Projects >> bio4j >>bd519008bea82aa249cc024b5da53bd84d5067dd

Chunk
Conflicting content 
            importProteinCitations          (entryXMLElem, graph, protein);
            importProteinKeywordsEdges      (entryXMLElem, graph, protein);
            importProteinGeneLocationEdges  (entryXMLElem, graph, protein);
<<<<<<< HEAD
            // importProteinGeneNameEdges      (entryXMLElem, graph, protein);
            importProteinOrganismsEdges     (entryXMLElem, graph, protein);
=======
            importProteinGeneNameEdges      (entryXMLElem, graph, protein);
>>>>>>> 9ba8790f25f91288b0b71f3e8b673f363c9c37f3
          }
        );
Solution content 
            importProteinCitations          (entryXMLElem, graph, protein);
            importProteinKeywordsEdges      (entryXMLElem, graph, protein);
            importProteinGeneLocationEdges  (entryXMLElem, graph, protein);
          }
        );
File
ImportUniProtEdges.java
Developer's decision
None
Kind of conflict
Comment
Chunk
Conflicting content 
  // {
    // }
  }

<<<<<<< HEAD
  // private void importProteinGeneNameEdges(
  // XMLElement entryXMLElem,
  // UniProtGraph graph,
  // Protein protein
  // )
  //
  //   Optional.ofNullable(entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME))
  //     .ifPresent(
  //       geneElement -> geneElement.getChildren(GENE_NAME_TAG_NAME)
  //         .stream()
  //         .forEach(
  //           geneNameElem -> {
  //             graph.geneNameNameIndex().getVertex(geneNameElem.getText()).ifPresent(
  //               geneName ->
  //               protein.addOutEdge(graph.ProteinGeneName(), geneName)
  //                 .set(graph.ProteinGeneName().geneNameType, geneNameElem.getAttributeValue("type"))
  //             );
  //           }
  //         )
  //     );
  //
  //   // Element geneElement = entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME);
  //   // if (geneElement != null) {
  //   //   List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);
  //   //
  //   //   for (Element geneNameElem : geneNamesList) {
  //   //     String geneNameSt = geneNameElem.getText();
  //   //     String typeSt = geneNameElem.getAttributeValue("type");
  //   //
  //   //     Optional> optionalGeneName = graph.geneNameNameIndex().getVertex(geneNameSt);
  //   //     vertexIndexCalls.add(1);
  //   //
  //   //     if(optionalGeneName.isPresent()){
  //   //       GeneName geneName = optionalGeneName.get();
  //   //       ProteinGeneName proteinGeneName = protein.addOutEdge(graph.ProteinGeneName(), geneName);
  //   //       edgeCounter.add(1);
  //   //       proteinGeneName.set(graph.ProteinGeneName().geneNameType, typeSt);
  //   //     }
  //   //   }
  //   // }
  // }
=======
  private void importProteinGeneNameEdges(
  Element entryXMLElem,
  UniProtGraph graph,
  Protein protein
  )
  {

    Optional.ofNullable(entryXMLElem.getChild(GENE_TAG_NAME))
      .ifPresent(
        geneElement -> geneElement.getChildren(GENE_NAME_TAG_NAME)
          .stream()
          .forEach(
            geneNameElem -> {
              graph.geneNameNameIndex().getVertex(geneNameElem.getText()).ifPresent(
                geneName ->
                protein.addOutEdge(graph.ProteinGeneName(), geneName)
                  .set(graph.ProteinGeneName().geneNameType, geneNameElem.getAttributeValue("type"))
              );
            }
          )
      );

    // Element geneElement = entryXMLElem.getChild(GENE_TAG_NAME);
    // if (geneElement != null) {
    //   List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);
    //
    //   for (Element geneNameElem : geneNamesList) {
    //     String geneNameSt = geneNameElem.getText();
    //     String typeSt = geneNameElem.getAttributeValue("type");
    //
    //     Optional> optionalGeneName = graph.geneNameNameIndex().getVertex(geneNameSt);
    //     vertexIndexCalls.add(1);
    //
    //     if(optionalGeneName.isPresent()){
    //       GeneName geneName = optionalGeneName.get();
    //       ProteinGeneName proteinGeneName = protein.addOutEdge(graph.ProteinGeneName(), geneName);
    //       edgeCounter.add(1);
    //       proteinGeneName.set(graph.ProteinGeneName().geneNameType, typeSt);
    //     }
    //   }
    // }
  }
>>>>>>> 9ba8790f25f91288b0b71f3e8b673f363c9c37f3

  private void importProteinCitations(
  Element entryXMLElem,
Solution content 
  //     .ifPresent(
  //
    // }
  }

