Examples with Annotation org.nextprot.api.core.domain.annotation.Annotation used on opensource projects

Example 56 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class PepXServiceTest method shouldReturnAnEmptryListIfTheVariantIsNotConaintedInThePeptide.

@Test
public void shouldReturnAnEmptryListIfTheVariantIsNotConaintedInThePeptide() throws Exception {
    // Taking example NX_Q9H6T3
    String peptide = "GANAP";
    boolean modeIsoleucine = true;
    String isoName = "NX_Q9H6T3-3";
    Isoform isoform = mock(Isoform.class);
    when(isoform.getIsoformAccession()).thenReturn(isoName);
    // https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/simple.html
    // (check that page to format the sequence)
    // GANAL is present instead of GANAP
    when(isoform.getSequence()).thenReturn("MDADPYNPVLPTNRASAYFRLKKFAVAESDCNLAVALNRSYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNNFEATNELRKISQALASKENSYPKEADIVIKSTEGERKQIEAQQNKQQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETVLLLEPGNKQAVTELSKIKKELIEKGHWDDVFLDSTQRQNVVKPIDNPPHPGSTKPLKKVIIEETGNLIQTIDVPDSTTAAAPENNPINLANVIAATGTTSKKNSSQDDLFPTSDTPRAKVLKIEEVSDTSSLQPQASLKQDVCQSYSEKMPIEIEQKPAQFATTVLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHDFYIEKEKPLLIFEILQRLSELKRFDMAVMFMSETEKKIARALFNHIDKSGLKDSSVEELKKRYGG");
    PepXIsoformMatch pepXIsoformMatch = new PepXIsoformMatch(isoName, 154);
    List<Annotation> annots = Arrays.asList(getMockedAnnotation("L", "Z", 158, isoName, true));
    List<Isoform> isoforms = Arrays.asList(isoform);
    // empty
    List<Annotation> result = PepXServiceImpl.buildEntryWithVirtualAnnotations(peptide, modeIsoleucine, Arrays.asList(pepXIsoformMatch), annots, isoforms);
    // or
    // null
    // annotations
    assertTrue(result.isEmpty());
}

Example 57 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class PepXServiceTest method shouldGiveAnExceptionIfTheOriginalIsNotPresentOnTheSequence.

/*
	 * Specification has changed look at:
	 * shouldReturnAnEmptryListIfTheVariantIsNotConaintedInThePeptide
	 * 
	 * @Test(expected=NextProtException.class) public void
	 * shouldGiveAnExceptionIfTheVariantIsNotConaintedInThePeptide() throws
	 * Exception { try {
	 * 
	 * //Taking example NX_Q9H6T3 String peptide = "GANAP"; boolean
	 * modeIsoleucine = true; String isoName = "NX_Q9H6T3-3";
	 * 
	 * Isoform isoform = mock(Isoform.class);
	 * when(isoform.getIsoformAccession()).thenReturn(isoName);
	 * //https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/
	 * simple.html (check that page to format the sequence) //GANAL is present
	 * instead of GANAP when(isoform.getSequence()).thenReturn(
	 * "MDADPYNPVLPTNRASAYFRLKKFAVAESDCNLAVALNRSYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNNFEATNELRKISQALASKENSYPKEADIVIKSTEGERKQIEAQQNKQQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETVLLLEPGNKQAVTELSKIKKELIEKGHWDDVFLDSTQRQNVVKPIDNPPHPGSTKPLKKVIIEETGNLIQTIDVPDSTTAAAPENNPINLANVIAATGTTSKKNSSQDDLFPTSDTPRAKVLKIEEVSDTSSLQPQASLKQDVCQSYSEKMPIEIEQKPAQFATTVLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHDFYIEKEKPLLIFEILQRLSELKRFDMAVMFMSETEKKIARALFNHIDKSGLKDSSVEELKKRYGG"
	 * );
	 * 
	 * List<Pair<String, Integer>> isosAndPositions = Arrays.asList(new
	 * Pair<String, Integer>(isoName, 154)); //Position of the begin of peptide
	 * List<Annotation> annots = Arrays.asList(getMockedAnnotation("L", "Z",
	 * 158, isoName, true)); List<Isoform> isoforms = Arrays.asList(isoform);
	 * 
	 * PepXServiceImpl.buildEntryWithVirtualAnnotations(peptide, modeIsoleucine,
	 * isosAndPositions, annots, isoforms); //empty or null annotations
	 * }catch(NextProtException e){ if(e.getMessage().contains(
