org.blueprint.seqhound
Class SeqHound

java.lang.Object
  |
  +--org.blueprint.seqhound.SeqHound

public class SeqHound

extends java.lang.Object

This class provides a remote interface to the SeqHound database. It provides a core set of functionality for obtaining bioinformatics data using alphanumeric keys such as the taxonomy id, gene info identifier, accession number, and various other identifiers.

Field Summary

static int	REPORT_ASN_TXT used by SHoundProteinReportSetDescription to specify the 'format' field.
static int	REPORT_XML used by SHoundProteinReportSetDescription to specify the 'format' field.
int	SEQHOUND_ABNORMAL Possible error codes returned by this API.
int	SEQHOUND_ERROR Possible error codes returned by this API.
int	SEQHOUND_NULL Possible error codes returned by this API.
int	SEQHOUND_OK Possible error codes returned by this API.

Constructor Summary

SeqHound()
Creates a SeqHound object and uses the default configuration file '.shoundremrc' and default log threshold 'INFO'.

SeqHound(java.lang.String config)
Creates a SeqHound object and using the specified configuration file and the default log threshold 'INFO'.

SeqHound(java.lang.String config, java.lang.String logThreshold)
Creates a SeqHound object using the specified configuration file and minimum level for logging.

Method Summary

protected int	_ParseError(java.lang.String content) determines whether seqhound server returned SEQHOUND_OK, SEQHOUND_ERROR, or SEQHOUND_NULL and returns the server response, else returns SEQHOUND_ABNORMAL.
protected java.lang.String	GetFunctionCall(java.lang.String func, java.lang.String args) Constructs the http call to seqrem.
protected int	ProcessContents(java.lang.String address, java.lang.StringBuffer result) takes a url address: http://server address/path to cgi?
protected int	ProcessContents(java.lang.String address, java.io.Writer out) takes a url address: http://server address/path to cgi?
java.util.Hashtable	ProcessRetStr(java.util.Hashtable h, java.lang.String str) Process the return string from server to a hashtable
void	setLogThreshold(java.lang.String minium) Set the threshold for logging.
int	SHound3DbWhat(int mmdbid) Finds out what kind of molecules are contained in a 3-D structure.
boolean	SHound3DExists(int mmdbid) Finds out whether a given structural ID (mmdbid) exists in the SeqHound database.
int	SHound3DFromGi(int gi) Get the MMDB identifier for a given gi
int[]	SHound3DFromGiList(int[] giList) Get an array of MMDB identifiers for a given gi array
int[]	SHound3DNeighboursFromGi(int gi, double eValue) Retrieves a list of protein BLAST neighbours possessing 3-D structure.
int[]	SHound3DNeighboursFromTaxID(int taxid, double eValue) Retrieves a list of protein BLAST neighbours possessing 3-D structure using a list of proteins belonging to a complete genome as a query.
java.lang.String	SHoundAccFromGi(int gi) Gets an accession value given a gi value.
java.lang.String[]	SHoundAccFromGiList(int[] giList) Retrieves a list of accession given a list of gi's
int[]	SHoundAllGenomes() Get an array of taxonomy identifiers for all complete genomes present in the SeqHound system.
java.lang.String[]	SHoundCDDIDFromGi(int gi) retrieves the domains for a specified gi.
java.lang.String[]	SHoundCDDIDFromGiList(int[] giList) retrieve the domain identifiers for a specified gi array
float	SHoundCDDScoreFromGi(int gi, java.lang.String cddid) Get the score for a Conserved domain database domain
int[]	SHoundChromosomeFromGenome(int taxid, int chromflags) Get all the chromosomes for a given taxonomy identifier and the molecule
int[]	SHoundChromosomeFromGenomeList(int[] taxList, int chromflags) Gets an array of chromosome identifiers for a given taxonomy list
int[]	SHoundDNAFromChromosome(int chromid) Get an array of dna gi's for a given chromosome identifier
int[]	SHoundDNAFromChromosomeList(int[] chromList) Get an array of dna gi's for an input of chromosome array
int[]	SHoundDNAFromOrganism(int taxid, int chromflags) Get an array of dna gi's for a given organism
int[]	SHoundDNAFromOrganismList(int[] taxList, int chromflags) Get an array of dna gi's for a given taxonomy array
int	SHoundDNAFromProtein(int gi) Get the dna gi fro a given gi
int[]	SHoundDNAFromProteinList(int[] giList) Get an array of dna gi for a given array of gi
int[]	SHoundDNAFromTaxID(int taxid) Get the DNA gi's for a given taxonomy id
int[]	SHoundDNAFromTaxIDIII(int taxid) Get the dna gi's for a given taxid.
int[]	SHoundDNAFromTaxIDList(int[] taxList) get an array of dna gi's for an array of taxonomy identifiers
boolean	SHoundExists(int gi) reports whether a given gi exists in the SeqHound database.
int	SHoundFindAcc(java.lang.String acc) Retrieves a gi from an accession value.
int[]	SHoundFindAccList(java.lang.String[] accList) Retrieves a list of gi's given a list of accession values.
int	SHoundFindName(java.lang.String name) Converts PDB, EMBL, Siwss-Prot, PIR sequence identifier into a GI.
int[]	SHoundFindNameList(java.lang.String[] nameList) Given a list of ID from PDB, SwissProt, or PIR sequence identifiers, retrieves a list of gi's.
boolean	SHoundFini() Clean up SeqHound
int	SHoundFirstOfRedundantGroupFromID(int group) Entrez collection of databases contains redundant entries i.e.
int[]	SHoundFirstOfRedundantGroupFromIDList(int[] group) Gets the gi of the best annotated sequence given an array of group id.
java.lang.String	SHoundGet3D(int mmdbid) Fetches ASN.1 representation of 3-D structure called Biostruc.
java.lang.String	SHoundGet3DfromPdbId(java.lang.String pdbid) Fetches ASN.1 representation of 3-D structure called Biostruc.
java.lang.String	SHoundGetAccFromRetiredGi(int gi) Returns accession number for the given retired gi.
int[]	SHoundGetAllTaxAncestors(int taxid) Retrieves all taxid (the whole subtree) above a given taxid
int[]	SHoundGetAllTaxProgeny(int taxid) operates on NCBI's taxonomy tree.
java.lang.String	SHoundGetBioseq(int gi) fetches a string formated in ASN representing a sequence information.
java.lang.String	SHoundGetBioseqList(int[] giList) Get a list of ASN.1 formatted sequence information and available annotations.
java.lang.String	SHoundGetBioseqSet(int gi) retrieves the fetches ASN.1 representation of a sequence called BioseqSet.
java.lang.String	SHoundGetBioseqSetList(int[] giList) retrieves a string contain the bioseqset for a list of gi's
java.lang.String	SHoundGetDefline(int gi) Defline contains the gi, accession number and other valuable information together with a short description of the sequence
java.lang.String[]	SHoundGetDeflineList(int[] giList) retrieves a list of defline lines
java.lang.String[]	SHoundGetDomainIdFromLabel(java.lang.String label) retrieves the domain id given a label
java.lang.String[]	SHoundGetDomainLabelFromDomainId(java.lang.String accession) Returns a short non-unique label given a domain for a Conserved Domain Database (CDD).
java.lang.String	SHoundGetDomainsFromGi(int gi) Fetches information about domains from the Conserved Domain Database (CDD) as assigned by Reverse Position Specific BLAST to a given protein sequence.
java.lang.String	SHoundGetDomainsFromGiWithEvalue(int gi, double eValue) Fetches information about domains from the Conserved Domain Database (CDD) as assigned by Reverse Position Specific BLAST to a given protein sequence.
java.lang.String	SHoundGetFasta(int gi) The FASTA format is widely used in bioinformatics community; it consists of a definition line, new line followed by a sequence terminated by a second new line.
java.lang.String	SHoundGetFastaFromRedundantGroupID(int gid) The FASTA format is widely used in bioinformatics community; it consists of a definition line, new line followed by a sequence terminated by a second new line.
java.util.Hashtable	SHoundGetFastaFromRedundantGroupIDKeyedList(int[] gidList) retrieves fasta list for the given redundant group id list
java.util.Hashtable	SHoundGetFastaKeyedList(int[] giList) retrieves fasta list for the given gilist
java.lang.String[]	SHoundGetFastaList(int[] giList) retrieves a list of fasta
boolean	SHoundGetFastaList(int[] giList, java.io.Writer out) writes a series of fasta data into a writer object pointed to by out.
java.lang.String	SHoundGetGenBankff(int gi) GenBank flat file contains comprehensive full annotation of a sequence.
java.lang.String[]	SHoundGetGenBankffList(int[] giList) retrieves an array of strings formated in genbank ff.
int[]	SHoundGetGisByDomainId(java.lang.String domain) retrieve the gi's having a domain id
int[]	SHoundGetGisByDomainIdAndEvalue(java.lang.String domain, double evalue) Fetches protein sequences on which a domain from the Conserved Domain Database (CDD) was identified by Reverse Position Specific BLAST.
int[]	SHoundGetGisByNumberOfDomains(int numdoms) retrieves all the gi's with the specified number of domains
int	SHoundGetLargestMMDBID() return the largest mmdbid
java.lang.String	SHoundGetPDB3D(int mmdbid) Retrieves an PDB representation of a 3-D structure
int[]	SHoundGetReferenceIDFromGi(int gi, int reftype) Retrieves the MUID or PMID for a given gi.