  // private void importProteinGeneNameEdges(
  // XMLElement entryXMLElem,
  // UniProtGraph graph,
  // Protein protein
  // )
  // {
  //   Optional.ofNullable(entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME))
  //       geneElement -> geneElement.getChildren(GENE_NAME_TAG_NAME)
  //         .stream()
  //         .forEach(
  //           geneNameElem -> {
  //             graph.geneNameNameIndex().getVertex(geneNameElem.getText()).ifPresent(
  //               geneName ->
  //               protein.addOutEdge(graph.ProteinGeneName(), geneName)
  //                 .set(graph.ProteinGeneName().geneNameType, geneNameElem.getAttributeValue("type"))
  //             );
  //           }
  //         )
  //     );
  //
  //   // Element geneElement = entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME);
  //   // if (geneElement != null) {
  //   //   List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);
  //   //
  //   //   for (Element geneNameElem : geneNamesList) {
  //   //     String geneNameSt = geneNameElem.getText();
  //   //     String typeSt = geneNameElem.getAttributeValue("type");
  //   //
  //   //     Optional> optionalGeneName = graph.geneNameNameIndex().getVertex(geneNameSt);
  //   //     vertexIndexCalls.add(1);
  //   //
  //   //     if(optionalGeneName.isPresent()){
  //   //       GeneName geneName = optionalGeneName.get();
  //   //       ProteinGeneName proteinGeneName = protein.addOutEdge(graph.ProteinGeneName(), geneName);
  //   //       edgeCounter.add(1);
  //   //       proteinGeneName.set(graph.ProteinGeneName().geneNameType, typeSt);
  //   //     }
  //   //   }
  //   // }
  // }

  private void importProteinCitations(
  Element entryXMLElem,
File
ImportUniProtEdges.java
Developer's decision
Version 1
Kind of conflict
Comment
Method declaration
Chunk
Conflicting content 
          importProteinCitations    (entryXMLElem, graph, protein);
          importProteinKeywords     (entryXMLElem, graph);
          importProteinGeneLocation (entryXMLElem, graph);
<<<<<<< HEAD
          // importProteinGeneNames    (entryXMLElem, graph);
          importProteinOrganisms    (entryXMLElem, graph);
=======
          importProteinGeneNames    (entryXMLElem, graph);
>>>>>>> 9ba8790f25f91288b0b71f3e8b673f363c9c37f3

          proteinCounter++;
Solution content 
          importProteinCitations    (entryXMLElem, graph, protein);
          importProteinKeywords     (entryXMLElem, graph);
          importProteinGeneLocation (entryXMLElem, graph);

          proteinCounter++;
File
ImportUniProtVertices.java
Developer's decision
None
Kind of conflict
Comment
Method invocation
Chunk
Conflicting content 
    }
  }

<<<<<<< HEAD
  // private void importProteinGeneNames(
  //   XMLElement entryXMLElem,
  //   UniProtGraph graph
  // )
  // {
  //
  //   final Element geneElement = entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME);
  //
  //   if(geneElement != null) {
  //
  //     final List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);
  //
  //     for(Element geneNameElem: geneNamesList) {
  //
  //       final String geneNameSt = geneNameElem.getText();
  //       final String typeSt     = geneNameElem.getAttributeValue("type");
  //
  //       if(!geneNameSet.contains(geneNameSt)) {
  //
  //         geneNameSet.add(geneNameSt);
  //
  //         if(!graph.geneNameNameIndex().getVertex(geneNameSt).isPresent()) {
  //
  //           final GeneName geneName = graph.addVertex(graph.GeneName());
  //           geneName.set(graph.GeneName().name, geneNameSt);
  //         }
  //       }
  //     }
  //   }
  // }
=======
  private void importProteinGeneNames(
    Element entryXMLElem,
    UniProtGraph graph
  )
  {

    final Element geneElement = entryXMLElem.getChild(GENE_TAG_NAME);

    if(geneElement != null) {

      final List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);

      for(Element geneNameElem: geneNamesList) {

        final String geneNameSt = geneNameElem.getText();
        final String typeSt     = geneNameElem.getAttributeValue("type");

        if(!geneNameSet.contains(geneNameSt)) {

          geneNameSet.add(geneNameSt);

          if(!graph.geneNameNameIndex().getVertex(geneNameSt).isPresent()) {

            final GeneName geneName = graph.addVertex(graph.GeneName());
            geneName.set(graph.GeneName().name, geneNameSt);
          }
        }
      }
    }
  }
>>>>>>> 9ba8790f25f91288b0b71f3e8b673f363c9c37f3

  private void importProteinComments(
    Element entryXMLElem,
Solution content 
    }
  }

  // private void importProteinGeneNames(
  //   XMLElement entryXMLElem,
  //   UniProtGraph graph
  // )
  // {
  //
  //   final Element geneElement = entryXMLElem.asJDomElement().getChild(GENE_TAG_NAME);
  //
  //   if(geneElement != null) {
  //
  //     final List geneNamesList = geneElement.getChildren(GENE_NAME_TAG_NAME);
  //
  //     for(Element geneNameElem: geneNamesList) {
  //
  //       final String geneNameSt = geneNameElem.getText();
  //       final String typeSt     = geneNameElem.getAttributeValue("type");
  //
  //       if(!geneNameSet.contains(geneNameSt)) {
  //
  //         geneNameSet.add(geneNameSt);
  //
  //         if(!graph.geneNameNameIndex().getVertex(geneNameSt).isPresent()) {
  //
  //           final GeneName geneName = graph.addVertex(graph.GeneName());
  //           geneName.set(graph.GeneName().name, geneNameSt);
  //         }
  //       }
  //     }
  //   }
  // }

  private void importProteinComments(
    Element entryXMLElem,
File
ImportUniProtVertices.java
Developer's decision
Version 1
Kind of conflict
Comment
Method declaration