Examples with Attribute net.sourceforge.ondex.core.Attribute used on opensource projects

Example 1 with Attribute

use of net.sourceforge.ondex.core.Attribute in project knetbuilder by Rothamsted.

the class ONDEXGraphCloner method cloneConcept.

/**
 * Clones a concept from the original graph to the new graph
 *
 * @param conceptToClone
 *            the concept to clone in the original graph
 * @return the new Concept
 */
public ONDEXConcept cloneConcept(ONDEXConcept conceptToClone) {
    if (!metaDataHasBeenCloned) {
        cloneMetaData();
    }
    if (old2newConceptIds.containsKey(conceptToClone.getId())) {
        // " already cloned returning previously cloned concept");
        return newGraph.getConcept(old2newConceptIds.get(conceptToClone.getId()));
    }
    ONDEXGraphMetaData nomd = newGraph.getMetaData();
    String pid = conceptToClone.getPID();
    String desc = conceptToClone.getDescription();
    String anno = conceptToClone.getAnnotation();
    ArrayList<EvidenceType> ets = new ArrayList<EvidenceType>();
    for (EvidenceType evidence : conceptToClone.getEvidence()) {
        ets.add(nomd.getEvidenceType(evidence.getId()));
    }
    DataSource dataSource = conceptToClone.getElementOf();
    DataSource newDataSource = nomd.getDataSource(dataSource.getId());
    ConceptClass cc = conceptToClone.getOfType();
    ConceptClass newCC = nomd.getConceptClass(cc.getId());
    ONDEXConcept newConcept = newGraph.createConcept(pid, anno, desc, newDataSource, newCC, ets);
    // required to prevent StackOverflow when adding itself as tag
    old2newConceptIds.put(conceptToClone.getId(), newConcept.getId());
    for (ONDEXConcept tag : conceptToClone.getTags()) {
        ONDEXConcept newTag;
        if (old2newConceptIds.containsKey(tag.getId())) {
            // check if
            // tag
            // concept
            // exists
            int cid = old2newConceptIds.get(tag.getId());
            newTag = newGraph.getConcept(cid);
        } else {
            // recursive
            newTag = cloneConcept(tag);
        }
        newConcept.addTag(newTag);
    }
    for (Attribute attribute : conceptToClone.getAttributes()) {
        AttributeName att = attribute.getOfType();
        AttributeName newAtt = nomd.getAttributeName(att.getId());
        newConcept.createAttribute(newAtt, attribute.getValue(), attribute.isDoIndex());
    }
    for (ConceptName name : conceptToClone.getConceptNames()) {
        newConcept.createConceptName(name.getName(), name.isPreferred());
    }
    for (ConceptAccession acc : conceptToClone.getConceptAccessions()) {
        dataSource = acc.getElementOf();
        newDataSource = nomd.getDataSource(dataSource.getId());
        newConcept.createConceptAccession(acc.getAccession(), newDataSource, acc.isAmbiguous());
    }
    return newConcept;
}

Example 2 with Attribute

use of net.sourceforge.ondex.core.Attribute in project knetbuilder by Rothamsted.

the class Subgraph method mapOnAttribute.

