The AJAX Library Documentation: CVS (developers) release

This documentation is automatically derived from the comments in the source file function headers. Function documentation and the source code are also indexed in SRS as databases EFUNCREL and EDATAREL.

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

Notes

This table is automatically generated.
"Notes" link to library file-specific documentation (bottom of this page). This documentation will be added as part of the general AJAX make-over.

LIBRARY	DATATYPES	FUNCTIONS	NOTES
General data definitions	Datatypes		Notes
System Specific Definitions	Datatypes		Notes
General data definitions	Datatypes		Notes
AJAX Command Definitions	Datatypes	Functions	Notes
Alignments	Datatypes	Functions	Notes
Array handling	Datatypes	Functions	Notes
Assembly functions	Datatypes	Functions	Notes
Assembly data	Datatypes		Notes
Assembly reading	Datatypes	Functions	Notes
Assembly writing	Datatypes	Functions	Notes
Assembly database	Datatypes	Functions	Notes
Assert function	Datatypes	Functions	Notes
Base Code Functions	Datatypes	Functions	Notes
Call Registration Functions	Datatypes	Functions	Notes
Codon Analysis Functions	Datatypes	Functions	Notes
DNA Melting Functions	Datatypes	Functions	Notes
DAS Functions	Datatypes	Functions	Notes
Domainatrix Functions	Datatypes	Functions	Notes
DOM parser	Datatypes	Functions	Notes
Domain Functions	Datatypes	Functions	Notes
Exception handling	Datatypes	Functions	Notes
Feature table functions	Datatypes	Functions	Notes
Feature table data	Datatypes		Notes
Features table reading	Datatypes	Functions	Notes
Feature table writing	Datatypes	Functions	Notes
Feature table database	Datatypes	Functions	Notes
File handling	Datatypes	Functions	Notes
Data file handling	Datatypes	Functions	Notes
File i/O handling	Datatypes	Functions	Notes
Formatted output	Datatypes	Functions	Notes
Graphical output	Datatypes	Functions	Notes
Histogram Graphical Functions	Datatypes	Functions	Notes
HTTP Functions	Datatypes	Functions	Notes
Indexing Functions	Datatypes	Functions	Notes
Java Functions	Datatypes	Functions	Notes
Lists	Datatypes	Functions	Notes
Mart: BioMart Functions	Datatypes	Functions	Notes
Maths utilities	Datatypes	Functions	Notes
Matrices: Comparison Matrix Functions	Datatypes	Functions	Notes
Memory allocation	Datatypes	Functions	Notes
Message handling	Datatypes	Functions	Notes
Names: Variables and database definitions	Datatypes	Functions	Notes
Nexus Data Functions	Datatypes	Functions	Notes
Obo term functions	Datatypes	Functions	Notes
Obo term data	Datatypes		Notes
Obo term reading	Datatypes	Functions	Notes
Obo term writing	Datatypes	Functions	Notes
Obo term database	Datatypes	Functions	Notes
Pattern Functions	Datatypes	Functions	Notes
Protein Databank Data Functions	Datatypes	Functions	Notes
Protein Databank Data I/O Functions	Datatypes	Functions	Notes
Phylogenetic Data Functions	Datatypes	Functions	Notes
Query language Functions	Datatypes	Functions	Notes
Sequence Range Functions	Datatypes	Functions	Notes
Regular expressions	Datatypes	Functions	Notes
Feature Report Functions	Datatypes	Functions	Notes
Resource functions	Datatypes	Functions	Notes
Resource data	Datatypes		Notes
Resource reading	Datatypes	Functions	Notes
Resource writing	Datatypes	Functions	Notes
Resource database	Datatypes	Functions	Notes
Sequence	Datatypes	Functions	Notes
Sequence ABI traces	Datatypes	Functions	Notes
Sequence data	Datatypes		Notes
Sequence database	Datatypes	Functions	Notes
Sequence reading	Datatypes	Functions	Notes
Sequence types	Datatypes	Functions	Notes
Sequence writing	Datatypes	Functions	Notes
SOAP Functions	Datatypes	Functions	Notes
Sort Utility Functions	Datatypes	Functions	Notes
SQL	Datatypes	Functions	Notes
String manipulation	Datatypes	Functions	Notes
System Utility Functions	Datatypes	Functions	Notes
Tables	Datatypes	Functions	Notes
Taxon functions	Datatypes	Functions	Notes
Taxon data	Datatypes		Notes
Taxon reading	Datatypes	Functions	Notes
Taxon writing	Datatypes	Functions	Notes
Taxon database	Datatypes	Functions	Notes
Text functions	Datatypes	Functions	Notes
Text data	Datatypes		Notes
Text reading	Datatypes	Functions	Notes
Text writing	Datatypes	Functions	Notes
Text database	Datatypes	Functions	Notes
Time Functions	Datatypes	Functions	Notes
Sequence Translation Functions	Datatypes	Functions	Notes
Phylogenetic Tree Functions	Datatypes	Functions	Notes
Url functions	Datatypes	Functions	Notes
Url data	Datatypes		Notes
Url reading	Datatypes	Functions	Notes
Url writing	Datatypes	Functions	Notes
Url database	Datatypes	Functions	Notes
Utilities	Datatypes	Functions	Notes
Variation functions	Datatypes	Functions	Notes
Variation data	Datatypes		Notes
Variation reading	Datatypes	Functions	Notes
Variation writing	Datatypes	Functions	Notes
Variation database	Datatypes	Functions	Notes
Vector: Cloning Vector Functions	Datatypes	Functions	Notes

