ubic.basecode.io.reader.AbstractMatrixReader.java Source code

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Here is the source code for ubic.basecode.io.reader.AbstractMatrixReader.java

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/*
 * The baseCode project
 * 
 * Copyright (c) 2006 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.basecode.io.reader;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import java.util.Vector;

import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import ubic.basecode.dataStructure.matrix.Matrix2D;

/**
 * Abstract class representing an object that can read in a {@link Matrix2D}from a file.
 * 
 * @author Paul Pavlidis
 * 
 */
public abstract class AbstractMatrixReader<M extends Matrix2D<String, String, V>, V> {

    protected static Logger log = LoggerFactory.getLogger(AbstractMatrixReader.class);

    public abstract M read(InputStream stream) throws IOException;

    public abstract M read(String filename) throws IOException;

    public abstract M read(String filename, int maxRows) throws IOException;

    /**
     * @param dis
     * @param skipColumns how many data columns shoul be ignored
     * @return
     * @throws IOException
     */
    protected List<String> readHeader(BufferedReader dis, int skipColumns) throws IOException {
        List<String> headerVec = new Vector<String>();
        String header = null;

        /*
         * Read past comments.
         */
        while ((header = dis.readLine()) != null) {
            if (header.startsWith("#") || header.startsWith("!") || StringUtils.isBlank(header)) {
                continue;
            }
            break;
        }

        if (header == null)
            return headerVec;

        if (header.startsWith("\t"))
            header = "c" + header;

        String[] tokens = StringUtils.splitPreserveAllTokens(header, "\t");
        // delims.

        String previousToken = "";
        int columnNumber = 0;

        for (int i = 0; i < tokens.length; i++) {
            String s = StringUtils.strip(tokens[i], " ");
            boolean missing = false;

            if (s.compareTo("\t") == 0) {

                if (previousToken.compareTo("\t") == 0) { /* two tabs in a row */
                    missing = true;
                } else if (i == tokens.length - 1) { // at end of line.
                    missing = true;
                } else {
                    previousToken = s;
                    continue;
                }
            } else if (StringUtils.isBlank(s)) {
                missing = true;
            }

            if (missing) {
                throw new IOException("Missing values are not allowed in the header (column " + columnNumber
                        + " at '" + header + "')");
            }
            if (columnNumber > 0) {

                if (skipColumns > 0 && columnNumber <= skipColumns) {

                    // ignore, but count it.
                } else {
                    headerVec.add(s);
                }
            } else {
                // corner string.
            }
            columnNumber++;

            previousToken = s;
        }

        return headerVec;

    }
}