	 * "No valid variants found for isoform ")){ throw e; //success tests }else
	 * fail(); }
	 * 
	 * }
	 */
// because we have variants in nextprot which do not have original aa is not equal to isoform aa at that variant position (inconsistency)
@Ignore
@Test(expected = NextProtException.class)
public void shouldGiveAnExceptionIfTheOriginalIsNotPresentOnTheSequence() throws Exception {
    try {
        // Taking example NX_Q9H6T3
        String peptide = "GANAP";
        boolean modeIsoleucine = true;
        String isoName = "NX_Q9H6T3-3";
        Isoform isoform = mock(Isoform.class);
        when(isoform.getIsoformAccession()).thenReturn(isoName);
        // https://cdn.rawgit.com/calipho-sib/sequence-viewer/master/examples/simple.html
        // (check that page to format the sequence)
        // GANAL is present instead of GANAP
        when(isoform.getSequence()).thenReturn("MDADPYNPVLPTNRASAYFRLKKFAVAESDCNLAVALNRSYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNNFEATNELRKISQALASKENSYPKEADIVIKSTEGERKQIEAQQNKQQAISEKDRGNGFFKEGKYERAIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTARTFLGKLNEAKQDFETVLLLEPGNKQAVTELSKIKKELIEKGHWDDVFLDSTQRQNVVKPIDNPPHPGSTKPLKKVIIEETGNLIQTIDVPDSTTAAAPENNPINLANVIAATGTTSKKNSSQDDLFPTSDTPRAKVLKIEEVSDTSSLQPQASLKQDVCQSYSEKMPIEIEQKPAQFATTVLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHDFYIEKEKPLLIFEILQRLSELKRFDMAVMFMSETEKKIARALFNHIDKSGLKDSSVEELKKRYGG");
        PepXIsoformMatch pepXIsoformMatch = new PepXIsoformMatch(isoName, 154);
        // Original is not contained in the sequence, should be a L L->P
        // (GANAL)
        List<Annotation> annots = Arrays.asList(getMockedAnnotation("O", "P", 158, isoName, true));
        List<Isoform> isoforms = Arrays.asList(isoform);
        // empty
        PepXServiceImpl.buildEntryWithVirtualAnnotations(peptide, modeIsoleucine, Arrays.asList(pepXIsoformMatch), annots, isoforms);
    // or
    // null
    // annotations
    } catch (NextProtException e) {
        if (e.getMessage().contains("The amino acid")) {
            // success tests
            throw e;
        } else
            fail();
    }
}

Example 58 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class AnnotationFieldBuilder method init.

@Override
protected void init(Entry entry) {
    // Function with canonical first
    List<String> function_canonical = EntryUtils.getFunctionInfoWithCanonicalFirst(entry);
    for (String finfo : function_canonical) {
        addField(Fields.FUNCTION_DESC, finfo);
        addField(Fields.ANNOTATIONS, finfo);
    }
    List<Annotation> annots = entry.getAnnotations();
    for (Annotation currannot : annots) {
        String category = currannot.getCategory();
        AnnotationCategory apiCategory = currannot.getAPICategory();
        String quality = currannot.getQualityQualifier();
        if (apiCategory.equals(AnnotationCategory.FUNCTION_INFO) || apiCategory.equals(AnnotationCategory.EXPRESSION_PROFILE))
            // and tissue specificity values are indexed under other fields
            continue;
        // We also should exclude uninformative category 'sequence conflict'
        // if(!category.equals("tissue specificity")) {//These values are
        // indexed under other fields
        // if(!apiCategory.equals(AnnotationCategory.) {//These values are
        // indexed under other fields
        String desc = currannot.getDescription();
        if (apiCategory.equals(AnnotationCategory.GLYCOSYLATION_SITE)) {
            String xref = currannot.getSynonym();
            if (xref != null)
                // It is actually not a synonym but the carbohydrate id from
                // glycosuitedb !
