2307 lines
148 KiB
Text
2307 lines
148 KiB
Text
<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<title>/c/readme</title>
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<base href="//www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/">
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<meta name="description" content="NCBI C Toolkit Cross Reference">
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<body>
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<h2 class="warning" style="padding:10pt">WARNING: C Toolkit is deprecated, please use C++ Toolkit instead</h2>
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<div class="nav-menu">
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<div class="nav-title">
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<h1 class="main">NCBI C Toolkit Cross Reference</h1>
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<h3 class="banner"><span class="banner"><a class="banner" href="/IEB/ToolBox/C_DOC/lxr/source/">c</a>/​<a class="banner" href="/IEB/ToolBox/C_DOC/lxr/source/readme">readme</a></span></h3>
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<div class="filecontent">
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<pre class="filecontent-src">
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NCBI SOFTWARE DEVELOPMENT TOOLKIT
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National Center for Biotechnology Information
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Bldg 38A, NIH
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8600 Rockville Pike
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Bethesda, MD 20894
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The NCBI Software Development Toolkit was developed for the production and
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distribution of GenBank, Entrez, BLAST, and related services by NCBI. We make
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it freely available to the public without restriction to facilitate the
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use of NCBI by the scientific community. However, please understand that
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while we feel we have done a high quality job, this is not commercial software.
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The documentation lags considerably behind the software and we must make any
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changes required by our data production needs. Nontheless, many people have
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found it a useful and stable basis for a number of tools and applications.
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The toolkit is available by anonymous ftp from ftp.ncbi.nih.gov
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cd toolbox
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cd ncbi_tools
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bin
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get ncbi.tar.Z (compressed UNIX tar file)
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quit
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In this same directory are also ncbiz.exe (DOS self extracting archive) and
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ncbi.hqx (Mac self extracting archive). All three files contain the same
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source code and will make the toolkit for all platforms.
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Please feel free to email questions/suggestions to:
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toolbox@ncbi.nlm.nih.gov
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If you would like hardcopy of the current documentation, send your mailing
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address with your request to the email address above.
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If you are considering a serious development project using this toolkit, please
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contact us. We are happy to discuss compatible strategies and inform you of
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our longer term plans. There is no limitation of the use of this code or in
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contacting us about its use for commercial, academic, or government groups.
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===========================================================================
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Version 6.1
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the date of release may be obtained from the file ncbi/VERSION
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===========================================================================
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Summary
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The procedure of building the toolkit on Unix was slightly changed.
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Now there is no need to download any binary NCBI product for your
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platform to obtain the platform-specific ncbi.mk file.
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To build the NCBI toolkit you need to look for platform-dependent instructions:
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For UNIX (including Linux and Mac OS X):
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look at the file make/readme.unx
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For alternative Mac instructions (using CodeWarrior):
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look at the file make/readme.mac
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For Microsoft Windows95/98/NT:
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look at the file make/readme.dos
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There is some information which may be useful for NCBI tookit building
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in the file doc/FAQ.txt
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This release includes source code for the new (2.0.9) version of BLAST.
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Look at the file doc/README.bls for more detailed documentation on
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stand-alone BLAST.
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The file doc/README.pbl has the information about PowerBLAST.
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And the description on Integrating Matrix Profiles And Local Alignments
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(IMPALA) is located in the file doc/README.imp
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The file doc/sequin.htm describes the SEQUIN and its configuration.
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If you have problems configuring Entrez with a firewall, look at the
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file doc/firewall.txt
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This file has a section called CONFIGURATION OR SETTINGS FILES,
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which explains in detail how our configuration system works. The ncbi
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config file (.ncbirc on UNIX, ncbi.ini on PC/Windows, and ncbi.cnf on
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Macintosh) is needed in order to find data files, such as
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gc.val (the genetic code table), provided in the toolkit or with programs
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like Sequin. (The asnload files containing dynamic versions of the ASN.1
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parse tables are no longer needed, since all platforms can now have large
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static data.)
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It has recently become possible to eliminate the need for the ncbi config
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file by calling UseLocalAsnloadDataAndErrMsg () at the beginning of your
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program. This looks for the data directory in the same directory as the
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running program. If it doesn't find it, it looks up one level, in case you
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are compiling programs in the build directory of the toolkit. If it finds
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the data directory in either of these places, it transiently sets the
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location, so code that loads these files is given the correct path.
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An even more recent change is that copies of several of our data files (gc,
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seqcode, and featdef) are now built into the source code, so if the data
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directory is not found, programs that require only these can still run.
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One final improvement is that access to our network services is now much
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simpler than before, so if you are not behind a firewall and have domain
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name server (DNS) available you can connect to our network without needing
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any configuration information in the ncbi config file. Operation behind a
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firewall, or with a proxy, requires very little in the ncbi config file, and
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this is easily created by asking Sequin to configure for network access.
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=============================================================================
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Notes from Previous Releases
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=============================================================================
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=============================================================================
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Version 6.0
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the date of release may be obtained from the file ncbi/VERSION
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=============================================================================
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This release includes source code for the new (2.0) version of BLAST.