int[]	SHoundGetReferenceIDFromGiList(int[] giList, int reftype) Retrieves the MUID or PMID for a given gi.
java.lang.String	SHoundGetSeqEntry(int gi) Fetches ASN.1 representation of a sequence called SeqEntry.
java.lang.String	SHoundGetSeqEntryList(int[] giList) Retrieves a list of seqentry from a list of gi
int[]	SHoundGetTaxChildNodes(int taxid) operates on NCBI's taxonomy tree.
int[]	SHoundGetTaxChildNodesList(int[] taxList) Get the children taxonomy id of an array of taxid inputs
java.lang.String	SHoundGetTaxLineageFromTaxID(int taxid, java.lang.String type) fetches a taxonomy lineage in a specified form.
java.lang.String	SHoundGetTaxNameFromTaxID(int taxid) fetches a taxonomy name in scientific form
java.lang.String	SHoundGetTaxNameFromTaxIDByClass(int taxid, java.lang.String nameClass) gets a taxon name in a specified style
int	SHoundGetTaxParent(int taxid) Retrieve the tax id situated directly above a given tax id
java.lang.String	SHoundGetXML3D(int mmdbid) Retrieves an XML representation of a 3-D structure
java.lang.String	SHoundGetXMLBioseq(int gi) Get an XML Formated Bioseq structure which contains sequence information and all available annotations.
java.lang.String	SHoundGetXMLSeqEntry(int gi) retrieves the a XML formated string of a seqentry
int[]	SHoundGiFrom3D(int mmdbid, boolean ProteinOnly) retrieves the gi given a mmdbid
int[]	SHoundGiFrom3DList(int[] mmdbidList, boolean ProteinOnly) retrieve an array of gi's from the MMDB identifiers
int[]	SHoundGiFromCDDID(java.lang.String cddid) retrieves an array of gi with the domain specified by input
int[]	SHoundGiFromCDDIDList(java.lang.String[] cddidList) get the gi's with the specified domains
int[]	SHoundGiFromGOID(int go) retrieves an array of gi with specified the specified gene ontology identifier
int[]	SHoundGiFromGOIDAndECode(int goid, java.lang.String ecode) Return all the gi's with the given goid and evidence code.
int[]	SHoundGiFromGOIDList(int[] goList) retrieves an array of gis that have been annotated with the specified goid
int[]	SHoundGiFromGOIDListAndECode(int[] goList, java.lang.String ecode) retrieves an array of gis that have been annotated with the specified goid list and the evidence code
int[]	SHoundGiFromLLID(int llid) Get gi associated with a locuslink identifier
int[]	SHoundGiFromLLIDList(int[] llidList) get the gi's associated with the locuslink id
int[]	SHoundGiFromOMIM(int omimid) retrieves gi's from an omim
int[]	SHoundGiFromOMIMList(int[] omimList) retrieves gi's associated with a omim
int	SHoundGiFromPDBchain(java.lang.String pdbcode, java.lang.String chain) retrieve an array of gi's from the PDB identifiers
int[]	SHoundGiFromReferenceID(int refid, int reftype) Retrieves the gi's associated with a publication.
int[]	SHoundGiFromReferenceList(int[] refList, int reftype) Retrieves the gi's associated with a publication list.
int[]	SHoundGODBGetAllAncestors(int goid) retrieves all the ancestors (parents, grandparents ...) of a given gene ontology id.
int[]	SHoundGODBGetAllChildren(int goid) retrieve all children of a given gene ontology id
int[]	SHoundGODBGetChildrenOf(int goid) retrieves all the children of a given gene ontology id
java.lang.String	SHoundGODBGetClassification(int goid) retrieve the ontology classification for a given goid
java.lang.String	SHoundGODBGetNameByID(int goid) retrieves the name of a given goid
int[]	SHoundGODBGetParentOf(int goid) retrieves an array of the parents of a given goid
int[]	SHoundGODBGetRecordByReference(java.lang.String refType) retrieve the gene ontology id by geneontology reference type
java.lang.String[]	SHoundGOECodeFromGiAndGOID(int gi, int goid) Retrieves all the evidence code from locuslink for a given gi and gene ontology id.
int[]	SHoundGOIDFromGi(int gi) retrieves an array of goid for a specified gi
int[]	SHoundGOIDFromGiList(int[] giList) retrieves an array of goid for a specified array of gi's
int[]	SHoundGOIDFromRedundantGi(int gi) retrieve an array of goid from a redundant gi
int[]	SHoundGOIDFromRedundantGiList(int[] giList) retrieve an array of goid for a given array of gi's
int[]	SHoundGOPMIDFromGiAndGOID(int gi, int goid) Retrieves the PMID's in the LocusLink database for a given gi and gene ontology id.
boolean	SHoundInit(boolean NetEntrezOnToo, java.lang.String appname) Initializes the SeqHound object.
boolean	SHoundIsInited() Check if SeqHound has been initialized.
boolean	SHoundIsNetEntrezOn() Checks if net entrez is enabled.
boolean	SHoundIsNRFirst(int gi) Reports if a given GI identifier represents the best annotated version from a group of database entries referring to the same protein sequence (so called redundant proteins).
boolean	SHoundIsProtein(int gi) Deprecated. replaced by SHoundMoleculeType(int)
protected boolean	SHoundIsServerAlive(java.lang.String configServerKey, java.lang.String path, java.lang.String args) Sends an http call to the servers to determine if they are up.
boolean	SHoundIsTaxDeleted(int taxid) reports whether a taxid has been deleted from the tree
boolean	SHoundIsTaxMerged(int taxid) reports if a given taxonomy identifier has been renamed
int[]	SHoundLLIDFromGi(int gi) retrieves locuslink id for a given gi
int[]	SHoundLLIDFromGiList(int[] giList) retrievs locuslink id for a given gi array
java.lang.String	SHoundLocusFromGi(int gi) retrieves the locus for a given gi
protected void	SHoundLogError(java.util.logging.Level level, java.lang.String msg) Logs information/error into the log file.
java.lang.String	SHoundMoleculeType(int gi) determines the molecular type given a gi
int[]	SHoundMuidFrom3D(int mmdbid) Get the MUID for a given MMDB identifier
int[]	SHoundMuidFrom3DList(int[] giList) Get the MUID list for a given gi array
int[]	SHoundMuidFromGi(int gi) Deprecated. replaced by SHoundGetReferenceIDFromGi(int, int)
int[]	SHoundMuidFromGiList(int[] giList) Deprecated. replaced by SHoundGetReferenceIDFromGiList(int[], int)
int[]	SHoundNeighboursFromGi(int gi, double eValue, boolean bLimit) Retrieves a list of protein BLAST neighbours.
int[]	SHoundNeighboursFromGiList(int[] giList, double eValue, boolean bLimit) Retrieves a list of protein BLAST neighbours.
int[]	SHoundNeighboursFromTaxID(int taxid, double eValue) Retrieves a list of protein BLAST neighbours using a list of proteins belonging to a complete genome as a query.
boolean	SHoundNetEntrezInit(java.lang.String appname) Initializes net entrez.
int[]	SHoundOMIMFromGi(int gi) retrieves omim associated with a gi
int[]	SHoundOMIMFromGiList(int[] giList) get the associated omim for an array of gi's
int[]	SHoundProteinFromDNA(int gi) Get the protein gi for a given gi
int[]	SHoundProteinFromDNAList(int[] giList) Get an array of protein gi's given an array of gi's
java.lang.String	SHoundProteinReportSetDescription(int gi, int format) Get a protein report set description for a given gi.
int[]	SHoundProteinsFromChromosome(int chromid) Get the protein gi's for a given chromosome identifier
int[]	SHoundProteinsFromChromosomeList(int[] chromList) Get the protein gi's for an array of chromosome identifiers
int[]	SHoundProteinsFromOrganism(int taxid, int chromflags) Get the proteins for a given taxonomy.
int[]	SHoundProteinsFromOrganismList(int[] taxList, int chromflags) Get the protein gi's for a given taxonomy array, use bit notation for chromflags
int[]	SHoundProteinsFromTaxID(int taxid) Get the protein gi's for a given taxonomy
int[]	SHoundProteinsFromTaxIDIII(int taxid) Get an array of protein gi's for a given taxonomy identifier.
int[]	SHoundProteinsFromTaxIDList(int[] taxList) get an array of proteins from an array of taxonomy identifier
int[]	SHoundRedundantGroup(int gi) Gets all protein entries with the same sequence from the system
int[]	SHoundRedundantGroupFromID(int group) returns an array of gi's in the same group.
int[]	SHoundRedundantGroupFromIDList(int[] groupList) returns an array of redundant protein gi's for an array of redundant group id's.
int	SHoundRedundantGroupIDFromGi(int gi) Entrez collection of databases contains redundant entries i.e.
int[]	SHoundRedundantGroupIDFromGiList(int[] giList) Entrez collection of databases contains redundant entries i.e.
java.util.Hashtable	SHoundRedundantGroupKeyedList(int[] giList) Gets all protein entries with the same sequence from the system
int[]	SHoundRedundantGroupList(int[] giList) Gets all protein entries with the same sequence from the system
java.lang.String	SHoundSeqIdFromGi(int gi) Gets a SeqId object given a gi.
java.lang.String	SHoundSeqIdFromGiList(int[] giList) Get the SeqId's given a gi list.
int	SHoundSequenceLength(int gi) retrieves the length of a sequence.
int	SHoundTaxIDFrom3D(int mmdbid) Get a taxid for a given gi
int[]	SHoundTaxIDFrom3DList(int[] mmdbidList) Get an array of taxid from an array of MMDB identifier
int	SHoundTaxIDFromGi(int gi) Get the taxid for a given gi
int[]	SHoundTaxIDFromGiList(int[] giList) Get an array of taxonomy identifiers from an array of gi
java.lang.String	SHoundXMLBioseq(int gi) A wrap function to get an XML Formated Bioseq structure which contains sequence information and all available annotations.