                addField(Fields.ANNOTATIONS, xref);
        } else if (apiCategory.equals(AnnotationCategory.DNA_BINDING_REGION))
            addField(Fields.ANNOTATIONS, category);
        else if (apiCategory.equals(AnnotationCategory.VARIANT))
            // We need to index them somehow for the GOLD/SILVER tests, or
            // do we ? in creates a lot of useless 'variant null' tokens
            desc = "Variant " + desc;
        if (desc != null) {
            // System.err.println(category + ": " + desc);
            if (apiCategory.equals(AnnotationCategory.SEQUENCE_CAUTION)) {
                int stringpos = 0;
                // The sequence
                desc = desc.split(":")[1].substring(1);
                // AAH70170 differs
                // from that shown.
                // Reason:
                // miscellaneous
                // discrepancy
                String[] desclevels = desc.split("\\.");
                String mainreason = desclevels[0];
                if ((stringpos = mainreason.indexOf(" at position")) != -1) {
                    // truncate the position
                    mainreason = mainreason.substring(0, stringpos);
                }
                addField(Fields.ANNOTATIONS, mainreason);
                if (desclevels.length > 1) {
                    if (// mainreason truncated
                    stringpos > 0)
                        desc = desc.substring(desc.indexOf(".") + 2);
                    else {
                        stringpos = desc.indexOf(mainreason) + mainreason.length();
                        desc = desc.substring(stringpos + 2);
                    }
                    addField(Fields.ANNOTATIONS, desc);
                }
            }
            if (!category.startsWith("go") && desc.length() > 1) {
                // description
                if (!this.isGold() || quality.equals("GOLD")) {
                    if (apiCategory.equals(AnnotationCategory.PHENOTYPIC_VARIATION)) {
                        // Get BED data (also get the notes ? )
                        Map<String, AnnotationIsoformSpecificity> annotSpecs = currannot.getTargetingIsoformsMap();
                        for (Map.Entry<String, AnnotationIsoformSpecificity> mapentry : annotSpecs.entrySet()) {
                            String subjectName = mapentry.getValue().getName();
                            // update description with the subject for each
                            // target isofotm
                            addField(Fields.ANNOTATIONS, subjectName + " " + desc);
                        // System.err.println("adding: " + subjectName +
                        // " " + desc);
                        }
                    } else
                        addField(Fields.ANNOTATIONS, desc);
                }
            }
        // in pathway and disease new annotations may appear due to
        // transformation of specific xrefs (orphanet...) into
        // annotations in the api
        }
        handleAnnotationTerm(currannot, entry);
        if (apiCategory.equals(AnnotationCategory.MATURE_PROTEIN) || apiCategory.equals(AnnotationCategory.MATURATION_PEPTIDE)) {
            String chainid = currannot.getSynonym();
            if (chainid != null) {
                // " synonyms: " + currannot.getAllSynonyms());
                if (chainid.contains("-"))
                    // Uniprot FT id,
                    addField(Fields.ANNOTATIONS, chainid);
                else // like
                // PRO_0000019235,
                // shouldn't be
                // called a
                // synonym
                {
                    List<String> chainsynonyms = currannot.getSynonyms();
                    if (chainsynonyms.size() == 1)
                        addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(desc + " | " + chainid));
                    else {
                        chainid = "";
                        for (String syno : chainsynonyms) {
                            chainid += syno + " | ";
                        }
                        addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(chainid));
                    }
                }
            }
        // else System.err.println("chainid null for: " + desc);
        // chainid 's null for the main chain, this is wrong
        }
        // variant xrefs and identifiers
        if (apiCategory.equals(AnnotationCategory.VARIANT)) {
            String evidxrefaccs = "";
            List<AnnotationEvidence> evidences = currannot.getEvidences();
            if (evidences != null)