General data definitions

General Type Definitions

These are general data types for dates, booleans (true/false) and so on.

Master AJAX Include File

System-Specific Type Definitions

AJAX Command Definitions

All EMBOSS applications depend on a complete user interface definition in an ACD (AJAX Command Definition) file. The ACD file specifies all the information the application needs. A single library call parses the definition, checks the command line, and prompts the user for any values still needed.

The ACD specification covers all the major data types read and written by EMBOSS applications and the internal functions needed to manage ACD file parsing, help text and conversions for other projects.

Alignments

Array handling

Assembly handling

See the links below.

Assembly data definitions

See the links below.

Assembly term reading

See the links below.

Assembly writing

See the links below.

Assembly database reading

See the links below.

Functions	Data types	Description
ajassem	ajassem	Assembly general handling
	ajassemdata	Assembly data types
ajassemread	ajassemread	Assembly reading
ajassemwrite	ajassemwrite	Assembly writing
ajassemdb		Assembly database access

Assert function

These functions control provide special handling of the "assert" function using AJAX message handling.

Base Code Functions

Call Registration Functions

Codon Analysis Functions

DNA Melting Functions

Domainatrix Functions

DOM XML Parser Functions

Domain Functions

Exception handling

Exception handling follows the model in David Hanson's book "C Interfaces and Implementations"

Feature table functions

See the links below.

Feature table data definitions

See the links below.

Feature table reading

See the links below.

Feature table writing

See the links below.

Feature table database reading

See the links below.

Functions	Data types	Description
ajfeat	ajfeat	Feature table general handling
	ajfeatdata	Feature table data types
ajfeatread	ajfeatread	Feature table reading
ajfeatwrite	ajfeatwrite	Feature table writing
ajfeatdb		Feature table database access

File object handling

AJAX provides input and output file data types with features such as lists of files to be processed and buffering of lines so that files can be read again from memory, useful for files which cannot be rewound like stdin.

Data File handling

File input/output handling

Formatted output

AJAX formatting is a superset of ANSI C, with additional types for strings, booleans and dates. Output can be to a string with automatic adjustment of memory allocation. Null pointers are checked for and reported rather than causing failures (for example with %s).

Graphical output

Graphical Data Types

See descriptions of functions and data types

Graphics in the current version use the PLplot graphics library. We continue to look for other graphics libraries available under the Library GPL and may change or allow alternatives in future.

Histogram Graphical Functions

Indexing Functions

Java Functions

Lists

Lists are tricky to handle because of the ownership of the data items. Data items are mostly of "any" data type (void* in ANSI C) which means that the list will not know how to free them.

Some lists assume the user will delete data when it is removed form the list. Others can automatically delete. See the function documentation for more information.

Separate string functions are provided because lists of strings can be very useful.

Maths utilities

Only a few utility functions are included so far. They cover rounding. Functions for sorting are planned as soon as they are needed by applications or by other library code.

Comparison Matrix Functions

Memory allocation

Only a few utility functions are included so far. They are basically malloc and friends with error messages on failure. There are also ANSI C macros to make life easier.

