com.hfg.bio.seq.alignment.blast.BLAST_DatabaseMgr 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.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

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

//==============================================================================
/**
 A BLAST sequence database manager.
 
 @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_DatabaseMgr
{
   private File mFile;
   private Map> mGroupMap;

   protected static XMLName XML_NAME = new XMLName("BLAST_DatabaseMgr");


   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################



   //---------------------------------------------------------------------------
   public BLAST_DatabaseMgr(File inFile)
         throws XMLException, IOException
   {
      mFile = inFile;

      XMLDoc doc = new XMLDoc(inFile);
      XMLTag rootNode = (XMLTag) doc.getRootNode();
      rootNode.verifyTagName(XML_NAME);

      List groupTags = rootNode.getSubtagsByName(BLAST_DatabaseGroup.XML_NAME);
      if (CollectionUtil.hasValues(groupTags))
      {
         for (XMLTag groupTag : groupTags)
         {
            addGroup(new BLAST_DatabaseGroup(groupTag));
         }
      }
   }

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

   //---------------------------------------------------------------------------
   public File getFile()
   {
      return mFile;
   }

   //---------------------------------------------------------------------------
   public BLAST_DatabaseMgr setFile(File inValue)
   {
      mFile = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public void persistToFile()
   {
      XMLDoc xmlDoc = toXMLDoc();
      xmlDoc.toIndentedXML(mFile, 0, 2);
   }

   //---------------------------------------------------------------------------
   public void addGroup(BLAST_DatabaseGroup inGroup)
   {
      if (inGroup != null)
      {
         if (null == mGroupMap)
         {
            mGroupMap = new HashMap<>(3);
         }

         List groupList = mGroupMap.get(inGroup.getSeqType());
         if (null == groupList)
         {
            groupList = new ArrayList<>(25);
            mGroupMap.put(inGroup.getSeqType(), groupList);
         }

         groupList.add(inGroup);
      }
   }


   //---------------------------------------------------------------------------
   public List getGroups(BioSequenceType inType)
   {
      return (mGroupMap != null ? mGroupMap.get(inType) : null);
   }


   //---------------------------------------------------------------------------
   public XMLDoc toXMLDoc()
   {
      XMLTag tag = new XMLTag(XML_NAME);

      if (CollectionUtil.hasValues(mGroupMap))
      {
         for (BioSequenceType bioSequenceType : mGroupMap.keySet())
         {
            for (BLAST_DatabaseGroup group : mGroupMap.get(bioSequenceType))
            {
               tag.addSubtag(group.toXMLTag());
            }
         }
      }

      XMLDoc doc = new XMLDoc();
      doc.setRootNode(tag);

      return doc;
   }

}