Program: 17012
Project: 17012
Buggy source:
/** 
 * #=GF <feature> <Generic per-File annotation, free text>
 * @param featureName 
 * @param value the line to be parsed
 */
private void handleFileAnnotation(String featureName,String value){
  if (featureName.equals(GF_ACCESSION_NUMBER)) {
    stockholmStructure.getFileAnnotation().setGFAccessionNumber(value);
  }
 else   if (featureName.equals(GF_IDENTIFICATION)) {
    stockholmStructure.getFileAnnotation().setGFIdentification(value);
  }
 else   if (featureName.equals(GF_DB_REFERENCE)) {
    stockholmStructure.getFileAnnotation().addDBReference(value);
  }
 else   if (featureName.equals(GF_DEFINITION)) {
    stockholmStructure.getFileAnnotation().setGFDefinition(value);
  }
 else   if (featureName.equals(GF_AUTHOR)) {
    stockholmStructure.getFileAnnotation().setGFAuthors(value);
  }
 else   if (featureName.equals(GF_ALIGNMENT_METHOD)) {
    stockholmStructure.getFileAnnotation().setAlignmentMethod(value);
  }
 else   if (featureName.equals(GF_BUILD_METHOD)) {
    stockholmStructure.getFileAnnotation().addGFBuildMethod(value);
  }
 else   if (featureName.equals(GF_SEARCH_METHOD)) {
    stockholmStructure.getFileAnnotation().setGFSearchMethod(value);
  }
 else   if (featureName.equals(GF_SOURCE_SEED)) {
    stockholmStructure.getFileAnnotation().setGFSourceSeed(value);
  }
 else   if (featureName.equals(GF_SOURCE_STRUCTURE)) {
    stockholmStructure.getFileAnnotation().setGFSourceStructure(value);
  }
 else   if (featureName.equals(GF_GATHERING_THRESHOLD)) {
    stockholmStructure.getFileAnnotation().setGFGatheringThreshs(value);
  }
 else   if (featureName.equals(GF_TRUSTED_CUTOFF)) {
    stockholmStructure.getFileAnnotation().setGFTrustedCutoffs(value);
  }
 else   if (featureName.equals(GF_NOISE_CUTOFF)) {
    stockholmStructure.getFileAnnotation().setGFNoiseCutoffs(value);
  }
 else   if (featureName.equals(GF_TYPE_FIELD)) {
    stockholmStructure.getFileAnnotation().setGFTypeField(value);
  }
 else   if (featureName.equals(GF_PREVIOUS_IDS)) {
    stockholmStructure.getFileAnnotation().setGFPreviousIDs(value);
  }
 else   if (featureName.equals(GF_SEQUENCE)) {
    status=STATUS_IN_SEQUENCE;
    stockholmStructure.getFileAnnotation().setGFNumSequences(value);
  }
 else   if (featureName.equals(GF_DB_COMMENT)) {
    stockholmStructure.getFileAnnotation().setGFDBComment(value);
  }
 else   if (featureName.equals(GF_REFERENCE_COMMENT)) {
    stockholmStructure.getFileAnnotation().setGFRefComment(value);
  }
 else   if (featureName.equals(GF_REFERENCE_NUMBER)) {
    StockholmFileAnnotationReference reference=new StockholmFileAnnotationReference();
    stockholmStructure.getFileAnnotation().getReferences().add(reference);
  }
 else   if (featureName.equals(GF_REFERENCE_MEDLINE)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefMedline(value);
  }
 else   if (featureName.equals(GF_REFERENCE_TITLE)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefTitle(value);
  }
 else   if (featureName.equals(GF_REFERENCE_AUTHOR)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefAuthor(value);
  }
 else   if (featureName.equals(GF_REFERENCE_LOCALTION)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefLocation(value);
  }
 else   if (featureName.equals(GF_KEYWORDS)) {
    stockholmStructure.getFileAnnotation().setGFKeywords(value);
  }
 else   if (featureName.equals(GF_COMMENT)) {
    stockholmStructure.getFileAnnotation().addToGFComment(value);
  }
 else   if (featureName.equals(GF_PFAM_ACCESSION)) {
    stockholmStructure.getFileAnnotation().setGFPfamAccession(value);
  }
 else   if (featureName.equals(GF_LOCATION)) {
    stockholmStructure.getFileAnnotation().setGFLocation(value);
  }
 else   if (featureName.equals(GF_WIKIPEDIA_LINK)) {
    stockholmStructure.getFileAnnotation().setGFWikipediaLink(value);
  }
 else   if (featureName.equals(GF_CLAN)) {
    stockholmStructure.getFileAnnotation().setGFClan(value);
  }
 else   if (featureName.equals(GF_MEMBERSHIP)) {
    stockholmStructure.getFileAnnotation().setGFMembership(value);
  }
 else   if (featureName.equals(GF_NEW_HAMPSHIRE)) {
    stockholmStructure.getFileAnnotation().addGFNewHampshire(value);
  }
 else   if (featureName.equals(GF_TREE_ID)) {
    stockholmStructure.getFileAnnotation().addGFTreeID(value);
  }
 else   if (featureName.equals(GF_FALSE_DISCOVERY_RATE)) {
    stockholmStructure.getFileAnnotation().addGFFalseDiscoveryRate(value);
  }
 else {
    System.err.println("String_Node_Str" + featureName + "String_Node_Str");
  }
}

