6.2. Programming Guides

6.2.1. AJAX

Programming guides (Table 6.1, “Programming Guides for the AJAX Library”) are available for most files in AJAX. These summarise the available C data structures and functions and methods for their use. For some files a programming guide is "Not available", others say "See" a guide only, without any deep coverage. In most cases, you are unlikely to need such files and should see the online library documentation for a description of the datatypes and functions included.

Table 6.1. Programming Guides for the AJAX Library
AJAX Library FileProgramming Guide
acd/ajacd.c/hHandling ACD Files
core/ajalign.c/cHandling Alignments
core/ajalign.h/cHandling Alignments
core/ajarch.hC Basic Datatypes
core/ajarr.c/hHandling Arrays. Also see Handling Simple
core/ajassert.h/cNot available
core/ajax.hC Basic Datatypes, Your First EMBOSS Application
core/ajbase.h/cHandling Sequences
core/ajcall.h/cSee Handling Graphics
core/ajcod.h/cHandling Codon
core/ajdan.h/cHandling Sequences
core/ajdmx.h/cNot available
core/ajdefine.hC Basic Datatypes
core/ajdomain.h/cNot available
core/ajdom.h/cSee Handling Graphics
core/ajexcept.h/cHandling Exceptions
core/ajfeat.h/cHandling Features
core/ajfeatdata.hHandling Features
core/ajfile.h/cHandling Files
core/ajfiledata.h/cNot available
core/ajfileio.h/cNot available
core/ajfmt.h/cHandling Strings
graphics/ajgraph.h/cHandling Graphics
graphics/ajgraphstruct.hHandling Graphics
graphics/ajgraphxml.h/cSee Handling Graphics
graphics/ajhist.h/cHandling Graphics
core/ajindex.h/cNot available
core/ajjava.h/cNot available
core/ajlist.h/cHandling Lists
core/ajmath.h/cHandling Maths
core/ajmatrices.h/cHandling Matrices
core/ajmem.h/cObjects (C Data Structures)
core/ajmess.h/cHandling Exceptions
core/ajnam.h/cNot available
core/ajnexus.h/cSee Handling Phylip
core/ajpat.h/cHandling Patterns. Also see Handling Simple
core/ajpdb.h/cNot available
core/ajpdbio.h/cNot available
core/ajphylo.h/cHandling Phylip
core/ajrange.h/cHandling Simple
core/ajreg.h/cHandlingPatterns. Also see Handling Simple
core/ajreport.h/cHandling Reports
core/ajseqabi.h/cSee Handling Sequences
core/ajseq.h/cHandling Sequences
core/ajseqdata.hHandling Sequences
ajaxdb/ajseqdb.h/cSee Handling Sequences
core/ajseqread.h/cHandling Sequences
core/ajseqtype.h/cHandling Sequences
core/ajseqwrite.h/cHandling Sequences
core/ajsort.h/cHandling Arrays
core/ajsql.h/cNot available
core/ajstr.h/cHandlingStrings. Also see Handling Simple
core/ajsys.h/cHandling System
core/ajtable.h/cHandling Tables
core/ajtime.h/cNot available
core/ajtranslate.h/cHandling Sequences
core/ajtree.h/cNot available
core/ajutil.h/cHandling System
core/ajvector.h/cSee Handling Maths
pcre/pcre.cSee HandlingPatterns
pcre/pcre_chartables.cSee HandlingPatterns
pcre/pcre_config.hSee HandlingPatterns
pcre/pcre_get.cSee HandlingPatterns
pcre/pcre.hSee HandlingPatterns
pcre/pcre_internal.hSee HandlingPatterns
pcre/pcreposix.cSee HandlingPatterns
pcre/pcreposix.hSee HandlingPatterns
pcre/pcre_printint.cSee HandlingPatterns
pcre/pcre_study.cSee HandlingPatterns

6.2.2. NUCLEUS

Programming guides are not currently available for the NUCLEUS library. In some cases algorithms and data structures that you might expect to find in NUCLEUS are in fact kept in AJAX. This is usually necessary for purposes of compilation. For example any functions that are called during ACD file processing, which is handled by a part of AJAX, must also live in AJAX.