[Toolbox] empty file handling in NetworkAnalysis

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/MetaboRank.java

@@ -144,10 +144,12 @@ public class MetaboRank extends AbstractMet4jApplication {
         System.err.println("transition probabilities computed (reverse graph)");
 
         importSeeds(seedsFilePath);
-
-        compute();
-
-        printCompoundTable(output);
+        if(seeds.isEmpty()){
+            System.err.println("no seed available, computation aborted");
+        }else{
+            compute();
+            printCompoundTable(output);
+        }
         System.err.println("done.");
 
     }

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/PrecursorNetwork.java

@@ -71,10 +71,14 @@ public class PrecursorNetwork extends AbstractMet4jApplication {
                 .map(BioReaction.class::cast)
                 .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
 
-        fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.PrecursorNetwork precursorComp =
-                new fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.PrecursorNetwork(graph, bootstraps, targets, forbidden);
-        BipartiteGraph precursorNet = precursorComp.getPrecursorNetwork();
-        ExportGraph.toGml(precursorNet, output);
+        if(targets.isEmpty()){
+            System.err.println("no target available, computation aborted");
+        }else {
+            fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.PrecursorNetwork precursorComp =
+                    new fr.inrae.toulouse.metexplore.met4j_graph.computation.analyze.PrecursorNetwork(graph, bootstraps, targets, forbidden);
+            BipartiteGraph precursorNet = precursorComp.getPrecursorNetwork();
+            ExportGraph.toGml(precursorNet, output);
+        }
     }
 
     @Override

met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/ScopeNetwork.java

@@ -79,14 +79,18 @@ public class ScopeNetwork extends AbstractMet4jApplication {
                     .map(BioReaction.class::cast)
                     .collect(BioCollection::new, BioCollection::add, BioCollection::addAll);
 
-        ScopeCompounds scopeComp = new ScopeCompounds(graph, seeds, bootstraps, forbidden);
-        if (includeSides) scopeComp.includeBootstrapsInScope();
-        if (trace) scopeComp.trace();
-        BipartiteGraph scope = scopeComp.getScopeNetwork();
-        if (trace) {
-            ExportGraph.toGmlWithAttributes(scope, output, scopeComp.getExpansionSteps(), "step");
-        } else {
-            ExportGraph.toGml(scope, output);
+        if(seeds.isEmpty()){
+            System.err.println("no seed available, computation aborted");
+        }else {
+            ScopeCompounds scopeComp = new ScopeCompounds(graph, seeds, bootstraps, forbidden);
+            if (includeSides) scopeComp.includeBootstrapsInScope();
+            if (trace) scopeComp.trace();
+            BipartiteGraph scope = scopeComp.getScopeNetwork();
+            if (trace) {
+                ExportGraph.toGmlWithAttributes(scope, output, scopeComp.getExpansionSteps(), "step");
+            } else {
+                ExportGraph.toGml(scope, output);
+            }
         }
 
     }