public final void mapOnAttribute() {
    Set<ONDEXConcept> allConcepts = this.getConcepts();
    Map<ArrayKey<Object>, List<Integer>> gdsToConceptIndex = new HashMap<ArrayKey<Object>, List<Integer>>();
    Map<Integer, List<ArrayKey<Object>>> conceptToGdsIndex = new HashMap<Integer, List<ArrayKey<Object>>>();
    Set<ConceptClass> ccs = StandardFunctions.getContainedConceptClasses(allConcepts);
    // Process a subset for each concept class separately
    for (ConceptClass cc : ccs) {
        Set<ONDEXConcept> subsetByCC = BitSetFunctions.and(allConcepts, graph.getConceptsOfConceptClass(cc));
        gdsToConceptIndex.clear();
        conceptToGdsIndex.clear();
        for (ONDEXConcept c : subsetByCC) {
            // Building the index on all gdss
            CategoryMapBuilder<ArrayKey<Object>, Integer> gdsToConceptIndexBuider = new CategoryMapBuilder<ArrayKey<Object>, Integer>(gdsToConceptIndex);
            CategoryMapBuilder<Integer, ArrayKey<Object>> conceptToGdsIndexBuider = new CategoryMapBuilder<Integer, ArrayKey<Object>>(conceptToGdsIndex);
            for (Attribute attribute : c.getAttributes()) {
                ArrayKey<Object> accessionKey = new ArrayKey<Object>(new Object[] { attribute.getOfType(), attribute.getValue() });
                gdsToConceptIndexBuider.addEntry(accessionKey, c.getId());
                conceptToGdsIndexBuider.addEntry(c.getId(), accessionKey);
            }
        }
        // Collapse equivalent entries
        System.err.println("Finished indexing concepts of " + cc.getId() + " concept class and started collapsing " + now("dd.MM.yyyy G 'at' HH:mm:ss z"));
        Entry<ArrayKey<Object>, List<Integer>> seed = null;
        while (gdsToConceptIndex.size() > 0) {
            Set<Integer> cluster = new HashSet<Integer>();
            seed = gdsToConceptIndex.entrySet().iterator().next();
            List<Integer> subCluster = new ArrayList<Integer>();
            subCluster.addAll(seed.getValue());
            while (true) {
                List<Integer> tempCluster = new ArrayList<Integer>();
                for (Integer nextSeed : subCluster) {
                    List<ArrayKey<Object>> gdss = conceptToGdsIndex.remove(nextSeed);
                    if (gdss != null) {
                        for (ArrayKey<Object> gds : gdss) {
                            List<Integer> list = gdsToConceptIndex.remove(gds);
                            if (list != null)
                                tempCluster.addAll(list);
                        }
                    }
                }
                cluster.addAll(subCluster);
                if (tempCluster.size() == 0) {
                    break;
                }
                subCluster = tempCluster;
            }
            mergeConcepts(cluster);
        }
        gdsToConceptIndex.clear();
        conceptToGdsIndex.clear();
    }
}

Example 3 with Attribute

use of net.sourceforge.ondex.core.Attribute in project knetbuilder by Rothamsted.

the class DecypherAlignment method writeDecypherFASTAFile.

