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com.hfg xml, html, svg, and bioinformatics utility library
package com.hfg.bio.taxonomy.ncbi;
import com.hfg.bio.taxonomy.SeqRepositoryDivision;
import com.hfg.util.StringUtil;
import java.util.HashMap;
import java.util.Map;
import java.util.Collection;
import java.io.Serializable;
//------------------------------------------------------------------------------
/**
* Enumerated list of NCBI GenBank divisions.
*
* Based on division.dmp file in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
*
* @author J. Alex Taylor, hairyfatguy.com
*/
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------
public class NCBIGenBankDivision implements SeqRepositoryDivision, Serializable
{
//**************************************************************************
// PRIVATE FIELDS
//**************************************************************************
private String mName;
private String mCode;
private Integer mId;
private static Map sUniqueIdMap = new HashMap<>(20);
private static Map sUniqueCodeMap = new HashMap<>(20);
//**************************************************************************
// PUBLIC FIELDS
//**************************************************************************
/** Bacteria BCT 0 */
public static NCBIGenBankDivision BACTERIA = new NCBIGenBankDivision("Bacteria", "BCT", 0);
/** Invertebrates INV 1 */
public static NCBIGenBankDivision INVERTEBRATES = new NCBIGenBankDivision("Invertebrates", "INV", 1);
/** Mammals MAM 2 */
public static NCBIGenBankDivision MAMMALS = new NCBIGenBankDivision("Mammals", "MAM", 2);
/** Phages PHG 3 */
public static NCBIGenBankDivision PHAGES = new NCBIGenBankDivision("Phages", "PHG", 3);
/** Plants PLN 4 */
public static NCBIGenBankDivision PLANTS = new NCBIGenBankDivision("Plants", "PLN", 4);
/** Primates PRI 5 */
public static NCBIGenBankDivision PRIMATES = new NCBIGenBankDivision("Primates", "PRI", 5);
/** Rodents ROD 6 */
public static NCBIGenBankDivision RODENTS = new NCBIGenBankDivision("Rodents", "ROD", 6);
/** Synthetic SYN 7 */
public static NCBIGenBankDivision SYNTHETIC = new NCBIGenBankDivision("Synthetic", "SYN", 7);
/** Unassigned UNA 8 (No species nodes should inherit this division assignment) */
public static NCBIGenBankDivision UNASSIGNED = new NCBIGenBankDivision("Unassigned", "UNA", 8);
/** Viruses VRL 9 */
public static NCBIGenBankDivision VIRUSES = new NCBIGenBankDivision("Viruses", "VRL", 9);
/** Vertebrates VRT 10 */
public static NCBIGenBankDivision VERTEBRATES = new NCBIGenBankDivision("Vertebrates", "VRT", 10);
/** Environmental samples ENV 11 (Anonymous sequences cloned directly from the environment) */
public static NCBIGenBankDivision ENVIRONMENTAL_SAMPLES = new NCBIGenBankDivision("Environmental samples", "ENV", 11);
// Functional divisions
/** Constructed sequences */
public static NCBIGenBankDivision CONSTRUCTED = new NCBIGenBankDivision("Constructed", "CON");
/** EST sequences (Expressed Sequence Tags) */
public static NCBIGenBankDivision EST = new NCBIGenBankDivision("EST", "EST");
/** Patent sequences */
public static NCBIGenBankDivision PATENT = new NCBIGenBankDivision("Patent", "PAT");
/** STS sequences (Sequence Tagged Sites) */
public static NCBIGenBankDivision STS = new NCBIGenBankDivision("STS", "STS");
/** GSS sequences (Genome Survey Sequences) */
public static NCBIGenBankDivision GSS = new NCBIGenBankDivision("GSS", "GSS");
/** HTGS sequences (High Throughput Genomic sequences) */
public static NCBIGenBankDivision HTG = new NCBIGenBankDivision("HTG", "HTG");
/** HTC sequences (High Throughput cDNA sequences) */
public static NCBIGenBankDivision HTC = new NCBIGenBankDivision("HTC", "HTC");
/** Transcriptome Shotgun Assembly sequences */
public static NCBIGenBankDivision TSA = new NCBIGenBankDivision("TSA", "TSA");
//**************************************************************************
// CONSTRUCTORS
//**************************************************************************
//--------------------------------------------------------------------------
private NCBIGenBankDivision(String inName, String inCode, int inId)
{
this(inName, inCode);
mId = inId;
if (sUniqueIdMap.containsKey(mId + ""))
{
throw new RuntimeException("A object already exists with the id '" + mId + "'!");
}
sUniqueIdMap.put(mId + "", this);
}
//--------------------------------------------------------------------------
private NCBIGenBankDivision(String inName, String inCode)
{
mName = inName;
mCode = inCode;
if (sUniqueCodeMap.containsKey(mCode))
{
throw new RuntimeException("A object already exists with the code '" + mCode + "'!");
}
sUniqueCodeMap.put(mCode, this);
}
//**************************************************************************
// PUBLIC METHODS
//**************************************************************************
//--------------------------------------------------------------------------
public static Collection values()
{
return sUniqueCodeMap.values();
}
//--------------------------------------------------------------------------
/**
Returns the corresponding NCBIGenBankDivision by comparing the id to the
id values of the enumerated set.
@param inId the id of the GenBank division to retrieve
@return NCBIGenBankDivsion object corresponding to the specified id
*/
public static NCBIGenBankDivision valueOf(int inId)
{
return sUniqueIdMap.get(inId + "");
}
//--------------------------------------------------------------------------
/**
Returns the corresponding NCBIGenBankDivision by comparing the value to the
name, code, and id values of the enumerated set.
@param inValue the name, code, or id of the GenBank division to retrieve
@return NCBIGenBankDivsion object corresponding to the specified value
*/
public static NCBIGenBankDivision valueOf(String inValue)
{
NCBIGenBankDivision value = null;
if (StringUtil.isSet(inValue))
{
for (NCBIGenBankDivision division : sUniqueCodeMap.values())
{
if (division.name().equalsIgnoreCase(inValue)
|| division.getCode().equalsIgnoreCase(inValue)
|| (division.getId() != null
&& (division.getId() + "").equals(inValue)))
{
value = division;
break;
}
}
}
return value;
}
//--------------------------------------------------------------------------
public String name()
{
return mName;
}
//--------------------------------------------------------------------------
/**
The same as name().
*/
@Override
public String toString()
{
return name();
}
//--------------------------------------------------------------------------
/**
Returns the 3-letter GenBank division code.
@return the 3-letter GenBank division code
*/
public String getCode()
{
return mCode;
}
//--------------------------------------------------------------------------
public Integer getId()
{
return mId;
}
//**************************************************************************
// PRIVATE METHODS
//**************************************************************************
//--------------------------------------------------------------------------
/**
* This method is called after de-serialization, allowing the object
* to nominate a replacement object to be used in the output
* graph instead of this object. We don't want multiple objects of each type
* to exist in a target VM, so instances replace themselves with
* local objects.
*/
private Object readResolve()
{
return sUniqueIdMap.get(mId + "");
}
}