test_class.declarator: directory
test_class.modifier: private static
test_class.original_string: private static Path directory;
test_class.type: Path
test_class.var_name: directory
test_class.declarator: target
test_class.modifier: private static
test_class.original_string: private static Structure target;
test_class.type: Structure
test_class.var_name: target
test_class.declarator: queryMotif
test_class.modifier: private static
test_class.original_string: private static StructuralMotif queryMotif;
test_class.type: StructuralMotif
test_class.var_name: queryMotif
test_class.file: singa-structure/src/test/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DMatchTest.java
test_class.identifier: Fit3DMatchTest
test_case.body: @Test
      void shouldGetCsvRepresentation() {
          Fit3D fit3d = Fit3DBuilder.create()
                  .query(queryMotif)
                  .target(target.getFirstChain())
                  .run();
          assertEquals("1gl0_E-57_E-102_E-195,4.680710257022384E-4,NaN,n/a,n/a,n/a,n/a", fit3d.getMatches().get(0).toCsvLine());
      }
test_case.class_method_signature: Fit3DMatchTest.shouldGetCsvRepresentation()
test_case.full_signature: @Test void shouldGetCsvRepresentation()
test_case.identifier: shouldGetCsvRepresentation
test_case.invocations: run target query create getFirstChain assertEquals toCsvLine get getMatches
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldGetCsvRepresentation()
focal_class.declarator: CSV_HEADER = "match,rmsd,p-value,title,UniProt,Pfam,EC\n"
focal_class.modifier: public static final
focal_class.original_string: public static final String CSV_HEADER = "match,rmsd,p-value,title,UniProt,Pfam,EC\n";
focal_class.type: String
focal_class.var_name: CSV_HEADER
focal_class.declarator: substructureSuperimposition
focal_class.modifier: private final
focal_class.original_string: private final SubstructureSuperimposition substructureSuperimposition;
focal_class.type: SubstructureSuperimposition
focal_class.var_name: substructureSuperimposition
focal_class.declarator: rmsd
focal_class.modifier: private final
focal_class.original_string: private final double rmsd;
focal_class.type: double
focal_class.var_name: rmsd
focal_class.declarator: pvalue
focal_class.modifier: private
focal_class.original_string: private double pvalue;
focal_class.type: double
focal_class.var_name: pvalue
focal_class.declarator: candidateMotif
focal_class.modifier: private
focal_class.original_string: private StructuralMotif candidateMotif;
focal_class.type: StructuralMotif
focal_class.var_name: candidateMotif
focal_class.declarator: matchType
focal_class.modifier: private
focal_class.original_string: private StructuralMotif.Type matchType;
focal_class.type: StructuralMotif.Type
focal_class.var_name: matchType
focal_class.declarator: uniProtIdentifiers
focal_class.modifier: private
focal_class.original_string: private Map<String, UniProtIdentifier> uniProtIdentifiers;
focal_class.type: Map<String, UniProtIdentifier>
focal_class.var_name: uniProtIdentifiers
focal_class.declarator: pfamIdentifiers
focal_class.modifier: private
focal_class.original_string: private Map<String, PfamIdentifier> pfamIdentifiers;
focal_class.type: Map<String, PfamIdentifier>
focal_class.var_name: pfamIdentifiers
focal_class.declarator: ecNumbers
focal_class.modifier: private
focal_class.original_string: private Map<String, ECNumber> ecNumbers;
focal_class.type: Map<String, ECNumber>
focal_class.var_name: ecNumbers
focal_class.declarator: alignedSequence
focal_class.modifier: private
focal_class.original_string: private String alignedSequence;
focal_class.type: String
focal_class.var_name: alignedSequence
focal_class.declarator: structureTitle
focal_class.modifier: private
focal_class.original_string: private String structureTitle;
focal_class.type: String
focal_class.var_name: structureTitle
focal_class.file: singa-structure/src/main/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DMatch.java
focal_class.identifier: Fit3DMatch
focal_class.interfaces: implements Comparable<Fit3DMatch>
focal_class.class_method_signature: Fit3DMatch.Fit3DMatch(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.full_signature: private  Fit3DMatch(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.identifier: Fit3DMatch
focal_class.modifiers: private
focal_class.parameters: (double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.signature:  Fit3DMatch(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.class_method_signature: Fit3DMatch.of(double rmsd)
