B.3. AJAX Library Files

Table B.1. 
TopicLibrary fileShort description
AJAX database reading library
Sequence databaseajseqdbDefines a sequence database reading object (SeqSAccess) used in the definition of AjPSeqin and static data structures and functions for handling all aspects of sequence database access.
AJAX graphics library
Graphical outputajgraphAll the basic functions you are likely to need for plotting and printing graphs.
Histogram graphical functionsajhistDefines the histogram object AjPHist object for handling histograms, which includes the histogram data object (AjPHistdata) as a substructure. It contains basic functions for handling histograms.
Graphical outputajgraphstructObjects for handling graphs, including the basic graph object (AjPGraph) and the PLplot graph data object (AjPGraphdata).
AJAX ACD library
AJAX command definitionsajacdThe ajAcdGet* family of functions that return AJAX objects for data definitions in the application ACD file.
AJAX core library files
AlignmentsajalignDefines the main alignment object (AjPAlign). It can be used for retrieving an input sequence alignment via ACD file processing. The header file contains most of the functions you will ever need for general handling of sequence alignments.
Array handlingajarrVarious array objects and functions for handling dynamic arrays.
Assert functionajassertFunctions for handling assertions.
Base code functionsajbaseFunctions for character conversion of nucleotide bases and other character conversion functions for use with molecular sequences.
Call registration functionsajcallA few functions to allow access to different graphics packages, should alternatives to PLplot be implemented in the future.
Codon analysis functionsajcodDefines the AjPCod object and functions for handling codon usage tables.
DNA melting functionsajdanFunctions for calculating properties of nucleotide sequences, mostly related to DNA melting/annealing.
Domainatrix functionsajdmxData structures and functions for handling structure as used by some of the EMBASSY structure applications.
DOM parserajdomDOM XML parser functions
Domain functionsajdomainDefines the scop object (AjPScop), cath object (AjPCath), and generic domain classification object (AjPDomain) object for storing protein structural domain data. It contains functions for handling protein domain data, including reading the SCOP and CATH domain classification database parsable files and for reading and writing the DCF (domain classification file) format files.
Exception handlingajexceptContains the ajExceptRaise function for raising an exception.
Feature table functionsajfeatMost of the functions you will ever need for general feature handling.
File handlingajfileObjects and functions for handling of data files, general files and directories and static functions for manipulating them at a low level.
Data file handlingajfiledataData file handling
File i/O handlingajfileioFile input/output handling
Formatted outputajfmtFunctions for string formatting. The functions are similar to the C functions printf, fprintf etc, but the set of conversion specifiers and other functionality is extended.
Indexing functionsajindexDatabase indexing functions.
Java functionsajjavaJava functions.
ListsajlistAll the functions you are likely to ever need for the creation and control of linked lists. They define the basic list object (AjPList) which includes the list node object (AjPListNode) as a nested substructure, and a list iteration object (AjIList).
Maths utilitiesajmathGeneral maths functions for rounding numbers, coordinate conversion, random number generation etc.
Comparison matrix functionsajmatricesDefines the AjPMatrix and AjPMatrixf objects and functions for handling comparison matrices.
Memory allocationajmemMemory allocation
Message handlingajmessDefines the error message object (AjPError) and functions for message handling.
Names: Variables and database definitionsajnamNames: Variables and database definitions
Nexus data functionsajnexusFunctions and objects (including static data structures and functions) for parsing the NEXUS file format.
Pattern functionsajpatDefines the sequence pattern list object (AjPPatlistSeq) and general pattern list object (AjPPatlistRegex) and functions for handling lists of regular expression patterns.
Protein databank data functionsajpdbProtein databank data functions.
Protein databank data I/O functionsajpdbioProtein databank data I/O functions.
Phylogenetic data functionsajphyloDefines the objects and functions for handling phylogenetic data.
Sequence range functionsajrangeDefines the range specification object (AjPRange) and contain functions for handling of range specifications (see Section A.2.1.5, “range).
Regular expressionsajregDefines the regular expression object (AjPRegexp) and functions for handling of regular expressions.
Feature report functionsajreportDefines the AjPReport object and functions for handling of reports.
SequenceajseqMost of the functions you will ever need for general sequence handling. They define the AjPSeqCvt object used for sequence conversion (Section 6.7.14, “Sequence Conversion”.
Sequence ABI tracesajseqabiProvides functions for parsing sequences (and other data) from ABI trace files.
Sequence readingajseqreadFunctions for handling the sequence query and sequence input objects and a few general sequence handling functions.
Sequence typesajseqtypeFunctions for handling of sequence types. They also contain static data structures and functions for validation and processing of sequence types at a low level.
Sequence writingajseqwriteDefines the sequence output object (AjPSeqout) and include functions for writing sequences to file. They define static data structures and functions for handling sequence output, in the supported formats, at a low level.
Sort utility functionsajsortFunctions for sorting arrays (Section 6.17.10, “Sorting Arrays”).
SQLajsqlSQL database access.
String manipulationajstrMost of the functions you will ever need for general string handling. They define the basic string object AjPStr, string iteration object (AjIStr and string token parser object (AjPStrTok) for use with the functions.
System utility functionsajsysSystem functions, mostly for low level handling of files and directories and system-specific functions.
TablesajtableDefines the hash table object (AjPTable) and functions for handling hash tables.
Time functionsajtimeTime functions.
Sequence translation functionsajtranslateDefines a sequence translation object (AjPTrn) and include functions for handling sequence translation (Section 6.8, “Handling Sequence Translation”).
Phylogenetic tree functionsajtreeCreate and manipulate phylogenetic trees.
UtilitiesajutilExit cleanly, memory cleanup, manipulate bytes and so on.
Mathematical vector functionsajvectorData structures and functions for handling vectors in 3D space.
System specific definitionsajarchSystem-specific type definitions.
General data definitionsajaxMaster AJAX include file.
General data definitionsajdefineGeneral type definitions.
Feature table dataajfeatdataBasic feature objects (AjPFeattable, AjPFeature and AjPFeattabOut) for general use, e.g. retrieving features via ACD file processing. It also defines a feature input object (AjPFeattabIn) used for low level feature input handling.
Sequence dataajseqdataDefine the basic sequence objects (AjPSeq, AjPSeqset and AjPSeqall) for general use e.g. retrieving sequences via ACD file processing. They also define a sequence input object (AjPSeqin) and a sequence query object (AjPSeqQuery) used for low level sequence retrieval.