Methods inherited from class java.lang.Object

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

Field Detail

REPORT_XML

public static final int REPORT_XML

used by SHoundProteinReportSetDescription to specify the 'format' field. Results in a XML string.

See Also:

SHoundProteinReportSetDescription(int, int), Constant Field Values

REPORT_ASN_TXT

public static final int REPORT_ASN_TXT

used by SHoundProteinReportSetDescription to specify the 'format' field. Results in a protein report string.

See Also:

SHoundProteinReportSetDescription(int, int), Constant Field Values

SEQHOUND_ERROR

public final int SEQHOUND_ERROR

Possible error codes returned by this API. A server error occurred.

See Also:

Constant Field Values

SEQHOUND_NULL

public final int SEQHOUND_NULL

Possible error codes returned by this API. A null value was returned.

See Also:

Constant Field Values

SEQHOUND_OK

public final int SEQHOUND_OK

Possible error codes returned by this API. Everything was okay.

See Also:

Constant Field Values

SEQHOUND_ABNORMAL

public final int SEQHOUND_ABNORMAL

Possible error codes returned by this API. An unknown error.

See Also:

Constant Field Values

Constructor Detail

SeqHound

public SeqHound()
         throws java.io.FileNotFoundException,
                java.io.IOException

Creates a SeqHound object and uses the default configuration file '.shoundremrc' and default log threshold 'INFO'.
To specify your own configuration file, use corresponding constructor.

Throws:

java.io.FileNotFoundException - if the default configuration file is not found

java.io.IOException - if there is an I/O exception

See Also:

SeqHound(String),SeqHound(String, String)

SeqHound

public SeqHound(java.lang.String config)
         throws java.io.FileNotFoundException,
                java.io.IOException

Creates a SeqHound object and using the specified configuration file and the default log threshold 'INFO'.
To use the default configuration file, use the corresponding constructor.

Throws:

java.io.FileNotFoundException - if the default configuration file is not found

java.io.IOException - if there is an I/O exception

See Also:

SeqHound(),SeqHound(String, String)

SeqHound

public SeqHound(java.lang.String config,
                java.lang.String logThreshold)
         throws java.io.FileNotFoundException,
                java.io.IOException

Creates a SeqHound object using the specified configuration file and minimum level for logging. Logging levels are as specified in java.util.logging.Level : SEVERE, WARNING, INFO, CONFIG, FINE, FINER, FINEST
To use the default configuration file, use the corresponding constructor.

Throws:

java.io.FileNotFoundException - if the default configuration file is not found

java.io.IOException - if there is an I/O exception

See Also:

SeqHound(),SeqHound(String)

Method Detail

SHoundLogError

protected void SHoundLogError(java.util.logging.Level level,
                              java.lang.String msg)

Logs information/error into the log file.

Parameters:

level - the level of the information or exception. There are 3 levels, SH_info, SH_warn, SH_severe

msg - the message to be logged

setLogThreshold

public void setLogThreshold(java.lang.String minium)

Set the threshold for logging. Messages at and above 'minimum' will get logged, below it, is not logged. 'minium' must be defined in java.util.logging.Level class: SEVERE, WARNING, INFO, CONFIG, FINE, FINER, FINEST, otherwise defaults to "INFO".

GetFunctionCall

protected java.lang.String GetFunctionCall(java.lang.String func,
                                           java.lang.String args)

Constructs the http call to seqrem. Ex:
http://seqhound.mshri.on.ca?fnct=SeqHoundInit&IsNetEntrezOnToo=TRUE&appname=value

Parameters:

func - the function being called on the cgi server

args - the querystring arguments to send to the server

Returns:

the http call

_ParseError

protected int _ParseError(java.lang.String content)

determines whether seqhound server returned SEQHOUND_OK, SEQHOUND_ERROR, or SEQHOUND_NULL and returns the server response, else returns SEQHOUND_ABNORMAL.

Parameters:

content - the string to parse the return value from

See Also:

SEQHOUND_ERROR,SEQHOUND_NULL,SEQHOUND_ABNORMAL,SEQHOUND_OK

ProcessContents

protected int ProcessContents(java.lang.String address,
                              java.lang.StringBuffer result)
                       throws java.io.IOException,
                              java.net.MalformedURLException

takes a url address: http://server address/path to cgi?querystring and sends the call to the remote server. Then it gets the response from the server and determines the return value of the url. and return SEQHOUND_OK, SEQHOUND_NULL, SEQHOUND_ERROR based on the server response.

Parameters:

address - the http address

result - a buffer in which to save the return value from the server

Returns:

SEQHOUND_OK, SEQHOUND_ERROR, SEQHOUND_NULL

Throws:

java.io.IOException - if there is an I/O exception

java.net.MalformedURLException - if the address is not valid

See Also:

SEQHOUND_OK,SEQHOUND_NULL,SEQHOUND_ERROR

ProcessContents

protected int ProcessContents(java.lang.String address,
                              java.io.Writer out)
                       throws java.io.IOException,
                              java.net.MalformedURLException

takes a url address: http://server address/path to cgi?querystring and sends the call to the remote server. Then it gets the response from the server and determines the return value of the url. and return SEQHOUND_OK, SEQHOUND_NULL, SEQHOUND_ERROR based on the server response.

Parameters:

address - the http address

out - an output where the server response should be directed

Returns:

SEQHOUND_OK, SEQHOUND_ERROR, SEQHOUND_NULL

Throws:

java.io.IOException - if there is an I/O exception

java.net.MalformedURLException - if the address is not valid

See Also:

SEQHOUND_OK,SEQHOUND_NULL,SEQHOUND_ERROR

SHoundIsServerAlive

protected boolean SHoundIsServerAlive(java.lang.String configServerKey,
                                      java.lang.String path,
                                      java.lang.String args)
                               throws java.io.IOException

Sends an http call to the servers to determine if they are up.

Parameters:

configServerKey - the key that specifies which server to use

path - the path to the cgi-bin

args - the http querystring

Returns:

true/false, is the specified server up

Throws:

java.io.IOException - if there is an I/O Exception

SHoundInit

public boolean SHoundInit(boolean NetEntrezOnToo,
                          java.lang.String appname)
                   throws java.io.IOException

Initializes the SeqHound object. this function must be called before any other seqhound functions can be used. It tests for an active seqhound server and sets this object to use that server.

Parameters:

NetEntrezOnToo - turn on net entrez on

appname - the applicaton name

Returns:

true if SeqHound initialized properly, else false

Throws:

java.io.IOException - if an I/O Exception occurred

SHoundFini

public boolean SHoundFini()
                   throws java.io.IOException

Clean up SeqHound

Returns:

true

Throws:

java.io.IOException

SHoundIsNetEntrezOn

public boolean SHoundIsNetEntrezOn()
                            throws java.io.IOException

Checks if net entrez is enabled. Returns true if enabled, else returns false;

Returns:

true if net entrez enabled, else false

Throws:

java.io.IOException

SHoundIsInited

public boolean SHoundIsInited()

Check if SeqHound has been initialized.

Returns:

true if initialized, else false

SHoundNetEntrezInit

public boolean SHoundNetEntrezInit(java.lang.String appname)
                            throws java.io.IOException

Initializes net entrez.

Parameters:

appname - the application name

Returns:

true if net entrez initialized else, false

Throws:

java.io.IOException

SHoundFindAcc

public int SHoundFindAcc(java.lang.String acc)
                  throws java.io.IOException

Retrieves a gi from an accession value.

Parameters:

acc - the accession value

Returns:

the gi or a SEQHOUND_ERROR, SEQHOUND_NULL, SEQHOUND_ABNORMAL if not found

Throws:

java.io.IOException

SHoundFindAccList

public int[] SHoundFindAccList(java.lang.String[] accList)
                        throws java.io.IOException

Retrieves a list of gi's given a list of accession values.

Parameters:

accList - the list of accession values

Returns:

a list of gi's, or null

Throws:

java.io.IOException

See Also:

SHoundFindAcc(String)

SHoundFindName

public int SHoundFindName(java.lang.String name)
                   throws java.io.IOException

Converts PDB, EMBL, Siwss-Prot, PIR sequence identifier into a GI. Note thatEMBL shares accession numbers with GenBank. EMBL GenInfo identifiers may be returned using these accessions; for example SHoundFindAcc(X13776) will return GI 45269. EMBL also has its own identifiers (which the NCBI and SeqHound refer to as 'name'). So the same GI may be returned by SHoundFindName(PAAMIR).