focal_class.full_signature: public static Fit3DMatch of(double rmsd)
focal_class.identifier: of
focal_class.modifiers: public static
focal_class.parameters: (double rmsd)
focal_class.return: Fit3DMatch
focal_class.signature: Fit3DMatch of(double rmsd)
focal_class.class_method_signature: Fit3DMatch.of(double rmsd, SubstructureSuperimposition substructureSuperimposition)
focal_class.full_signature: public static Fit3DMatch of(double rmsd, SubstructureSuperimposition substructureSuperimposition)
focal_class.identifier: of
focal_class.modifiers: public static
focal_class.parameters: (double rmsd, SubstructureSuperimposition substructureSuperimposition)
focal_class.return: Fit3DMatch
focal_class.signature: Fit3DMatch of(double rmsd, SubstructureSuperimposition substructureSuperimposition)
focal_class.class_method_signature: Fit3DMatch.of(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.full_signature: public static Fit3DMatch of(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.identifier: of
focal_class.modifiers: public static
focal_class.parameters: (double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.return: Fit3DMatch
focal_class.signature: Fit3DMatch of(double rmsd, SubstructureSuperimposition substructureSuperimposition, double pvalue)
focal_class.class_method_signature: Fit3DMatch.analyzeMatch()
focal_class.full_signature: private void analyzeMatch()
focal_class.identifier: analyzeMatch
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void analyzeMatch()
focal_class.class_method_signature: Fit3DMatch.getAlignedSequence()
focal_class.full_signature: public String getAlignedSequence()
focal_class.identifier: getAlignedSequence
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAlignedSequence()
focal_class.class_method_signature: Fit3DMatch.getCandidateMotif()
focal_class.full_signature: public StructuralMotif getCandidateMotif()
focal_class.identifier: getCandidateMotif
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: StructuralMotif
focal_class.signature: StructuralMotif getCandidateMotif()
focal_class.class_method_signature: Fit3DMatch.getMatchType()
focal_class.full_signature: public StructuralMotif.Type getMatchType()
focal_class.identifier: getMatchType
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: StructuralMotif.Type
focal_class.signature: StructuralMotif.Type getMatchType()
focal_class.class_method_signature: Fit3DMatch.getUniProtIdentifiers()
focal_class.full_signature: public Optional<Map<String, UniProtIdentifier>> getUniProtIdentifiers()
focal_class.identifier: getUniProtIdentifiers
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Optional<Map<String, UniProtIdentifier>>
focal_class.signature: Optional<Map<String, UniProtIdentifier>> getUniProtIdentifiers()
focal_class.class_method_signature: Fit3DMatch.setUniProtIdentifiers(Map<String, UniProtIdentifier> uniProtIdentifiers)
focal_class.full_signature:  void setUniProtIdentifiers(Map<String, UniProtIdentifier> uniProtIdentifiers)
focal_class.identifier: setUniProtIdentifiers
focal_class.parameters: (Map<String, UniProtIdentifier> uniProtIdentifiers)
focal_class.return: void
focal_class.signature: void setUniProtIdentifiers(Map<String, UniProtIdentifier> uniProtIdentifiers)
focal_class.class_method_signature: Fit3DMatch.getPfamIdentifiers()
focal_class.full_signature: public Optional<Map<String, PfamIdentifier>> getPfamIdentifiers()
focal_class.identifier: getPfamIdentifiers
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Optional<Map<String, PfamIdentifier>>
focal_class.signature: Optional<Map<String, PfamIdentifier>> getPfamIdentifiers()
focal_class.class_method_signature: Fit3DMatch.setPfamIdentifiers(Map<String, PfamIdentifier> pfamIdentifiers)
focal_class.full_signature:  void setPfamIdentifiers(Map<String, PfamIdentifier> pfamIdentifiers)
focal_class.identifier: setPfamIdentifiers
focal_class.parameters: (Map<String, PfamIdentifier> pfamIdentifiers)
focal_class.return: void
focal_class.signature: void setPfamIdentifiers(Map<String, PfamIdentifier> pfamIdentifiers)
focal_class.class_method_signature: Fit3DMatch.getEcNumbers()
focal_class.full_signature: public Optional<Map<String, ECNumber>> getEcNumbers()
focal_class.identifier: getEcNumbers
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Optional<Map<String, ECNumber>>
focal_class.signature: Optional<Map<String, ECNumber>> getEcNumbers()