/**
 * @param og                  the current graph
 * @param seqs                the Concepts containing the sequences to write
 * @param filename            the file to write to
 * @param sequenceType        the type of sequence @see net.sourceforge.ondex.programcalls.SequenceType
 * @param includeOnlyTaxIdSeq include only sequences with taxid
 * @return
 * @throws IOException
 */
public static int writeDecypherFASTAFile(ONDEXGraph og, Set<ONDEXConcept> seqs, String filename, SequenceType sequenceType, boolean includeOnlyTaxIdSeq) throws IOException {
    int seqWritten = 0;
    String attSeq = null;
    if (sequenceType.equals(AA)) {
        attSeq = MetaData.Att_AA;
    } else if (sequenceType.equals(NA)) {
        attSeq = MetaData.Att_NA;
    } else {
        System.err.println("Unknow attribute sequence type");
    }
    AttributeName defaultAt = og.getMetaData().getAttributeName(attSeq);
    List<AttributeName> attributesOfSequenceType = new ArrayList<AttributeName>();
    attributesOfSequenceType.add(defaultAt);
    for (int i = 1; i < Integer.MAX_VALUE; i++) {
        AttributeName next = og.getMetaData().getAttributeName(attSeq + ':' + i);
        if (next == null) {
            break;
        } else {
            System.out.println("Found " + attSeq + ':' + i);
            attributesOfSequenceType.add(next);
        }
    }
    AttributeName aTaxID = og.getMetaData().getAttributeName("TAXID");
    if (includeOnlyTaxIdSeq) {
        // filter out concepts without taxid
        Set<ONDEXConcept> taxIdConcepts = og.getConceptsOfAttributeName(aTaxID);
        seqs.retainAll(taxIdConcepts);
    }
    // find concepts with sequences
    Set<ONDEXConcept> attConcepts = null;
    for (AttributeName att : attributesOfSequenceType) {
        Set<ONDEXConcept> sequenceConcepts = og.getConceptsOfAttributeName(att);
        System.out.println(att.getId() + " " + sequenceConcepts.size());
        if (attConcepts == null) {
            attConcepts = sequenceConcepts;
            continue;
        }
        attConcepts.addAll(sequenceConcepts);
        System.out.println("Including " + att.getId());
    }
    // concepts with sequences and TAXID
    seqs.retainAll(attConcepts);
    System.out.println("Writing " + seqs.size() + " concepts with sequences");
    if (seqs.size() == 0) {
        return 0;
    }
    File f = new File(filename);
    f.createNewFile();
    // new buffered writer
    BufferedWriter out = new BufferedWriter(new FileWriter(f));
    StringBuilder line = new StringBuilder(70);
    for (ONDEXConcept concept : seqs) {
        int cid = concept.getId();
        Attribute taxIdAttribute = concept.getAttribute(aTaxID);
        String taxId = null;
        if (taxIdAttribute != null) {
            taxId = (String) taxIdAttribute.getValue();
            if (taxId.trim().length() == 0) {
                if (includeOnlyTaxIdSeq)
                    continue;
            }
        } else {
            if (includeOnlyTaxIdSeq)
                continue;
        }
        for (AttributeName aSeq : attributesOfSequenceType) {
            Attribute attribute = concept.getAttribute(aSeq);
            if (attribute == null) {
                continue;
            }
            Object value = attribute.getValue();
            String[] sequences = null;
            if (value instanceof String)
                sequences = new String[] { ((String) value).toUpperCase().trim() };
            else if (value instanceof Collection) {
                sequences = (String[]) ((Collection) value).toArray();
            } else if (value instanceof String[]) {
                sequences = (String[]) value;
            } else {
                System.err.println(value.getClass() + " is an unknown format for " + aSeq.getId());
                continue;
            }
            for (String seq : sequences) {
                if (seq == null || seq.length() == 0) {
                    System.err.println("empty seq");
                    continue;
                }
                seq = seq.toUpperCase();
                line.append(headerLineStart);
                line.append(cid);
                line.append(TAXID_DELIMINATOR);
                if (taxId != null) {
                    line.append(taxId);
                } else {
                    line.append(EMPTY_TAXID);
                }
                line.append(TAXID_DELIMINATOR);
                line.append(aSeq.getId());
                out.write(line.toString());
                line.setLength(0);
                out.newLine();
                String stringToWrite = null;
                if (sequenceType.equals(NA)) {
                    stringToWrite = replaceAllNonIUPAC_NA_Notation_Chars.matcher(seq).replaceAll("");
                } else {
                    stringToWrite = replaceAllNonChars.matcher(seq).replaceAll("");
                }
                if (stringToWrite == null || stringToWrite.length() == 0) {
                    System.err.println("nout to write");
                    continue;
                }
                for (int i = 0; i < stringToWrite.length(); i = i + 70) {
                    int end = i + 70;
                    if (end > stringToWrite.length() - 1) {
                        end = stringToWrite.length() - 1;
                    }
                    String toWrite = stringToWrite.substring(i, end);
                    if (toWrite.length() > 0) {
                        out.write(toWrite);
                        out.newLine();
                    }
                }
                seqWritten++;
            }
        }
    }
    out.flush();
    out.close();
    return seqWritten;
}

Example 4 with Attribute

use of net.sourceforge.ondex.core.Attribute in project knetbuilder by Rothamsted.

the class Parser method start.

