1. 28 May, 2021 9 commits
    • cfrainay's avatar
      Create CHANGELOG · 3a845268
      cfrainay authored
      3a845268
    • cfrainay's avatar
      fix graph javadoc · 81703355
      cfrainay authored
      81703355
    • cfrainay's avatar
      Clean graph package · ffdc00dd
      cfrainay authored
      ffdc00dd
    • cfrainay's avatar
      Merge remote-tracking branch 'origin/feature/GraphMilestone' into develop · 901c2ae0
      cfrainay authored
      # Conflicts:
      #	README.md
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/algo/RandomWalk.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/analyze/GraphLocalMeasure.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/analyze/GraphMeasure.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/analyze/ScopeCompounds.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/analyze/centrality/EigenVectorCentrality.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/KShortestPath.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/SimilarityWeightPolicy.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/WeightsFromFile.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/GraphOperation.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/utils/ComputeAdjacencyMatrix.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/utils/RankUtils.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/BioPathUtils.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/GraphFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/bipartite/BipartiteEdge.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/bipartite/BipartiteEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/compound/CompoundGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/compound/ReactionEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/compressed/CompressedGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/compressed/PathEdge.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/compressed/PathEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MergedGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdge.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/parallel/MetaEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/pathway/PathwayGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/pathway/PathwayGraphEdge.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/pathway/PathwayGraphEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/reaction/CompoundEdgeFactory.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/core/reaction/ReactionGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/BioGraph2Sif.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/BioGraph2XGMML.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/Bionetwork2BioGraph.java
      #	met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/io/ExportGraph.java
      901c2ae0
    • cfrainay's avatar
      Isolate RandomWalkCentrality · 88e7b045
      cfrainay authored
      Unexpected behavior regarding starting nodes incident edges, lower centrality than expected. Centrality from transient matrix is fine. Further investigation needed regarding expected number of walks for terminal nodes
      88e7b045
    • cfrainay's avatar
      Add test for RandomWalkCentrality · 1738bcdb
      cfrainay authored
      + remove duplicated code
      1738bcdb
    • cfrainay's avatar
      [ToolBox] Add sbml convertion to reaciton graph · a5bc071c
      cfrainay authored
      a5bc071c
    • cfrainay's avatar
      [ToolBox] Update NetworkSummary description · 82f7717c
      cfrainay authored
      82f7717c
    • cfrainay's avatar
      [graph-core] add bioGraph edge reversing implementation · 8b32c9e3
      cfrainay authored
      + asUndirected method which add a reversed copy for each edge
      8b32c9e3
  2. 18 May, 2021 1 commit
  3. 17 May, 2021 3 commits
  4. 12 May, 2021 4 commits
  5. 11 May, 2021 2 commits
  6. 10 May, 2021 1 commit
  7. 07 May, 2021 3 commits
  8. 05 May, 2021 1 commit
  9. 03 May, 2021 1 commit
  10. 29 Apr, 2021 3 commits
  11. 27 Apr, 2021 8 commits
  12. 16 Apr, 2021 4 commits