Parameters:

name - the name

Returns:

gi or a negative value

Throws:

java.io.IOException

SHoundFindNameList

public int[] SHoundFindNameList(java.lang.String[] nameList)
                         throws java.io.IOException

Given a list of ID from PDB, SwissProt, or PIR sequence identifiers, retrieves a list of gi's. Note that EMBL shares accession numbers with GenBank. EMBL GenInfo identifiers may be returned using these accessions; for example SHoundFindAcc(X13776) will return GI 45269. EMBL also has its own identifiers (which the NCBI and SeqHound refer to as 'name'). So the same GI may be returned by SHoundFindName("PAAMIR").

Parameters:

nameList - the list of names

Returns:

list of gi's or null

Throws:

java.io.IOException

See Also:

SHoundFindName(String)

SHoundAccFromGi

public java.lang.String SHoundAccFromGi(int gi)
                                 throws java.io.IOException

Gets an accession value given a gi value.

Parameters:

gi - the gi to look up

Returns:

the accession value

Throws:

java.io.IOException

SHoundAccFromGiList

public java.lang.String[] SHoundAccFromGiList(int[] giList)
                                       throws java.io.IOException

Retrieves a list of accession given a list of gi's

Parameters:

giList - the list of gi's

Returns:

the list of accessions or null

Throws:

java.io.IOException

See Also:

SHoundAccFromGi(int)

SHoundSeqIdFromGi

public java.lang.String SHoundSeqIdFromGi(int gi)
                                   throws java.io.IOException

Gets a SeqId object given a gi. SeqId object is an ASN formatted string with relevant gi information.

Parameters:

gi - the gi to retrieve the SeqId for

Returns:

the SeqId

Throws:

java.io.IOException

SHoundSeqIdFromGiList

public java.lang.String SHoundSeqIdFromGiList(int[] giList)
                                       throws java.io.IOException

Get the SeqId's given a gi list. The SeqId's will be one big string formatted in ASN.

Parameters:

giList - the list of gi

Returns:

the ASN formatted string or null

Throws:

java.io.IOException

See Also:

SHoundSeqIdFromGi(int)

SHoundMoleculeType

public java.lang.String SHoundMoleculeType(int gi)
                                    throws java.io.IOException

determines the molecular type given a gi

Parameters:

gi - the gi to be determined

Returns:

a string description of the molecule type. Possible values include: protein, DNA, RNA or a null

Throws:

java.io.IOException

SHoundSequenceLength

public int SHoundSequenceLength(int gi)
                         throws java.io.IOException

retrieves the length of a sequence.

Parameters:

gi - the sequence to get the length of

Returns:

the length of the sequence

Throws:

java.io.IOException

SHoundIsProtein

public boolean SHoundIsProtein(int gi)
                        throws java.io.IOException

Deprecated. replaced by SHoundMoleculeType(int)

Returns where a given gi is a protein or not.

Parameters:

gi - the gi to determine

Returns:

true if gi is protein, else false

Throws:

java.io.IOException

SHoundIsNRFirst

public boolean SHoundIsNRFirst(int gi)
                        throws java.io.IOException

Reports if a given GI identifier represents the best annotated version from a group of database entries referring to the same protein sequence (so called redundant proteins).

Parameters:

gi - the gi

Returns:

true if best annotated else false

Throws:

java.io.IOException

SHoundExists

public boolean SHoundExists(int gi)
                     throws java.io.IOException

reports whether a given gi exists in the SeqHound database.

Parameters:

gi - the gi to request

Returns:

true if the gi is present in SeqHound, else false

Throws:

java.io.IOException

SHound3DbWhat

public int SHound3DbWhat(int mmdbid)
                  throws java.io.IOException

Finds out what kind of molecules are contained in a 3-D structure.

Parameters:

mmdbid - the 3D structure ID

Returns:

1 is a polymer, 2 is a protein, 4 is a DNA, 8 is a heteroatom 16 is solvent, 32 is water, 64 is RNA, 138 is ion

Throws:

java.io.IOException

SHoundGetLargestMMDBID

public int SHoundGetLargestMMDBID()
                           throws java.io.IOException

return the largest mmdbid

Returns:

mmdbid the 3D structure ID

Throws:

java.io.IOException

SHound3DExists

public boolean SHound3DExists(int mmdbid)
                       throws java.io.IOException

Finds out whether a given structural ID (mmdbid) exists in the SeqHound database.

Parameters:

mmdbid - the structural ID

Returns:

true if in SeqHound, else false

Throws:

java.io.IOException

SHoundGOPMIDFromGiAndGOID

public int[] SHoundGOPMIDFromGiAndGOID(int gi,
                                       int goid)
                                throws java.io.IOException

Retrieves the PMID's in the LocusLink database for a given gi and gene ontology id.

Parameters:

gi - the gene info id

goid - a geneontology id

Returns:

an array of PMID associated with the inputs

Throws:

java.io.IOException

SHoundGOECodeFromGiAndGOID

public java.lang.String[] SHoundGOECodeFromGiAndGOID(int gi,
                                                     int goid)
                                              throws java.io.IOException

Retrieves all the evidence code from locuslink for a given gi and gene ontology id.

Parameters:

gi - the gi

goid - the gene ontology id

Returns:

an array of evidence code from the locuslink database.

Throws:

java.io.IOException

SHoundGetReferenceIDFromGi

public int[] SHoundGetReferenceIDFromGi(int gi,
                                        int reftype)
                                 throws java.io.IOException

Retrieves the MUID or PMID for a given gi.

Parameters:

gi - the gi

reftype - specifies whether to return PMID or MUID. Set reftype to 1 for MUID, 2 for PMID.

Returns:

an array of reference ids.

java.io.IOException

SHoundGetReferenceIDFromGiList

public int[] SHoundGetReferenceIDFromGiList(int[] giList,
                                            int reftype)
                                     throws java.io.IOException

Retrieves the MUID or PMID for a given gi.

Parameters:

giList - the gilist

reftype - specifies whether to return PMID or MUID. Set reftype to 1 for MUID, 2 for PMID.

Returns:

an array of reference ids.

java.io.IOException

SHoundGiFromReferenceID

public int[] SHoundGiFromReferenceID(int refid,
                                     int reftype)
                              throws java.io.IOException

Retrieves the gi's associated with a publication.

Parameters:

refid - the publication id

reftype - the publication type. Set reftype to 1 if refid is a PMID Set reftype to 2 if refid is a MUID.

Returns:

an array of integers that are gis, or null

Throws:

java.io.IOException

SHoundGiFromReferenceList

public int[] SHoundGiFromReferenceList(int[] refList,
                                       int reftype)
                                throws java.io.IOException

Retrieves the gi's associated with a publication list.

Parameters:

refList - the publication list

reftype - the publication type. Set reftype to 1 if refid is a PMID Set reftype to 2 if refid is a MUID.

Returns:

an array of integers that are gis, or null

Throws:

java.io.IOException

SHoundGetBioseq

public java.lang.String SHoundGetBioseq(int gi)
                                 throws java.io.IOException

fetches a string formated in ASN representing a sequence information. The seqence information is called a Bioseq and it contains all the available annotation.

Parameters:

gi - the gi

Returns:

the string ASN Bioseq

Throws:

java.io.IOException

SHoundGetBioseqList

public java.lang.String SHoundGetBioseqList(int[] giList)
                                     throws java.io.IOException

Get a list of ASN.1 formatted sequence information and available annotations.

Parameters:

giList - the list of gi

Returns:

a string ASN

Throws:

java.io.IOException

See Also:

SHoundGetBioseq(int)

SHoundGetXMLBioseq

public java.lang.String SHoundGetXMLBioseq(int gi)
                                    throws java.io.IOException

Get an XML Formated Bioseq structure which contains sequence information and all available annotations.

Parameters:

gi - the gi

Returns:

the XML string

Throws:

java.io.IOException

See Also:

SHoundGetBioseq(int)

SHoundXMLBioseq

public java.lang.String SHoundXMLBioseq(int gi)
                                 throws java.io.IOException

A wrap function to get an XML Formated Bioseq structure which contains sequence information and all available annotations. To consist with other remote APIs

Parameters:

gi - the gi

Returns:

the XML string

Throws:

java.io.IOException

SHoundGetSeqEntry

public java.lang.String SHoundGetSeqEntry(int gi)
                                   throws java.io.IOException

Fetches ASN.1 representation of a sequence called SeqEntry. SeqEntry contains a single sequence or a group of sequences if they are logically related (e.g. gene and its protein product).

