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com.hfg xml, html, svg, and bioinformatics utility library
package com.hfg.bio;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import com.hfg.setting.FloatSetting;
import com.hfg.setting.IntSetting;
import com.hfg.setting.Settings;
import com.hfg.setting.StringListSetting;
import com.hfg.setting.StringSetting;
import com.hfg.util.StringUtil;
import com.hfg.util.collection.CollectionUtil;
//------------------------------------------------------------------------------
/**
Settings for protein digestion via protease(s).
@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 extends Settings implements Cloneable
{
public static final String PROTEASE = "protease";
public static final String MAX_MISSED_CLEAVAGES = "maxMissedCleavages";
public static final String MIN_FRAG_LENGTH = "minFragLength";
public static final String MAX_FRAG_LENGTH = "maxFragLength";
public static final String MIN_FRAG_MASS = "minFragMass";
public static final String MAX_FRAG_MASS = "maxFragMass";
public static final String ALKYLATED_CYS = "alkylatedCys";
private static int sDefaultMaxMissedCleavages = 0;
private static int sDefaultMinFragmentLength = 1;
//###########################################################################
// CONSTRUCTORS
//###########################################################################
//---------------------------------------------------------------------------
public DigestSettings()
{
super();
init();
}
//---------------------------------------------------------------------------
@Override
protected void init()
{
add(new StringListSetting(PROTEASE));
add(new IntSetting(MAX_MISSED_CLEAVAGES, sDefaultMaxMissedCleavages));
add(new IntSetting(MIN_FRAG_LENGTH, sDefaultMinFragmentLength));
add(new IntSetting(MAX_FRAG_LENGTH));
add(new FloatSetting(MIN_FRAG_MASS));
add(new FloatSetting(MAX_FRAG_MASS));
add(new StringSetting(ALKYLATED_CYS));
}
//###########################################################################
// PUBLIC METHODS
//###########################################################################
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setProtease(Protease inValue)
{
List list = new ArrayList<>(1);
list.add(inValue);
return setProteases(list);
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setProteases(Collection inValues)
{
List stringListValue = null;
if (CollectionUtil.hasValues(inValues))
{
stringListValue = new ArrayList<>(inValues.size());
for (Protease protease : inValues)
{
stringListValue.add(protease.name());
}
}
get(PROTEASE).setValue(stringListValue);
return this;
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public Set getProteases()
{
Set proteases = null;
List proteaseNames = (List) get(PROTEASE).getValue();
if (CollectionUtil.hasValues(proteaseNames))
{
proteases = new HashSet<>(proteaseNames.size());
for (String proteaseName : proteaseNames)
{
proteases.add(Protease.valueOf(proteaseName));
}
}
return proteases;
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setMaxMissedCleavages(int inValue)
{
get(MAX_MISSED_CLEAVAGES).setValue(inValue);
return this;
}
//---------------------------------------------------------------------------
public Integer getMaxMissedCleavages()
{
return (Integer) get(MAX_MISSED_CLEAVAGES).getValue();
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setMinFragmentLength(Integer inValue)
{
get(MIN_FRAG_LENGTH).setValue(inValue);
return this;
}
//---------------------------------------------------------------------------
public Integer getMinFragmentLength()
{
return (Integer) get(MIN_FRAG_LENGTH).getValue();
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setMaxFragmentLength(Integer inValue)
{
get(MAX_FRAG_LENGTH).setValue(inValue);
return this;
}
//---------------------------------------------------------------------------
public Integer getMaxFragmentLength()
{
return (Integer) get(MAX_FRAG_LENGTH).getValue();
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setMinFragmentMass(Float inValue)
{
get(MIN_FRAG_MASS).setValue(inValue);
return this;
}
//---------------------------------------------------------------------------
public Float getMinFragmentMass()
{
return (Float) get(MIN_FRAG_MASS).getValue();
}
//---------------------------------------------------------------------------
@SuppressWarnings("unchecked")
public DigestSettings setMaxFragmentMass(Float inValue)
{
get(MAX_FRAG_MASS).setValue(inValue);
return this;
}
//---------------------------------------------------------------------------
public Float getMaxFragmentMass()
{
return (Float) get(MAX_FRAG_MASS).getValue();
}
//---------------------------------------------------------------------------
/**
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 setAlkylatedCys(AminoAcid inValue)
{
get(ALKYLATED_CYS).setValue(inValue != null ? inValue.name() : null);
return this;
}
//---------------------------------------------------------------------------
public AminoAcid getAlkylatedCys()
{
AminoAcid aa = null;
String stringValue = (String) get(ALKYLATED_CYS).getValue();
if (StringUtil.isSet(stringValue))
{
aa = AminoAcid.valueOf(stringValue);
}
return aa;
}
//---------------------------------------------------------------------------
/**
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 ( (getMinFragmentLength() != null && inFrag.length() < getMinFragmentLength())
|| (getMinFragmentMass() != null && inFrag.getMonoisotopicMass() < getMinFragmentMass())
|| (getMaxFragmentLength() != null && inFrag.length() > getMaxFragmentLength())
|| (getMaxFragmentMass() != null && inFrag.getMonoisotopicMass() > getMaxFragmentMass()))
{
result = false;
}
return result;
}
//---------------------------------------------------------------------------
@Override
public DigestSettings clone()
{
DigestSettings copy;
try
{
copy = (DigestSettings) super.clone();
}
catch (CloneNotSupportedException e)
{
throw new RuntimeException(e);
}
return copy;
}
}