org.strbio.net
Class SCOP

java.lang.Object
  org.strbio.net.SCOP

public class SCOP
extends java.lang.Object

Class to access SCOP over the web.

  Version 1.1, 3/13/1 - added getRawAnnotPDB, use IO.getURLData
  Version 1.0, 3/6/1 - original version
  

Version:

1.1, 3/13/1

Author:

JMC

Constructor Summary

SCOP()

Method Summary

static java.lang.String	getClassName(java.lang.String rawdata) returns name of class from query, if found, or null if not found.
static java.lang.String	getFamilyName(java.lang.String rawdata) returns name of family from query, if found, or null if not found.
static java.lang.String	getFoldName(java.lang.String rawdata) returns name of fold from query, if found, or null if not found.
static SCOPInfo	getInfo(java.lang.String rawdata) returns numbers and domain name from query, if found, or null if not found.
static SCOPInfo[]	getInfoLinks(java.lang.String rawdata) returns numbers in links from query, if found, or null if not found
static java.lang.String[]	getPDBDomains(java.lang.String rawdata) returns pdb entry domains if not found
static java.lang.String	getProteinName(java.lang.String rawdata) returns name of protein from query, if found, or null if not found.
static java.lang.String	getRawAnnot(java.lang.String code, Printf outfile) Query the server for annotation data
static java.lang.String	getRawAnnotNumeric(SCOPInfo si, Printf outfile) Query the server for annotation data, using numeric entries in SCOPInfo.
static java.lang.String	getRawAnnotPDB(java.lang.String code, Printf outfile) Query the server for annotation data for a given pdb string
static java.lang.String	getSpeciesName(java.lang.String rawdata) returns name of species from query, if found, or null if not found.
static java.lang.String	getSuperfamilyName(java.lang.String rawdata) returns name of superfamily from query, if found, or null if not found.

Methods inherited from class java.lang.Object

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

Constructor Detail

SCOP

public SCOP()

Method Detail

getRawAnnot

public static java.lang.String getRawAnnot(java.lang.String code,
                                           Printf outfile)

Query the server for annotation data

getRawAnnotNumeric

public static java.lang.String getRawAnnotNumeric(SCOPInfo si,
                                                  Printf outfile)

Query the server for annotation data, using numeric entries in SCOPInfo.

getRawAnnotPDB

public static java.lang.String getRawAnnotPDB(java.lang.String code,
                                              Printf outfile)

Query the server for annotation data for a given pdb string

getInfoLinks

public static final SCOPInfo[] getInfoLinks(java.lang.String rawdata)

returns numbers in links from query, if found, or null if not found

getPDBDomains

public static final java.lang.String[] getPDBDomains(java.lang.String rawdata)

returns pdb entry domains if not found

getInfo

public static final SCOPInfo getInfo(java.lang.String rawdata)

returns numbers and domain name from query, if found, or null if not found.

getClassName

public static final java.lang.String getClassName(java.lang.String rawdata)

returns name of class from query, if found, or null if not found.

getFoldName

public static final java.lang.String getFoldName(java.lang.String rawdata)

returns name of fold from query, if found, or null if not found.

getSuperfamilyName

public static final java.lang.String getSuperfamilyName(java.lang.String rawdata)

returns name of superfamily from query, if found, or null if not found.

getFamilyName

public static final java.lang.String getFamilyName(java.lang.String rawdata)

returns name of family from query, if found, or null if not found.

getProteinName

public static final java.lang.String getProteinName(java.lang.String rawdata)

returns name of protein from query, if found, or null if not found.

getSpeciesName

public static final java.lang.String getSpeciesName(java.lang.String rawdata)

returns name of species from query, if found, or null if not found.