| AJAX database reading library |
| Sequence database | ajseqdb | Defines 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. |
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| AJAX graphics library |
| Graphical output | ajgraph | All the basic functions you are likely to need for plotting and printing graphs. |
| Histogram graphical functions | ajhist | Defines 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 output | ajgraphstruct | Objects for handling graphs, including the basic graph object (AjPGraph) and the PLplot graph data object (AjPGraphdata). |
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| AJAX ACD library |
| AJAX command definitions | ajacd | The ajAcdGet* family of functions that return AJAX objects for data definitions in the application ACD file. |
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| AJAX core library files |
| Alignments | ajalign | Defines 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 handling | ajarr | Various array objects and functions for handling dynamic arrays. |
| Assert function | ajassert | Functions for handling assertions. |
| Base code functions | ajbase | Functions for character conversion of nucleotide bases and other character conversion functions for use with molecular sequences. |
| Call registration functions | ajcall | A few functions to allow access to different graphics packages, should alternatives to PLplot be implemented in the future. |
| Codon analysis functions | ajcod | Defines the AjPCod object and functions for handling codon usage tables. |
| DNA melting functions | ajdan | Functions for calculating properties of nucleotide sequences, mostly related to DNA melting/annealing. |
| Domainatrix functions | ajdmx | Data structures and functions for handling structure as used by some of the EMBASSY structure applications. |
| DOM parser | ajdom | DOM XML parser functions |
| Domain functions | ajdomain | Defines 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 handling | ajexcept | Contains the ajExceptRaise function for raising an exception. |
| Feature table functions | ajfeat | Most of the functions you will ever need for general feature handling. |
| File handling | ajfile | Objects and functions for handling of data files, general files and directories and static functions for manipulating them at a low level. |
| Data file handling | ajfiledata | Data file handling |
| File i/O handling | ajfileio | File input/output handling |
| Formatted output | ajfmt | Functions 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 functions | ajindex | Database indexing functions. |
| Java functions | ajjava | Java functions. |
| Lists | ajlist | All 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 utilities | ajmath | General maths functions for rounding numbers, coordinate conversion, random number generation etc. |
| Comparison matrix functions | ajmatrices | Defines the AjPMatrix and AjPMatrixf objects and functions for handling comparison matrices. |
| Memory allocation | ajmem | Memory allocation |
| Message handling | ajmess | Defines the error message object (AjPError) and functions for message handling. |
| Names: Variables and database definitions | ajnam | Names: Variables and database definitions |
| Nexus data functions | ajnexus | Functions and objects (including static data structures and functions) for parsing the NEXUS file format. |
| Pattern functions | ajpat | Defines the sequence pattern list object (AjPPatlistSeq) and general pattern list object (AjPPatlistRegex) and functions for handling lists of regular expression patterns. |
| Protein databank data functions | ajpdb | Protein databank data functions. |
| Protein databank data I/O functions | ajpdbio | Protein databank data I/O functions. |
| Phylogenetic data functions | ajphylo | Defines the objects and functions for handling phylogenetic data. |
| Sequence range functions | ajrange | Defines the range specification object (AjPRange) and contain functions for handling of range specifications (see Section A.2.1.5, “range”). |
| Regular expressions | ajreg | Defines the regular expression object (AjPRegexp) and functions for handling of regular expressions. |
| Feature report functions | ajreport | Defines the AjPReport object and functions for handling of reports. |
| Sequence | ajseq | Most 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 traces | ajseqabi | Provides functions for parsing sequences (and other data) from ABI trace files. |
| Sequence reading | ajseqread | Functions for handling the sequence query and sequence input objects and a few general sequence handling functions. |
| Sequence types | ajseqtype | Functions 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 writing | ajseqwrite | Defines 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 functions | ajsort | Functions for sorting arrays (Section 6.17.10, “Sorting Arrays”). |
| SQL | ajsql | SQL database access. |
| String manipulation | ajstr | Most 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 functions | ajsys | System functions, mostly for low level handling of files and directories and system-specific functions. |
| Tables | ajtable | Defines the hash table object (AjPTable) and functions for handling hash tables. |
| Time functions | ajtime | Time functions. |
| Sequence translation functions | ajtranslate | Defines a sequence translation object (AjPTrn) and include functions for handling sequence translation (Section 6.8, “Handling Sequence Translation”). |
| Phylogenetic tree functions | ajtree | Create and manipulate phylogenetic trees. |
| Utilities | ajutil | Exit cleanly, memory cleanup, manipulate bytes and so on. |
| Mathematical vector functions | ajvector | Data structures and functions for handling vectors in 3D space. |
| System specific definitions | ajarch | System-specific type definitions. |
| General data definitions | ajax | Master AJAX include file. |
| General data definitions | ajdefine | General type definitions. |
| Feature table data | ajfeatdata | Basic 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 data | ajseqdata | Define 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. |