Uses of Class
org.strbio.mol.Profile

Packages that use Profile

org.strbio.local	These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.mol.lib.pred2ary	These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes.
org.strbio.net	These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page).

Uses of Profile in org.strbio.local

Methods in org.strbio.local that return Profile

Profile	PSIBlastP2.blastAll(Printf outfile) Blast, and get the checkpoint info.
Profile	PSIBlastP.blastAll(Printf outfile) Blast, and get the checkpoint info.
Profile	BlastP.blastAll(Printf outfile) Return a profile containing responses to the blast query.
protected Profile	BlastP.blastPBlastAll(Printf outfile) kludge to allow super.super() reference to blastAll method.
Profile	BlastPAdapter.blastProfile(Printf outfile) Return a profile containing responses to the blast query.
Profile	ClustalW.getProfile(java.lang.String raw) return the profile stored in the raw clustal output

Uses of Profile in org.strbio.mol

Subclasses of Profile in org.strbio.mol

class

ProfilePSI Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

Methods in org.strbio.mol that return Profile

Profile

Profile.choose(int seqNum) Make a profile based on this one, featuring one of the sub- sequences.

Methods in org.strbio.mol with parameters of type Profile

void	Profile.addSeqsDirectlyFrom(Profile q) Add additional sequences from another profile of the same length.
void	Profile.addSeqsFrom(Profile q) add sequence info from another profile; aligns and copies.
void	Profile.copySeqsDirectlyFrom(Profile q) Copy additional sequences from another profile of the same length, eliminating current sequences.
void	Profile.copySeqsFrom(Profile q) copy sequence info from another profile; aligns and copies, replacing current sequence info.
protected void	Profile.splitCopy(Profile q) When a Profile is split, sequence names should go to each child.

Constructors in org.strbio.mol with parameters of type Profile

Profile(Profile q)
Copy a Profile, including all data in it.

ProfilePSI(Profile q)
Create from a regular profile.

ProteinSet(Profile q)
Make a protein set from a profile... the protein set will contain newly created Proteins, one per sequence in the profile.

Uses of Profile in org.strbio.mol.lib

Methods in org.strbio.mol.lib that return Profile

Profile	Blast.blastAll(Printf outfile) Return a profile containing responses to the blast query.
Profile	BlastAdapter.blastProfile(Printf outfile) Return a profile containing responses to the blast query.
Profile	Blast.blastProfile(Printf outfile) Return a profile containing responses to the blast query.

Uses of Profile in org.strbio.mol.lib.pred2ary

Subclasses of Profile in org.strbio.mol.lib.pred2ary

class

PredClassProfile Class to represent a single protein, with class routines and lots of stats.

Constructors in org.strbio.mol.lib.pred2ary with parameters of type Profile

PredClassProfile(Profile q)

Uses of Profile in org.strbio.net

Methods in org.strbio.net that return Profile

Profile

BlastWeb.blastAll(Printf outfile) Returns a profile with all responses to the query.