com.hfg.bio.seq.genomic.assembly

Class NCBIGenomicAssemblyInfo

java.lang.Object

com.hfg.bio.seq.genomic.assembly.NCBIGenomicAssemblyInfo

All Implemented Interfaces:

Comparable<NCBIGenomicAssemblyInfo>

public class NCBIGenomicAssemblyInfo
extends Object
implements Comparable<NCBIGenomicAssemblyInfo>

Information about an NCBI genomic assembly. See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the fields.

Constructor Summary

Constructors

Constructor and Description
NCBIGenomicAssemblyInfo()
NCBIGenomicAssemblyInfo(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
int	compareTo(NCBIGenomicAssemblyInfo inObj2) Compares this object with the specified object for order.
static Map<NCBITaxon,List<NCBIGenomicAssemblyInfo>>	extractInfoFromAssemblySummaryFile(File inFile) Use for processing an assembly_summary.txt file from the NCBI ftp site.
String	getAssemblyAccession()
GenomicAssemblyLevel	getAssemblyLevel()
String	getAssemblyName()
GenomicAssemblyReleaseType	getAssemblyReleaseType()
GenomicAssemblyVersionStatus	getAssemblyVersionStatus()
String	getBioprojectAccession()
String	getBiosampleAccession()
boolean	getExcludedFromRefSeq()
String	getFTP_Path()
String	getGenBankRefSeqPairedAssembly()
GenomicRepresentation	getGenomicRepresentation()
String	getInfraspecificName()
String	getIsolate()
NCBITaxon	getOrganismTaxon()
GenomicPairedAssemblyComparison	getPairedAssemblyComparison()
GenomicRefSeqCategory	getRefSeqCategory()
GenomicRelationToTypeMaterial	getRelationToTypeMaterial()
Date	getReleaseDate()
NCBITaxon	getSpeciesTaxon()
String	getSubmitter()
String	getWGSAccession()
NCBIGenomicAssemblyInfo	setAssemblyAccession(String inValue)
NCBIGenomicAssemblyInfo	setAssemblyLevel(GenomicAssemblyLevel inValue)
NCBIGenomicAssemblyInfo	setAssemblyName(String inValue)
NCBIGenomicAssemblyInfo	setAssemblyReleaseType(GenomicAssemblyReleaseType inValue)
NCBIGenomicAssemblyInfo	setAssemblyVersionStatus(GenomicAssemblyVersionStatus inValue)
NCBIGenomicAssemblyInfo	setBioprojectAccession(String inValue)
NCBIGenomicAssemblyInfo	setBiosampleAccession(String inValue)
NCBIGenomicAssemblyInfo	setExcludedFromRefSeq(boolean inValue)
NCBIGenomicAssemblyInfo	setFTP_Path(String inValue)
NCBIGenomicAssemblyInfo	setGenBankRefSeqPairedAssembly(String inValue)
NCBIGenomicAssemblyInfo	setGenomicRepresentation(GenomicRepresentation inValue)
NCBIGenomicAssemblyInfo	setInfraspecificName(String inValue)
NCBIGenomicAssemblyInfo	setIsolate(String inValue)
NCBIGenomicAssemblyInfo	setOrganismTaxon(NCBITaxon inValue)
NCBIGenomicAssemblyInfo	setPairedAssemblyComparison(GenomicPairedAssemblyComparison inValue)
NCBIGenomicAssemblyInfo	setRefSeqCategory(GenomicRefSeqCategory inValue)
NCBIGenomicAssemblyInfo	setRelationToTypeMaterial(GenomicRelationToTypeMaterial inValue)
NCBIGenomicAssemblyInfo	setReleaseDate(Date inValue)
NCBIGenomicAssemblyInfo	setSpeciesTaxon(NCBITaxon inValue)
NCBIGenomicAssemblyInfo	setSubmitter(String inValue)
NCBIGenomicAssemblyInfo	setWGSAccession(String inValue)
String	toString()
XMLTag	toXMLTag()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

NCBIGenomicAssemblyInfo

public NCBIGenomicAssemblyInfo()

NCBIGenomicAssemblyInfo

public NCBIGenomicAssemblyInfo(XMLTag inXMLTag)

Method Detail

extractInfoFromAssemblySummaryFile

public static Map<NCBITaxon,List<NCBIGenomicAssemblyInfo>> extractInfoFromAssemblySummaryFile(File inFile)
                                                                                       throws IOException,
                                                                                              ParseException

Use for processing an assembly_summary.txt file from the NCBI ftp site.