focal_class.class_method_signature: Fit3DMatch.setEcNumbers(Map<String, ECNumber> ecNumbers)
focal_class.full_signature:  void setEcNumbers(Map<String, ECNumber> ecNumbers)
focal_class.identifier: setEcNumbers
focal_class.parameters: (Map<String, ECNumber> ecNumbers)
focal_class.return: void
focal_class.signature: void setEcNumbers(Map<String, ECNumber> ecNumbers)
focal_class.class_method_signature: Fit3DMatch.getStructureTitle()
focal_class.full_signature: public String getStructureTitle()
focal_class.identifier: getStructureTitle
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getStructureTitle()
focal_class.class_method_signature: Fit3DMatch.setStructureTitle(String structureTitle)
focal_class.full_signature:  void setStructureTitle(String structureTitle)
focal_class.identifier: setStructureTitle
focal_class.parameters: (String structureTitle)
focal_class.return: void
focal_class.signature: void setStructureTitle(String structureTitle)
focal_class.class_method_signature: Fit3DMatch.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.class_method_signature: Fit3DMatch.getSubstructureSuperimposition()
focal_class.full_signature: public SubstructureSuperimposition getSubstructureSuperimposition()
focal_class.identifier: getSubstructureSuperimposition
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition getSubstructureSuperimposition()
focal_class.class_method_signature: Fit3DMatch.getRmsd()
focal_class.full_signature: public double getRmsd()
focal_class.identifier: getRmsd
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getRmsd()
focal_class.class_method_signature: Fit3DMatch.getPvalue()
focal_class.full_signature: public double getPvalue()
focal_class.identifier: getPvalue
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getPvalue()
focal_class.class_method_signature: Fit3DMatch.setPvalue(double pvalue)
focal_class.full_signature: public void setPvalue(double pvalue)
focal_class.identifier: setPvalue
focal_class.modifiers: public
focal_class.parameters: (double pvalue)
focal_class.return: void
focal_class.signature: void setPvalue(double pvalue)
focal_class.class_method_signature: Fit3DMatch.toCsvLine()
focal_class.full_signature: public String toCsvLine()
focal_class.identifier: toCsvLine
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toCsvLine()
focal_class.class_method_signature: Fit3DMatch.compareTo(Fit3DMatch other)
focal_class.full_signature: @Override public int compareTo(Fit3DMatch other)
focal_class.identifier: compareTo
focal_class.modifiers: @Override public
focal_class.parameters: (Fit3DMatch other)
focal_class.return: int
focal_class.signature: int compareTo(Fit3DMatch other)
focal_method.body: public String toCsvLine() {
          StringJoiner stringJoiner = new StringJoiner(",");
          String stringRepresentation = substructureSuperimposition.getStringRepresentation();
          stringJoiner.add(stringRepresentation.replaceFirst("\\d+\\.\\d+_", ""));
          stringJoiner.add(String.valueOf(rmsd));
          stringJoiner.add(String.valueOf(pvalue));
          stringJoiner.add(((structureTitle != null) ? "\"" + structureTitle.replaceAll("\"", "") + "\"" : "n/a"));
          stringJoiner.add(((uniProtIdentifiers != null) ? uniProtIdentifiers.entrySet().stream()
                  .map(entry -> entry.getKey() + ":" + entry.getValue())
                  .collect(Collectors.joining(",", "[", "]")) : "n/a"));
          stringJoiner.add(((pfamIdentifiers != null) ? pfamIdentifiers.entrySet().stream()
                  .map(entry -> entry.getKey() + ":" + entry.getValue())
                  .collect(Collectors.joining(",", "[", "]")) : "n/a"));
          stringJoiner.add(((ecNumbers != null) ? ecNumbers.entrySet().stream()
                  .map(entry -> entry.getKey() + ":" + entry.getValue())
                  .collect(Collectors.joining(",", "[", "]")) : "n/a"));
          return stringJoiner.toString();
      }
focal_method.class_method_signature: Fit3DMatch.toCsvLine()
focal_method.full_signature: public String toCsvLine()
focal_method.identifier: toCsvLine
focal_method.invocations: getStringRepresentation add replaceFirst add valueOf add valueOf add replaceAll add collect map stream entrySet getKey getValue joining add collect map stream entrySet getKey getValue joining add collect map stream entrySet getKey getValue joining toString
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: String
focal_method.signature: String toCsvLine()