/*
* 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.core.sequence.ProteinSequence;
import java.util.Map;
public interface IProfeatProperties {
/**
* Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
* An interface class to generate the properties of a protein sequence based on its converted attributes.<br/>
* The seven different attributes are<p/>
* Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
* Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)<br/>
* Charge (Positive, Neutral, Negative)<br/>
* Secondary structure (Helix, Strand, Coil)<br/>
* Solvent accessibility (Buried, Exposed, Intermediate)<br/>
*
* @author kohchuanhock
* @version 2011.06.16
* @since 3.0.2
*/
/**
* Enumeration of the seven different attributes
*/
public enum ATTRIBUTE {HYDROPHOBICITY, VOLUME, POLARITY, POLARIZABILITY, CHARGE, SECONDARYSTRUCTURE, SOLVENTACCESSIBILITY};
/**
* Enumeration of the three different groupings for each attributes
*/
public enum GROUPING {GROUP1, GROUP2, GROUP3};
/**
* Enumeration of the transition between groupA and groupB
*/
public enum TRANSITION {BETWEEN_11, BETWEEN_22, BETWEEN_33, BETWEEN_12, BETWEEN_13, BETWEEN_23};
/**
* Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
*/
public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
/**
* 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 double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
public Map<GROUPING, Double> getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
public Map<ATTRIBUTE, Map<GROUPING, Double>> getComposition(ProteinSequence sequence) throws Exception;
/**
* 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 double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception;
public Map<TRANSITION, Double> getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
public Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(ProteinSequence sequence) throws Exception;
/**
* 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 double getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group, DISTRIBUTION distribution) throws Exception;
public Map<DISTRIBUTION, Double> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception;
public Map<GROUPING, Map<DISTRIBUTION, Double>> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception;
public Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception;
}