Commits · 3a84526805d354f3a074344d22b30cff5dd75f45 · metexplore / met4j

28 May, 2021 9 commits

Create CHANGELOG · 3a845268
cfrainay authored May 28, 2021

3a845268
fix graph javadoc · 81703355
cfrainay authored May 28, 2021

81703355
Clean graph package · ffdc00dd
cfrainay authored May 28, 2021

ffdc00dd

Merge remote-tracking branch 'origin/feature/GraphMilestone' into develop · 901c2ae0

cfrainay authored May 28, 2021

# 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

Isolate RandomWalkCentrality · 88e7b045

cfrainay authored May 28, 2021

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

Add test for RandomWalkCentrality · 1738bcdb
cfrainay authored May 28, 2021
```
+ remove duplicated code
```
1738bcdb
[ToolBox] Add sbml convertion to reaciton graph · a5bc071c
cfrainay authored May 28, 2021

a5bc071c
[ToolBox] Update NetworkSummary description · 82f7717c
cfrainay authored May 28, 2021

82f7717c
[graph-core] add bioGraph edge reversing implementation · 8b32c9e3
cfrainay authored May 28, 2021
```
+ asUndirected method which add a reversed copy for each edge
```
8b32c9e3

18 May, 2021 1 commit
- Code clean-up · 53ad904f
  cfrainay authored May 18, 2021
  
  53ad904f
17 May, 2021 3 commits
- Keep most efficient reaction graph creation · 54513f43
  cfrainay authored May 17, 2021
```
+ add cofactor filter
```
  54513f43
- fix reaction graph creation · 8dd45f44
  cfrainay authored May 17, 2021
  
  8dd45f44
- Update test class names · 43c4848f
  cfrainay authored May 17, 2021
  
  43c4848f
12 May, 2021 4 commits
- [Toolbox] Create App for Network Extraction · 26628637
  cfrainay authored May 12, 2021
```
include shortest paths, k-shortest path, Steiner Tree, with degree², chemical sim or custom weighting. Output compound graph gml for now
```
  26628637
- fix scope network trace, add trace to gml, update app · 935babe0
  cfrainay authored May 12, 2021
  
  935babe0
- add generic vertex attribute export for gml · b0b6aa36
  cfrainay authored May 12, 2021
  
  b0b6aa36
- Allow inclusion of bootstrap compounds in scope · 40f12fbb
  cfrainay authored May 12, 2021
```
+ add test case
```
  40f12fbb
11 May, 2021 2 commits
- Allow to store index of addition in compounds scope computation · d829128d
  cfrainay authored May 11, 2021
  
  d829128d
- Change SideCompoundsScan manual for better clarity · 64e60265
  cfrainay authored May 11, 2021
```
+For coherency and clarity, reporting only ids imply reporting only flagged side compounds
```
  64e60265
10 May, 2021 1 commit
- Checks if the reactionToIgnoreFile is provided · 8694ed25
  lcottret authored May 10, 2021
  
  8694ed25
07 May, 2021 3 commits
- add test for node mapping · 25bd19a3
  cfrainay authored May 07, 2021
```
+fix separator interpreted as regex
```
  25bd19a3
- Fix error messages with bad number of lines · 198099c5
  lcottret authored May 07, 2021
  
  198099c5
- adds smiles and inchis to metabolite table · 573a05ec
  lcottret authored May 07, 2021
  
  573a05ec
05 May, 2021 1 commit
- Change in weights import, made more flexible in handled file format · eebc81d0
  cfrainay authored May 05, 2021
```
Now accept parameter to set separator, header, column indexes.
New test case added
```
  eebc81d0
03 May, 2021 1 commit
- Class to set bound flux from file · ac5e298b
  lcottret authored May 03, 2021
  
  ac5e298b
29 Apr, 2021 3 commits
- Merge tag 'hotfix-removeflexfluxlink' into develop · 95c73de5
  lcottret authored Apr 29, 2021
```
Finish hotfix-removeflexfluxlink
```
  95c73de5
- Finish hotfix-removeflexfluxlink · 92dc70ab
  lcottret authored Apr 29, 2021
  
  92dc70ab
- remove flexflux link · 0d57e5f1
  lcottret authored Apr 29, 2021
  
  0d57e5f1
27 Apr, 2021 8 commits
- Merge tag 'hotfix_0.5.2' into develop · 2b8e45fe
  lcottret authored Apr 27, 2021
```
Finish hotfix_0.5.2
```
  2b8e45fe
- Finish hotfix_0.5.2 · 2ce89a0b
  lcottret authored Apr 27, 2021
  
  2ce89a0b
- mvn perform is launched from the local checkout · abca4d80
  lcottret authored Apr 27, 2021
  
  abca4d80
- [skip ci]rollback changes from release preparation of met4j-0.5.1 · 8378ece2
  GITLAB_USER_NAME authored Apr 27, 2021
  
  8378ece2
- [skip ci] prepare release met4j-0.5.1 · b833572c
  GITLAB_USER_NAME authored Apr 27, 2021
  
  b833572c
- Merge tag 'hotfix_0.5.1' into develop · bb788c8d
  lcottret authored Apr 27, 2021
```
Finish hotfix_0.5.1
```
  bb788c8d
- Finish hotfix_0.5.1 · 495b96ed
  lcottret authored Apr 27, 2021
  
  495b96ed
- push changes in prepare-release · ad7438e3
  lcottret authored Apr 27, 2021
  
  ad7438e3
16 Apr, 2021 4 commits
- [Toolbox] Create App precursor network extraction · b46c7c40
  cfrainay authored Apr 16, 2021
  
  b46c7c40
- [Toolbox] Create App scope network extraction · 54229553
  cfrainay authored Apr 16, 2021
  
  54229553
- Merge tag 'hotfix-yml' into develop · 97df772c
  lcottret authored Apr 16, 2021
```
Finish hotfix hotfix-yml
```
  97df772c
- Finish hotfix hotfix-yml · 4d7634c5
  lcottret authored Apr 16, 2021
  
  4d7634c5