edu.scripps.fl.pubchem.promiscuity.servlet.PCPromiscuityRunnable.java Source code

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Here is the source code for edu.scripps.fl.pubchem.promiscuity.servlet.PCPromiscuityRunnable.java

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/*               
 * Copyright 2011 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.promiscuity.servlet;

import java.io.File;
import java.util.Map;

import org.apache.commons.io.FilenameUtils;

import edu.scripps.fl.pubchem.promiscuity.PCPromiscuityMain;
import edu.scripps.fl.pubchem.promiscuity.PCPromiscuityOutput;
import edu.scripps.fl.pubchem.promiscuity.model.CompoundPromiscuityInfo;
import edu.scripps.fl.pubchem.promiscuity.model.PCPromiscuityParameters;

public class PCPromiscuityRunnable implements Runnable {

    private final PCPromiscuityParameters params;
    private final File tmpFile;

    public PCPromiscuityRunnable(PCPromiscuityParameters params, File tmpFile) {
        this.params = params;
        this.tmpFile = tmpFile;
    }

    public void run() {
        try {
            Map<Long, CompoundPromiscuityInfo> map = new PCPromiscuityMain(params).getCompoundPromiscuityInfoMap();
            PCPromiscuityOutput output = new PCPromiscuityOutput();
            output.compoundPromiscuityToXML(map, params, tmpFile);
            String csvName = FilenameUtils.removeExtension(tmpFile.getAbsolutePath()) + ".csv";
            File file = new File(csvName);
            output.compoundPromiscuityToCSV(map, params, file);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

}