Example usage for org.jdom2 Element getText

List of usage examples for org.jdom2 Element getText

  1. HOME
  2. Java
  3. org.jdom2
  4. org.jdom2.*
  5. Element
  6. getText

Introduction

In this page you can find the example usage for org.jdom2 Element getText.

Prototype

public String getText()

Source Link

Document

Returns the textual content directly held under this element as a string.

Usage

From source file:com.bio4j.neo4jdb.programs.ImportUniprot.java

License:Open Source License

private static void importProteinComments(XMLElement entryXMLElem, BatchInserter inserter,
        BatchInserterIndexProvider indexProvider, long currentProteinId, String proteinSequence,
        UniprotDataXML uniprotDataXML) {

    //---------------indexes declaration---------------------------
    BatchInserterIndex commentTypeNameIndex = indexProvider.nodeIndex(CommentTypeNode.COMMENT_TYPE_NAME_INDEX,
            MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST));
    BatchInserterIndex subcellularLocationNameIndex = indexProvider.nodeIndex(
            SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX,
            MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST));
    BatchInserterIndex isoformIdIndex = indexProvider.nodeIndex(IsoformNode.ISOFORM_ID_INDEX,
            MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST));
    BatchInserterIndex nodeTypeIndex = indexProvider.nodeIndex(Bio4jManager.NODE_TYPE_INDEX_NAME,
            MapUtil.stringMap(PROVIDER_ST, LUCENE_ST, TYPE_ST, EXACT_ST));
    //-----------------------------------------------------------

    List<Element> comments = entryXMLElem.asJDomElement().getChildren(UniprotStuff.COMMENT_TAG_NAME);

    for (Element commentElem : comments) {

        String commentTypeSt = commentElem.getAttributeValue(UniprotStuff.COMMENT_TYPE_ATTRIBUTE);

        Element textElem = commentElem.getChild("text");
        String commentTextSt = "";
        String commentStatusSt = "";
        String commentEvidenceSt = "";
        if (textElem != null) {
            commentTextSt = textElem.getText();
            commentStatusSt = textElem.getAttributeValue("status");
            if (commentStatusSt == null) {
                commentStatusSt = "";
            }/*  w  w w .j a  v a  2 s  .  c  om*/
            commentEvidenceSt = textElem.getAttributeValue("evidence");
            if (commentEvidenceSt == null) {
                commentEvidenceSt = "";
            }
        }

        commentProperties.put(BasicCommentRel.TEXT_PROPERTY, commentTextSt);
        commentProperties.put(BasicCommentRel.STATUS_PROPERTY, commentStatusSt);
        commentProperties.put(BasicCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt);

        //-----------------COMMENT TYPE NODE RETRIEVING/CREATION---------------------- 
        //long commentTypeId = indexService.getSingleNode(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt);
        IndexHits<Long> commentTypeNameIndexHits = commentTypeNameIndex
                .get(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt);
        long commentTypeId = -1;
        if (commentTypeNameIndexHits.hasNext()) {
            commentTypeId = commentTypeNameIndexHits.getSingle();
        }
        commentTypeNameIndexHits.close();
        if (commentTypeId < 0) {
            commentTypeProperties.put(CommentTypeNode.NAME_PROPERTY, commentTypeSt);
            commentTypeId = inserter.createNode(commentTypeProperties);
            commentTypeNameIndex.add(commentTypeId,
                    MapUtil.map(CommentTypeNode.COMMENT_TYPE_NAME_INDEX, commentTypeSt));

            //----flushing the indexation----
            commentTypeNameIndex.flush();

