Merge branch 'feature/mergedSideCompounds' into 'develop'

handling mutliple compartments in side compound scan

See merge request !8

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

@@ -4,19 +4,22 @@ import fr.inrae.toulouse.metexplore.met4j_chemUtils.FormulaParser;
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
 import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.DefaultWeightPolicy;
+import fr.inrae.toulouse.metexplore.met4j_graph.computation.transform.VertexContraction;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
 import fr.inrae.toulouse.metexplore.met4j_graph.io.Bionetwork2BioGraph;
 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.JsbmlReader;
 import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
-import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
 import fr.inrae.toulouse.metexplore.met4j_toolbox.generic.AbstractMet4jApplication;
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
 import org.kohsuke.args4j.Option;
 
 import java.io.FileWriter;
 import java.io.IOException;
-import java.util.regex.Pattern;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
 
 /**
  *
@@ -50,6 +53,11 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
     @Option(name = "-er", aliases = {"--edgeRedundancy"}, usage = "flag as side compound any compound with a number of redundancy in incident edges (parallel edges connecting to the same neighbor) above the given threshold")
     public double parallelEdge = Double.NaN;
 
+    enum strategy {by_name,by_id}
+    @Option(name = "-m", aliases = {"--merge"}, usage = "Degree is shared between compounds in different compartments. " +
+            "Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form \"xxx_y\" with xxx as base identifier and y as compartment label).")
+    public strategy mergingStrat = null;
+
 
     public static void main(String[] args) throws IOException, Met4jSbmlReaderException {
 
@@ -86,12 +94,32 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
         //perform scan
         //------------
         System.err.println("Scaning...");
+
+        //if merging compartment
+        Map<String, Integer> mergedDegree = new HashMap<>();
+        Boolean merge = (mergingStrat!=null);
+        Function<BioMetabolite,String> getSharedId = BioMetabolite::getName;
+        if(merge){
+            if(mergingStrat.equals(strategy.by_id)) getSharedId = (new VertexContraction.MapByIdSubString("^(\\w+)_\\w$"))::commonField;
+
+            mergedDegree = graph.vertexSet().stream().collect(
+                    Collectors.groupingBy(
+                            getSharedId,
+                            Collectors.summingInt(v -> graph.degreeOf(v))
+                    )
+            );
+        }
+
         //degree statistics
         DescriptiveStatistics degreeStats = new DescriptiveStatistics();
         double dt = degree;
         if (!Double.isNaN(degreePrecentile)) {
             for (BioMetabolite v : graph.vertexSet()) {
-                degreeStats.addValue(graph.degreeOf(v));
+                if (merge){
+                    degreeStats.addValue(mergedDegree.get(getSharedId.apply(v)));
+                }else{
+                    degreeStats.addValue(graph.degreeOf(v));
+                }
             }
             dt = degreeStats.getPercentile(degreePrecentile);
         }
@@ -120,7 +148,7 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
             StringBuffer l = new StringBuffer(v.getId());
             if (reportValue) l.append("\t" + v.getName());
 
-            int d = graph.degreeOf(v);
+            int d = merge ? mergedDegree.get(getSharedId.apply(v)) : graph.degreeOf(v);
             boolean sideFromDegree = (d >= degree);
             if (sideFromDegree) side = true;
             if (reportValue) l.append("\t" + d);
@@ -137,7 +165,7 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
             if (flagInorganic || flagNoFormula) {
                 String formula = v.getChemicalFormula();
                 String inorganic = "?";
-                String validForumla = "true";
+                String validFormula = "true";
                 try{
                     FormulaParser fp = new FormulaParser(formula);
                     if(flagInorganic){
@@ -150,14 +178,14 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
                     }
                 }catch(IllegalArgumentException e){
                     if(flagNoFormula){
-                        validForumla = "false";
+                        validFormula = "false";
                         side = true;
                     }
 
                 }
                 if (reportValue){
                     if(flagInorganic) l.append("\t" + inorganic);
-                    if(flagNoFormula) l.append("\t" + validForumla);
+                    if(flagNoFormula) l.append("\t" + validFormula);
                 }
             }
 
@@ -185,7 +213,7 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
     public String getLongDescription() {
         return this.getShortDescription() + "\n" +
                 "Side compounds are metabolites of small relevance for topological analysis. Their definition can be quite subjective and varies between sources.\n" +
-                "Side compounds tends to be ubiquitous and not specific to a particular biochemical or physiological process.\n" +
+                "Side compounds tend to be ubiquitous and not specific to a particular biochemical or physiological process." +
                 "Compounds usually considered as side compounds include water, atp or carbon dioxide. By being involved in many reactions and thus connected to many compounds, " +
                 "they tend to significantly lower the average shortest path distances beyond expected metabolic relatedness.\n" +
                 "This tool attempts to propose a list of side compounds according to specific criteria:  \n" +