Parameters:

gi - the gi

Returns:

an XML formatted string represented the SeqEntry or null

Throws:

java.io.IOException

SHoundGetSeqEntryList

public java.lang.String SHoundGetSeqEntryList(int[] giList)
                                       throws java.io.IOException

Retrieves a list of seqentry from a list of gi

Parameters:

giList - the gi list

Returns:

an ASN formated string containing the seqentry

Throws:

java.io.IOException

See Also:

SHoundGetSeqEntry(int)

SHoundGetXMLSeqEntry

public java.lang.String SHoundGetXMLSeqEntry(int gi)
                                      throws java.io.IOException

retrieves the a XML formated string of a seqentry

Parameters:

gi - the gi

Returns:

the string in xml format

Throws:

java.io.IOException

See Also:

SHoundGetSeqEntry(int)

SHoundGetBioseqSet

public java.lang.String SHoundGetBioseqSet(int gi)
                                    throws java.io.IOException

retrieves the fetches ASN.1 representation of a sequence called BioseqSet. BioseqSet exists only if there is more than one sequence in logical group of sequences (e.g. gene and its protein product).

Parameters:

gi - the gi

Returns:

an ASN formatted string containing the bioseqset

Throws:

java.io.IOException

SHoundGetBioseqSetList

public java.lang.String SHoundGetBioseqSetList(int[] giList)
                                        throws java.io.IOException

retrieves a string contain the bioseqset for a list of gi's

Parameters:

giList - an array of gi's

Returns:

an ASN formated string

Throws:

java.io.IOException

See Also:

SHoundGetBioseqSet(int)

SHoundGetDefline

public java.lang.String SHoundGetDefline(int gi)
                                  throws java.io.IOException

Defline contains the gi, accession number and other valuable information together with a short description of the sequence

Parameters:

gi - the gi

Returns:

the definition line

Throws:

java.io.IOException

SHoundGetDeflineList

public java.lang.String[] SHoundGetDeflineList(int[] giList)
                                        throws java.io.IOException

retrieves a list of defline lines

Parameters:

giList - the array of gi's

Returns:

an array of deflines

Throws:

java.io.IOException

See Also:

SHoundGetDefline(int)

SHoundGetFasta

public java.lang.String SHoundGetFasta(int gi)
                                throws java.io.IOException

The FASTA format is widely used in bioinformatics community; it consists of a definition line, new line followed by a sequence terminated by a second new line.

Parameters:

gi - the gi

Returns:

a string fasta

Throws:

java.io.IOException

SHoundGetFastaList

public java.lang.String[] SHoundGetFastaList(int[] giList)
                                      throws java.io.IOException

retrieves a list of fasta

Parameters:

giList - an array of gi's

Returns:

an array of fasta strings

Throws:

java.io.IOException

See Also:

SHoundGetFasta(int)

SHoundGetFastaList

public boolean SHoundGetFastaList(int[] giList,
                                  java.io.Writer out)
                           throws java.io.IOException

writes a series of fasta data into a writer object pointed to by out. Use this function to print a list of fasta data to a file.

Parameters:

giList - array of gi's

out - the writer object

Returns:

true if successfully wrote to out, else false

Throws:

java.io.IOException

See Also:

SHoundGetFastaList(int[])

SHoundGetGenBankff

public java.lang.String SHoundGetGenBankff(int gi)
                                    throws java.io.IOException

GenBank flat file contains comprehensive full annotation of a sequence.

Parameters:

gi - the gi to retrieve

Returns:

a string of the genbank format

Throws:

java.io.IOException

SHoundGetGenBankffList

public java.lang.String[] SHoundGetGenBankffList(int[] giList)
                                          throws java.io.IOException

retrieves an array of strings formated in genbank ff.

Parameters:

giList - an array of gi's

Returns:

an array of genbank ff

Throws:

java.io.IOException

See Also:

SHoundGetGenBankff(int)

SHoundGet3D

public java.lang.String SHoundGet3D(int mmdbid)
                             throws java.io.IOException

Fetches ASN.1 representation of 3-D structure called Biostruc. Biostrucs represent data model in Molecular Modeling database.

Parameters:

mmdbid - the mmdb id

Returns:

a string ASN.1 formated 3-D biostruc

Throws:

java.io.IOException

SHoundGet3DfromPdbId

public java.lang.String SHoundGet3DfromPdbId(java.lang.String pdbid)
                                      throws java.io.IOException

Fetches ASN.1 representation of 3-D structure called Biostruc. Biostrucs represent data model in Molecular Modeling database.

Parameters:

pdbid - the PDB identifier

Returns:

a string ASN.1 representation

Throws:

java.io.IOException

SHoundGetXML3D

public java.lang.String SHoundGetXML3D(int mmdbid)
                                throws java.io.IOException

Retrieves an XML representation of a 3-D structure

Parameters:

mmdbid - the MMDB identifier

Returns:

a string XML formated biostruc

Throws:

java.io.IOException

SHoundGetPDB3D

public java.lang.String SHoundGetPDB3D(int mmdbid)
                                throws java.io.IOException

Retrieves an PDB representation of a 3-D structure

Parameters:

mmdbid - the MMDB identifier

Returns:

a string PDB formated biostruc

Throws:

java.io.IOException

SHoundGiFrom3D

public int[] SHoundGiFrom3D(int mmdbid,
                            boolean ProteinOnly)
                     throws java.io.IOException

retrieves the gi given a mmdbid

Parameters:

mmdbid - the MMDB identifier

ProteinOnly - get the protein gi

Returns:

an array of the gi's in the 3 D structure

Throws:

java.io.IOException

SHoundGiFrom3DList

public int[] SHoundGiFrom3DList(int[] mmdbidList,
                                boolean ProteinOnly)
                         throws java.io.IOException

retrieve an array of gi's from the MMDB identifiers

Parameters:

mmdbidList - the list of MMDB identifiers

ProteinOnly - protein or non-protein gi's to retrieve

Returns:

array of gi's

Throws:

java.io.IOException

See Also:

SHoundGiFrom3D(int, boolean)

SHoundGiFromPDBchain

public int SHoundGiFromPDBchain(java.lang.String pdbcode,
                                java.lang.String chain)
                         throws java.io.IOException

retrieve an array of gi's from the PDB identifiers

Parameters:

pdbcode - the PDB identifier

chain - the chain on the PDB structure

Returns:

gi in the chain, -1 if not found or zero

Throws:

java.io.IOException

See Also:

SHoundGiFromPDBchain(String, String)

SHound3DFromGi

public int SHound3DFromGi(int gi)
                   throws java.io.IOException

Get the MMDB identifier for a given gi

Parameters:

gi - the gi

Returns:

an MMDB identifier or -1 or zero

Throws:

java.io.IOException

SHound3DFromGiList

public int[] SHound3DFromGiList(int[] giList)
                         throws java.io.IOException

Get an array of MMDB identifiers for a given gi array

Parameters:

giList - the array of gi's

Returns:

an array of MMDB identifier or null

Throws:

java.io.IOException

SHoundDNAFromProtein

public int SHoundDNAFromProtein(int gi)
                         throws java.io.IOException

Get the dna gi fro a given gi

Parameters:

gi - the gi

Returns:

the corresponding dna gi

Throws:

java.io.IOException

SHoundDNAFromProteinList

public int[] SHoundDNAFromProteinList(int[] giList)
                               throws java.io.IOException

Get an array of dna gi for a given array of gi

Parameters:

giList - the array of gi

Returns:

an array of dna gi or null

Throws:

java.io.IOException

See Also:

SHoundDNAFromProtein(int)

SHoundProteinFromDNA

public int[] SHoundProteinFromDNA(int gi)
                           throws java.io.IOException

Get the protein gi for a given gi

Parameters:

gi - the gi

Returns:

a protein gi

Throws:

java.io.IOException

SHoundProteinFromDNAList

public int[] SHoundProteinFromDNAList(int[] giList)
                               throws java.io.IOException

Get an array of protein gi's given an array of gi's

Parameters:

giList - the array of gi

Returns:

an array of gi's

Throws:

java.io.IOException

See Also:

SHoundProteinFromDNA(int)

SHoundMuidFromGi

public int[] SHoundMuidFromGi(int gi)
                       throws java.io.IOException

Deprecated. replaced by SHoundGetReferenceIDFromGi(int, int)

Get the MUID for a given gi

Parameters:

gi - the gi

Returns:

an array of MUID or -1 or zero

Throws:

java.io.IOException

SHoundMuidFromGiList

public int[] SHoundMuidFromGiList(int[] giList)
                           throws java.io.IOException

Deprecated. replaced by SHoundGetReferenceIDFromGiList(int[], int)

Get the MUIDs for a given array of gi's

Parameters:

giList - the gi array

Returns:

an array of MUID or null

Throws:

java.io.IOException

SHoundMuidFrom3D

public int[] SHoundMuidFrom3D(int mmdbid)
                       throws java.io.IOException

Get the MUID for a given MMDB identifier

Parameters:

mmdbid - MMDB identifier

Returns:

an MUID or -1 or zero

Throws:

java.io.IOException

SHoundMuidFrom3DList

public int[] SHoundMuidFrom3DList(int[] giList)
                           throws java.io.IOException

Get the MUID list for a given gi array

Parameters:

giList - the gi array

Returns:

an MUID array or null

Throws:

java.io.IOException

SHoundTaxIDFromGi

public int SHoundTaxIDFromGi(int gi)
                      throws java.io.IOException

Get the taxid for a given gi

Parameters:

gi - the gi

Returns:

an taxonomy identifier or -1 or zero

Throws:

java.io.IOException

SHoundTaxIDFromGiList

public int[] SHoundTaxIDFromGiList(int[] giList)
                            throws java.io.IOException