Parameters:

inFile - the assembly_summary.txt file

Returns:

a Map with species taxons as the keys

Throws:

IOException

ParseException

toString

public String toString()

Overrides:

toString in class Object

toXMLTag

public XMLTag toXMLTag()

setAssemblyAccession

public NCBIGenomicAssemblyInfo setAssemblyAccession(String inValue)

getAssemblyAccession

public String getAssemblyAccession()

setBioprojectAccession

public NCBIGenomicAssemblyInfo setBioprojectAccession(String inValue)

getBioprojectAccession

public String getBioprojectAccession()

setBiosampleAccession

public NCBIGenomicAssemblyInfo setBiosampleAccession(String inValue)

getBiosampleAccession

public String getBiosampleAccession()

setWGSAccession

public NCBIGenomicAssemblyInfo setWGSAccession(String inValue)

getWGSAccession

public String getWGSAccession()

setRefSeqCategory

public NCBIGenomicAssemblyInfo setRefSeqCategory(GenomicRefSeqCategory inValue)

getRefSeqCategory

public GenomicRefSeqCategory getRefSeqCategory()

setOrganismTaxon

public NCBIGenomicAssemblyInfo setOrganismTaxon(NCBITaxon inValue)

getOrganismTaxon

public NCBITaxon getOrganismTaxon()

setSpeciesTaxon

public NCBIGenomicAssemblyInfo setSpeciesTaxon(NCBITaxon inValue)

getSpeciesTaxon

public NCBITaxon getSpeciesTaxon()

setInfraspecificName

public NCBIGenomicAssemblyInfo setInfraspecificName(String inValue)

getInfraspecificName

public String getInfraspecificName()

setIsolate

public NCBIGenomicAssemblyInfo setIsolate(String inValue)

getIsolate

public String getIsolate()

setAssemblyVersionStatus

public NCBIGenomicAssemblyInfo setAssemblyVersionStatus(GenomicAssemblyVersionStatus inValue)

getAssemblyVersionStatus

public GenomicAssemblyVersionStatus getAssemblyVersionStatus()

setAssemblyLevel

public NCBIGenomicAssemblyInfo setAssemblyLevel(GenomicAssemblyLevel inValue)

getAssemblyLevel

public GenomicAssemblyLevel getAssemblyLevel()

setAssemblyReleaseType

public NCBIGenomicAssemblyInfo setAssemblyReleaseType(GenomicAssemblyReleaseType inValue)

getAssemblyReleaseType

public GenomicAssemblyReleaseType getAssemblyReleaseType()

setGenomicRepresentation

public NCBIGenomicAssemblyInfo setGenomicRepresentation(GenomicRepresentation inValue)

getGenomicRepresentation

public GenomicRepresentation getGenomicRepresentation()

setReleaseDate

public NCBIGenomicAssemblyInfo setReleaseDate(Date inValue)

getReleaseDate

public Date getReleaseDate()

setAssemblyName

public NCBIGenomicAssemblyInfo setAssemblyName(String inValue)

getAssemblyName

public String getAssemblyName()

setSubmitter

public NCBIGenomicAssemblyInfo setSubmitter(String inValue)

getSubmitter

public String getSubmitter()

setGenBankRefSeqPairedAssembly

public NCBIGenomicAssemblyInfo setGenBankRefSeqPairedAssembly(String inValue)

getGenBankRefSeqPairedAssembly

public String getGenBankRefSeqPairedAssembly()

setPairedAssemblyComparison

public NCBIGenomicAssemblyInfo setPairedAssemblyComparison(GenomicPairedAssemblyComparison inValue)

getPairedAssemblyComparison

public GenomicPairedAssemblyComparison getPairedAssemblyComparison()

setFTP_Path

public NCBIGenomicAssemblyInfo setFTP_Path(String inValue)

getFTP_Path

public String getFTP_Path()

setExcludedFromRefSeq

public NCBIGenomicAssemblyInfo setExcludedFromRefSeq(boolean inValue)

getExcludedFromRefSeq

public boolean getExcludedFromRefSeq()

setRelationToTypeMaterial

public NCBIGenomicAssemblyInfo setRelationToTypeMaterial(GenomicRelationToTypeMaterial inValue)

getRelationToTypeMaterial

public GenomicRelationToTypeMaterial getRelationToTypeMaterial()

compareTo

public int compareTo(NCBIGenomicAssemblyInfo inObj2)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

The implementor must ensure sgn(x.compareTo(y)) == -sgn(y.compareTo(x)) for all x and y. (This implies that x.compareTo(y) must throw an exception iff y.compareTo(x) throws an exception.)

The implementor must also ensure that the relation is transitive: (x.compareTo(y) > 0 && y.compareTo(z) > 0) implies x.compareTo(z) > 0.

Finally, the implementor must ensure that x.compareTo(y)==0 implies that sgn(x.compareTo(z)) == sgn(y.compareTo(z)), for all z.

It is strongly recommended, but not strictly required that (x.compareTo(y)==0) == (x.equals(y)). Generally speaking, any class that implements the Comparable interface and violates this condition should clearly indicate this fact. The recommended language is "Note: this class has a natural ordering that is inconsistent with equals."

In the foregoing description, the notation sgn(expression) designates the mathematical signum function, which is defined to return one of -1, 0, or 1 according to whether the value of expression is negative, zero, or positive, respectively.

Specified by:

compareTo in interface Comparable<NCBIGenomicAssemblyInfo>

Parameters:

inObj2 - the object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type prevents it from being compared to this object.