            //---adding comment type node to node_type index----
            nodeTypeIndex.add(commentTypeId,
                    MapUtil.map(Bio4jManager.NODE_TYPE_INDEX_NAME, CommentTypeNode.NODE_TYPE));
        }
        //-----toxic dose----------------
        switch (commentTypeSt) {
        case ToxicDoseCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, toxicDoseCommentRel,
                    commentProperties);
            break;
        case CautionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, cautionCommentRel, commentProperties);
            break;
        case CofactorCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, cofactorCommentRel, commentProperties);
            break;
        case DiseaseCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, diseaseCommentRel, commentProperties);
            break;
        case OnlineInformationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            onlineInformationCommentProperties.put(OnlineInformationCommentRel.STATUS_PROPERTY,
                    commentStatusSt);
            onlineInformationCommentProperties.put(OnlineInformationCommentRel.EVIDENCE_PROPERTY,
                    commentEvidenceSt);
            onlineInformationCommentProperties.put(OnlineInformationCommentRel.TEXT_PROPERTY, commentTextSt);
            String nameSt = commentElem.getAttributeValue("name");
            if (nameSt == null) {
                nameSt = "";
            }
            String linkSt = "";
            Element linkElem = commentElem.getChild("link");
            if (linkElem != null) {
                String uriSt = linkElem.getAttributeValue("uri");
                if (uriSt != null) {
                    linkSt = uriSt;
                }
            }
            onlineInformationCommentProperties.put(OnlineInformationCommentRel.NAME_PROPERTY, nameSt);
            onlineInformationCommentProperties.put(OnlineInformationCommentRel.LINK_PROPERTY, linkSt);
            inserter.createRelationship(currentProteinId, commentTypeId, onlineInformationCommentRel,
                    onlineInformationCommentProperties);
            break;
        case TissueSpecificityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, tissueSpecificityCommentRel,
                    commentProperties);
            break;
        case FunctionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, functionCommentRel, commentProperties);
            break;
        case BiotechnologyCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, biotechnologyCommentRel,
                    commentProperties);
            break;
        case SubunitCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, subunitCommentRel, commentProperties);
            break;
        case PolymorphismCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, polymorphismCommentRel,
                    commentProperties);
            break;
        case DomainCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, domainCommentRel, commentProperties);
            break;
        case PostTranslationalModificationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId,
                    postTranslationalModificationCommentRel, commentProperties);
            break;
        case CatalyticActivityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, catalyticActivityCommentRel,
                    commentProperties);
            break;
        case DisruptionPhenotypeCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, disruptionPhenotypeCommentRel,
                    commentProperties);
            break;
        case BioPhysicoChemicalPropertiesCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.STATUS_PROPERTY,
                    commentStatusSt);
            biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.EVIDENCE_PROPERTY,
                    commentEvidenceSt);
            biophysicochemicalCommentProperties.put(BioPhysicoChemicalPropertiesCommentRel.TEXT_PROPERTY,
                    commentTextSt);
            String phDependenceSt = commentElem.getChildText("phDependence");
            String temperatureDependenceSt = commentElem.getChildText("temperatureDependence");
            if (phDependenceSt == null) {
                phDependenceSt = "";
            }
            if (temperatureDependenceSt == null) {
                temperatureDependenceSt = "";
            }
            String absorptionMaxSt = "";
            String absorptionTextSt = "";
            Element absorptionElem = commentElem.getChild("absorption");
            if (absorptionElem != null) {
                absorptionMaxSt = absorptionElem.getChildText("max");
                absorptionTextSt = absorptionElem.getChildText("text");
                if (absorptionMaxSt == null) {
                    absorptionMaxSt = "";
                }
                if (absorptionTextSt == null) {
                    absorptionTextSt = "";
                }
            }
            String kineticsSt = "";
            Element kineticsElem = commentElem.getChild("kinetics");
            if (kineticsElem != null) {
                kineticsSt = new XMLElement(kineticsElem).toString();
            }
            String redoxPotentialSt = "";
            String redoxPotentialEvidenceSt = "";
            Element redoxPotentialElem = commentElem.getChild("redoxPotential");
            if (redoxPotentialElem != null) {
                redoxPotentialSt = redoxPotentialElem.getText();
                redoxPotentialEvidenceSt = redoxPotentialElem.getAttributeValue("evidence");
                if (redoxPotentialSt == null) {
                    redoxPotentialSt = "";
                }
                if (redoxPotentialEvidenceSt == null) {
                    redoxPotentialEvidenceSt = "";
                }
            }
            biophysicochemicalCommentProperties.put(
                    BioPhysicoChemicalPropertiesCommentRel.TEMPERATURE_DEPENDENCE_PROPERTY,
                    temperatureDependenceSt);
            biophysicochemicalCommentProperties
                    .put(BioPhysicoChemicalPropertiesCommentRel.PH_DEPENDENCE_PROPERTY, phDependenceSt);
            biophysicochemicalCommentProperties
                    .put(BioPhysicoChemicalPropertiesCommentRel.KINETICS_XML_PROPERTY, kineticsSt);
            biophysicochemicalCommentProperties
                    .put(BioPhysicoChemicalPropertiesCommentRel.ABSORPTION_MAX_PROPERTY, absorptionMaxSt);
            biophysicochemicalCommentProperties
                    .put(BioPhysicoChemicalPropertiesCommentRel.ABSORPTION_TEXT_PROPERTY, absorptionTextSt);
            biophysicochemicalCommentProperties.put(
                    BioPhysicoChemicalPropertiesCommentRel.REDOX_POTENTIAL_EVIDENCE_PROPERTY,
                    redoxPotentialEvidenceSt);
            biophysicochemicalCommentProperties
                    .put(BioPhysicoChemicalPropertiesCommentRel.REDOX_POTENTIAL_PROPERTY, redoxPotentialSt);
            inserter.createRelationship(currentProteinId, commentTypeId, bioPhysicoChemicalPropertiesCommentRel,
                    biophysicochemicalCommentProperties);
            break;
        case AllergenCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, allergenCommentRel, commentProperties);
            break;
        case PathwayCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, pathwayCommentRel, commentProperties);
            break;
        case InductionCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, inductionCommentRel,
                    commentProperties);
            break;
        case ProteinSubcellularLocationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            if (uniprotDataXML.getSubcellularLocations()) {
                List<Element> subcLocations = commentElem
                        .getChildren(UniprotStuff.SUBCELLULAR_LOCATION_TAG_NAME);