Get an array of taxonomy identifiers from an array of gi

Parameters:

giList - an array of gi's

Returns:

an array of taxonomy id's or null

Throws:

java.io.IOException

See Also:

SHoundTaxIDFromGi(int)

SHoundTaxIDFrom3D

public int SHoundTaxIDFrom3D(int mmdbid)
                      throws java.io.IOException

Get a taxid for a given gi

Parameters:

mmdbid - the gi

Returns:

an taxid

Throws:

java.io.IOException

SHoundTaxIDFrom3DList

public int[] SHoundTaxIDFrom3DList(int[] mmdbidList)
                            throws java.io.IOException

Get an array of taxid from an array of MMDB identifier

Parameters:

mmdbidList - an array of MMDB identifier

Returns:

an array of taxonomy identifier

Throws:

java.io.IOException

See Also:

SHoundTaxIDFrom3D(int)

SHoundProteinsFromTaxID

public int[] SHoundProteinsFromTaxID(int taxid)
                              throws java.io.IOException

Get the protein gi's for a given taxonomy

Parameters:

taxid - the taxonomy identifier

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundProteinsFromTaxIDList

public int[] SHoundProteinsFromTaxIDList(int[] taxList)
                                  throws java.io.IOException

get an array of proteins from an array of taxonomy identifier

Parameters:

taxList - the array of taxonomy

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundProteinsFromTaxIDIII

public int[] SHoundProteinsFromTaxIDIII(int taxid)
                                 throws java.io.IOException

Get an array of protein gi's for a given taxonomy identifier. Uses precomputed searches if appropriate, to speed up the search.

Parameters:

taxid - the given taxonomy identifier

Returns:

an array of taxonomy identifier

Throws:

java.io.IOException

SHoundDNAFromTaxID

public int[] SHoundDNAFromTaxID(int taxid)
                         throws java.io.IOException

Get the DNA gi's for a given taxonomy id

Parameters:

taxid - the taxonomy identifier

Returns:

an array of dna gi's

Throws:

java.io.IOException

SHoundDNAFromTaxIDList

public int[] SHoundDNAFromTaxIDList(int[] taxList)
                             throws java.io.IOException

get an array of dna gi's for an array of taxonomy identifiers

Parameters:

taxList - an array of taxid

Returns:

an array of dna gi's

Throws:

java.io.IOException

SHoundDNAFromTaxIDIII

public int[] SHoundDNAFromTaxIDIII(int taxid)
                            throws java.io.IOException

Get the dna gi's for a given taxid. Uses precomputed searches to speed up search where appropriate.

Parameters:

taxid -

Returns:

an array of DNA gi's

Throws:

java.io.IOException

SHoundProteinsFromOrganism

public int[] SHoundProteinsFromOrganism(int taxid,
                                        int chromflags)
                                 throws java.io.IOException

Get the proteins for a given taxonomy. Chromflags is the DNA molecule type, where each bit is reserved for one kind of DNA molecule.

Parameters:

taxid - the taxonomy identifier

chromflags - use hex notations: 0x40 for phage, 0x10 extra-chromosomal, 0x08 plasmid, 0x04 chloroplast, 0x02 mitochondrion, 0x01 chromosome, 0xFF all

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundProteinsFromOrganismList

public int[] SHoundProteinsFromOrganismList(int[] taxList,
                                            int chromflags)
                                     throws java.io.IOException

Get the protein gi's for a given taxonomy array, use bit notation for chromflags

Parameters:

taxList - the array of taxonomy identifier

chromflags - see SHoundProteinsFromOrganism(int, int)

Returns:

an array of protein identifiers

Throws:

java.io.IOException

SHoundProteinsFromChromosome

public int[] SHoundProteinsFromChromosome(int chromid)
                                   throws java.io.IOException

Get the protein gi's for a given chromosome identifier

Parameters:

chromid - the chromosome identifier

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundProteinsFromChromosomeList

public int[] SHoundProteinsFromChromosomeList(int[] chromList)
                                       throws java.io.IOException

Get the protein gi's for an array of chromosome identifiers

Parameters:

chromList - an array of chromosomes

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundAllGenomes

public int[] SHoundAllGenomes()
                       throws java.io.IOException

Get an array of taxonomy identifiers for all complete genomes present in the SeqHound system.

Returns:

an array of taxonomy identifiers

Throws:

java.io.IOException

SHoundChromosomeFromGenome

public int[] SHoundChromosomeFromGenome(int taxid,
                                        int chromflags)
                                 throws java.io.IOException

Get all the chromosomes for a given taxonomy identifier and the molecule

Parameters:

taxid - the taxonomy identifier

chromflags - see SHoundProteinsFromOrganism(int, int)

Returns:

an array of chromsome identifier or null

Throws:

java.io.IOException

SHoundChromosomeFromGenomeList

public int[] SHoundChromosomeFromGenomeList(int[] taxList,
                                            int chromflags)
                                     throws java.io.IOException

Gets an array of chromosome identifiers for a given taxonomy list

Parameters:

taxList - the taxonomy list

chromflags - see SHoundProteinsFromOrganism(int, int)

Returns:

an array of chromosome identifiers

Throws:

java.io.IOException

SHoundDNAFromOrganism

public int[] SHoundDNAFromOrganism(int taxid,
                                   int chromflags)
                            throws java.io.IOException

Get an array of dna gi's for a given organism

Parameters:

taxid - the taxonomy identifier

chromflags - see SHoundProteinsFromOrganism(int, int)

Returns:

array of dna identifier

Throws:

java.io.IOException

SHoundDNAFromOrganismList

public int[] SHoundDNAFromOrganismList(int[] taxList,
                                       int chromflags)
                                throws java.io.IOException

Get an array of dna gi's for a given taxonomy array

Parameters:

taxList - the taxonomy array

chromflags - see SHoundProteinsFromOrganism(int, int)

Returns:

an array of DNA gi's

Throws:

java.io.IOException

SHoundDNAFromChromosome

public int[] SHoundDNAFromChromosome(int chromid)
                              throws java.io.IOException

Get an array of dna gi's for a given chromosome identifier

Parameters:

chromid - the chromosome identifier

Returns:

an array fo dna gi's

Throws:

java.io.IOException

SHoundDNAFromChromosomeList

public int[] SHoundDNAFromChromosomeList(int[] chromList)
                                  throws java.io.IOException

Get an array of dna gi's for an input of chromosome array

Parameters:

chromList - an array of chromsome identifiers

Returns:

an array of dna gi's

Throws:

java.io.IOException

SHoundRedundantGroup

public int[] SHoundRedundantGroup(int gi)
                           throws java.io.IOException

Gets all protein entries with the same sequence from the system

Parameters:

gi - the gi

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundRedundantGroupList

public int[] SHoundRedundantGroupList(int[] giList)
                               throws java.io.IOException

Gets all protein entries with the same sequence from the system

Parameters:

giList -

Returns:

an array of protein gi's

Throws:

java.io.IOException

SHoundRedundantGroupIDFromGi

public int SHoundRedundantGroupIDFromGi(int gi)
                                 throws java.io.IOException

Entrez collection of databases contains redundant entries i.e. proteins with the same sequence but different annotations. The function gets an arbitrary redundant group identifier for a protein sequence. The redundant group identifiers can only be used temporarily, they change every day.

Parameters:

gi - the gi

Returns:

a temporary group id

Throws:

java.io.IOException

SHoundRedundantGroupIDFromGiList

public int[] SHoundRedundantGroupIDFromGiList(int[] giList)
                                       throws java.io.IOException

Entrez collection of databases contains redundant entries i.e. proteins with the same sequence but different annotations. The function gets an arbitrary redundant group identifier for a list of protein sequences. The redundant group identifiers can only be used temporarily, they change every day.

Parameters:

giList - an arrary of gi

Returns:

an array of group id

Throws:

java.io.IOException

SHoundRedundantGroupFromID

public int[] SHoundRedundantGroupFromID(int group)
                                 throws java.io.IOException

returns an array of gi's in the same group. The group id changes everyday

Parameters:

group - id the group identifier

Returns:

array of gi in the same group

Throws:

java.io.IOException

SHoundRedundantGroupFromIDList

public int[] SHoundRedundantGroupFromIDList(int[] groupList)
                                     throws java.io.IOException

returns an array of redundant protein gi's for an array of redundant group id's. The group id's change daily.

Parameters:

groupList - an array of group id

Returns:

an array of redundant protein gi's

Throws:

java.io.IOException

SHoundFirstOfRedundantGroupFromID

public int SHoundFirstOfRedundantGroupFromID(int group)
                                      throws java.io.IOException

Entrez collection of databases contains redundant entries i.e. proteins with the same sequence but different annotations. The function gets a representative entry (generally the one with best annotation such as PDB, RefSeq or SwissProt entry) given a redundant group identifier. The redundant group identifiers can only be used temporarily, they change every day.

Parameters:

group - the group id

Returns:

the best annotation gi for a given group

Throws:

java.io.IOException

SHoundFirstOfRedundantGroupFromIDList

public int[] SHoundFirstOfRedundantGroupFromIDList(int[] group)
                                            throws java.io.IOException

Gets the gi of the best annotated sequence given an array of group id.

