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 | |
| AJAX Command Definitions | Datatypes | Functions | Notes |
| Alignments | Datatypes | Functions | Notes |
| Array handling | 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 |
| Domainatrix Functions | Datatypes | Functions | Notes |
| Domain Functions | Datatypes | Functions | Notes |
| Exception handling | Datatypes | Functions | Notes |
| Feature Table Functions | Datatypes | Functions | Notes |
| Feature Table Data | Datatypes | Notes | |
| File handling | Datatypes | Functions | Notes |
| Formatted output | Datatypes | Functions | Notes |
| Graphical output | Datatypes | Functions | Notes |
| Histogram Graphical Functions | Datatypes | Functions | Notes |
| Indexing Functions | Datatypes | Functions | Notes |
| Java Functions | Datatypes | Functions | Notes |
| Lists | Datatypes | Functions | Notes |
| Maths utilities | Datatypes | Functions | Notes |
| 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 |
| Protein Databank Data Functions | Datatypes | Functions | Notes |
| Protein Databank Data I/O Functions | Datatypes | Functions | Notes |
| Phylogenetic Data Functions | Datatypes | Functions | Notes |
| Sequence Range Functions | Datatypes | Functions | Notes |
| Regular expressions | Datatypes | Functions | Notes |
| Feature Report Functions | 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 |
| Sort Utility Functions | Datatypes | Functions | Notes |
| String manipulation | Datatypes | Functions | Notes |
| System Utility Functions | Datatypes | Functions | Notes |
| Tables | Datatypes | Functions | Notes |
| Time Functions | Datatypes | Functions | Notes |
| Sequence Translation Functions | Datatypes | Functions | Notes |
| Phylogenetic Tree Functions | Datatypes | Functions | Notes |
| Utilities | Datatypes | Functions | Notes |
| Cloning Vector Functions | Datatypes | Functions | Notes |
General data definitions
These are general data types for dates, booleans (true/false) and so on.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 is relatively simple at present, but will expand rapidly to cover all the major data types required by EMBOSS applications.
Alignments
Array handling
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
Domain Functions
Exception handling
Exception handling follows the model in David Hanson's book "C Interfaces and Implementations"Feature Table Functions
File 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.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
See descriptions of functions and data types and XML data typesGraphics 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
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: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
Sequence reading and writing
See the links below.
| Functions | Data types | Description |
|---|---|---|
| ajseq | ajseq | General sequence handling |
| ajseqdata | Sequence data types | |
| ajseqabi | Sequence ABI trace data | |
| ajseqdb | Sequence database access | |
| ajseqread | ajseqread | Sequence reading |
| ajseqtype | Sequence types | |
| ajseqwrite | ajseqwrite | Sequence writing |
Sort Utility Functions
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.