org.csml.tommo.sugar.analysis.CachedFile.java Source code

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Here is the source code for org.csml.tommo.sugar.analysis.CachedFile.java

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/**
 *    Copyright Masao Nagasaki
 *    Nagasaki Lab
 *    Laboratory of Biomedical Information Analysis,
 *    Department of Integrative Genomics,
 *    Tohoku Medical Megabank Organization, Tohoku University 
 *    @since 2013
 *
 *    This file is part of SUGAR (Subtile-based GUI-Assisted Refiner).
 *    SUGAR is an extension of FastQC (copyright 2010-12 Simon Andrews)
 *
 *    SUGAR 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.
 *
 *    SUGAR 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 SUGAR; if not, write to the Free Software
 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
package org.csml.tommo.sugar.analysis;

import java.io.File;
import java.io.IOException;
import java.io.Writer;

import org.json.simple.JSONObject;
import org.json.simple.JSONValue;

public class CachedFile implements JSONSerializable {

    private final static int CACHE_VERSION = 1;

    private static final String JSON_ATTR_VERSION = "version";
    private static final String JSON_ATTR_MATRIX_SIZE = "matrixSize";
    private static final String JSON_ATTR_FILE_SIZE = "fileSize";
    private static final String JSON_ATTR_LAST_MODIFIED = "lastModified";
    private static final String JSON_ATTR_FILE_PATH = "filePath";
    private static final String JSON_ATTR_QUALITY_THRESHOLD = "qualityThreshold";

    protected String filePath;
    protected Long lastModified;
    protected Long fileSize;

    protected int matrixSize;
    protected int qualityThreshold;
    protected int version;

    public CachedFile(File file, int matrixSize, int qualityThreshold) {
        filePath = file.getAbsolutePath();
        lastModified = file.lastModified();
        fileSize = file.length();
        this.matrixSize = matrixSize;
        this.qualityThreshold = qualityThreshold;
        version = CACHE_VERSION;
    }

    // customized JSON Serialization

    protected CachedFile() {
    }

    @Override
    public String toJSONString() {
        JSONObject obj = toJSONObject();
        return obj.toString();
    }

    @Override
    public void writeJSONString(Writer out) throws IOException {
        JSONObject obj = toJSONObject();
        JSONValue.writeJSONString(obj, out);
    }

    public JSONObject toJSONObject() {
        JSONObject obj = new JSONObject();
        obj.put(JSON_ATTR_FILE_PATH, filePath);
        obj.put(JSON_ATTR_LAST_MODIFIED, lastModified);
        obj.put(JSON_ATTR_FILE_SIZE, fileSize);
        obj.put(JSON_ATTR_MATRIX_SIZE, matrixSize);
        obj.put(JSON_ATTR_QUALITY_THRESHOLD, qualityThreshold);
        obj.put(JSON_ATTR_VERSION, version);
        return obj;
    }

    @Override
    public void fromJSONObject(JSONObject jsonObject) {

        filePath = jsonObject.get(JSON_ATTR_FILE_PATH).toString();
        lastModified = new Long(jsonObject.get(JSON_ATTR_LAST_MODIFIED).toString());
        fileSize = new Long(jsonObject.get(JSON_ATTR_FILE_SIZE).toString());
        matrixSize = new Integer(jsonObject.get(JSON_ATTR_MATRIX_SIZE).toString());
        qualityThreshold = new Integer(jsonObject.get(JSON_ATTR_QUALITY_THRESHOLD).toString());
        version = new Integer(jsonObject.get(JSON_ATTR_VERSION).toString());

    }

    // customized JSON Serialization

    @Override
    public String toString() {
        return "CachedFile [filePath=" + filePath + ", lastModified=" + lastModified + ", fileSize=" + fileSize
                + ", matrixSize=" + matrixSize + ", qualityThreshold=" + qualityThreshold + ", version=" + version
                + "]";
    }

    @Override
    public int hashCode() {
        final int prime = 31;
        int result = 1;
        result = prime * result + ((filePath == null) ? 0 : filePath.hashCode());
        result = prime * result + ((fileSize == null) ? 0 : fileSize.hashCode());
        result = prime * result + ((lastModified == null) ? 0 : lastModified.hashCode());
        result = prime * result + matrixSize;
        result = prime * result + qualityThreshold;
        result = prime * result + version;
        return result;
    }

    @Override
    public boolean equals(Object obj) {
        if (this == obj)
            return true;
        if (obj == null)
            return false;
        if (getClass() != obj.getClass())
            return false;
        CachedFile other = (CachedFile) obj;
        if (filePath == null) {
            if (other.filePath != null)
                return false;
        } else if (!filePath.equals(other.filePath))
            return false;
        if (fileSize == null) {
            if (other.fileSize != null)
                return false;
        } else if (!fileSize.equals(other.fileSize))
            return false;
        if (lastModified == null) {
            if (other.lastModified != null)
                return false;
        } else if (!lastModified.equals(other.lastModified))
            return false;
        if (matrixSize != other.matrixSize)
            return false;
        if (qualityThreshold != other.qualityThreshold)
            return false;
        if (version != other.version)
            return false;
        return true;
    }

    public File getFile() {
        return new File(filePath);
    }

    public int getMatrixSize() {
        return matrixSize;
    }

    public int getQualityThreshold() {
        return qualityThreshold;
    }

}