/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.gwas;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
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() {
PreferenceManager prefs = PreferenceManager.getInstance();
this.maxSize = prefs.getAsInt(PreferenceManager.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;
}
}