org.cytoscape.MetScape.data.ConceptData.java Source code

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Here is the source code for org.cytoscape.MetScape.data.ConceptData.java

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/*************************************************************************
 * Copyright 2012 Regents of the University of Michigan 
 * 
 * NCIBI - The National Center for Integrative Biomedical Informatics (NCIBI)
 *         http://www.ncib.org.
 * 
 * This product may includes software developed by others; in that case see specific notes in the code. 
 * 
 * This program 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, along with the following terms:
 * 1.   You may convey a work based on this program in accordance with section 5, 
 *      provided that you retain the above notices.
 * 2.   You may convey verbatim copies of this program code as you receive it, 
 *      in any medium, provided that you retain the above notices.
 * 
 * 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 General Public License for more details, http://www.gnu.org/licenses/.
 * 
 * This work was supported in part by National Institutes of Health Grant #U54DA021519
 *
 ******************************************************************/
package org.cytoscape.MetScape.data;

import java.io.File;
import java.util.ArrayList;
import java.util.List;

import org.apache.commons.io.FilenameUtils;
import org.ncibi.commons.file.DataFile;
import org.ncibi.commons.file.ExcelFile;
import org.ncibi.commons.file.TextFile;
import org.ncibi.commons.lang.NumUtils;
import org.ncibi.commons.lang.StrUtils;

import com.google.common.base.CharMatcher;

public class ConceptData {

    private List<Concept> allConcepts = new ArrayList<Concept>();
    private String name = "(none)";
    private ConceptMapping mapping = new ConceptMapping();

    public static ConceptData parse(File conceptFile) {

        ConceptData ret = null;
        try {
            ConceptData ex = new ConceptData();
            DataFile base;
            if (conceptFile.getName().endsWith(".xls") || conceptFile.getName().endsWith(".xlsx"))
                base = new ExcelFile(conceptFile);
            else
                base = new TextFile(conceptFile);
            ex.name = FilenameUtils.removeExtension(conceptFile.getName());
            int startRow = base.getStartRowIndex();
            int endRow = base.getEndRowIndex();
            // first row - labels; ignore for now
            startRow++;
            for (int row = startRow; row < (endRow + 1); row++) {
                if (base.getString(row, 0) == null || base.getString(row, 0).equals("")
                        || StrUtils.splitCommaOrSpaceSeparatedString(base.getString(row, 8)) == null
                        || StrUtils.splitCommaOrSpaceSeparatedString(base.getString(row, 8)).isEmpty()
                        || CharMatcher.WHITESPACE.trimFrom(base.getString(row, 8)).equals(""))
                    continue;
                Concept rec = ex.makeRecord();

                rec.setConceptName(base.getString(row, 0));
                rec.setConceptType(base.getString(row, 1));
                rec.setNumUniqueGenes(base.getInteger(row, 2));
                rec.setCoeff(base.getDouble(row, 3));
                rec.setOddsRatio(base.getDouble(row, 4));
                rec.setPvalue(base.getDouble(row, 5));
                rec.setFdr(base.getDouble(row, 6));
                rec.setDirection(base.getString(row, 7));
                rec.setGeneIdsOrSymbols(
                        StrUtils.splitCommaOrSpaceSeparatedString(makeIdValue(base.getString(row, 8))));
                ex.addRecord(rec);
            }
            ret = ex;
        } catch (Throwable t) {
            t.printStackTrace();
        }
        return ret;
    }

    private static String makeIdValue(String string) {
        Integer probe = NumUtils.toInteger(string);
        if (probe != null)
            return probe.toString();
        return string;
    }

    private Concept makeRecord() {
        return new Concept();
    }

    private void addRecord(Concept rec) {
        allConcepts.add(rec);
    }

    public List<Concept> getAllConcepts() {
        return allConcepts;
    }

    public void setAllConcepts(List<Concept> allConcepts) {
        this.allConcepts = allConcepts;
    }

    public void setName(String name) {
        this.name = name;
    }

    public String getName() {
        return name;
    }

    public ConceptMapping getMapping() {
        return mapping;
    }

    public void setMapping(ConceptMapping mapping) {
        this.mapping = mapping;
    }

    @Override
    public int hashCode() {
        final int prime = 31;
        int result = 1;
        result = prime * result + ((allConcepts == null) ? 0 : allConcepts.hashCode());
        result = prime * result + ((name == null) ? 0 : name.hashCode());
        return result;
    }

    @Override
    public boolean equals(Object obj) {
        if (this == obj)
            return true;
        if (obj == null)
            return false;
        if (getClass() != obj.getClass())
            return false;
        ConceptData other = (ConceptData) obj;
        if (allConcepts == null) {
            if (other.allConcepts != null)
                return false;
        } else if (!allConcepts.equals(other.allConcepts))
            return false;
        if (name == null) {
            if (other.name != null)
                return false;
        } else if (!name.equals(other.name))
            return false;
        return true;
    }

    public boolean isEmpty() {
        return allConcepts.isEmpty();
    }

    public String toString() {
        return name;
    }

}