DescriptionCache.java

/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package org.broad.igv.gwas;

import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.IGVPreferences;
import org.broad.igv.prefs.PreferencesManager;

import java.util.ArrayList;


/**
 * Created by IntelliJ IDEA.
 * User: jussi
 * Date: 2/7/11
 * Time: 1:32 PM
 * To change this template use File | Settings | File Templates.
 */
public class DescriptionCache {

    private static final Logger log = Logger.getLogger(DescriptionCache.class);


    // Maximum amount of values stored in the cache
    private int maxSize;

    private ArrayList<String> chrs = new ArrayList<String>();
    private ArrayList<Integer> locations = new ArrayList<Integer>();
    private ArrayList<Double> values = new ArrayList<Double>();
    private ArrayList<String> descriptions = new ArrayList<String>();
    // Storage for the header tokens
    private String[] headerTokens = new String[1000];

    public DescriptionCache() {

        IGVPreferences prefs = PreferencesManager.getPreferences();
        this.maxSize = prefs.getAsInt(Constants.GWAS_DESCRIPTION_CACHE_SIZE);

    }

    public int getMaxSize() {
        return maxSize;
    }

    /**
     * Set size of the cache in lines. Minimum size is 10.
     *
     * @param maxSize
     */
    public void setMaxSize(int maxSize) {
        if (maxSize < 10)
            maxSize = 10;
        this.maxSize = maxSize;
    }

    public String[] getHeaderTokens() {
        return headerTokens;
    }

    public void setHeaderTokens(String[] headerTokens) {
        this.headerTokens = headerTokens;
    }

    public void setHeaderTokens(String headerString) {
        headerString = headerString.trim();
         this.headerTokens = Globals.singleTabMultiSpacePattern.split(headerString);
    }


    public void clear() {

        this.chrs = new ArrayList<String>();
        this.locations = new ArrayList<Integer>();
        this.descriptions = new ArrayList<String>();
    }


    public boolean add(String chr, int location, double value, String description) {

        if (this.locations.size() >= this.maxSize) {
            this.locations.remove(0);
            this.chrs.remove(0);
            this.descriptions.remove(0);
            this.values.remove(0);
        }

        return this.chrs.add(chr) && this.locations.add(location) && this.descriptions.add(description) && this.values.add(value);
    }

    public String getDescription(String chr, int location, double value) {

        String description = null;

        int indexCounter = 0;
        boolean descriptionFound = false;

        while (indexCounter < this.descriptions.size() && !descriptionFound) {
            if (this.chrs.get(indexCounter).equals(chr) && this.locations.get(indexCounter) == location && this.values.get(indexCounter) == value) {
                description = this.descriptions.get(indexCounter);
                descriptionFound = true;

            }
            indexCounter++;
        }

        return description;

    }


    public String getDescriptionString(String chr, int location, double value) {

        String description = this.getDescription(chr, location, value);
        String descriptionString = null;

        if (description != null) {
            descriptionString = "";
            int headersSize = this.getHeaderTokens().length;
            String[] tokens = Globals.singleTabMultiSpacePattern.split(description);

            for (int i = 0; i < headersSize; i++) {
                String tmpHeaderToken = this.getHeaderTokens()[i];
                if (tmpHeaderToken != null)
                    descriptionString += tmpHeaderToken + ": " + tokens[i] + "<br>";
            }

        }
        return descriptionString;

    }


}