@Override
public void start() throws Exception {
    initaliseMetaData();
    // Get entity factory
    ef = graph.getFactory();
    // holder for things to come
    TabArrayObject tao;
    File dir = new File((String) args.getUniqueValue(FileArgumentDefinition.INPUT_DIR));
    // grab files folder
    String input_dir = dir.getAbsolutePath() + File.separator;
    // TODO:
    /*
           * Start of parsing of td_phenotype
           *
           */
    TabDelimited td_phenotype = new TabDelimited(input_dir + "phenotype.csv");
    // create wildtype phenotype
    ONDEXConcept wildtype = ef.createConcept("", dataSourceAHD, ccAHDPO, etIMPD);
    wildtype.createConceptName("wild type", true);
    while ((tao = td_phenotype.getNext()) != null) {
        // deal with the top level ontology elements
        String organ = (String) tao.getElement(2);
        ONDEXConcept first_level_element = null;
        if (organ.equals("") || organ == null) {
            System.out.println("Error");
        } else {
            if (first_level_elements.containsKey(organ)) {
                first_level_element = first_level_elements.get(organ);
            } else {
                first_level_element = ef.createConcept("", dataSourceAHD, ccAHDPO, etIMPD);
                first_level_element.createConceptName(organ, true);
                first_level_elements.put(organ, first_level_element);
            }
        }
        // deal with second level ontology elements
        String attribute = (String) tao.getElement(3);
        ONDEXConcept second_level_element = null;
        Pair oa = new Pair(organ, attribute);
        if (attribute.equals("") || attribute == null) {
            System.out.println("Error");
        } else {
            if (second_level_elements.containsKey(oa)) {
                second_level_element = second_level_elements.get(oa);
            } else {
                second_level_element = ef.createConcept("", dataSourceAHD, ccAHDPO, etIMPD);
                second_level_element.createConceptName(attribute, true);
                second_level_elements.put(oa, second_level_element);
                // create relation between first and second level elements
                ef.createRelation(second_level_element, first_level_element, rtISA, etIMPD);
            }
        }
        // deal with third level ontology elements
        String phenotype_desc = (String) tao.getElement(6);
        ONDEXConcept third_level_element = null;
        Triple oap = new Triple(organ, attribute, phenotype_desc);
        if (phenotype_desc.equals("") || phenotype_desc == null) {
            System.out.println("Error");
        } else {
            if (third_level_elements.containsKey(oap)) {
                third_level_element = third_level_elements.get(oap);
            } else {
                third_level_element = ef.createConcept("", dataSourceAHD, ccAHDPO, etIMPD);
                third_level_element.createConceptName(phenotype_desc, true);
                third_level_elements.put(oap, third_level_element);
                // create relation between third and second level elements
                ef.createRelation(third_level_element, second_level_element, rtISA, etIMPD);
            }
        }
        // get or creating hormones
        ONDEXConcept hormone = getHormone((String) tao.getElement(5));
        // get or creating plants
        ONDEXConcept plant = getPlant((String) tao.getElement(1));
        // create experiments
        ONDEXConcept experiment = ef.createConcept("", dataSourceAHD, ccExp, etIMPD);
        experiment.createConceptAccession((String) tao.getElement(0), dataSourceAHD, false);
        // linking experiments to phenotypes
        ef.createRelation(experiment, third_level_element, rtOP, etIMPD);
        // linking experiments to plants
        ef.createRelation(plant, experiment, rtPP, etIMPD);
        // linking experiments to hormone
        String has_hormone = (String) tao.getElement(4);
        if (has_hormone.equals("0")) {
            ef.createRelation(experiment, hormone, rtNotTreat, etIMPD);
        } else if (has_hormone.equals("1")) {
            ef.createRelation(experiment, hormone, rtTreat, etIMPD);
        } else if (has_hormone.equals("2")) {
            ef.createRelation(experiment, hormone, rtAssoc, etIMPD);
        } else {
            System.err.println("Error in phenotype - column 4");
            tao.debug();
        }
    }
    // reset tab array object
    tao = null;
    td_phenotype = null;
    /*
           * Start of parsing of td_plant_hormone
