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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.seq;


//------------------------------------------------------------------------------
/**
 Simple container for sequence mapping stats.
 
  @see com.hfg.graphics.Gene2D
  @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 SeqMappingCoverage
{
   private Integer mQueryLength;
   private Integer mMappedLength;
   private Float   mPctIdentity;

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

   //--------------------------------------------------------------------------
   /**
    Sets the summed length of the query sequence that was successfully mapped.
    @param inValue the length of the query seq portions that were covered by mapping
    @return this SeqMappingCoverage object (for potential method chaining)
    */
   public SeqMappingCoverage setMappedLength(Integer inValue)
   {
      mMappedLength = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   /**
    Returns the summed length of the query sequence that was successfully mapped.
    @return the summed length of the query sequence that was successfully mapped
    */
   public Integer getMappedLength()
   {
      return mMappedLength;
   }

   //--------------------------------------------------------------------------
   /**
    Sets the length of the query sequence that was mapped.
    @param inValue the query seq length
    @return this SeqMappingCoverage object (for potential method chaining)
    */
   public SeqMappingCoverage setQueryLength(Integer inValue)
   {
      mQueryLength = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   /**
    Returns the length of the query sequence that was mapped.
    @return the query length
    */
   public Integer getQueryLength()
   {
      return mQueryLength;
   }

   //--------------------------------------------------------------------------
   /**
    Sets the percent identity of the query sequence to the mapping target for the
    region(s) mapped.
    @param inValue the pct. identity of the query seq to the mapping target
    @return this SeqMappingCoverage object (for potential method chaining)
    */
   public SeqMappingCoverage setPercentIdentity(Float inValue)
   {
      mPctIdentity = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   /**
    Returns the percent identity of the query sequence to the mapping target for the
    region(s) mapped.
    @return the pct. identity of the query sequence to the mapping target sequence for the mapped region(s)
    */
   public Float getPercentIdentity()
   {
      return mPctIdentity;
   }
}