                for (AnnotationEvidence ev : evidences) {
                    if (ev.isResourceAXref()) {
                        String db = ev.getResourceDb();
                        if (db == null)
                            System.err.println("db is null for evidence in variant annot: " + desc);
                        else {
                            if (!evidxrefaccs.isEmpty())
                                evidxrefaccs += " | ";
                            if (db.equals("Cosmic"))
                                evidxrefaccs += db.toLowerCase() + ":" + ev.getResourceAccession();
                            else if (// Just to allow
                            db.equals("dbSNP"))
                                // comparison with
                                // incoherent
                                // current solr
                                // implementation
                                evidxrefaccs += ev.getResourceAccession();
                            else
                                // Uniprot
                                evidxrefaccs += currannot.getSynonym();
                        // FT
                        // id,
                        // like
                        // VAR_056577
                        }
                    }
                }
            if (!this.isGold() || quality.equals("GOLD")) {
                if (!evidxrefaccs.isEmpty())
                    addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(evidxrefaccs));
                Collection<AnnotationProperty> props = currannot.getProperties();
                for (AnnotationProperty prop : props) if (prop.getName().equals("mutation AA"))
                    // eg: p.D1685E, it is unclear why this property
                    // exists only in cosmic variants
                    addField(Fields.ANNOTATIONS, prop.getValue());
            }
        }
    }
    // Families (why not part of Annotations ?), always GOLD
    for (Family family : entry.getOverview().getFamilies()) {
        String ac = family.getAccession();
        int stringpos = 0;
        addField(Fields.ANNOTATIONS, ac);
        String famdesc = family.getDescription();
        // There is no get_synonyms() method for families -> can't access
        // PERVR for FA-04785
        addField(Fields.ANNOTATIONS, famdesc);
        stringpos = famdesc.indexOf("elongs to ") + 14;
        // Skip the 'Belongs to' and
        famdesc = famdesc.substring(stringpos);
        // what may come before (eg:
        // NX_P19021)
        // remove
        famdesc = famdesc.substring(0, famdesc.length() - 1);
        // final dot
        addField(Fields.ANNOTATIONS, famdesc);
        // are there subfamilies
        String[] families = famdesc.split("\\. ");
        // ?
        if (families.length > 1) {
            // Always GOLD
            for (int i = 0; i < families.length; i++) {
                addField(Fields.ANNOTATIONS, families[i]);
                if (families[i].contains(") superfamily")) {
                    // index one
                    // more time
                    // without
                    // parenthesis
                    famdesc = families[i].substring(0, families[i].indexOf("(")) + "superfamily";
                    addField(Fields.ANNOTATIONS, famdesc);
                }
            }
        }
        // Sonetimes these synonymes are wrong eg: NX_Q6NUT3 -> Major
        // facilitator (TC 2.A.1) superfamily
        List<String> famsynonyms = this.terminologyservice.findCvTermByAccession(ac).getSynonyms();
        if (famsynonyms != null)
            for (String famsynonym : famsynonyms) addField(Fields.ANNOTATIONS, famsynonym.trim());
    }
}

Example 59 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class XrefFieldBuilder method init.

@Override
protected void init(Entry entry) {
    String[] extraNameCat = { "entry name", "family name", "allergen name", "reaction ID", "toxin name" };
    // Xrefs
    List<DbXref> xrefs = entry.getXrefs();
    for (DbXref xref : xrefs) {
        String acc = xref.getAccession();
        String db = xref.getDatabaseName();
        if (db.equals(NEXTPROT_SUBMISSION.getName()))
            continue;
        if (db.equals(HPA.getName()) && !acc.contains(ENSG.getName())) {
            // HPA with ENSG are for expression
            addField(Fields.ANTIBODY, acc);
        }
        if (db.equals(ENSEMBL.getName())) {
            addField(Fields.ENSEMBL, acc);
        }
        // but for mrnas BC040557 -> protein sequence ID=AAH40557.1, the pid is just a property of the xref...
