/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.aaproperties.profeat;
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE;
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION;
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING;
import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION;
import org.biojava.nbio.core.sequence.ProteinSequence;
import java.util.Map;
/**
* This is an adaptor class which enable the ease of generating profeat properties.
* At least one adaptor method is written for each available properties provided in IProfeatProperties.
*
* @author kohchuanhock
* @version 2011.06.16
* @since 3.0.2
* @see IProfeatProperties
* @see ProfeatPropertiesImpl
*/
public class ProfeatProperties {
/**
* An adaptor method which returns the composition of the specific grouping for the given attribute.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param attribute
* one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
* @param group
* the grouping to be computed
* @return
* returns the composition of the specific grouping for the given attribute
* @throws Exception
* throws Exception if attribute or group are unknown
*/
public static double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return new ProfeatPropertiesImpl().getComposition(sequence, attribute, group);
}
public static Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception{
return new ProfeatPropertiesImpl().getComposition(sequence, attribute);
}
public static Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception{
return new ProfeatPropertiesImpl().getComposition(sequence);
}
public static double getComposition(String sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return ProfeatProperties.getComposition(new ProteinSequence(sequence), attribute, group);
}
public static Map<GROUPING, Double> getComposition(String sequence, ATTRIBUTE attribute) throws Exception{
return ProfeatProperties.getComposition(new ProteinSequence(sequence), attribute);
}
public static Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(String sequence) throws Exception{
return ProfeatProperties.getComposition(new ProteinSequence(sequence));
}
/**
* An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param attribute
* one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
* @param transition
* the interested transition between the groups
* @return
* returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
* @throws Exception
* throws Exception if attribute or group are unknown
*/
public static double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
return new ProfeatPropertiesImpl().getTransition(sequence, attribute, transition);
}
public static Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception{
return new ProfeatPropertiesImpl().getTransition(sequence, attribute);
}
public static Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception{
return new ProfeatPropertiesImpl().getTransition(sequence);
}
public static double getTransition(String sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
return ProfeatProperties.getTransition(new ProteinSequence(sequence), attribute, transition);
}
public static Map<TRANSITION, Double> getTransition(String sequence, ATTRIBUTE attribute) throws Exception{
return ProfeatProperties.getTransition(new ProteinSequence(sequence), attribute);
}
public static Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(String sequence) throws Exception{
return ProfeatProperties.getTransition(new ProteinSequence(sequence));
}
/**
* An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
* Example: "1111122222"<br/>
* For the above example,<br/>
* position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
* position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param attribute
* one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
* @param group
* one the three groups for the attribute
* @param distribution
* the distribution of the grouping
*
* @return
* the position with respect to the length of sequence where the given distribution of the grouping can be found.<br/>
* @throws Exception
* throws Exception if attribute or group are unknown
*/
public static double getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception{
return new ProfeatPropertiesImpl().getDistributionPosition(sequence, attribute, group, distribution);
}
public static Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return new ProfeatPropertiesImpl().getDistributionPosition(sequence, attribute, group);
}
public static Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception{
return new ProfeatPropertiesImpl().getDistributionPosition(sequence, attribute);
}
public static Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception{
return new ProfeatPropertiesImpl().getDistributionPosition(sequence);
}
public static double getDistributionPosition(String sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception{
return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence), attribute, group, distribution);
}
public static Map<DISTRIBUTION, Double> getDistributionPosition(String sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence), attribute, group);
}
public static Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(String sequence, ATTRIBUTE attribute) throws Exception{
return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence), attribute);
}
public static Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(String sequence) throws Exception{
return ProfeatProperties.getDistributionPosition(new ProteinSequence(sequence));
}
}