The NUCLEUS Library Documentation: CVS (developers) release

Notes

This documentation is automatically derived from the comments in the source file function headers.

The functions are documented in the order in which they appear in the source files.

This documentation and the source code are also indexed in SRS as databases EFUNC and EDATA.

The pages are generated by a Perl script which is easily modifiable.

The most useful libraries for new developers are given in bold italics.

Notes


LIBRARY DATATYPES FUNCTIONS NOTES
Include file for all applications Datatypes   Notes
Pattern list file reading   Functions Notes
Pattern matching algorithms Datatypes Functions Notes
Signatures of protein domains Datatypes Functions Notes
N-mer (word) algorithms   Functions Notes
Reading data files   Functions Notes
Groups of applications Datatypes Functions Notes
Data file utilities   Functions Notes
Alignments   Functions Notes
Comparison matrices Datatypes Functions Notes
Properties of protein sequences   Functions Notes
Miscellaneos methods   Functions Notes
Isoelectric point utilities   Functions Notes
Comments   Functions Notes
Consensus sequences   Functions Notes
Exit calls for applications   Functions Notes
EST algorithms Datatypes Functions Notes
Indexing databases using B+ trees Datatypes Functions Notes
Showing sequences in pretty formats Datatypes Functions Notes
Initialising internals   Functions Notes
Database indexing using EMBL-CD indices Datatypes Functions Notes
Domainatrix package algorithms Datatypes Functions Notes
Word matching algorithms Datatypes Functions Notes
Protein databank (PDB) structure file utilities   Functions Notes
Molecular fragment algorithms Datatypes Functions Notes
Domain algorithms   Functions Notes
XYZ 3D coordinate algorithms   Functions Notes


Master Include File

The emboss.h include file brings in every NUCLEUS and AJAX include file so there is no need to add include files for eqach function or datatype.

Sequence Alignment

See descriptions of
functions

Complexity

See descriptions of
functions

Consensus

See descriptions of
functions

Data Files

See descriptions of
functions

Database Index

See descriptions of
functions and data types

Domainatrix Methods

See descriptions of
functions

Domain Methods

See descriptions of
functions

EST Methods

See descriptions of
functions and data types

Exit Methods

See descriptions of
functions

Groups

See descriptions of
functions and data types

Protein properties

See descriptions of
functions

Indexing

See descriptions of
functions and data types

Initialization

See descriptions of
functions

Comparison Matrices

See descriptions of
functions and data types

Miscellaneous Methods

See descriptions of
functions and data types

Molecular fragments

See descriptions of
functions and data types

Word (n-mer) Methods

See descriptions of
functions

Pattern Matching Methods

See descriptions of
functions and data types

Pattern List Input Methods

See descriptions of
functions

Protein data bank

See descriptions of
functions

Sequence Properties

See descriptions of
functions

Reading data files

See descriptions of
functions

Show (Display) Methods

See descriptions of
functions and data types

Signature Methods

See descriptions of
functions and data types

Word Methods

See descriptions of
functions

Xyz Coordinate Methods

See descriptions of
functions