edu.scripps.fl.pubchem.xml.extract.XrefExtractor.java Source code

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Here is the source code for edu.scripps.fl.pubchem.xml.extract.XrefExtractor.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem.xml.extract;

import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import org.apache.commons.beanutils.BeanUtils;
import org.dom4j.Document;
import org.dom4j.Node;

import com.googlecode.exceltablemodel.ExcelTableModel;

import edu.scripps.fl.pubchem.xml.model.Panel;
import edu.scripps.fl.pubchem.xml.model.PanelTarget;
import edu.scripps.fl.pubchem.xml.model.Xref;

/*
 * @author S Canny (scanny at scripps dot edu)
 */
public class XrefExtractor {

    public void checkXrefAgainstPanel(List<Xref> xrefs, List<Panel> panel) {
        for (Panel yy : panel) {
            for (int ii = 0; ii < xrefs.size(); ii++) {
                Xref xx = xrefs.get(ii);
                String type = xx.getXrefType();
                if (type.equalsIgnoreCase("gene") || type.equalsIgnoreCase("protein")
                        || type.equalsIgnoreCase("nucleotide")) {
                    Double idD = Double.parseDouble(xx.getXrefValue().toString());
                    Integer id = idD.intValue();
                    if (type.equalsIgnoreCase("gene")) {
                        List<Integer> genes = yy.getPanelGene();
                        if (genes != null) {
                            if (genes.contains(id))
                                xrefs.remove(xx);
                        }
                    } else if (type.equalsIgnoreCase("protein") || type.equalsIgnoreCase("nucleotide")) {
                        List<PanelTarget> targets = yy.getPanelTarget();
                        if (targets != null) {
                            for (PanelTarget target : targets) {
                                if (target.getPanelTargetGi().equals(id)) {
                                    xrefs.remove(xx);
                                }
                            }
                        }
                    } else if (type.equalsIgnoreCase("taxonomy")) {
                        List<Integer> taxonomies = yy.getPanelTaxonomy();
                        if (taxonomies != null) {
                            if (taxonomies.contains(id))
                                xrefs.remove(xx);
                        }
                    }
                }
            }
        }

    }

    public void fillXrefExcelTemplate(ExcelTableModel model, List<Xref> xrefs)
            throws IllegalAccessException, InvocationTargetException, NoSuchMethodException {
        model.setSheet("Xrefs");
        Map<Integer, String> map = new XMLExtractor().getColumnsMap(model);
        String[] xrefProperties = { "xrefType", "xrefValue", "xrefComment", "isTarget", "isPrimaryCitation" };
        for (int ii = 0; ii <= xrefs.size() - 1; ii++) {
            Xref xref = xrefs.get(ii);
            for (String property : xrefProperties) {
                for (int jj = 0; jj <= map.size() - 1; jj++) {
                    if (property.equalsIgnoreCase(map.get(jj))) {
                        model.setValueAt(BeanUtils.getProperty(xref, property), ii, jj);
                    }
                }
            }
        }
        new XMLExtractor().autoSizeSheet(model);
    }

    public List<Xref> getXrefValuesFromXML(Document doc, List<Panel> panel) throws Exception {
        List<Xref> xrefs = new ArrayList<Xref>();
        List<Node> nodes = doc.selectNodes("//PC-AssayDescription_xref/PC-AnnotatedXRef");
        for (Node nn : nodes) {
            Xref xref = new Xref();
            Node node = nn.selectSingleNode("PC-AnnotatedXRef_xref/PC-XRefData");
            selectXref(xref, node, "PC-XRefData_aid", "AID");
            selectXref(xref, node, "PC-XRefData_protein-gi", "Protein");
            selectXref(xref, node, "PC-XRefData_gene", "Gene");
            selectXref(xref, node, "PC-XRefData_taxonomy", "Taxonomy");
            selectXref(xref, node, "PC-XRefData_mim", "OMIM");
            selectXref(xref, node, "PC-XRefData_dburl", "Source Database Homepage");
            selectXref(xref, node, "PC-XRefData_mesh", "MESH");
            selectXref(xref, node, "PC-XRefData_sburl", "Substance Homepage");
            selectXref(xref, node, "PC-XRefData_asurl", "Assay Homepage");
            selectXref(xref, node, "PC-XRefData_rn", "Substance Registry #");
            selectXref(xref, node, "PC-XRefData_pmid", "PMID");
            selectXref(xref, node, "PC-XRefData_sid", "SID");
            selectXref(xref, node, "PC-XRefData_cid", "CID");
            selectXref(xref, node, "PC-XRefData_nucleotide-gi", "Nucleotide");
            selectXref(xref, node, "PC-XRefData_gi", "GenBank");
            selectXref(xref, node, "PC-XRefData_mmdb", "MMDB");
            selectXref(xref, node, "PC-XRefData_biosystem", "Biosystems Id");
            if (nn.selectSingleNode("PC-AnnotatedXRef_comment") != null)
                xref.setXrefComment(nn.selectSingleNode("PC-AnnotatedXRef_comment").getText());
            Node citationNode = nn.selectSingleNode("PC-AnnotatedXRef_type");
            if (citationNode != null) {
                if (citationNode.getText().equals("1"))
                    xref.setIsPrimaryCitation(true);
            }
            xrefs.add(xref);
        }
        nodes = doc.selectNodes("//PC-AssayDescription_target/PC-AssayTargetInfo");
        for (Node nn : nodes) {
            Xref xref = new Xref();
            BeanUtils.setProperty(xref, "xrefValue", nn.selectSingleNode("PC-AssayTargetInfo_mol-id").getText());
            BeanUtils.setProperty(xref, "xrefTargetValue",
                    nn.selectSingleNode("PC-AssayTargetInfo_molecule-type").getText());
            BeanUtils.setProperty(xref, "isTarget", true);
            xrefs.add(xref);
        }
        if (panel != null)
            checkXrefAgainstPanel(xrefs, panel);
        return xrefs;
    }

    public void selectXref(Xref xref, Node nn, String xrefNode, String xrefType)
            throws IllegalAccessException, InvocationTargetException {
        if (nn.selectSingleNode(xrefNode) != null) {
            BeanUtils.setProperty(xref, "xrefValue", nn.selectSingleNode(xrefNode).getText());
            xref.setXrefType(xrefType);
        }
    }

}