- 10 Jan, 2023 6 commits
- 06 Jan, 2023 2 commits
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Clement Frainay authored
Fix handling of weighted metabolic graphs as undirected: Weights are now copied to reverse edges. Correction added in DistanceMatrix and CompoundGraph apps for non-symmetric degree weighting under undirected option. For convenience, use of java8 lambda for weighting and weight processing. See merge request !26
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Clement Frainay authored
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- 20 Dec, 2022 1 commit
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cfrainay authored
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- 15 Dec, 2022 1 commit
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cfrainay authored
Add case for unorthodox format C1xx instead of Cxx. New test cases added
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- 07 Dec, 2022 3 commits
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Clement Frainay authored
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Clement Frainay authored
Feature/get distance manyto many See merge request !18
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Improve shortest path union computation using jgrapht many-to-many implementation. Provides utilities to easily get distance matrix from path computation. DefaultWeightingPolicy name changed to "Unweighted" policy, that need to be explicitly used for unweighted shortest path computation, rather than deprecated ShortestPath methods' parameters
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- 02 Dec, 2022 4 commits
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Clement Frainay authored
Expand SBML Mapping. Expand mapping of chemical data onto metabolic networks (i.e. retrieving chemical entities within a metabolic network) As datasets sometimes provides only chemical names, provides fuzzy matching to get entries with most similar names See merge request !24
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Clement Frainay authored
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Ludovic Cottret authored
reaction balance See merge request !23
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Ludovic Cottret authored
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- 17 Nov, 2022 2 commits
- 15 Nov, 2022 7 commits
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lcottret authored
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lcottret authored
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lcottret authored
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lcottret authored
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lcottret authored
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Ludovic Cottret authored
Feature/set ids from file See merge request !22
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Ludovic Cottret authored
See merge request !22
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- 21 Oct, 2022 3 commits
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Clement Frainay authored
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Clement Frainay authored
Feature/get seeds See merge request !20
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Clement Frainay authored
Identify sources and/or targets in whole model or in external/exchange compartment.
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- 04 Oct, 2022 7 commits
- 22 Sep, 2022 2 commits
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Clement Frainay authored
create apps to export degree and chemical similarity weights for compound graphs See merge request !19
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Clement Frainay authored
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- 16 Sep, 2022 2 commits
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Clement Frainay authored
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Clement Frainay authored
Create RPAIRS-like tags from carbon-skeleton graph, with edge redundancy-based estimation of side transition See merge request !16
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