Fixed version (ground truth):
/** 
 * #=GF &lt;feature&gt; &lt;Generic per-File annotation, free text&gt;
 * @param featureName 
 * @param value the line to be parsed
 */
private void handleFileAnnotation(String featureName,String value){
  if (featureName.equals(GF_ACCESSION_NUMBER)) {
    stockholmStructure.getFileAnnotation().setGFAccessionNumber(value);
  }
 else   if (featureName.equals(GF_IDENTIFICATION)) {
    stockholmStructure.getFileAnnotation().setGFIdentification(value);
  }
 else   if (featureName.equals(GF_DB_REFERENCE)) {
    stockholmStructure.getFileAnnotation().addDBReference(value);
  }
 else   if (featureName.equals(GF_DEFINITION)) {
    stockholmStructure.getFileAnnotation().setGFDefinition(value);
  }
 else   if (featureName.equals(GF_AUTHOR)) {
    stockholmStructure.getFileAnnotation().setGFAuthors(value);
  }
 else   if (featureName.equals(GF_ALIGNMENT_METHOD)) {
    stockholmStructure.getFileAnnotation().setAlignmentMethod(value);
  }
 else   if (featureName.equals(GF_BUILD_METHOD)) {
    stockholmStructure.getFileAnnotation().addGFBuildMethod(value);
  }
 else   if (featureName.equals(GF_SEARCH_METHOD)) {
    stockholmStructure.getFileAnnotation().setGFSearchMethod(value);
  }
 else   if (featureName.equals(GF_SOURCE_SEED)) {
    stockholmStructure.getFileAnnotation().setGFSourceSeed(value);
  }
 else   if (featureName.equals(GF_SOURCE_STRUCTURE)) {
    stockholmStructure.getFileAnnotation().setGFSourceStructure(value);
  }
 else   if (featureName.equals(GF_GATHERING_THRESHOLD)) {
    stockholmStructure.getFileAnnotation().setGFGatheringThreshs(value);
  }
 else   if (featureName.equals(GF_TRUSTED_CUTOFF)) {
    stockholmStructure.getFileAnnotation().setGFTrustedCutoffs(value);
  }
 else   if (featureName.equals(GF_NOISE_CUTOFF)) {
    stockholmStructure.getFileAnnotation().setGFNoiseCutoffs(value);
  }
 else   if (featureName.equals(GF_TYPE_FIELD)) {
    stockholmStructure.getFileAnnotation().setGFTypeField(value);
  }
 else   if (featureName.equals(GF_PREVIOUS_IDS)) {
    stockholmStructure.getFileAnnotation().setGFPreviousIDs(value);
  }
 else   if (featureName.equals(GF_SEQUENCE)) {
    status=STATUS_IN_SEQUENCE;
    stockholmStructure.getFileAnnotation().setGFNumSequences(value);
  }
 else   if (featureName.equals(GF_DB_COMMENT)) {
    stockholmStructure.getFileAnnotation().setGFDBComment(value);
  }
 else   if (featureName.equals(GF_REFERENCE_COMMENT)) {
    stockholmStructure.getFileAnnotation().setGFRefComment(value);
  }
 else   if (featureName.equals(GF_REFERENCE_NUMBER)) {
    StockholmFileAnnotationReference reference=new StockholmFileAnnotationReference();
    stockholmStructure.getFileAnnotation().getReferences().add(reference);
  }
 else   if (featureName.equals(GF_REFERENCE_MEDLINE)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefMedline(value);
  }
 else   if (featureName.equals(GF_REFERENCE_TITLE)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefTitle(value);
  }
 else   if (featureName.equals(GF_REFERENCE_AUTHOR)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefAuthor(value);
  }
 else   if (featureName.equals(GF_REFERENCE_LOCALTION)) {
    stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefLocation(value);
  }
 else   if (featureName.equals(GF_KEYWORDS)) {
    stockholmStructure.getFileAnnotation().setGFKeywords(value);
  }
 else   if (featureName.equals(GF_COMMENT)) {
    stockholmStructure.getFileAnnotation().addToGFComment(value);
  }
 else   if (featureName.equals(GF_PFAM_ACCESSION)) {
    stockholmStructure.getFileAnnotation().setGFPfamAccession(value);
  }
 else   if (featureName.equals(GF_LOCATION)) {
    stockholmStructure.getFileAnnotation().setGFLocation(value);
  }
 else   if (featureName.equals(GF_WIKIPEDIA_LINK)) {
    stockholmStructure.getFileAnnotation().setGFWikipediaLink(value);
  }
 else   if (featureName.equals(GF_CLAN)) {
    stockholmStructure.getFileAnnotation().setGFClan(value);
  }
 else   if (featureName.equals(GF_MEMBERSHIP)) {
    stockholmStructure.getFileAnnotation().setGFMembership(value);
  }
 else   if (featureName.equals(GF_NEW_HAMPSHIRE)) {
    stockholmStructure.getFileAnnotation().addGFNewHampshire(value);
  }
 else   if (featureName.equals(GF_TREE_ID)) {
    stockholmStructure.getFileAnnotation().addGFTreeID(value);
  }
 else   if (featureName.equals(GF_FALSE_DISCOVERY_RATE)) {
    stockholmStructure.getFileAnnotation().addGFFalseDiscoveryRate(value);
  }
 else {
    System.err.println("String_Node_Str" + featureName + "String_Node_Str");
  }
}