GeneUtils.java

package org.genedb.web.mvc.controller;

import org.gmod.schema.feature.MRNA;
import org.gmod.schema.mapped.Feature;
import org.gmod.schema.mapped.FeatureRelationship;

import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;

public class GeneUtils {

    private static String[] geneNameParts = {"gene", "mRNA", "polypeptide", "intron", "exon"};
    private static Set<String> geneParts = new HashSet<String>();
    
    static {
        geneParts.addAll(Arrays.asList(geneNameParts));
    }
    
    // FIXME - This is just it's possible, not certain
    public static boolean isPartOfGene(Feature feature) {
        if (geneParts.contains(feature.getType().getName())) {
            //System.err.println("Returning true for "+feature.getUniqueName());
            return true;
        }
        //System.err.println("Returning false for "+feature.getUniqueName());
        return false;
    }

    public static Feature getGeneFromPart(Feature feature) {
        if ("polypeptide".equals(feature.getType().getName())) {
            //System.err.println("Looking for gene for "+feature.getUniqueName());
            Feature gene = null;
            Feature mRNA = null;
            Collection<FeatureRelationship> frs = feature.getFeatureRelationshipsForSubjectId();
            for (FeatureRelationship relationship : frs) {
                //System.err.println("FeatureRealtionship for mRNA is "+relationship.getFeatureByObjectId().getUniqueName());
                if(relationship.getType().getName().equals("derives_from")){
                    mRNA = relationship.getObjectFeature();
                }
            }
            if (mRNA != null) {
                frs = mRNA.getFeatureRelationshipsForSubjectId();
                for (FeatureRelationship relationship : frs) {
                    if(relationship.getType().getName().equals("part_of")) {
                        gene = relationship.getObjectFeature();
                    }
                    //Feature feat = relationship.getFeatureByObjectId();
                    
                }
            }
            return gene;
        }
        return feature;
    }

    

}