Uses of Class
org.strbio.mol.ProfileSet

Packages that use ProfileSet

org.strbio.app	These classes are stand-alone applications.
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.util.ui	These classes are general purpose utility functions related to a program's user interface.

Uses of ProfileSet in org.strbio.app

Fields in org.strbio.app declared as ProfileSet

ProfileSet

JThreadText.p

Methods in org.strbio.app that return ProfileSet

protected ProfileSet	JThreadText.newProfileSet()
protected ProfileSet	JThread.newProfileSet()

Uses of ProfileSet in org.strbio.mol

Subclasses of ProfileSet in org.strbio.mol

class

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

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

ProfileSet(ProfileSet q)
Copy another profile set, but not the profiles themselves.

Uses of ProfileSet in org.strbio.mol.lib

Subclasses of ProfileSet in org.strbio.mol.lib

class	FoldLibrary A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.
class	TOMFoldLibrary The TOM fold library.
class	UserFoldLibrary A standard fold library for threading, loaded in by the user.

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

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

class	PCPSet Class to represent a set of profiles with information for 2ary structure prediction.
class	PredictionSet Class to represent a set of profiles being used in 2ary structure prediction as a prediction set.
class	TPSet Class to represent a set of profiles being used in 2ary structure prediction; this might be either a training or prediction set.
class	TrainingSet Class to represent a set of profiles being used in 2ary structure prediction as a training set.

Fields in org.strbio.mol.lib.pred2ary declared as ProfileSet

ProfileSet

ProfileDisplayArea.p Profiles to display.

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

ProfileDisplayArea(ProfileSet ps, java.awt.Component par, int fontSize)
Initialize with given parent container.

Uses of ProfileSet in org.strbio.util.ui

Fields in org.strbio.util.ui declared as ProfileSet

ProfileSet

ProfileGUIApp.p

Methods in org.strbio.util.ui that return ProfileSet

protected ProfileSet

ProfileGUIApp.newProfileSet() Return a new profile set of whatever subclass is wanted.

Methods in org.strbio.util.ui with parameters of type ProfileSet

protected void

ProfileGUIApp.setProteins(ProfileSet set) set the current protein set.