                for (Element subcLocation : subcLocations) {

                    List<Element> locations = subcLocation.getChildren(UniprotStuff.LOCATION_TAG_NAME);
                    Element firstLocation = locations.get(0);
                    //long firstLocationId = indexService.getSingleNode(SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX, firstLocation.getTextTrim());
                    long firstLocationId = -1;
                    IndexHits<Long> firstLocationIndexHits = subcellularLocationNameIndex.get(
                            SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX,
                            firstLocation.getTextTrim());
                    if (firstLocationIndexHits.hasNext()) {
                        firstLocationId = firstLocationIndexHits.getSingle();
                    }
                    firstLocationIndexHits.close();
                    long lastLocationId = firstLocationId;

                    if (firstLocationId < 0) {
                        subcellularLocationProperties.put(SubcellularLocationNode.NAME_PROPERTY,
                                firstLocation.getTextTrim());
                        lastLocationId = createSubcellularLocationNode(subcellularLocationProperties, inserter,
                                subcellularLocationNameIndex, nodeTypeIndex);
                        //---flushing subcellular location name index---
                        subcellularLocationNameIndex.flush();
                    }

                    for (int i = 1; i < locations.size(); i++) {

                        long tempLocationId;
                        IndexHits<Long> tempLocationIndexHits = subcellularLocationNameIndex.get(
                                SubcellularLocationNode.SUBCELLULAR_LOCATION_NAME_INDEX,
                                locations.get(i).getTextTrim());
                        if (tempLocationIndexHits.hasNext()) {
                            tempLocationId = tempLocationIndexHits.getSingle();
                            tempLocationIndexHits.close();
                        } else {
                            subcellularLocationProperties.put(SubcellularLocationNode.NAME_PROPERTY,
                                    locations.get(i).getTextTrim());
                            tempLocationId = createSubcellularLocationNode(subcellularLocationProperties,
                                    inserter, subcellularLocationNameIndex, nodeTypeIndex);
                            subcellularLocationNameIndex.flush();
                        }

