User's Guide

Ultimate Parser Library

last updated September 20, 1996

for version 1.0

• Contributors to the Ultimate Parser C++ library
• Ultimate Parser library aims, objectives, and limitations
• C++ library stylistic conventions
• The Base class
  • Constructors
  • Variants and Wildcards
  • Implementation
  • Indexing
  • Matching
• The Alphabet Classes
  • Generic Alphabet Class
    • General Alphabet Functions
    • Base Manipulation
    • Alphabet Lengths
    • Implementation
    • Alphabet Creation
  • Specific Alphabets
    • Nucleic Acid Alphabets
    • Amino Acid Alphabets
  • Alph Class
    • Member Functions
• Sequence
  • Sequence Constructors
  • Subsequences
    • Sequence Initialization
  • The SeqRep Class
  • Reference Counting
  • Const and Reference Counting
    • Design Note:
  • Sequence Subscripting
  • Sequence Sizes and Offsets
  • Sequence Comparisons
  • Setting The Sequence Conversion Alphabet
  • String Conversions
    • Design Note
  • Sequence I/O
    • Sequence I/O Formats
  • Automatic Resizing of Sequences
    • Design Note
  • Speeding up Sequence Access in Library Code
    • Sequence Conversion to C-style arrays
• SeqList: Sets of Sequences
  • SeqList Constructors
  • SeqList Destructors
  • SeqList Initialization
    • Design Note
  • Appending to SeqList
  • SeqList Copy Constructor and Copy Semantics
  • Subscripting and Other Info
  • Input and Output
  • SeqList Automatic Resizing
• ASN Sequence Streams
  • The BaseStream Class
    • Constructors
    • Public Methods
    • Protected Methods
    • Flags and States
  • The AsnStream Class
    • Constructors
    • Public Methods
    • Private Methods
  • The EntrezStream Class
    • Constructors
    • Public Methods
  • Configuration for Accessing Entrez/ASN databases
• AlphabetTuple and BaseTuple Classes
  • AlphabetTuple Class
  • BaseTuple Class
• The Prob, ShortProb, LargeReal, ShortLargeReal classes
  • Prob and ShortProb
    • Constructors
    • Usage
    • Member Functions
  • LargeReal and ShortLargeReal
    • Constructors
    • Usage
    • Member Functions
    • printing
  • Prob and LargeReal Implementation
• Histogram Classes
  • Constructors
  • Adding and subtracting instances
  • Setting smoothing parameters
  • Retrieving count information
    • Raw Count Information
  • Input and Output
  • Run-time Type Information
• Input
• The ClassNameRegistry
• NamedObject Class
• IdObject Class
• NamedClass Class
  • NamedClass methods
  • Deriving a class from NamedClass
    • An Example
  • NamedClass commands
• NameToPtr Class
• Command Class
• EqualStrings
• OrderSort
• Log2
• LogGamma
• Multinomial
• Regularizer Class
  • Regularizer methods
  • Regularizer commands
  • MLPReg Class
    • MLPReg methods
    • MLPReg commands
  • MLZReg Class
    • MLZReg methods
    • MLZReg commands
  • DirichletReg Class
    • DirichletReg methods
    • DirichletReg commands
  • GribskovReg Class
    • GribskovReg methods
    • GribskovReg commands
  • SubstPseudoReg Class
    • SubstPseudoReg methods
    • SubstPseudoReg commands
  • FeatureReg Class
    • FeatureReg methods
    • FeatureReg commands
    • FeaturePartition class
• Hash Table Functions
  • The SimpleHashClass class
    • Constructors
    • Methods
    • Printing
  • The DictionaryClass class
    • Constructors
    • Methods
    • Printing
  • The UserDefinitions class
    • Constructors
    • Methods
    • Printing
  • The StringListClass class
    • Constructors
    • Methods
• MasPar Support
  • Linear Array Support
    • Linear Shift Operations
    • Linear Host to PE Array Functions
  • Probabilities in MPL
    • Singular Probability Functions
    • Plural Probability Functions
  • Linking G++ with MPL
• Projects and other things left to do
  • Coming Attractions
  • Wish List
• Index

This document was generated on 28 October 1996 using the texi2html translator version 1.51.