org.strbio.util.db
Class CATHInfo

java.lang.Object
  org.strbio.util.db.Info
      org.strbio.util.db.ProteinInfo
          org.strbio.util.db.ProteinStructureInfo
              org.strbio.util.db.CATHInfo

public class CATHInfo
extends ProteinStructureInfo

This is a class containing info that is found in CATH.

  Version 1.0, 7/21/99 - original version.
  

Version:

1.0, 7/21/99

Author:

JMC

Field Summary

java.lang.String	domainCode CATH code for the domain; i.e. 1abcA1
int	endRes ending residue in domain, or -1 for whole chain.
java.lang.String	number CATH number; i.e. 2.20.200.10...
int	startRes starting residue number in domain, or -1 for whole chain.

Fields inherited from class org.strbio.util.db.ProteinInfo

protein

Fields inherited from class org.strbio.util.db.Info

related

Constructor Summary

CATHInfo()
Default initialization has -1 for start/end res, and null for everything else.

Method Summary

int	getA() return the architecture number
int	getC() return the class number.
int	getH() return the homologous superfamily number
int	getLevel(int n) Get the part of the number corresponding to the classification at level N (starting at 0 to mean the leftmost, or Class).
int	getT() return the topology number
int	matchesLevel(CATHInfo y) What is the highest level this matches another record at?
boolean	matchesUpTo(CATHInfo y, int n) Does this match another CATH record up to level N?
void	processYAPF(java.lang.String buffer) Initialize this Info from a line in a YAPF file, if applicable.
void	stripLeading0() strip leading 0's from the number.
void	writeYAPF(Printf outfile) write this info to a single line of a file, so it can be read later.

Methods inherited from class org.strbio.util.db.Info

getClass

Methods inherited from class java.lang.Object

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

Field Detail

domainCode

public java.lang.String domainCode

CATH code for the domain; i.e. 1abcA1

number

public java.lang.String number

CATH number; i.e. 2.20.200.10...

startRes

public int startRes

starting residue number in domain, or -1 for whole chain.

endRes

public int endRes

ending residue in domain, or -1 for whole chain.

Constructor Detail

CATHInfo

public CATHInfo()

Default initialization has -1 for start/end res, and null for everything else.

Method Detail

getLevel

public int getLevel(int n)

Get the part of the number corresponding to the classification at level N (starting at 0 to mean the leftmost, or Class). Returns 0 to mean unknown/unclassified.

getC

public int getC()

return the class number. I can't call this getClass() or class() due to incompatibility with Java language.

getA

public int getA()

return the architecture number

getT

public int getT()

return the topology number

getH

public int getH()

return the homologous superfamily number

matchesUpTo

public boolean matchesUpTo(CATHInfo y,
                           int n)

Does this match another CATH record up to level N? 0==class, etc. This will be false if the level doesn't exist for one or the other entries.

matchesLevel

public int matchesLevel(CATHInfo y)

What is the highest level this matches another record at? 0=class. -1 means this doesn't even match at the class level.

writeYAPF

public void writeYAPF(Printf outfile)
               throws java.io.IOException

write this info to a single line of a file, so it can be read later.

Overrides:

writeYAPF in class Info

Throws:

java.io.IOException

processYAPF

public void processYAPF(java.lang.String buffer)

Initialize this Info from a line in a YAPF file, if applicable.

Overrides:

processYAPF in class Info

stripLeading0

public void stripLeading0()

strip leading 0's from the number.