test_class.declarator: logger = LoggerFactory.getLogger(PlipParserTest.class)
test_class.modifier: private static final
test_class.original_string: private static final Logger logger = LoggerFactory.getLogger(PlipParserTest.class);
test_class.type: Logger
test_class.var_name: logger
test_class.declarator: structureCount = 0
test_class.modifier: private static
test_class.original_string: private static int structureCount = 0;
test_class.type: int
test_class.var_name: structureCount
test_class.file: singa-structure/src/test/java/bio/singa/structure/parser/plip/PlipParserTest.java
test_class.identifier: PlipParserTest
test_case.body: @Test
      void shouldParseInteractionsWithInsertionCodes() {
          InputStream inputStream = getResourceAsStream("plip/1k1i.xml");
          InteractionContainer interactionContainer = PlipParser.parse("1k1i", inputStream);
          OakStructure structure = (OakStructure) StructureParser.pdb()
                  .pdbIdentifier("1k1i")
                  .chainIdentifier("A")
                  .parse();
          interactionContainer.validateWithStructure(structure);
      }
test_case.class_method_signature: PlipParserTest.shouldParseInteractionsWithInsertionCodes()
test_case.full_signature: @Test void shouldParseInteractionsWithInsertionCodes()
test_case.identifier: shouldParseInteractionsWithInsertionCodes
test_case.invocations: getResourceAsStream parse parse chainIdentifier pdbIdentifier pdb validateWithStructure
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldParseInteractionsWithInsertionCodes()
focal_class.declarator: logger = LoggerFactory.getLogger(PlipParser.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(PlipParser.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.file: singa-structure/src/main/java/bio/singa/structure/parser/plip/PlipParser.java
focal_class.identifier: PlipParser
focal_class.class_method_signature: PlipParser.PlipParser(String pdbIdentifier, InputStream inputStream)
focal_class.full_signature: private  PlipParser(String pdbIdentifier, InputStream inputStream)
focal_class.identifier: PlipParser
focal_class.modifiers: private
focal_class.parameters: (String pdbIdentifier, InputStream inputStream)
focal_class.signature:  PlipParser(String pdbIdentifier, InputStream inputStream)
focal_class.class_method_signature: PlipParser.PlipParser(String pdbIdentifier)
focal_class.full_signature: private  PlipParser(String pdbIdentifier)
focal_class.identifier: PlipParser
focal_class.modifiers: private
focal_class.parameters: (String pdbIdentifier)
focal_class.signature:  PlipParser(String pdbIdentifier)
focal_class.class_method_signature: PlipParser.parse(String pdbIdentifier, String plipXml)
focal_class.full_signature: public static InteractionContainer parse(String pdbIdentifier, String plipXml)
focal_class.identifier: parse
focal_class.modifiers: public static
focal_class.parameters: (String pdbIdentifier, String plipXml)
focal_class.return: InteractionContainer
focal_class.signature: InteractionContainer parse(String pdbIdentifier, String plipXml)
focal_class.class_method_signature: PlipParser.parse(String pdbIdentifier, InputStream inputStream)
focal_class.full_signature: public static InteractionContainer parse(String pdbIdentifier, InputStream inputStream)
focal_class.identifier: parse
focal_class.modifiers: public static
focal_class.parameters: (String pdbIdentifier, InputStream inputStream)
focal_class.return: InteractionContainer
focal_class.signature: InteractionContainer parse(String pdbIdentifier, InputStream inputStream)
focal_class.class_method_signature: PlipParser.parse()
focal_class.full_signature: @Override public InteractionContainer parse()
focal_class.identifier: parse
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: InteractionContainer
focal_class.signature: InteractionContainer parse()
focal_class.class_method_signature: PlipParser.parseXML()
focal_class.full_signature: private void parseXML()
focal_class.identifier: parseXML
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void parseXML()
focal_class.superclass: extends AbstractXMLParser<InteractionContainer>
focal_method.body: public static InteractionContainer parse(String pdbIdentifier, String plipXml) {
          PlipParser parser = new PlipParser(pdbIdentifier);
          try {
              parser.getXmlReader().parse(new InputSource(new StringReader(plipXml)));
              return ((PlipContentHandler) parser.getXmlReader().getContentHandler()).getInteractionContainer();
          } catch (IOException e) {
              throw new UncheckedIOException("Could not parse XML from fetch result, the server seems to be unavailable.", e);
          } catch (SAXException e) {
              throw new IllegalStateException("Could not parse XML from fetch result, the XML seems to be malformed.", e);
          }
      }
focal_method.class_method_signature: PlipParser.parse(String pdbIdentifier, String plipXml)
focal_method.full_signature: public static InteractionContainer parse(String pdbIdentifier, String plipXml)
focal_method.identifier: parse
focal_method.invocations: parse getXmlReader getInteractionContainer getContentHandler getXmlReader
focal_method.modifiers: public static
focal_method.parameters: (String pdbIdentifier, String plipXml)
focal_method.return: InteractionContainer
focal_method.signature: InteractionContainer parse(String pdbIdentifier, String plipXml)