Message handling

The message functions names are rather confusing. There are a set of macros to make them easier to use, and typical applications will only use these and avoid the direct function calls.

Names: Variables and database definitions

AJAX checks variable names first as environment variables (on Unix) and then as definitions in either the user's ~/.embossrc file or in the site wide emboss.defaults file.

Sequence databases are defined in the same files, and handled by a related set of functions. Database definitions are very flexible, and are summarised in the database definition guide.

Nexus Data Functions

Obo term handling

See the links below.

Obo term data definitions

See the links below.

Obo term reading

See the links below.

Obo term writing

See the links below.

Obo term database reading

See the links below.

Functions	Data types	Description
ajobo	ajobo	Obo term general handling
	ajobodata	Obo term data types
ajoboread	ajoboread	Obo term reading
ajobowrite	ajobowrite	Obo term writing
ajobodb		Obo term database access

Pattern matching functions

Protein Databank Data Functions

Protein Databank Data I/O Functions

Phylogenetic Data Functions

Sequence Range Functions

Regular expressions

Internal functions are documented in the following categories:

PCRE

Internal data structures are documented in the PCRE Internals and PCRE Posix

AJAX regular expressions are based on the PCRE (Perl Compatible Regular Expressions) library.

Feature Report Functions

Data resource handling

See the links below.

Data resource data definitions

See the links below.

Data resource reading

See the links below.

Data resource writing

See the links below.

Data resource database reading

See the links below.

Functions	Data types	Description
ajresource	ajresource	Data resource general handling
	ajresourcedata	Data resource data types
ajresourceread	ajresourceread	Data resource reading
ajresourcewrite	ajresourcewrite	Data resource writing
ajresourcedb		Data resource database access

Sequence data definitions

See the links below.

Sequence handling

See the links below.

Sequence ABI Trace handling

See the links below.

Sequence reading

See the links below.

Management of Sequence Types

See the links below.

Sequence writing

See the links below.

Sequence database reading

See the links below.

Functions	Data types	Description
ajseq	ajseq	Sequence general handling
	ajseqdata	Sequence data types
	ajseqabi	Sequence ABI trace data
ajseqread	ajseqread	Sequence reading
ajseqtype		Sequence types
ajseqwrite	ajseqwrite	Sequence writing
ajseqdb		Sequence database access

Sort Utility Functions

SQL Database Access

String manipulation

String handling is the most extensive part of the library so far. String data structures are fundamental to many of the internal routines and are the internal representation of sequence data.

System Utility Functions

Tables

Table handling was initially based on David Hanson's book "C Interfaces and Implementations".

The hash functions and comparison functions have been revised to work better with strings. Further changes will be made in future.

Taxon handling

See the links below.

Taxon data definitions

See the links below.

Taxon reading

See the links below.

Taxon writing

See the links below.

Taxon database reading

See the links below.

Functions	Data types	Description
ajtax	ajtax	Taxon general handling
	ajtaxdata	Taxon data types
ajtaxread	ajtaxread	Taxon reading
ajtaxwrite	ajtaxwrite	Taxon writing
ajtaxdb		Taxon database access

Text handling

See the links below.

Text data definitions

See the links below.

Text reading

See the links below.

Text writing

See the links below.

Text database reading

See the links below.

Functions	Data types	Description
ajtext	ajtext	Text general handling
	ajtextdata	Text data types
ajtextread	ajtextread	Text reading
ajtextwrite	ajtextwrite	Text writing
ajtextdb		Text database access

Time Functions

Sequence Translation Functions

Phylogenetic Tree Functions

Url handling

See the links below.

Url data definitions

See the links below.

Url reading

See the links below.

Url writing

See the links below.

Url database reading

See the links below.

Functions	Data types	Description
ajurl	ajurl	Url general handling
	ajurldata	Url data types
ajurlread	ajurlread	Url reading
ajurlwrite	ajurlwrite	Url writing
ajurldb		Url database access

Utilities

Only a few utility functions are included so far. These cover aborting applications and testing for bigendian or littleendian machines.

Variation handling

See the links below.

Variation data definitions

See the links below.

Variation reading

See the links below.

Variation writing

See the links below.

Variation database reading

See the links below.

Functions	Data types	Description
ajvar	ajvar	Variation general handling
	ajvardata	Variation data types
ajvarread	ajvarread	Variation reading
ajvarwrite	ajvarwrite	Variation writing
ajvardb		Variation database access