLine.ensembleFreq.regex, sline)) :\r
error + "Found 'freeEnergy' line on its own";\r
- structs.add("Free energy of ensemble (kcal/mol) followed by "\r
- + "frequency of mfe structure in ensemble");\r
+ structs.add("Free energy of ensemble (kcal/mol) followed by frequency of mfe structure in ensemble");\r
scores.add(Float.parseFloat(sc.findInLine(floatP)));\r
scores.add(Float.parseFloat(nsc.findInLine(floatP)));\r
data.add(newSetScore(AlifoldResult.ensembleValues, scores));\r
// jump line\r
sline = reader.readLine();\r
}\r
- \r
\r
assert(!ftype.equals(AlifoldLine.ensembleFreq)) :\r
error + "Wasn't expecting 'frequency of mfe structure'!";\r
error + "Wasn't expecting an alignment sequence!";\r
assert(!ftype.equals(AlifoldLine.OTHER)) :\r
error + "Wasn't expecting this whatever it is: " + fline;\r
- if (Pattern.matches("^\\s*$", fline)) {\r
- log.warn("While parsing alifold stdout: A line is either empty or"\r
- + " contains only whitespace");\r
- }\r
- \r
+\r
fline = sline;\r
}\r
\r
} else if (Pattern.matches(freqP, token)) {\r
return RNAOut.FREQ;\r
}\r
- \r
+\r
return RNAOut.OTHER;\r
}\r
\r
public static enum AlifoldResult {\r
mfeStructure, contactProbabilityStructure, MEAStucture, centroidStructure, stochBTStructure, consensusAlignment, ensembleValues, contactProbabilities\r
}\r
- \r
\r
// Print the full regex Strings for testing \r
public static void main(String[] args) {\r
System.out.println(l.toString() + ": " + l.regex.replace("^","").replace("$",""));\r
}\r
}\r
- \r
\r
- \r
-} \r
+}\r