A B C D E F G H I J K L M N O P Q R S T U V W

P

Pair<O> - Class in PIP.Collections

Pair(O, O) - Constructor for class PIP.Collections.Pair

PairsIterator<E> - Class in PIP.Collections

PairsIterator(Pairs<E>) - Constructor for class PIP.Collections.PairsIterator

pairWiseBlast(String, String) - Static method in class PIP.IO.Blast.Blaster

pairWiseBlastNucleotide(String, String) - Static method in class PIP.IO.Blast.Blaster

ParseBlastOutput - Class in PIP.IO.Blast

ParseBlastOutput() - Constructor for class PIP.IO.Blast.ParseBlastOutput

parsePairWiseBlastOutput(String, int) - Static method in class PIP.IO.Blast.ParseBlastOutput

PBFactory - Class in PIP.IO

PBFactory() - Constructor for class PIP.IO.PBFactory

pdbFile(String) - Static method in class PIP.Core.App

PDBFile - Class in PIP.IO.CreatePeripheralData

PDBFile(PrintStream) - Constructor for class PIP.IO.CreatePeripheralData.PDBFile

PDBFileChainBased - Class in PIP.IO.CreatePeripheralData

PDBFileChainBased(PrintStream) - Constructor for class PIP.IO.CreatePeripheralData.PDBFileChainBased

This class outputs residue details into PDB format and outputs them to the PrintStream passed into the constructor.

PDBFileDomainBased - Class in PIP.IO.CreatePeripheralData

PDBFileDomainBased(PrintStream) - Constructor for class PIP.IO.CreatePeripheralData.PDBFileDomainBased

PersistDatabase - Class in PIP.IO.CreateJDODatabase

This class creates the structure of the database so that the data can then be added to it.

PersistDatabase() - Constructor for class PIP.IO.CreateJDODatabase.PersistDatabase

PersistDomainInteractions - Class in PIP.IO.CreateJDODatabase

This class stores all the domain-domain interactions in the database and puts them in a usefull container for quick look up based on family classification.

PersistDomainInteractions() - Constructor for class PIP.IO.CreateJDODatabase.PersistDomainInteractions

persistDomainsByFamily(FamilyType) - Method in class PIP.Domains.Domains

PersistEntries - Class in PIP.IO.CreateJDODatabase

This class gets out all the relevant information from the MSD which needs to be querried in a fast manner and stores the info in the JDO database.

PersistEntries() - Constructor for class PIP.IO.CreateJDODatabase.PersistEntries

persistFamilyToDomainInteractions(FamilyType) - Method in class PIP.Domains.Interactions.DomainInteractions

PersistOritentationInteractions - Class in PIP.IO.CreateJDODatabase

This class reads in all of the results of files generated by PIP.IO.CreatePeripheralData.GenerateOrientationFiles and reads the results into objects which are then persisted in the databse.

PersistOritentationInteractions() - Constructor for class PIP.IO.CreateJDODatabase.PersistOritentationInteractions

persistPairFamilyToDomainInteractions(FamilyType) - Method in class PIP.Domains.Interactions.DomainInteractions

persistPairFamilyToDomainInteractions(FamilyType) - Method in class PIP.Domains.Orientation.OrientationSimilarInteractions

PersistPeripheral - Class in PIP.IO.CreateJDODatabase

To reduce the storage space of repeated data within the database all of the atom and residue names are

PersistPeripheral() - Constructor for class PIP.IO.CreateJDODatabase.PersistPeripheral

Pfam - Class in PIP.Domains.Family

Pfam(String) - Constructor for class PIP.Domains.Family.Pfam

PfamReader - Class in PIP.IO.MSD

PfamReader(Connection) - Constructor for class PIP.IO.MSD.PfamReader

Piecewise<T> - Class in PIP.Collections

Piecewise() - Constructor for class PIP.Collections.Piecewise

PIP.Collections - package PIP.Collections

PIP.Collections.Distribution - package PIP.Collections.Distribution

PIP.Collections.Map - package PIP.Collections.Map

PIP.Collections.Persistent - package PIP.Collections.Persistent

PIP.Core - package PIP.Core

PIP.Domains - package PIP.Domains

PIP.Domains.Family - package PIP.Domains.Family

PIP.Domains.Interactions - package PIP.Domains.Interactions

PIP.Domains.Orientation - package PIP.Domains.Orientation

PIP.Domains.SequenceSimilarity - package PIP.Domains.SequenceSimilarity

PIP.ExampleCode - package PIP.ExampleCode

PIP.IO - package PIP.IO

PIP.IO.Blast - package PIP.IO.Blast

PIP.IO.CreateJDODatabase - package PIP.IO.CreateJDODatabase

PIP.IO.CreatePeripheralData - package PIP.IO.CreatePeripheralData

PIP.IO.MSD - package PIP.IO.MSD

PIP.IO.StampPackage - package PIP.IO.StampPackage

printAll(Collection, PrintStream) - Static method in class PIP.Collections.CollectionUtility

printMap(Collection<Map.Entry<K, V>>, PrintStream) - Static method in class PIP.Collections.CollectionUtility

printMultiMap(Collection<Map.Entry<K, V>>, PrintStream) - Static method in class PIP.Collections.CollectionUtility

printOutFormatDBFileAll(Family, Collection<Domain>, PrintStream) - Static method in class PIP.IO.Blast.FormatDBFileCreator

printOutSummaryDomainInteractionsToKeep(List<DomainInteraction>, String, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

put(K, V) - Method in class PIP.Collections.Persistent.AbstractMap

Associates the specified value with the specified key in this map (optional operation).

put(K, V) - Method in class PIP.Collections.Persistent.SHashMap

putAll(Map<? extends K, ? extends V>) - Method in class PIP.Collections.Persistent.AbstractMap

Copies all of the mappings from the specified map to this map (optional operation).

PymolScript - Class in PIP.IO

PymolScript(DomainInteraction, String, FamilyType) - Constructor for class PIP.IO.PymolScript

PymolScript(String, DomainInteraction, FamilyType) - Constructor for class PIP.IO.PymolScript

PymolScript(Domain, String, Collection<Residue>, String, String, String) - Constructor for class PIP.IO.PymolScript

PymolScript(DomainInteraction, Domain, FamilyType) - Constructor for class PIP.IO.PymolScript

PymolScript(String, Entry, Domain, String) - Constructor for class PIP.IO.PymolScript

PymolScript(String, Assembly, DomainInteraction, Domain, String) - Constructor for class PIP.IO.PymolScript

PymolScript(DomainInteraction, String, String, FamilyType) - Constructor for class PIP.IO.PymolScript