Clean up logging system

[jabaws.git] / datamodel / compbio / data / sequence / RNAStructReader.java

diff --git a/datamodel/compbio/data/sequence/RNAStructReader.java b/datamodel/compbio/data/sequence/RNAStructReader.java
index 4292554..4fd364a 100644 (file)
--- a/datamodel/compbio/data/sequence/RNAStructReader.java
+++ b/datamodel/compbio/data/sequence/RNAStructReader.java
@@ -17,8 +17,6 @@ import org.apache.log4j.Logger;
 \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
@@ -124,15 +122,13 @@ public class RNAStructReader {
                                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
@@ -142,11 +138,7 @@ public class RNAStructReader {
                                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*$", fline)) {\r
-                               log.warn("While parsing alifold stdout: A line is either empty or"\r
-                                               + " contains only whitespace");\r
-                       }\r
-                       \r
+\r
                        fline = sline;\r
                }\r
                                \r
@@ -237,7 +229,7 @@ public class RNAStructReader {
                } else if (Pattern.matches(freqP, token)) {\r
                        return RNAOut.FREQ;\r
                }\r
-               \r
+\r
                return RNAOut.OTHER;\r
        }\r
        \r
@@ -277,7 +269,6 @@ public class RNAStructReader {
        public static enum AlifoldResult {\r
                mfeStructure, contactProbabilityStructure, MEAStucture, centroidStructure, stochBTStructure, consensusAlignment, ensembleValues, contactProbabilities\r
        }\r
-       \r
 \r
        // Print the full regex Strings for testing \r
        public static void main(String[] args) {\r
@@ -285,7 +276,5 @@ public class RNAStructReader {
                        System.out.println(l.toString() + ": " + l.regex.replace("^","").replace("$",""));\r
                }\r
        }\r
-       \r
 \r
-       \r
-}      \r
+}\r