           *
           */
    TabDelimited td_plant_hormone = new TabDelimited(input_dir + "plant_hormone.csv");
    while ((tao = td_plant_hormone.getNext()) != null) {
        String plantName = (String) tao.getElement(1);
        String hormoneName = (String) tao.getElement(2);
        ONDEXConcept plant = getPlant(plantName);
        ONDEXConcept hormone = getHormone(hormoneName);
        ONDEXRelation r = ef.createRelation(plant, hormone, rtAssoc, etIMPD);
        if (tao.getElement(3).equals("yes")) {
            r.createAttribute(anTLConf, true, false);
        } else if (tao.getElement(3).equals("no")) {
            r.createAttribute(anTLConf, false, false);
        } else {
            System.err.println("Error in plant hormone - column 3");
            tao.debug();
        }
    }
    // reset tab array object
    tao = null;
    td_plant_hormone = null;
    /*
           * Start of parsing of td_plant_info
           *
           */
    TabDelimited td_plant_info = new TabDelimited(input_dir + "plant_info.csv");
    while ((tao = td_plant_info.getNext()) != null) {
        ONDEXConcept plant = getPlant((String) tao.getElement(0));
        String eco = (String) tao.getElement(1);
        if (!eco.equals("")) {
            plant.createAttribute(anEco, eco, false);
        }
        String mut = (String) tao.getElement(2);
        if (!mut.equals("")) {
            plant.createAttribute(anMut, mut, false);
        }
        String dom = (String) tao.getElement(3);
        if (!dom.equals("")) {
            plant.createAttribute(anDominance, dom, false);
        }
        String plantType = (String) tao.getElement(6);
        if (!plantType.equals("")) {
            plant.createAttribute(anPlantType, plantType, false);
        }
        String desc = (String) tao.getElement(5);
        if (!desc.equals("")) {
            plant.createAttribute(anDesc, desc, false);
        }
        String pmidsList = (String) tao.getElement(4);
        if (!pmidsList.equals("")) {
            if (pmidsList.contains(";")) {
                String[] pmidsL = pmidsList.split(";");
                for (String n : pmidsL) {
                    ONDEXConcept pub = getPub(n);
                    ef.createRelation(plant, pub, rtPub, etIMPD);
                }
            } else {
                ONDEXConcept pub = getPub(pmidsList);
                ef.createRelation(plant, pub, rtPub, etIMPD);
            }
        }
    }
    // reset tab array object
    tao = null;
    td_plant_info = null;
    TabDelimited td_gene_hormone_plant = new TabDelimited(input_dir + "gene_hormone_plant.csv");
    while ((tao = td_gene_hormone_plant.getNext()) != null) {
        String geneAcc = (String) tao.getElement(1);
        ONDEXConcept g = getGene(geneAcc);
        // AHD names
        String geneName = (String) tao.getElement(2);
        if (!geneName.equals("")) {
            if (geneName.contains(",")) {
                String[] gNames = geneName.split(",");
                for (String n : gNames) {
                    if (g.getConceptName(n) == null) {
                        g.createConceptName(n, true);
                    }
                }
            } else {
                if (g.getConceptName(geneName) == null) {
                    g.createConceptName(geneName, true);
                }
            }
        }
        // linking genes to plants
        String plantName = (String) tao.getElement(4);
        ONDEXConcept plant = getPlant(plantName);
        ONDEXRelation hasMutatedGene = graph.getRelation(plant, g, rtHasMutatedGene);
        if (graph.getRelation(plant, g, rtHasMutatedGene) == null) {
            hasMutatedGene = ef.createRelation(plant, g, rtHasMutatedGene, etIMPD);
        }
        // linking genes to hormones
        // TODO: Find better relation
        String hormoneName = (String) tao.getElement(3);
        ONDEXConcept hormone = getHormone(hormoneName);
        if (graph.getRelation(g, hormone, rtAssoc) == null) {
            ef.createRelation(g, hormone, rtAssoc, etIMPD);
        }
        try {
            String site = (String) tao.getElement(5);
            if (!site.equals("")) {
                if (!hasMutatedGene.getAttribute(anSite).getValue().equals(site)) {
                    hasMutatedGene.createAttribute(anSite, site, false);
                }
            }
        } catch (Exception e) {
        // do nothing
        }
    }
    // reset tab array object
    tao = null;
    td_gene_hormone_plant = null;
