/*
 * Copyright (c) 2007-2012 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * 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.
 */

package org.broad.igv.plugin.mongovariant;

import org.broad.igv.variant.vcf.VCFVariant;
import org.broadinstitute.sting.gatk.walkers.na12878kb.core.MongoVariantContext;
import org.broadinstitute.sting.gatk.walkers.na12878kb.core.TruthStatus;

/**
 * Wrapper for VCFVariant so we can include additional fields from MongoDB
 * User: jacob
 * Date: 2013-Jan-28
 */
public class MongoVCFVariant extends VCFVariant{

    private final MongoVariantContext mongoVariantContext;

    public MongoVCFVariant(MongoVariantContext mongoVariantContext, String chr) {
        super(mongoVariantContext.getVariantContext(), chr);
        this.mongoVariantContext = mongoVariantContext;
    }

    public TruthStatus getTruthStatus() {
        return mongoVariantContext.getType();
    }

    public boolean isReviewed(){
        return mongoVariantContext.isReviewed();
    }
}

@@ -586,16 +586,48 @@
 riant;%0A%0A
+import org.apache.log4j.Logger;%0A
 import o
@@ -818,16 +818,75 @@
 tatus;%0A%0A
+import java.text.SimpleDateFormat;%0Aimport java.util.Date;%0A%0A
 /**%0A * W
@@ -1043,16 +1043,17 @@
 FVariant
+ 
 %7B%0A%0A    p
@@ -1063,54 +1063,763 @@
 ate 
-final MongoVariantContext mongoVariantContext;
+static Logger log = Logger.getLogger(MongoVCFVariant.class);%0A%0A    private final MongoVariantContext mongoVariantContext;%0A%0A    @Override%0A    public String getAttributeAsString(String key) %7B%0A        if (key.equalsIgnoreCase(%22date%22)) %7B%0A            try %7B%0A                long date = (Long) super.getAttributes().get(key);%0A                SimpleDateFormat formatter = new SimpleDateFormat(%22MMM dd, yyyy. HH:mm%22);%0A                return formatter.format(new Date(date));%0A            %7D catch (Exception e) %7B%0A                //Don't much care, but if we drop the ball and the API changes%0A                //we don't want to crash everything%0A                log.error(e.getMessage(), e);%0A            %7D%0A        %7D%0A        return super.getAttributeAsString(key);%0A    %7D
 %0A%0A  
@@ -2148,16 +2148,17 @@
 viewed()
+ 
 %7B%0A      

Improve date formatting in tooltip for MongoVCFVariant