com.hfg.bio.seq.alignment.blast.BLAST_DatabaseGroup Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.bio.seq.alignment.blast;


import java.util.ArrayList;
import java.util.List;

import com.hfg.bio.seq.BioSequenceType;
import com.hfg.util.StringUtil;
import com.hfg.util.collection.CollectionUtil;
import com.hfg.xml.XMLName;
import com.hfg.xml.XMLTag;

//==============================================================================
/**
 Container for a group of BLAST sequence databases.
 
 @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 BLAST_DatabaseGroup
{

   private String mName;
   private BioSequenceType mSeqType;
   private List mDatabases;

   protected static XMLName XML_NAME = new XMLName("BLAST_DatabaseGroup");
   private static XMLName XML_NAME_ATT = new XMLName("name");
   private static XMLName XML_SEQ_TYPE_ATT = new XMLName("seqType");



   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public BLAST_DatabaseGroup(String inName, BioSequenceType inType)
   {
      mName = inName;
      mSeqType = inType;
   }

   //---------------------------------------------------------------------------
   public BLAST_DatabaseGroup(XMLTag inXMLTag)
   {
      inXMLTag.verifyTagName(XML_NAME);
      mName = inXMLTag.getAttributeValue(XML_NAME_ATT);

      String bioSequenceTypeString = inXMLTag.getAttributeValue(XML_SEQ_TYPE_ATT);
      if (! StringUtil.isSet(bioSequenceTypeString))
      {
         throw new RuntimeException("No " + StringUtil.singleQuote(XML_SEQ_TYPE_ATT) + " specified for group " + StringUtil.singleQuote(mName) + "!");
      }

      mSeqType = BioSequenceType.valueOf(bioSequenceTypeString);

      List dbTags = inXMLTag.getSubtagsByName(BLAST_Database.XML_NAME);
      if (CollectionUtil.hasValues(dbTags))
      {
         for (XMLTag dbTag : dbTags)
         {
            addDatabase(new BLAST_Database(dbTag));
         }
      }
   }


   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public XMLTag toXMLTag()
   {
      XMLTag tag = new XMLTag(XML_NAME);
      tag.setAttribute(XML_NAME_ATT, name());
      tag.setAttribute(XML_SEQ_TYPE_ATT, getSeqType());

      if (CollectionUtil.hasValues(getDatabases()))
      {
         for (BLAST_Database db : getDatabases())
         {
            tag.addSubtag(db.toXMLTag());
         }
      }

      return tag;
   }

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return name();
   }

   //---------------------------------------------------------------------------
   public String name()
   {
      return mName;
   }

   //---------------------------------------------------------------------------
   public BioSequenceType getSeqType()
   {
      return mSeqType;
   }

   //---------------------------------------------------------------------------
   public void addDatabase(BLAST_Database inValue)
   {
      if (null == mDatabases)
      {
         mDatabases = new ArrayList<>(10);
      }

      mDatabases.add(inValue);
   }

   //---------------------------------------------------------------------------
   public List getDatabases()
   {
      return mDatabases;
   }

}