    TabDelimited td_gene_hormone_info = new TabDelimited(input_dir + "gene_hormone_info.csv");
    while ((tao = td_gene_hormone_info.getNext()) != null) {
        String gAcc = (String) tao.getElement(1);
        String gName = (String) tao.getElement(2);
        ONDEXConcept gene = getGene(gAcc);
        if ((!gName.equals("")) && gene.getConceptName(gName) == null) {
            gene.createConceptName(gName, true);
        }
        String hormoneName = (String) tao.getElement(3);
        ONDEXConcept hormone = getHormone(hormoneName);
        ONDEXRelation geneToHormone = graph.getRelation(gene, hormone, rtAssoc);
        if (geneToHormone == null) {
            geneToHormone = ef.createRelation(gene, hormone, rtAssoc, etIMPD);
        }
        String hormoneRole = (String) tao.getElement(4);
        if (!hormoneRole.equals("-") && !hormoneRole.equals("")) {
            if (geneToHormone.getAttribute(anGeneRole) == null) {
                geneToHormone.createAttribute(anGeneRole, hormoneRole, false);
            } else if (geneToHormone.getAttribute(anGeneRole).getValue().equals(hormoneRole)) {
            // do nothing
            } else {
                // some kind of duplication going on...
                tao.debug();
            }
        }
        String geneDesc = (String) tao.getElement(5);
        if (!geneDesc.equals("")) {
            Attribute attribute = geneToHormone.getAttribute(anDesc);
            if (attribute == null) {
                geneToHormone.createAttribute(anDesc, geneDesc, false);
            } else if (attribute.getValue().equals(geneDesc)) {
            // do nothing
            } else {
                // System.err.println("problem here " + (String) tao.getElement(1));
                // appending the new description onto the old one
                attribute.setValue(attribute.getValue() + " ; " + geneDesc);
            }
        }
        // still potentially same problems as above
        Attribute sureattribute = geneToHormone.getAttribute(anTLConf);
        String sure = (String) tao.getElement(7);
        if (sureattribute == null) {
            if (sure.equals("yes")) {
                geneToHormone.createAttribute(anTLConf, true, false);
            } else if (sure.equals("no")) {
                geneToHormone.createAttribute(anTLConf, false, false);
            } else {
                System.err.println("Error in gene-hormone info - column 7");
                tao.debug();
            }
        } else if (sureattribute.getValue().equals(sure)) {
        // do nothing
        } else {
            // default to no if there's a conflict
            sureattribute.setValue(false);
        }
        // still same problem as above
        // evidence issue, when 2 or more things have one from and one not from go
        // defaults to go if there's a clash
        Attribute goaattribute = geneToHormone.getAttribute(anGOA);
        String go = (String) tao.getElement(8);
        if (goaattribute == null) {
            if (go == null || go.isEmpty()) {
                geneToHormone.addEvidenceType(etGI);
            } else if (go.equals("GO")) {
                geneToHormone.addEvidenceType(etGOA);
            // geneToHormone.createGDS(anGOA, "yes", false);
            } else if (go.equals("other")) {
                geneToHormone.addEvidenceType(etIMPD);
            }
        } else if (goaattribute.getValue().equals(go)) {
        // do nothing
        } else {
            // default to go if there's a conflict
            goaattribute.setValue("GO");
        }
        // tying all publication information to the gene only, even though it's not quite true..
        // the publication should really be tied to the relations, but one cannot set up a relation
        // between a relation and a node
        String pimds = (String) tao.getElement(6);
        if (pimds.equals("")) {
        } else if (pimds.contains(";")) {
            String[] pids = pimds.split(";");
            for (String p : pids) {
                ONDEXConcept pub = getPub(p);
                if (graph.getRelation(gene, pub, rtPub) == null) {
                    ef.createRelation(gene, pub, rtPub, etIMPD);
                }
            }
        } else {
            // get publication or create
            ONDEXConcept pub = getPub(pimds);
            // make relation if none already exists
            if (graph.getRelation(gene, pub, rtPub) == null) {
                ef.createRelation(gene, pub, rtPub, etIMPD);
            }
        }
    }
/*
           * Microarray stuff follows here
           *