Parameters:

group - array of group identifier

Returns:

an array of the best annotated gi

Throws:

java.io.IOException

SHoundGetTaxChildNodes

public int[] SHoundGetTaxChildNodes(int taxid)
                             throws java.io.IOException

operates on NCBI's taxonomy tree. It retrieves all taxons situated directly below a given taxon in the taxonomy tree.

Parameters:

taxid - the taxonomy

Returns:

an array of taxonomy id that are children of taxid

Throws:

java.io.IOException

SHoundGetTaxChildNodesList

public int[] SHoundGetTaxChildNodesList(int[] taxList)
                                 throws java.io.IOException

Get the children taxonomy id of an array of taxid inputs

Parameters:

taxList - an array of taxonomy

Returns:

an array of taxonomy id

Throws:

java.io.IOException

SHoundGetAllTaxProgeny

public int[] SHoundGetAllTaxProgeny(int taxid)
                             throws java.io.IOException

operates on NCBI's taxonomy tree. It retrieves all taxons (the whole subtree) situated below a given taxon in the taxonomy tree.

Parameters:

taxid - the taxonomy id

Returns:

an array of taxid

Throws:

java.io.IOException

SHoundGetTaxParent

public int SHoundGetTaxParent(int taxid)
                       throws java.io.IOException

Retrieve the tax id situated directly above a given tax id

Parameters:

taxid - a taxonomy identifier

Returns:

a taxid

Throws:

java.io.IOException

SHoundGetAllTaxAncestors

public int[] SHoundGetAllTaxAncestors(int taxid)
                               throws java.io.IOException

Retrieves all taxid (the whole subtree) above a given taxid

Parameters:

taxid - a taxonomy identifier

Returns:

a taxonomy identifier

Throws:

java.io.IOException

SHoundIsTaxMerged

public boolean SHoundIsTaxMerged(int taxid)
                          throws java.io.IOException

reports if a given taxonomy identifier has been renamed

Parameters:

taxid - a taxonomy identifier

Returns:

true if taxid has been renamed, else false

Throws:

java.io.IOException

SHoundIsTaxDeleted

public boolean SHoundIsTaxDeleted(int taxid)
                           throws java.io.IOException

reports whether a taxid has been deleted from the tree

Parameters:

taxid - an taxon id

Returns:

true if taxid deleted, else false

Throws:

java.io.IOException

SHoundGetTaxNameFromTaxIDByClass

public java.lang.String SHoundGetTaxNameFromTaxIDByClass(int taxid,
                                                         java.lang.String nameClass)
                                                  throws java.io.IOException

gets a taxon name in a specified style

Parameters:

taxid - a taxonomy identifier

nameClass - one of:
SLRI_taxon_name_name_class_none
SLRI_taxon_name_name_class_acronym
SLRI_taxon_name_name_class_anamorph
SLRI_taxon_name_name_class_blast_name
SLRI_taxon_name_name_class_common_name
SLRI_taxon_name_name_class_equivalent_name
SLRI_taxon_name_name_class_includes
SLRI_taxon_name_name_class_in_part
SLRI_taxon_name_name_class_misnomer
SLRI_taxon_name_name_class_misspelling
SLRI_taxon_name_name_class_preferred_acronym
SLRI_taxon_name_name_class_preferred_common_name
SLRI_taxon_name_name_class_scientific_name
SLRI_taxon_name_name_class_synonym
SLRI_taxon_name_name_class_teleomorph
SLRI_taxon_name_name_class_other

Returns:

a taxon name

Throws:

java.io.IOException

SHoundGetTaxNameFromTaxID

public java.lang.String SHoundGetTaxNameFromTaxID(int taxid)
                                           throws java.io.IOException

fetches a taxonomy name in scientific form

Parameters:

taxid -

Returns:

a taxonomy name

Throws:

java.io.IOException

SHoundGetTaxLineageFromTaxID

public java.lang.String SHoundGetTaxLineageFromTaxID(int taxid,
                                                     java.lang.String type)
                                              throws java.io.IOException

fetches a taxonomy lineage in a specified form.

Parameters:

taxid - a taxonomy id

type - a string specifying the form. One of:
SHoundGetTaxLineage_FULL
SHoundGetTaxLineage_GENBANK
SHoundGetTaxLineage_TAXDBSHORT

Returns:

a taxonomy lineage

Throws:

java.io.IOException

SHoundGiFromGOID

public int[] SHoundGiFromGOID(int go)
                       throws java.io.IOException

retrieves an array of gi with specified the specified gene ontology identifier

Parameters:

go - the gene ontology identifier

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGiFromGOIDList

public int[] SHoundGiFromGOIDList(int[] goList)
                           throws java.io.IOException

retrieves an array of gis that have been annotated with the specified goid

Parameters:

goList - the array of goid

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGiFromGOIDListAndECode

public int[] SHoundGiFromGOIDListAndECode(int[] goList,
                                          java.lang.String ecode)
                                   throws java.io.IOException

retrieves an array of gis that have been annotated with the specified goid list and the evidence code

Parameters:

goList - the array of goid

ecode - the go evidence code

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGOIDFromGi

public int[] SHoundGOIDFromGi(int gi)
                       throws java.io.IOException

retrieves an array of goid for a specified gi

Parameters:

gi - the gi

Returns:

an array of goid's

Throws:

java.io.IOException

SHoundGOIDFromGiList

public int[] SHoundGOIDFromGiList(int[] giList)
                           throws java.io.IOException

retrieves an array of goid for a specified array of gi's

Parameters:

giList - the array of gi's

Returns:

an array of goid's

Throws:

java.io.IOException

SHoundGiFromGOIDAndECode

public int[] SHoundGiFromGOIDAndECode(int goid,
                                      java.lang.String ecode)
                               throws java.io.IOException

Return all the gi's with the given goid and evidence code.

Parameters:

goid - a gene ontology identifier

ecode - an evidence code

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGOIDFromRedundantGi

public int[] SHoundGOIDFromRedundantGi(int gi)
                                throws java.io.IOException

retrieve an array of goid from a redundant gi

Parameters:

gi - the gi

Returns:

an array of goid

Throws:

java.io.IOException

SHoundGOIDFromRedundantGiList

public int[] SHoundGOIDFromRedundantGiList(int[] giList)
                                    throws java.io.IOException

retrieve an array of goid for a given array of gi's

Parameters:

giList - the gi array

Returns:

an array of goid

Throws:

java.io.IOException

SHoundGiFromCDDID

public int[] SHoundGiFromCDDID(java.lang.String cddid)
                        throws java.io.IOException

retrieves an array of gi with the domain specified by input

Parameters:

cddid - the domain identifier

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGiFromCDDIDList

public int[] SHoundGiFromCDDIDList(java.lang.String[] cddidList)
                            throws java.io.IOException

get the gi's with the specified domains

Parameters:

cddidList - an array of domain identifiers

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundCDDIDFromGi

public java.lang.String[] SHoundCDDIDFromGi(int gi)
                                     throws java.io.IOException

retrieves the domains for a specified gi.

Parameters:

gi - the gi

Returns:

an array og domain identifiers

Throws:

java.io.IOException

SHoundCDDIDFromGiList

public java.lang.String[] SHoundCDDIDFromGiList(int[] giList)
                                         throws java.io.IOException

retrieve the domain identifiers for a specified gi array

Parameters:

giList - an array of gi's

Returns:

an array of domain names

Throws:

java.io.IOException

SHoundGiFromOMIM

public int[] SHoundGiFromOMIM(int omimid)
                       throws java.io.IOException

retrieves gi's from an omim

Parameters:

omimid - the omid identifier

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGiFromOMIMList

public int[] SHoundGiFromOMIMList(int[] omimList)
                           throws java.io.IOException

retrieves gi's associated with a omim

Parameters:

omimList - an array of omim

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundOMIMFromGi

public int[] SHoundOMIMFromGi(int gi)
                       throws java.io.IOException

retrieves omim associated with a gi

Parameters:

gi - the gi

Returns:

an array of omim

Throws:

java.io.IOException

SHoundOMIMFromGiList

public int[] SHoundOMIMFromGiList(int[] giList)
                           throws java.io.IOException

get the associated omim for an array of gi's

Parameters:

giList - the gi array

Returns:

an array of omim's

Throws:

java.io.IOException

SHoundCDDScoreFromGi

public float SHoundCDDScoreFromGi(int gi,
                                  java.lang.String cddid)
                           throws java.io.IOException

Get the score for a Conserved domain database domain

Parameters:

gi - the gi

cddid - the CDD identifier

Returns:

an CDD score

Throws:

java.io.IOException

SHoundGiFromLLID

public int[] SHoundGiFromLLID(int llid)
                       throws java.io.IOException

