Java tutorial
/* * Copyright (C) 2010-2012 "Oh no sequences!" * * This is free software: you can redistribute it and/or modify * it under the terms of the GNU Affero General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Affero General Public License for more details. * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/> */ package com.ohnosequences.xml.model.go; import com.ohnosequences.xml.model.uniprot.ProteinXML; import com.ohnosequences.xml.api.model.XMLElement; import java.util.ArrayList; import java.util.List; import org.jdom2.Element; /** * * @author ppareja */ public class GoAnnotationXML extends XMLElement { public static final String TAG_NAME = "go_annotation"; public static final String SAMPLE_GENE_NUMBER_TAG_NAME = "sample_gene_number"; public static final String ANNOTATOR_GO_TERMS_TAG_NAME = "annotator_go_terms"; public static final String PROTEIN_ANNOTATIONS_TAG_NAME = "protein_annotations"; public GoAnnotationXML() { super(new Element(TAG_NAME)); } public GoAnnotationXML(String value) throws Exception { super(value); } public GoAnnotationXML(Element element) { super(element); } public void addAnnotatorGoTerm(GoTermXML term) { initAnnotatorGoTermsTag(); Element annotators = root.getChild(ANNOTATOR_GO_TERMS_TAG_NAME); annotators.addContent(term.asJDomElement()); } public void addProteinAnnotation(ProteinXML protein) { initProteinAnnotatiosTag(); Element proteins = root.getChild(PROTEIN_ANNOTATIONS_TAG_NAME); proteins.addContent(protein.asJDomElement()); } private void initProteinAnnotatiosTag() { Element proteins = root.getChild(PROTEIN_ANNOTATIONS_TAG_NAME); if (proteins == null) { proteins = new Element(PROTEIN_ANNOTATIONS_TAG_NAME); root.addContent(proteins); } } private void initAnnotatorGoTermsTag() { Element annotators = root.getChild(ANNOTATOR_GO_TERMS_TAG_NAME); if (annotators == null) { annotators = new Element(ANNOTATOR_GO_TERMS_TAG_NAME); root.addContent(annotators); } } //----------------SETTERS------------------- public void setSampleGeneNumber(int value) { setNodeText(SAMPLE_GENE_NUMBER_TAG_NAME, String.valueOf(value)); } //----------------GETTERS--------------------- public int getSampleGeneNumber() throws NumberFormatException { return Integer.parseInt(getNodeText(SAMPLE_GENE_NUMBER_TAG_NAME)); } public Element getProteinAnnotations() { return root.getChild(PROTEIN_ANNOTATIONS_TAG_NAME); } public List<GoTermXML> getAnnotatorGoTerms() { Element tempElem = root.getChild(ANNOTATOR_GO_TERMS_TAG_NAME); if (tempElem != null) { List<GoTermXML> result = new ArrayList<GoTermXML>(); List<Element> tempList = tempElem.getChildren(GoTermXML.TAG_NAME); for (Element element : tempList) { result.add(new GoTermXML(element)); } return result; } else { return null; } } }