          // reset tab array object
          tao = null;
          td_gene_hormone_info = null;

          TabDelimited td_gene_hormone_microarray = new TabDelimited(input_dir+"gene_hormone_microarray.csv");

          while ((tao = td_gene_hormone_microarray.getNext()) != null) {

              String row_id = (String) tao.getElement(0);
              String exp_id = (String) tao.getElement(1);
              String hormoneName = (String) tao.getElement(2);
              String locusName = (String) tao.getElement(3);
              String microArrayData = (String) tao.getElement(4);

              ONDEXConcept hormone = getHormone(hormoneName);
              ONDEXConcept gene = getGene(locusName);
              ONDEXConcept mexp = getExp(exp_id);

              ONDEXConcept c = ef.createConcept("", dataSourceAHD, ccExp, etIMPD);
              c.createConceptAccession(row_id, dataSourceAHD, false);

              ef.createRelation(c, mexp, rtContrib, etIMPD);
              ef.createRelation(c, hormone, rtAssoc, etIMPD);
              ef.createRelation(gene, c, rtPP, etIMPD);

              c.createGDS(anMicro, microArrayData, false);


          }

          // reset tab array object
          tao = null;
          td_gene_hormone_microarray = null;

          // microarray info
          // there is some stuff not parsed, but not sure about the value of them
          TabDelimited microarray_info = new TabDelimited(input_dir+"microarray_info.csv");

          while ((tao = microarray_info.getNext()) != null) {

              String exp_id = (String) tao.getElement(0);
              String plantName = (String) tao.getElement(2);
              String hormoneName = (String) tao.getElement(4);
              String pmid = ((String) tao.getElement(9)).substring(6); // trim the "PMID: "
              String url = (String) tao.getElement(11);



              ONDEXConcept mexp = getExp(exp_id);
              ONDEXConcept pub = getPub(pmid);
              ONDEXConcept hormone = getHormone(hormoneName);
              ONDEXConcept plant = getPlant(plantName);


              ef.createRelation(mexp, pub, rtPub, etIMPD);
              ef.createRelation(hormone, mexp, rtAssoc, etIMPD);
              ef.createRelation(plant, mexp, rtPP, etIMPD);

              mexp.createGDS(anMicro, url, false);




          }

          */
}

Example 5 with Attribute

use of net.sourceforge.ondex.core.Attribute in project knetbuilder by Rothamsted.

the class Parser method mergeRelations.

/**
 * Merges relations occurrences and attributes across two ONDEX graphs into
 * first one.
 *
 * @param graph1
 * @param graph2
 */
private void mergeRelations(ONDEXGraph graph1, ONDEXGraph graph2) {
    // iterate over all relations in second graph
    for (ONDEXRelation r : graph2.getRelations()) {
        // check if relation already present in first graph
        ONDEXRelation r1 = graph1.getRelation(r.getFromConcept(), r.getToConcept(), r.getOfType());
        if (r1 == null) {
            // create new relation in first graph
            r1 = graph1.createRelation(r.getFromConcept(), r.getToConcept(), r.getOfType(), r.getEvidence());
        }
        // synchronise tags
        Set<ONDEXConcept> newTags = new HashSet<ONDEXConcept>(r.getTags());
        newTags.removeAll(r1.getTags());
        for (ONDEXConcept c : newTags) {
            if (graph1.getConcept(c.getId()) != null)
                r1.addTag(c);
        }
        // synchronise evidence
        Set<EvidenceType> newEvidence = new HashSet<EvidenceType>(r.getEvidence());
        newEvidence.removeAll(r1.getEvidence());
        for (EvidenceType et : newEvidence) {
            // create new evidence type if not existing
            if (graph1.getMetaData().getEvidenceType(et.getId()) == null)
                graph1.getMetaData().createEvidenceType(et.getId(), et.getFullname(), et.getDescription());
            r1.addEvidenceType(et);
        }
        // synchronise attributes
        Set<Attribute> newAttributes = new HashSet<Attribute>(r.getAttributes());
        newAttributes.removeAll(r1.getAttributes());
        for (Attribute attr : newAttributes) {
            AttributeName an = attr.getOfType();
            // create new attribute name if not existing
            if (graph1.getMetaData().getAttributeName(an.getId()) == null)
                graph1.getMetaData().createAttributeName(an.getId(), an.getFullname(), an.getDescription(), an.getUnit(), an.getDataType(), an.getSpecialisationOf());
            r1.createAttribute(an, attr.getValue(), attr.isDoIndex());
        }
    }
}