Get gi associated with a locuslink identifier

Parameters:

llid - a locuslink id

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGiFromLLIDList

public int[] SHoundGiFromLLIDList(int[] llidList)
                           throws java.io.IOException

get the gi's associated with the locuslink id

Parameters:

llidList - an array of locuslink id

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundLLIDFromGi

public int[] SHoundLLIDFromGi(int gi)
                       throws java.io.IOException

retrieves locuslink id for a given gi

Parameters:

gi - the gi

Returns:

an array of locuslink id

Throws:

java.io.IOException

SHoundLLIDFromGiList

public int[] SHoundLLIDFromGiList(int[] giList)
                           throws java.io.IOException

retrievs locuslink id for a given gi array

Parameters:

giList - the array of gi's

Returns:

an array of locuslink id

Throws:

java.io.IOException

SHoundLocusFromGi

public java.lang.String SHoundLocusFromGi(int gi)
                                   throws java.io.IOException

retrieves the locus for a given gi

Parameters:

gi - the gi

Returns:

a locuslink locus

Throws:

java.io.IOException

SHoundGODBGetRecordByReference

public int[] SHoundGODBGetRecordByReference(java.lang.String refType)
                                     throws java.io.IOException

retrieve the gene ontology id by geneontology reference type

Parameters:

refType - the reference type, eg "EC",

Returns:

an array of goid

Throws:

java.io.IOException

SHoundGODBGetChildrenOf

public int[] SHoundGODBGetChildrenOf(int goid)
                              throws java.io.IOException

retrieves all the children of a given gene ontology id

Parameters:

goid - the gene ontology id

Returns:

an array of the goid

Throws:

java.io.IOException

SHoundGODBGetParentOf

public int[] SHoundGODBGetParentOf(int goid)
                            throws java.io.IOException

retrieves an array of the parents of a given goid

Parameters:

goid - the input gene ontology id

Returns:

an array of goid that are the parent of the input

Throws:

java.io.IOException

SHoundGODBGetAllAncestors

public int[] SHoundGODBGetAllAncestors(int goid)
                                throws java.io.IOException

retrieves all the ancestors (parents, grandparents ...) of a given gene ontology id.

Parameters:

goid - the goid

Returns:

an array of goid

Throws:

java.io.IOException

SHoundGODBGetAllChildren

public int[] SHoundGODBGetAllChildren(int goid)
                               throws java.io.IOException

retrieve all children of a given gene ontology id

Parameters:

goid - a given goid

Returns:

an array of the children of the input

Throws:

java.io.IOException

SHoundGODBGetNameByID

public java.lang.String SHoundGODBGetNameByID(int goid)
                                       throws java.io.IOException

retrieves the name of a given goid

Parameters:

goid - the goid

Returns:

the name

Throws:

java.io.IOException

SHoundGODBGetClassification

public java.lang.String SHoundGODBGetClassification(int goid)
                                             throws java.io.IOException

retrieve the ontology classification for a given goid

Parameters:

goid - the given goid

Returns:

the classification goid falls into

Throws:

java.io.IOException

SHoundNeighboursFromGi

public int[] SHoundNeighboursFromGi(int gi,
                                    double eValue,
                                    boolean bLimit)
                             throws java.io.IOException

Retrieves a list of protein BLAST neighbours. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.

Parameters:

gi - the gi

eValue - the e-value cutoff

bLimit - limit the return list to 100 gi's

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundNeighboursFromGiList

public int[] SHoundNeighboursFromGiList(int[] giList,
                                        double eValue,
                                        boolean bLimit)
                                 throws java.io.IOException

Retrieves a list of protein BLAST neighbours. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.

Parameters:

giList - the list of gi

eValue - the e value cutoff

bLimit - limit the return to 100 gi's

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundNeighboursFromTaxID

public int[] SHoundNeighboursFromTaxID(int taxid,
                                       double eValue)
                                throws java.io.IOException

Retrieves a list of protein BLAST neighbours using a list of proteins belonging to a complete genome as a query. Uses redundancy information for the query proteins. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.

Parameters:

taxid - the taxonomy identifier

eValue - the evalue cutoff

Returns:

an array of gi's

Throws:

java.io.IOException

SHound3DNeighboursFromGi

public int[] SHound3DNeighboursFromGi(int gi,
                                      double eValue)
                               throws java.io.IOException

Retrieves a list of protein BLAST neighbours possessing 3-D structure. Uses redundancy information for the query protein. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.

Parameters:

gi - the gi

eValue - the evalue cutoff

Returns:

an array of gi's

Throws:

java.io.IOException

SHound3DNeighboursFromTaxID

public int[] SHound3DNeighboursFromTaxID(int taxid,
                                         double eValue)
                                  throws java.io.IOException

Retrieves a list of protein BLAST neighbours possessing 3-D structure using a list of proteins belonging to a complete genome as a query. Uses redundancy information for the query protein. The BLAST protein neighbours were calculated using 0.01 maximum E-value cutoff.

Parameters:

taxid - the taxonomy id

eValue - the evalue cutoff

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGetGisByNumberOfDomains

public int[] SHoundGetGisByNumberOfDomains(int numdoms)
                                    throws java.io.IOException

retrieves all the gi's with the specified number of domains

Parameters:

numdoms - the number of domains

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGetDomainIdFromLabel

public java.lang.String[] SHoundGetDomainIdFromLabel(java.lang.String label)
                                              throws java.io.IOException

retrieves the domain id given a label

Parameters:

label - the domain label

Returns:

an array of domain id

Throws:

java.io.IOException

SHoundGetGisByDomainId

public int[] SHoundGetGisByDomainId(java.lang.String domain)
                             throws java.io.IOException

retrieve the gi's having a domain id

Parameters:

domain - the domain id

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGetDomainLabelFromDomainId

public java.lang.String[] SHoundGetDomainLabelFromDomainId(java.lang.String accession)
                                                    throws java.io.IOException

Returns a short non-unique label given a domain for a Conserved Domain Database (CDD). The above labels are preferred amongst scientific community.

Parameters:

accession - the accession number

Returns:

an array of domain labels

Throws:

java.io.IOException

SHoundGetGisByDomainIdAndEvalue

public int[] SHoundGetGisByDomainIdAndEvalue(java.lang.String domain,
                                             double evalue)
                                      throws java.io.IOException

Fetches protein sequences on which a domain from the Conserved Domain Database (CDD) was identified by Reverse Position Specific BLAST. The function uses an E-value cutoff for reporting results.

Parameters:

domain - the domain id

evalue - the evalue cutoff

Returns:

an array of gi's

Throws:

java.io.IOException

SHoundGetDomainsFromGi

public java.lang.String SHoundGetDomainsFromGi(int gi)
                                        throws java.io.IOException

Fetches information about domains from the Conserved Domain Database (CDD) as assigned by Reverse Position Specific BLAST to a given protein sequence.

Parameters:

gi - the gi

Returns:

domain identifier

Throws:

java.io.IOException

SHoundGetDomainsFromGiWithEvalue

public java.lang.String SHoundGetDomainsFromGiWithEvalue(int gi,
                                                         double eValue)
                                                  throws java.io.IOException

Fetches information about domains from the Conserved Domain Database (CDD) as assigned by Reverse Position Specific BLAST to a given protein sequence. The function uses an E-value cutoff for reporting results.

Parameters:

gi - the gi

eValue - the evalue cutoff

Returns:

an MMDB identifier or -1 or zero

Throws:

java.io.IOException

SHoundGetAccFromRetiredGi

public java.lang.String SHoundGetAccFromRetiredGi(int gi)
                                           throws java.io.IOException

Returns accession number for the given retired gi.

Parameters:

gi - a retired gi

Returns:

an accession string or null.

Throws:

java.io.IOException

SHoundProteinReportSetDescription

public java.lang.String SHoundProteinReportSetDescription(int gi,
                                                          int format)
                                                   throws java.io.IOException

Get a protein report set description for a given gi. The set description is a comprehensive description for a gi.

Parameters:

gi - the gi

format - the format of the description. Either REPORT_XML or REPORT_ASN_TXT

Returns:

the protein report string

Throws:

java.io.IOException

SHoundGetFastaKeyedList

public java.util.Hashtable SHoundGetFastaKeyedList(int[] giList)
                                            throws java.io.IOException

retrieves fasta list for the given gilist

Parameters:

giList - an array of gi's

Returns:

a hashtable with gi-fasta pair

Throws:

java.io.IOException

SHoundRedundantGroupKeyedList

public java.util.Hashtable SHoundRedundantGroupKeyedList(int[] giList)
                                                  throws java.io.IOException

Gets all protein entries with the same sequence from the system

Returns:

a hashtable of query gi and associated return protein gi's

Throws:

java.io.IOException

SHoundGetFastaFromRedundantGroupID

public java.lang.String SHoundGetFastaFromRedundantGroupID(int gid)
                                                    throws java.io.IOException

The FASTA format is widely used in bioinformatics community; it consists of a definition line, new line followed by a sequence terminated by a second new line.

Parameters:

gid - the redundant group id

Returns:

a string fasta

Throws:

java.io.IOException

SHoundGetFastaFromRedundantGroupIDKeyedList

public java.util.Hashtable SHoundGetFastaFromRedundantGroupIDKeyedList(int[] gidList)
                                                                throws java.io.IOException

retrieves fasta list for the given redundant group id list

Parameters:

gidList - an array of redundant group ids

Returns:

a hashtable with groupid-fasta pair

Throws:

java.io.IOException

ProcessRetStr

public java.util.Hashtable ProcessRetStr(java.util.Hashtable h,
                                         java.lang.String str)
                                  throws java.io.IOException

Process the return string from server to a hashtable

Parameters:

str - is the return string from server

Returns:

a hashtable with query-return pair

Throws:

java.io.IOException