com.hfg.bio.DigestSettings Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation
com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio;


//------------------------------------------------------------------------------
/**
 Settings for protease cleavage.
 
  @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 DigestSettings implements Cloneable
{
   private Integer   mMaxMissedCleavages = 0;
   private Integer   mMinFragmentLength  = 1;
   private Integer   mMaxFragmentLength;
   private Float     mMinFragmentMass;
   private Float     mMaxFragmentMass;
   private AminoAcid mAlkylatedCys;

   //---------------------------------------------------------------------------
   public DigestSettings setMaxMissedCleavages(Integer inValue)
   {
      mMaxMissedCleavages = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Integer getMaxMissedCleavages()
   {
      return mMaxMissedCleavages;
   }


   //---------------------------------------------------------------------------
   public DigestSettings setMinFragmentLength(Integer inValue)
   {
      mMinFragmentLength = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Integer getMinFragmentLength()
   {
      return mMinFragmentLength;
   }


   //---------------------------------------------------------------------------
   public DigestSettings setMaxFragmentLength(Integer inValue)
   {
      mMaxFragmentLength = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Integer getMaxFragmentLength()
   {
      return mMaxFragmentLength;
   }


   //---------------------------------------------------------------------------
   public DigestSettings setMinFragmentMass(Float inValue)
   {
      mMinFragmentMass = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Float getMinFragmentMass()
   {
      return mMinFragmentMass;
   }

   //---------------------------------------------------------------------------
   public DigestSettings setMaxFragmentMass(Float inValue)
   {
      mMaxFragmentMass = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Float getMaxFragmentMass()
   {
      return mMaxFragmentMass;
   }


   //---------------------------------------------------------------------------
   /**
    By specifying a modified cysteine a "virtual reduction" will be performed on
    the protein before digestion.
    @param inValue AminoAcid to substitute for x-linked or free cysteines
    @return this DigestSettings object to enable method chaining
    */
   public DigestSettings setAlkyatedCys(AminoAcid inValue)
   {
      mAlkylatedCys = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public AminoAcid getAlkyatedCys()
   {
      return mAlkylatedCys;
   }

   //---------------------------------------------------------------------------
   /**
    Returns whether the specified DigestFragment meets criteria for inclusion.
    @param inFrag the DigestFragment to test for inclusion
    @return whether the specified DigestFragment meets criteria for inclusion
    */
   public boolean meetsCriteria(DigestFragment inFrag)
   {
      boolean result = true;

      if (   (mMinFragmentLength != null && inFrag.length() < mMinFragmentLength)
          || (mMinFragmentMass   != null && inFrag.getMonoisotopicMass() < mMinFragmentMass)
          || (mMaxFragmentLength != null && inFrag.length() > mMaxFragmentLength)
          || (mMaxFragmentMass   != null && inFrag.getMonoisotopicMass() > mMaxFragmentMass))
      {
         result = false;
      }

      return result;
   }

   //---------------------------------------------------------------------------
   @Override
   public DigestSettings clone()
   {
      DigestSettings copy;
      try
      {
         copy = (DigestSettings) super.clone();
      }
      catch (CloneNotSupportedException e)
      {
         throw new RuntimeException(e);  
      }

      return copy;
   }
}