ubic.BAMSandAllen.AllenDataLoaders.AllenTop50DataLoader.java Source code

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Here is the source code for ubic.BAMSandAllen.AllenDataLoaders.AllenTop50DataLoader.java

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/*******************************************************************************
 * The ABAMS project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * 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 ubic.BAMSandAllen.AllenDataLoaders;

import java.io.FileInputStream;
import java.io.IOException;
import java.util.HashSet;
import java.util.Set;

import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;

import ubic.BAMSandAllen.NeuroNamesMappingLoader;
import ubic.BAMSandAllen.NomenClatureEntry;
import ubic.BAMSandAllen.SetupParameters;
import ubic.basecode.io.excel.ExcelUtil;

public class AllenTop50DataLoader {
    private final String spreadSheetLocation = SetupParameters.config.getString("abams.dataFolder")
            + "EnrichedGenesMasterList.xls";

    private Set<String> allenRegions;
    private Set<NomenClatureEntry> allenEnrichedEntries;

    public AllenTop50DataLoader() {
        try {
            NeuroNamesMappingLoader NNLoader = new NeuroNamesMappingLoader();

            allenRegions = new HashSet<String>();

            POIFSFileSystem fs = new POIFSFileSystem(new FileInputStream(spreadSheetLocation));
            HSSFWorkbook allen = new HSSFWorkbook(fs);
            HSSFSheet sheet;
            for (int i = 0; i < allen.getNumberOfSheets(); i++) {
                sheet = allen.getSheetAt(i);
                allenRegions.add(allen.getSheetName(i));
                // System.out.println( allen.getSheetName( i ) );
            }

            Set<String> allenRegions = getAllenRegions();
            Set<NomenClatureEntry> dongEntries = NNLoader.getDongEntries();
            allenEnrichedEntries = new HashSet<NomenClatureEntry>();

            for (String allenEnrichedAcro : allenRegions) {
                for (NomenClatureEntry dongEntry : dongEntries) {
                    if (allenEnrichedAcro.equals(dongEntry.acro)) {
                        allenEnrichedEntries.add(dongEntry);
                    }
                }
            }

            // make entry <-> gene links
            for (NomenClatureEntry dongEntry : allenEnrichedEntries) {
                sheet = allen.getSheet(dongEntry.acro);
                // System.out.println(dongEntry.acro);
                for (short i = 2; true; i++) {
                    String gene = ExcelUtil.getValue(sheet, i, (short) 0);
                    if (gene == null)
                        break;
                    dongEntry.expressedGenes.add(gene);
                    // System.out.println( gene );

                }
            }

        } catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }

    }

    public Set<String> getAllenRegions() {
        return allenRegions;
    }

    public Set<NomenClatureEntry> getAllenEnrichedEntries() throws IOException {
        return allenEnrichedEntries;
    }

    public Set<String> getGenesForDongRegion(String fullName) {
        for (NomenClatureEntry dongEntry : allenEnrichedEntries) {
            if (dongEntry.name.equalsIgnoreCase(fullName))
                return dongEntry.expressedGenes;
        }
        return null;
    }

    public static void main(String args[]) {
        new AllenTop50DataLoader();
    }
}