                        inserter.createRelationship(tempLocationId, lastLocationId,
                                subcellularLocationParentRel, null);
                        lastLocationId = tempLocationId;
                    }
                    Element lastLocation = locations.get(locations.size() - 1);
                    String evidenceSt = lastLocation.getAttributeValue(UniprotStuff.EVIDENCE_ATTRIBUTE);
                    String statusSt = lastLocation.getAttributeValue(UniprotStuff.STATUS_ATTRIBUTE);
                    String topologyStatusSt = "";
                    String topologySt = "";
                    Element topologyElem = subcLocation.getChild("topology");
                    if (topologyElem != null) {
                        topologySt = topologyElem.getText();
                        topologyStatusSt = topologyElem.getAttributeValue("status");
                    }
                    if (topologyStatusSt == null) {
                        topologyStatusSt = "";
                    }
                    if (topologySt == null) {
                        topologySt = "";
                    }
                    if (evidenceSt == null) {
                        evidenceSt = "";
                    }
                    if (statusSt == null) {
                        statusSt = "";
                    }
                    proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.EVIDENCE_PROPERTY,
                            evidenceSt);
                    proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.STATUS_PROPERTY,
                            statusSt);
                    proteinSubcellularLocationProperties.put(ProteinSubcellularLocationRel.TOPOLOGY_PROPERTY,
                            topologySt);
                    proteinSubcellularLocationProperties
                            .put(ProteinSubcellularLocationRel.TOPOLOGY_STATUS_PROPERTY, topologyStatusSt);
                    inserter.createRelationship(currentProteinId, lastLocationId, proteinSubcellularLocationRel,
                            proteinSubcellularLocationProperties);

                }
            }
            break;
        case UniprotStuff.COMMENT_ALTERNATIVE_PRODUCTS_TYPE:
            if (uniprotDataXML.getIsoforms()) {
                List<Element> eventList = commentElem.getChildren("event");
                List<Element> isoformList = commentElem.getChildren("isoform");

                for (Element isoformElem : isoformList) {
                    String isoformIdSt = isoformElem.getChildText("id");
                    String isoformNoteSt = isoformElem.getChildText("note");
                    String isoformNameSt = isoformElem.getChildText("name");
                    String isoformSeqSt = "";
                    Element isoSeqElem = isoformElem.getChild("sequence");
                    if (isoSeqElem != null) {
                        String isoSeqTypeSt = isoSeqElem.getAttributeValue("type");
                        if (isoSeqTypeSt.equals("displayed")) {
                            isoformSeqSt = proteinSequence;
                        }
                    }
                    if (isoformNoteSt == null) {
                        isoformNoteSt = "";
                    }
                    if (isoformNameSt == null) {
                        isoformNameSt = "";
                    }
                    isoformProperties.put(IsoformNode.ID_PROPERTY, isoformIdSt);
                    isoformProperties.put(IsoformNode.NOTE_PROPERTY, isoformNoteSt);
                    isoformProperties.put(IsoformNode.NAME_PROPERTY, isoformNameSt);
                    isoformProperties.put(IsoformNode.SEQUENCE_PROPERTY, isoformSeqSt);
                    //--------------------------------------------------------
                    //long isoformId = indexService.getSingleNode(IsoformNode.ISOFORM_ID_INDEX, isoformIdSt);
                    long isoformId = -1;
                    IndexHits<Long> isoformIdIndexHits = isoformIdIndex.get(IsoformNode.ISOFORM_ID_INDEX,
                            isoformIdSt);
                    if (isoformIdIndexHits.hasNext()) {
                        isoformId = isoformIdIndexHits.getSingle();
                    }
                    isoformIdIndexHits.close();
                    if (isoformId < 0) {
                        isoformId = createIsoformNode(isoformProperties, inserter, isoformIdIndex,
                                nodeTypeIndex);
                    }

                    for (Element eventElem : eventList) {

                        String eventTypeSt = eventElem.getAttributeValue("type");
                        switch (eventTypeSt) {
                        case AlternativeProductInitiationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                            inserter.createRelationship(isoformId, alternativeProductInitiationId,
                                    isoformEventGeneratorRel, null);
                            break;
                        case AlternativeProductPromoterRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                            inserter.createRelationship(isoformId, alternativeProductPromoterId,
                                    isoformEventGeneratorRel, null);
                            break;
                        case AlternativeProductRibosomalFrameshiftingRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                            inserter.createRelationship(isoformId, alternativeProductRibosomalFrameshiftingId,
                                    isoformEventGeneratorRel, null);
                            break;
                        case AlternativeProductSplicingRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                            inserter.createRelationship(isoformId, alternativeProductSplicingId,
                                    isoformEventGeneratorRel, null);
                            break;
                        }
                    }