        if (!(db.equals(PEPTIDE_ATLAS.getName()) || db.equals(SRM_ATLAS.getName()))) {
            if (db.equals(EMBL.getName())) {
                String propvalue = xref.getPropertyValue("protein sequence ID");
                if (propvalue != null) {
                    addField(Fields.XREFS, "EMBL:" + propvalue + ", " + propvalue);
                    addField(Fields.XREFS, "EMBL:" + acc + ", " + acc);
                } else {
                    propvalue = xref.getPropertyValue("genomic sequence ID");
                    if (propvalue != null || !acc.contains(".")) {
                        addField(Fields.XREFS, "EMBL:" + acc + ", " + acc);
                    }
                }
            } else {
                addField(Fields.XREFS, db + ":" + acc + ", " + acc);
                for (String category : extraNameCat) {
                    String extraName = xref.getPropertyValue(category);
                    if (extraName != null) {
                        // Can be found for dbs: "InterPro", "Pfam", "PROSITE"), "TIGRFAMs", "SMART", "PRINTS", "HAMAP",
                        // "PeroxiBase", "PIRSF", "PIR", "TCDB", "CAZy", "ESTHER", UniPathway
                        addField(Fields.XREFS, db + ":" + extraName + ", " + extraName);
                        break;
                    }
                }
            }
        }
    }
    // It is weird to have to go thru this to get the CAB antibodies, they should come with getXrefs()
    List<Annotation> annots = entry.getAnnotations();
    for (Annotation currannot : annots) {
        String category = currannot.getCategory();
        if ("pathway".equals(category)) {
            addField(Fields.XREFS, "Pathway:" + currannot.getDescription() + ", " + currannot.getDescription());
        } else if ("disease".equals(category)) {
            // Same remark
            DbXref parentXref = currannot.getParentXref();
            if (parentXref != null && parentXref.getDatabaseName().equals(ORPHANET.getName())) {
                String disName = parentXref.getPropertyValue("disease");
                addField(Fields.XREFS, "Disease:" + disName + ", " + disName);
            }
        } else if ("SmallMoleculeInteraction".equals(category)) {
            // Same remark
            addField(Fields.XREFS, "generic name:" + currannot.getDescription() + ", " + currannot.getDescription());
        }
    }
    // Isoform ids
    List<Isoform> isoforms = entry.getIsoforms();
    for (Isoform iso : isoforms) {
        String isoId = iso.getIsoformAccession().substring(3);
        addField(Fields.XREFS, "isoform ID:" + isoId + ", " + isoId);
    }
    // Xrefs to publications (PubMed, DOIs)
    for (Publication currpubli : entry.getPublications()) {
        List<PublicationDbXref> pubxrefs = currpubli.getDbXrefs();
        for (DbXref pubxref : pubxrefs) {
            // It happens to have a trailing \t (like 10.1080/13547500802063240 in NX_P14635)
            String acc = pubxref.getAccession().trim();
            String db = pubxref.getDatabaseName();
            addField(Fields.XREFS, db + ":" + acc + ", " + acc);
        }
    }
}

Example 60 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class IsoformSequencePositionMapperIntegrationTest method getErrorsDuringPropagationOnVariantsOfSingleEntry.

