Commit 9b494617 authored by Clement Frainay's avatar Clement Frainay
Browse files

Update output info

parent a9510ada
......@@ -37,9 +37,9 @@ public class ExtractPathways extends AbstractMet4jApplication {
//read smbl
JsbmlReader reader = new JsbmlReader(this.inputPath, false);
BioNetwork network = reader.read();
System.out.println("reaction in network: "+network.getReactionsView().size());
System.out.println("species in network: "+network.getMetabolitesView().size());
System.out.println("genes in network: "+network.getGenesView().size());
System.out.println("Number of reactions in original network: "+network.getReactionsView().size());
System.out.println("Number of species in original network: "+network.getMetabolitesView().size());
System.out.println("Number of genes in original network: "+network.getGenesView().size());
//get all reactions & metabolites
......@@ -52,9 +52,9 @@ public class ExtractPathways extends AbstractMet4jApplication {
for(String id : pathwayId.split("\\+")){
BioPathway pathway = network.getPathwaysView().get(id);
if(pathway!=null) pathways.add(pathway);
System.out.println("reaction in pathway "+pathway.getName()+" ("+id+"): "+network.getReactionsFromPathways(pathway).size());
System.out.println("species in pathway "+pathway.getName()+" ("+id+"): "+network.getMetabolitesFromPathway(pathway).size());
System.out.println("genes in pathway "+pathway.getName()+" ("+id+"): "+network.getGenesFromPathways(pathway).size());
System.out.println("Number of reactions in pathway "+pathway.getName()+" ("+id+"): "+network.getReactionsFromPathways(pathway).size());
System.out.println("Number of species in pathway "+pathway.getName()+" ("+id+"): "+network.getMetabolitesFromPathway(pathway).size());
System.out.println("Number of genes in pathway "+pathway.getName()+" ("+id+"): "+network.getGenesFromPathways(pathway).size());
}
//remove pathway's reactions and metabolites from list
......@@ -67,9 +67,9 @@ public class ExtractPathways extends AbstractMet4jApplication {
network.removeOnCascade(reactions);
network.removeOnCascade(metabolites);
network.removeOnCascade(genes);
System.out.println("reaction in network: "+network.getReactionsView().size());
System.out.println("species in network: "+network.getMetabolitesView().size());
System.out.println("genes in network: "+network.getGenesView().size());
System.out.println("Number of reactions in network: "+network.getReactionsView().size());
System.out.println("Number of species in network: "+network.getMetabolitesView().size());
System.out.println("Number of genes in network: "+network.getGenesView().size());
//export network
JsbmlWriter w = new JsbmlWriter(outputPath, network);
......
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