                    //protein isoform relationship
                    inserter.createRelationship(currentProteinId, isoformId, proteinIsoformRel, null);

                }
            }
            break;
        case UniprotStuff.COMMENT_SEQUENCE_CAUTION_TYPE:
            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.EVIDENCE_PROPERTY, commentEvidenceSt);
            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.STATUS_PROPERTY, commentStatusSt);
            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.TEXT_PROPERTY, commentTextSt);
            Element conflictElem = commentElem.getChild("conflict");
            if (conflictElem != null) {

                String conflictTypeSt = conflictElem.getAttributeValue("type");
                String resourceSt = "";
                String idSt = "";
                String versionSt = "";

                ArrayList<String> positionsList = new ArrayList<>();

                Element sequenceElem = conflictElem.getChild("sequence");
                if (sequenceElem != null) {
                    resourceSt = sequenceElem.getAttributeValue("resource");
                    if (resourceSt == null) {
                        resourceSt = "";
                    }
                    idSt = sequenceElem.getAttributeValue("id");
                    if (idSt == null) {
                        idSt = "";
                    }
                    versionSt = sequenceElem.getAttributeValue("version");
                    if (versionSt == null) {
                        versionSt = "";
                    }
                }

                Element locationElem = commentElem.getChild("location");
                if (locationElem != null) {
                    Element positionElem = locationElem.getChild("position");
                    if (positionElem != null) {
                        String tempPos = positionElem.getAttributeValue("position");
                        if (tempPos != null) {
                            positionsList.add(tempPos);
                        }
                    }
                }

