Fix Issue #53, #83: Predict possible species and gene ID

[AkMo3]

Fixes: #53, #83

New Task Created:

• OrganismAndGeneIdAssertionTask.java

Workflow:

1. While initialisation of EnrichmentCytoPanel, we call methods to set organism and gene ID. https://github.com/cytoscape/enrichment-table-app/blob/e216d18e6167c76520ecb51766842a15146a62b4/src/main/java/org/nrnb/gsoc/enrichment/ui/EnrichmentCytoPanel.java#L271-L274 https://github.com/cytoscape/enrichment-table-app/blob/e216d18e6167c76520ecb51766842a15146a62b4/src/main/java/org/nrnb/gsoc/enrichment/ui/EnrichmentCytoPanel.java#L280-L281

2. In setOrganism(final CyNetwork network):

   • First check if the organism is already present in the network, if present return.
   • Get list of all possible column that may contain species/organism information from OrganismNetworkEntry Enum
   • Iterate through values and check if any of the present values are also present in our list of organisms retrieved from GProfiler. Select the first value that matches.
   • Set the value in the network.

3. In setGeneId(final CyNetwork network, final CyServiceRegistrar registrar):

   • First check if geneID is already present in network
   • If not, check network type and select appropriate column. Eg: getGeneIdFromNetworkName
   • If gene not found, get information from NODE_LABEL style. https://github.com/cytoscape/enrichment-table-app/blob/e216d18e6167c76520ecb51766842a15146a62b4/src/main/java/org/nrnb/gsoc/enrichment/tasks/OrganismAndGeneIdAssertionTask.java#L72-L78