org.gitools.datasources.obo.OBOStream.java Source code

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Here is the source code for org.gitools.datasources.obo.OBOStream.java

Source

/*
 * #%L
 * gitools-obo
 * %%
 * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
 * %%
 * 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.
 * 
 * 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.
 * 
 * You should have received a copy of the GNU General Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/gpl-3.0.html>.
 * #L%
 */
package org.gitools.datasources.obo;

import org.apache.commons.net.ftp.FTPClient;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;

class OBOStream {

    private URL baseUrl;

    private BufferedReader reader;

    private int linePos;

    public OBOStream(BufferedReader reader) {
        this.reader = reader;
        this.linePos = 0;
    }

    public OBOStream(URL baseUrl) throws IOException {
        this.baseUrl = baseUrl;

        // Workaround for FTP problem connecting ftp.geneontology.org with URL.openStream()
        if (baseUrl.getProtocol().equalsIgnoreCase("ftp")) {
            FTPClient ftp = new FTPClient();
            if (baseUrl.getPort() != -1) {
                ftp.connect(baseUrl.getHost(), baseUrl.getPort());
            } else {
                ftp.connect(baseUrl.getHost());
            }
            ftp.login("anonymous", "");
            ftp.enterLocalPassiveMode();
            ftp.setControlKeepAliveTimeout(60);
            InputStream is = ftp.retrieveFileStream(baseUrl.getPath());
            this.reader = new BufferedReader(new InputStreamReader(is));
        } else {
            this.reader = new BufferedReader(new InputStreamReader(baseUrl.openStream()));
        }

        this.linePos = 0;
    }

    /**
     * @noinspection UnusedDeclaration
     */
    public URL getBaseUrl() {
        return baseUrl;
    }

    public BufferedReader getReader() {
        return reader;
    }

    public int getLinePos() {
        return linePos;
    }

    /**
     * returns a non empty line or null if EOF
     */

    public String nextLine() throws IOException {
        String line = readLine();
        while (line != null && isEmptyLine(line))
            line = readLine();

        return line;
    }

    public void close() throws IOException {
        if (reader != null) {
            reader.close();
            reader = null;
        }
    }

    /**
     * returns the next line or null if EOF
     */

    private String readLine() throws IOException {
        if (reader == null) {
            return null;
        }

        StringBuilder completeLine = new StringBuilder();

        String line = reader.readLine();
        linePos++;

        if (line != null) {
            line = line.trim();
        }

        while (line != null && line.endsWith("\\")) {
            line = line.substring(0, line.length() - 1);
            completeLine.append(line);
            line = reader.readLine();
            linePos++;
            if (line != null) {
                line = line.trim();
            }
        }

        if (line != null) {
            completeLine.append(line);
        }

        if (line == null && completeLine.length() == 0) {
            return null;
        }

        return completeLine.toString();
    }

    private boolean isEmptyLine(String line) {
        return line.replaceAll("\\s", "").isEmpty();
    }
}