public int getErrorsDuringPropagationOnVariantsOfSingleEntry(String entry_ac) throws Exception {
    Entry entry = entryBuilderService.build(EntryConfig.newConfig(entry_ac).withTargetIsoforms().withAnnotations());
    int delCount = 0;
    int subCount = 0;
    int insCount = 0;
    int otherCount = 0;
    int errorCount = 0;
    for (Annotation a : entry.getAnnotations()) {
        if (a.getAPICategory().equals(AnnotationCategory.VARIANT)) {
            // for each variant annotation
            String ori = a.getVariant().getOriginal();
            String mut = a.getVariant().getVariant();
            if (ori.length() == 1 && mut.length() == 1) {
                subCount++;
            } else if (ori.length() == 1 && mut.length() == 0) {
                delCount++;
            } else if (ori.length() == 0 && mut.length() == 1) {
                insCount++;
            } else if (sout) {
                System.out.println("Other variant:" + a.getUniqueName());
                otherCount++;
            }
            Map<String, Integer> isoExpectedPos = getExpectedPosForEachIsoform(entry, a);
            printExpectedPosForEachIsoform(isoExpectedPos, a);
            boolean errorOnVariant = false;
            for (String iso1name : isoExpectedPos.keySet()) {
                Integer iso1ExpectedPos = isoExpectedPos.get(iso1name);
                Isoform iso1 = IsoformUtils.getIsoformByName(entry, iso1name);
                if (iso1ExpectedPos != null) {
                    GeneMasterCodonPosition nuPos = IsoformSequencePositionMapper.getCodonPositionsOnMaster(iso1ExpectedPos, iso1);
                    if (!nuPos.isValid()) {
                        errorOnVariant = true;
                        if (sout)
                            System.out.println("ERROR1: codon positions not found for " + iso1name + " for variant at position: " + iso1ExpectedPos);
                        continue;
                    }
                    printIsoLengthAndRangesNuCount(iso1.getUniqueName(), iso1.getSequence(), iso1.getMasterMapping());
                    if (sout) {
                        System.out.println("Starting variant propagation from isoform " + iso1name + " at position " + iso1ExpectedPos);
                        System.out.println(getSequenceWithHighlighedPos(iso1.getSequence(), iso1ExpectedPos));
                    }
                    for (Isoform iso2 : entry.getIsoforms()) {
                        String iso2name = iso2.getUniqueName();
                        if (iso2name.equals(iso1name))
                            continue;
                        CodonNucleotideIndices nuIdx = IsoformSequencePositionMapper.getCodonNucleotideIndices(nuPos, iso2);
                        Integer iso2ActualPos = nuIdx.getAminoAcidPosition();
                        Integer iso2ExpectedPos = isoExpectedPos.get(iso2name);
                        if (sout)
                            System.out.println("Variant " + a.getUniqueName() + " position on isoform " + iso2name + " is " + iso2ActualPos);
                        printIsoLengthAndRangesNuCount(iso2.getUniqueName(), iso2.getSequence(), iso2.getMasterMapping());
                        if (iso2ExpectedPos != null)
                            if (sout)
                                System.out.println("Expected:" + getSequenceWithHighlighedPos(iso2.getSequence(), iso2ExpectedPos));
                        if (iso2ActualPos != null)
                            if (sout)
                                System.out.println("Actual  :" + getSequenceWithHighlighedPos(iso2.getSequence(), iso2ActualPos));
                        if (iso2ActualPos == null && iso2ExpectedPos == null) {
                        // OK
                        } else if (iso2ActualPos == null || iso2ExpectedPos == null) {
                            errorOnVariant = true;
                            if (sout)
                                System.out.println("ERROR2: variant position on isoform " + iso2name + " is " + iso2ActualPos + ", expected " + iso2ExpectedPos);
                        } else if (!iso2ActualPos.equals(iso2ExpectedPos)) {
                            errorOnVariant = true;
                            if (sout)
                                System.out.println("ERROR3: variant position on isoform " + iso2name + " is " + iso2ActualPos + ", expected " + iso2ExpectedPos);
                        }
                    }
                }
            }
            if (errorOnVariant)
                errorCount++;
            if (errorOnVariant)
                break;
        }
    }
    if (sout) {
        System.out.println("Summary " + entry.getUniqueName());
        System.out.println("insCount:" + insCount);
        System.out.println("delCount:" + delCount);
        System.out.println("subCount:" + subCount);
        System.out.println("otherCount:" + otherCount);
        System.out.println("errorCount:" + errorCount);
    }
    return errorCount;
}