                sequenceCautionProperties.put(BasicProteinSequenceCautionRel.RESOURCE_PROPERTY, resourceSt);
                sequenceCautionProperties.put(BasicProteinSequenceCautionRel.ID_PROPERTY, idSt);
                sequenceCautionProperties.put(BasicProteinSequenceCautionRel.VERSION_PROPERTY, versionSt);
                switch (conflictTypeSt) {
                case ProteinErroneousGeneModelPredictionRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId,
                                    seqCautionErroneousGeneModelPredictionId,
                                    proteinErroneousGeneModelPredictionRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionErroneousGeneModelPredictionId,
                                proteinErroneousGeneModelPredictionRel, sequenceCautionProperties);
                    }
                    break;
                case ProteinErroneousInitiationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId, seqCautionErroneousInitiationId,
                                    proteinErroneousInitiationRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionErroneousInitiationId,
                                proteinErroneousInitiationRel, sequenceCautionProperties);
                    }
                    break;
                case ProteinErroneousTranslationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId, seqCautionErroneousTranslationId,
                                    proteinErroneousTranslationRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionErroneousTranslationId,
                                proteinErroneousTranslationRel, sequenceCautionProperties);
                    }
                    break;
                case ProteinErroneousTerminationRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId, seqCautionErroneousTerminationId,
                                    proteinErroneousTerminationRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionErroneousTerminationId,
                                proteinErroneousTerminationRel, sequenceCautionProperties);
                    }
                    break;
                case ProteinFrameshiftRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId, seqCautionFrameshiftId,
                                    proteinFrameshiftRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionFrameshiftId,
                                proteinFrameshiftRel, sequenceCautionProperties);
                    }
                    break;
                case ProteinMiscellaneousDiscrepancyRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
                    if (positionsList.size() > 0) {
                        for (String tempPosition : positionsList) {
                            sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY,
                                    tempPosition);
                            inserter.createRelationship(currentProteinId, seqCautionMiscellaneousDiscrepancyId,
                                    proteinMiscellaneousDiscrepancyRel, sequenceCautionProperties);
                        }
                    } else {
                        sequenceCautionProperties.put(BasicProteinSequenceCautionRel.POSITION_PROPERTY, "");
                        inserter.createRelationship(currentProteinId, seqCautionMiscellaneousDiscrepancyId,
                                proteinMiscellaneousDiscrepancyRel, sequenceCautionProperties);
                    }
                    break;
                }
            }
            break;
        case DevelopmentalStageCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, developmentalStageCommentRel,
                    commentProperties);
            break;
        case MiscellaneousCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, miscellaneousCommentRel,
                    commentProperties);
            break;
        case SimilarityCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, similarityCommentRel,
                    commentProperties);
            break;
        case RnaEditingCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            rnaEditingCommentProperties.put(RnaEditingCommentRel.STATUS_PROPERTY, commentStatusSt);
            rnaEditingCommentProperties.put(RnaEditingCommentRel.EVIDENCE_PROPERTY, commentEvidenceSt);
            rnaEditingCommentProperties.put(RnaEditingCommentRel.TEXT_PROPERTY, commentTextSt);
            List<Element> locationsList = commentElem.getChildren("location");
            for (Element tempLoc : locationsList) {
                String positionSt = tempLoc.getChild("position").getAttributeValue("position");
                rnaEditingCommentProperties.put(RnaEditingCommentRel.POSITION_PROPERTY, positionSt);
                inserter.createRelationship(currentProteinId, commentTypeId, rnaEditingCommentRel,
                        rnaEditingCommentProperties);
            }
            break;
        case PharmaceuticalCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, pharmaceuticalCommentRel,
                    commentProperties);
            break;
        case EnzymeRegulationCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            inserter.createRelationship(currentProteinId, commentTypeId, enzymeRegulationCommentRel,
                    commentProperties);
            break;
        case MassSpectrometryCommentRel.UNIPROT_ATTRIBUTE_TYPE_VALUE:
            String methodSt = commentElem.getAttributeValue("method");
            String massSt = commentElem.getAttributeValue("mass");
            if (methodSt == null) {
                methodSt = "";
            }
            if (massSt == null) {
                massSt = "";
            }
            String beginSt = "";
            String endSt = "";
            Element locationElem = commentElem.getChild("location");
            if (locationElem != null) {
                Element beginElem = commentElem.getChild("begin");
                Element endElem = commentElem.getChild("end");
                if (beginElem != null) {
                    beginSt = beginElem.getAttributeValue("position");
                }

                if (endElem != null) {
                    endSt = endElem.getAttributeValue("position");
                }
            }
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.STATUS_PROPERTY, commentStatusSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.EVIDENCE_PROPERTY,
                    commentEvidenceSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.TEXT_PROPERTY, commentTextSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.METHOD_PROPERTY, methodSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.MASS_PROPERTY, massSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.BEGIN_PROPERTY, beginSt);
            massSpectrometryCommentProperties.put(MassSpectrometryCommentRel.END_PROPERTY, endSt);
            inserter.createRelationship(currentProteinId, commentTypeId, massSpectrometryCommentRel,
                    massSpectrometryCommentProperties);
            break;
        }

    }

}

From source file:com.cats.version.VersionCfgParseAndSave.java

License:Apache License

public List<VersionInfo> getVersionInfo(String fullPath) {
    SAXBuilder builder = new SAXBuilder();
    List<VersionInfo> infos = new ArrayList<VersionInfo>();
    try {/*from   w  w  w .ja v  a  2  s.  c  o m*/
        Document doc = builder.build(new File(fullPath));
        Element root = doc.getRootElement();
        List<Element> softEles = root.getChildren("software");
        for (Element softEle : softEles) {
            String appName = softEle.getAttribute("name").getValue();
            String versionCode = softEle.getChildText("latest-version-code");
            String versionName = softEle.getChildText("latest-version");
            String versionPath = softEle.getChildText("latest-version-abspath");
            String startupName = softEle.getChildText("latest-version-startup");

