statalign.io
Class ProteinSkeletons

java.lang.Object
  statalign.io.ProteinSkeletons

All Implemented Interfaces:

DataType

public class ProteinSkeletons
extends java.lang.Object
implements DataType

Represents simplified tertiary structures of a set of sequences (primarily proteins), only one 3d-coordinate per character (amino acid) is stored. For amino acids, this is normally the spatial location of the alpha-carbon atom.

Author:

novak, herman

Field Summary

java.util.List<java.util.List<java.lang.Double>>	bFactors
java.util.List<java.util.List<double[]>>	coords coordinates
java.util.List<java.lang.String>	names names of sequences
RawSequences	seqs

Constructor Summary

ProteinSkeletons()

Method Summary

RawSequences	getSeqs()
java.lang.String	getSummaryAssociatedWith(java.lang.String sequenceName)
boolean	perSequenceData()
void	removeDataAssociatedWith(java.lang.String sequenceName)
void	setSeqs(RawSequences rs)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

seqs

public RawSequences seqs

names

public java.util.List<java.lang.String> names

names of sequences

coords

public java.util.List<java.util.List<double[]>> coords

coordinates

bFactors

public java.util.List<java.util.List<java.lang.Double>> bFactors

Constructor Detail

ProteinSkeletons

public ProteinSkeletons()

Method Detail

perSequenceData

public boolean perSequenceData()

Specified by:

perSequenceData in interface DataType

Returns:

true if the DataType contains a List of items, each of which is associated with one of the input sequences, for example protein structure coordinates.

getSeqs

public RawSequences getSeqs()

Specified by:

getSeqs in interface DataType

setSeqs

public void setSeqs(RawSequences rs)

Specified by:

setSeqs in interface DataType

removeDataAssociatedWith

public void removeDataAssociatedWith(java.lang.String sequenceName)

Specified by:

removeDataAssociatedWith in interface DataType

getSummaryAssociatedWith

public java.lang.String getSummaryAssociatedWith(java.lang.String sequenceName)

Specified by:

getSummaryAssociatedWith in interface DataType