// Path: src/main/java/org/cruk/util/OrderedProperties.java
// public class OrderedProperties extends LinkedMap<String, String>
// {
//     private static final long serialVersionUID = 8837732667981161564L;
// 
//     /**
//      * Get the key set as an array.
//      *
//      * @return The key set as an array.
//      *
//      * @deprecated Use {@link #keySet()} instead and work with the collection.
//      */
//     @Deprecated
//     public String[] getPropertyNames()
//     {
//         return keySet().toArray(new String[0]);
//     }
// 
//     /**
//      * Set a key to a value.
//      *
//      * @param name The key.
//      * @param value The value;
//      *
//      * @deprecated Use {@link #put(String, String)} instead.
//      */
//     @Deprecated
//     public void setProperty(String name, String value)
//     {
//         put(name, value);
//     }
// 
//     /**
//      * Get a value by key.
//      *
//      * @param name The key of the value to get.
//      *
//      * @return The value matching the given key, or null if there is no match.
//      *
//      * @deprecated Use {@link #get(Object)} instead.
//      */
//     public String getProperty(String name)
//     {
//         return get(name);
//     }
// 
//     /**
//      * Returns the value of the property matching the first of the given
//      * set of names.
//      *
//      * @param names the possible names for the property.
//      * @return the property value.
//      */
//     public String getProperty(String[] names)
//     {
//         for (String name : names)
//         {
//             String value = get(name);
//             if (value != null) return value;
//         }
//         return null;
//     }
// 
//     /**
//      * Remove a key and value from the map.
//      *
//      * @param name The key.
//      * @return The value removed, or null.
//      *
//      * @deprecated Use {@link #remove(Object)} instead.
//      */
//     @Deprecated
//     public String removeProperty(String name)
//     {
//         return remove(name);
//     }
// }


import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.cruk.util.OrderedProperties;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2017 Cancer Research UK Cambridge 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.cruk.mga;



/**
 * Class used to represent the summary of alignments of a sequence
 * dataset against a multiple reference genomes.
 *
 * @author eldrid01
 *
 */
public class MultiGenomeAlignmentSummary implements Serializable
{
    private static final long serialVersionUID = 7594987898110254817L;

    private String datasetId;
    private long sequenceCount;
    private int sampledCount;
    private int trimLength;
    private int adapterCount;
    private int alignedCount;
    private Map<String, AlignmentSummary> alignmentSummaries = new HashMap<String, AlignmentSummary>();
// Path: src/main/java/org/cruk/util/OrderedProperties.java
// public class OrderedProperties extends LinkedMap<String, String>
// {
//     private static final long serialVersionUID = 8837732667981161564L;
// 
//     /**
//      * Get the key set as an array.
//      *
//      * @return The key set as an array.
//      *
//      * @deprecated Use {@link #keySet()} instead and work with the collection.
//      */
//     @Deprecated
//     public String[] getPropertyNames()
//     {
//         return keySet().toArray(new String[0]);
//     }
// 
//     /**
//      * Set a key to a value.
//      *
//      * @param name The key.
//      * @param value The value;
//      *
//      * @deprecated Use {@link #put(String, String)} instead.
//      */
//     @Deprecated
//     public void setProperty(String name, String value)
//     {
//         put(name, value);
//     }
// 
//     /**
//      * Get a value by key.
//      *
//      * @param name The key of the value to get.
//      *
//      * @return The value matching the given key, or null if there is no match.
//      *
//      * @deprecated Use {@link #get(Object)} instead.
//      */
//     public String getProperty(String name)
//     {
//         return get(name);
//     }
// 
//     /**
//      * Returns the value of the property matching the first of the given
//      * set of names.
//      *
//      * @param names the possible names for the property.
//      * @return the property value.
//      */
//     public String getProperty(String[] names)
//     {
//         for (String name : names)
//         {
//             String value = get(name);
//             if (value != null) return value;
//         }
//         return null;
//     }
// 
//     /**
//      * Remove a key and value from the map.
//      *
//      * @param name The key.
//      * @return The value removed, or null.
//      *
//      * @deprecated Use {@link #remove(Object)} instead.
//      */
//     @Deprecated
//     public String removeProperty(String name)
//     {
//         return remove(name);
//     }
// }


// Path: src/main/java/org/cruk/mga/MultiGenomeAlignmentSummary.java
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.cruk.util.OrderedProperties;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2017 Cancer Research UK Cambridge 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.cruk.mga;



/**
 * Class used to represent the summary of alignments of a sequence
 * dataset against a multiple reference genomes.
 *
 * @author eldrid01
 *
 */
public class MultiGenomeAlignmentSummary implements Serializable
{
    private static final long serialVersionUID = 7594987898110254817L;

    private String datasetId;
    private long sequenceCount;
    private int sampledCount;
    private int trimLength;
    private int adapterCount;
    private int alignedCount;
    private Map<String, AlignmentSummary> alignmentSummaries = new HashMap<String, AlignmentSummary>();
    private List<OrderedProperties> sampleProperties = new ArrayList<OrderedProperties>();