            Element detailEles = softEle.getChild("latest-version-detail");
            List<Element> detailItemEles = detailEles.getChildren("item");
            List<VersionInfoDetail> details = new ArrayList<VersionInfoDetail>();
            for (Element detailItem : detailItemEles) {
                String title = detailItem.getAttributeValue("name");
                List<Element> detailEleList = detailItem.getChildren("detail");
                List<String> detailList = new ArrayList<String>();
                for (Element detailEle : detailEleList) {
                    String strDetail = detailEle.getText();
                    detailList.add(strDetail);
                }
                details.add(new VersionInfoDetail(title, detailList));
            }

            Element ignoreEles = softEle.getChild("ignore-files");
            List<String> ignoreFiles = new ArrayList<String>();
            if (ignoreEles != null) {
                List<Element> ignoreItems = ignoreEles.getChildren("item");
                for (Element ignoreItem : ignoreItems) {
                    ignoreFiles.add(ignoreItem.getText());
                }
            }

            VersionInfo versionInfo = new VersionInfo();
            versionInfo.setAppName(appName);
            versionInfo.setVersion(versionName);
            versionInfo.setStartupName(startupName);
            versionInfo.setVersionCode(Integer.parseInt(versionCode));
            versionInfo.setPath(versionPath);
            versionInfo.setDetails(details);
            versionInfo.setIgnoreFiles(ignoreFiles);
            infos.add(versionInfo);
        }
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
    return infos;
}

From source file:com.cedarsoft.serialization.test.performance.XmlParserPerformance.java

License:Open Source License

public void benchJdom() {
    runBenchmark(new Runnable() {
        @Override/*from w  w  w .j  av a 2 s .c o  m*/
        public void run() {
            try {
                for (int i = 0; i < SMALL; i++) {
                    Document doc = new SAXBuilder().build(new StringReader(CONTENT_SAMPLE));

                    Element fileTypeElement = doc.getRootElement();
                    Element extensionElement = fileTypeElement.getChild("extension");

                    Extension extension = new Extension(extensionElement.getAttributeValue("delimiter"),
                            extensionElement.getText(),
                            extensionElement.getAttribute("default").getBooleanValue());
                    FileType fileType = new FileType(fileTypeElement.getChildText("id"), extension,
                            fileTypeElement.getAttribute("dependent").getBooleanValue());

                    assertNotNull(fileType);
                }
            } catch (Exception e) {
                throw new RuntimeException(e);
            }
        }
    }, 4);
}

From source file:com.dexterapps.android.translator.TranslateTextForAndroid.java

License:Apache License

private void parseXMLAndGenerateDom(String sourceFile) {
    SAXBuilder builder = new SAXBuilder();
    File xmlFile = new File(sourceFile);
    //System.out.println(xmlFile.getAbsolutePath());
    try {//from w  w  w.ja  v a2s .  c  o  m

        /*Navigate the XML DOM and populate the string array for translation
          We also map the XML in java object so we can use to navigate it again for generating the xml back
         */
        Document document = (Document) builder.build(xmlFile);
        Element rootNode = document.getRootElement();
        List list = rootNode.getChildren();
        for (int i = 0; i < list.size(); i++) {

            AndroidStringMapping stringElement = new AndroidStringMapping();

            Element stringNode = (Element) list.get(i);
            if (stringNode.getName().equalsIgnoreCase("string")) {
                stringElement.setType("string");
                stringElement.setAttributeName(stringNode.getAttributeValue("name"));
                stringElement.setAttributeValue(stringNode.getText());

                baseLanguageStringForTranslation.add(stringNode.getText());
                baseStringResourcesMapping.put(stringNode.getText(), i);
            } else if (stringNode.getName().equalsIgnoreCase("string-array")) {
                List stringArrayNodeList = stringNode.getChildren();
                ArrayList<String> stringArrayItems = new ArrayList<String>();

                for (int j = 0; j < stringArrayNodeList.size(); j++) {
                    Element stringArrayNode = (Element) stringArrayNodeList.get(j);

                    baseLanguageStringForTranslation.add(stringArrayNode.getText());
                    baseStringResourcesMapping.put(stringArrayNode.getText(), i + j);

                    stringArrayItems.add(stringArrayNode.getText());
                }

                stringElement.setType("string-array");
                stringElement.setAttributeName(stringNode.getAttributeValue("name"));
                stringElement.setAttributeValue(stringArrayItems);

