es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.ExperimentUtils.java Source code

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Here is the source code for es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.ExperimentUtils.java

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/*
   This file is part of RUbioSeq-GUI.
    
   RUbioSeq-GUI is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
    
   RUbioSeq-GUI 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 General Public License for more details.
    
   You should have received a copy of the GNU General Public License
   along with RUbioSeq-GUI.  If not, see <http://www.gnu.org/licenses/>.
*/
package es.uvigo.ei.sing.rubioseq.gui.view.models.experiments;

import java.io.File;
import java.io.IOException;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;

import es.uvigo.ei.sing.rubioseq.ExperimentType;

/**
 * 
 * @author hlfernandez
 *
 */
public class ExperimentUtils {

    public static final String BRANCH = "branch";
    public static final String BRANCH_SNV = "SNV";
    public static final String BRANCH_CNV = "CNV";
    public static final String BRANCH_METHYLATION = "Methylation";
    public static final String BRANCH_CHIPSEQ = "ChipSeq";
    private static final String BRANCH_MISSING_MESSAGE = "The attribute \'branch\' of the \'configData\' "
            + "element is missing. Please, update your XML to add this attribute which indicates the RUbioSeq branch "
            + "of this configuration file.\n\n " + "Allowed values:" + "\n\t<configData branch=\"SNV\">"
            + "\n\t<configData branch=\"CNV\"> " + "\n\t<configData branch=\"Methylation\">"
            + "\n\t<configData branch=\"ChipSeq\"> ";

    //   public static ExperimentType getExperimentType(File inputFile){
    //      if (inputFile.isDirectory() 
    //            || !inputFile.canRead()
    //            || !inputFile.getName().endsWith(".xml")) {
    //         return null;
    //      }
    //      SAXBuilder saxBuilder = new SAXBuilder();
    //      try {
    //         Document document = saxBuilder.build(inputFile);
    //         Element configData = document.getRootElement(); 
    //         
    //         Element methylType = configData.getChild(MethylationExperiment.METHYLTYPE);
    //         if(methylType!=null){
    //            return ExperimentType.Methylation;
    //         } else{
    //            Element csExperiment = configData.getChild(ChipSeqExperiment.EXPERIMENT);
    //            if(csExperiment!=null){
    //               return ExperimentType.CHIPSeq;
    //            } else{
    //               Element genomes1000 = configData.getChild(SingleNucleotideVariantExperiment.GENOMES1000ANNOT);
    //               if(genomes1000!=null){
    //                  return ExperimentType.SNV;
    //               } else{
    //                  return ExperimentType.CNV;
    //               }
    //            }
    //         }
    //      } catch (JDOMException e) {
    //         e.printStackTrace();
    //      } catch (IOException e) {
    //         e.printStackTrace();
    //      }
    //      return null;
    //   }

    public static ExperimentType getExperimentType(File inputFile) throws InvalidRubioSeqParameterException {
        if (inputFile.isDirectory() || !inputFile.canRead() || !inputFile.getName().endsWith(".xml")) {
            return null;
        }
        SAXBuilder saxBuilder = new SAXBuilder();
        try {
            Document document = saxBuilder.build(inputFile);
            Element configData = document.getRootElement();
            String branch = configData.getAttributeValue(ExperimentUtils.BRANCH);
            if (branch == null) {
                throw new InvalidRubioSeqParameterException(ExperimentUtils.BRANCH_MISSING_MESSAGE);
            } else {
                if (branch.equals(BRANCH_METHYLATION)) {
                    return ExperimentType.Methylation;
                } else if (branch.equals(BRANCH_SNV)) {
                    return ExperimentType.SNV;
                } else if (branch.equals(BRANCH_CNV)) {
                    return ExperimentType.CNV;
                } else if (branch.equals(BRANCH_CHIPSEQ)) {
                    return ExperimentType.CHIPSeq;
                }
            }
        } catch (JDOMException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
        return null;
    }
}