            } else {
                List stringPluralNodeList = stringNode.getChildren();
                ArrayList<AndroidStringPlurals> stringPluralsItems = new ArrayList<AndroidStringPlurals>();

                for (int j = 0; j < stringPluralNodeList.size(); j++) {
                    Element stringPluralNode = (Element) stringPluralNodeList.get(j);

                    baseLanguageStringForTranslation.add(stringPluralNode.getText());
                    baseStringResourcesMapping.put(stringPluralNode.getText(), i + j);

                    AndroidStringPlurals pluralItem = new AndroidStringPlurals();

                    pluralItem.setAttributeName(stringPluralNode.getAttributeValue("quantity"));
                    pluralItem.setAttributeValue(stringPluralNode.getText());

                    stringPluralsItems.add(pluralItem);
                }

                stringElement.setType("plurals");
                stringElement.setAttributeName(stringNode.getAttributeValue("name"));
                stringElement.setAttributeValue(stringPluralsItems);

            }

            stringXmlDOM.add(stringElement);

        }

    } catch (IOException io) {
        System.out.println(io.getMessage());
    } catch (JDOMException jdomex) {
        System.out.println(jdomex.getMessage());
    }
}

From source file:com.hotaviano.tableexporter.csv.CSVExporter.java

License:Open Source License

private void createBody(Document doc, PrintWriter writer) {
    Element tbody = doc.getRootElement().getChild("tbody");

    for (Element tr : tbody.getChildren()) {
        String line = "";
        for (Element td : tr.getChildren()) {
            line += td.getText() + ",";
        }//from  w  w w  .j a va  2s .c  om

        writer.println(line.substring(0, line.length() - 1));
    }
}

From source file:com.hotaviano.tableexporter.csv.CSVExporter.java

License:Open Source License

private void createHeader(Document doc, PrintWriter writer) {
    Element thead = doc.getRootElement().getChild("thead").getChildren().get(0);

    String header = "";
    for (Element elem : thead.getChildren()) {
        header += elem.getText() + ",";
    }/*from  w ww  . ja v  a2s .  c o  m*/

    writer.println(header.subSequence(0, header.length() - 1));
}

From source file:com.hotaviano.tableexporter.docx.DOCXExporter.java

License:Open Source License

private void createHeaderTable(XWPFTable table, Document document) {
    List<Element> elements = document.getRootElement().getChild("thead").getChildren().get(0).getChildren();
    int i = 0;/*ww  w.  j a va2 s.  c  om*/
    for (Element element : elements) {
        table.getRow(0).getCell(i++).setText(element.getText());
    }
}

From source file:com.hotaviano.tableexporter.docx.DOCXExporter.java

License:Open Source License

private void createBodyTable(XWPFTable table, Document document) {
    List<Element> elements = document.getRootElement().getChild("tbody").getChildren();

    int row = 1;/*from w  w w.  j a v a2s. c  o  m*/

    for (Element element : elements) {
        XWPFTableRow tableRow = table.getRow(row++);

        int col = 0;
        for (Element td : element.getChildren()) {
            tableRow.getCell(col++).setText(td.getText());
        }
    }
}

From source file:com.hotaviano.tableexporter.pdf.PDFExporter.java

License:Open Source License

private List<PdfPCell> getHeaders(Document document) {
    List<PdfPCell> result = new ArrayList<>();

    Element tr = document.getRootElement().getChild("thead").getChildren().get(0);

    for (Element th : tr.getChildren()) {
        PdfPCell cell = new PdfPCell(new Phrase(th.getText(), new Font(Font.BOLD)));
        result.add(cell);/*from  w ww.  java  2 s.c  o  m*/
    }

    return result;
}

From source file:com.hotaviano.tableexporter.pdf.PDFExporter.java

License:Open Source License

private List<String> getBodyValues(Document document) {
    List<String> result = new ArrayList<>();

    List<Element> trs = document.getRootElement().getChild("tbody").getChildren();

    for (Element tr : trs) {
        for (Element td : tr.getChildren()) {
            result.add(td.getText());
        }// w ww.  ja va  2s .  c om
    }

    return result;
}