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Also included are a small number of incremental changes in the ASN.1
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specification.
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BLAST 2.0 - BLAST 2.0 can produce gapped alignments and is capable of
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position-specific-iterated BLASTp (PSI-BLAST). Compared to the 1.4 release of
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BLAST, there are also signficant performance enhancements as well as extensive
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changes to the text report and the format of the databases. BLAST 2.0
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uses threads for multi-processing, using the NCBI threads library.
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Three BLAST programs may be compiled in the demo directory. They are:
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formatdb: formats FASTA files as BLAST databases for BLAST 2.0.
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blastall: perform all five flavors of blast comparison.
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blastn and blastp offer fully gapped alignments.
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blastx and tblastn have 'in-frame' gapped alignments and use sum
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statistics to link alignments from different frames.
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tblastx provides only ungapped alignments.
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blastpgp: performs gapped blastp searches and can be used to perform
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iterative searches in psi-blast mode.
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Additional information may be obtained from the README in the BLAST
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directory of the FTP site and from the NCBI BLAST pages.
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ASN.1 Spec Changes for 1997
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biblio.asn
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Cit-pat - some fields made optional to allow patent applications to be legal
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Cit-pat.number OPTIONAL
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Cit-pat.date-issue OPTIONAL
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-- Patent number and date-issue were made optional in 1997 to
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-- support patent applications being issued from the USPTO
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-- Semantically a Cit-pat must have either a patent number or
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-- an application number (or both) to be valid
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medline.asn
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added ML-field to support other MEDLINE line types
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Medline-entry ::= SEQUENCE {
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uid INTEGER OPTIONAL , -- MEDLINE UID, sometimes not yet available if from PubMed
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em Date , -- Entry Month
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... (not shown)
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pmid PubMedId OPTIONAL , -- MEDLINE records may include the PubMedId
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pub-type SET OF VisibleString OPTIONAL, -- may show publication types (review, etc)
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mlfield SET OF Medline-field OPTIONAL } -- additional Medline field types
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Medline-field ::= SEQUENCE {
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type INTEGER { -- Keyed type
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other (0) , -- look in line code
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comment (1) , -- comment line
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erratum (2) } , -- retracted, corrected, etc
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str VisibleString , -- the text
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ids SEQUENCE OF DocRef OPTIONAL } -- pointers relevant to this text
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DocRef ::= SEQUENCE { -- reference to a document
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type INTEGER {
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medline (1) ,
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pubmed (2) ,
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ncbigi (3) } ,
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uid INTEGER }
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seq.asn
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MolInfo.tech - added names for HTG classes already implemented
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Annotdesc.region - added seqloc. If present, all annots in this SeqAnnot
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are within this region. Optimization on big seqs.
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seqfeat.asn
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added OrgMod.specimen-voucher - new organism qualifier
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added OrgMod.old-name - used internally at NCBI
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added BioSource.is-focus - for distinguishing biological focus of
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multiple source features.
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added Seq-feat.pseudo so any feature can be flagged explicitly as
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belonging to a pseudogene
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added Seq-feat.except-text for an explanation of the exception when
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Seq-feat.except is TRUE. Currently this text is in Seq-feat.comment
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in backbone records and GBQuals in some other genbank records.
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=============================================================================
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Notes from Previous Releases
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=============================================================================
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Version 5.0
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Summary
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This release includes a small number of incremental changes in the ASN.1
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specification. Most significant is the addition of the PubMedID, a
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bibliographic citation identifier similar to a MEDLINE UID. PubMed is a new
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citation database being developed at NCBI which is a superset of MEDLINE. It
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will be an avenue by which publishers can deposit electronic versions of their
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citations and abstracts to allow them timely linking to network entrez from
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the publishers on-line services. PubMed will route these citations to MEDLINE
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and they will appear in MEDLINE (and Entrez) after the usual MEDLINE indexing.
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However, for some period of time, such articles will have only a PubMedID.
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We would like to switch Entrez over to supporting PubMedIDs as early as
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possible. WE STRONGLY ENCOURAGE DEVELOPERS TO RECOMPILE AND RELINK WITH THIS
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VERSION OF THE TOOLKIT AS SOON AS POSSIBLE. The changes in this specification
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should not cause problems with existing software, so a simple compile and
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link should be enough to make you compatible. Details of ASN.1 specification
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changes are listed below.
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There has been considerable development of the toolkit in other aspects as
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well, many of which are embodied in sequin, the new NCBI direct submission
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tool, which is included in the toolkit as well. In the interest of getting the
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PubMed changes into the specification and developers hands promptly, we have
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not included much on that aspect of this toolkit at this time.
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Changes in the 1996 NCBI ASN.1 (version 5.0) specification
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Once again, there are very few changes to the NCBI ASN.1 specification this
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year. The biggest change is the addition of the PubMed ID to support the new
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NCBI PubMed database. There are also small additions to the medline and
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organism specifications, detailed below. As usual, these changes are also
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backward compatible with old data. However, you should recompile and relink
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your applications as soon as possible, since the old applications will not be
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compatible with the new datatypes.
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1) PubMed - NCBI is building a new citation database that is a superset of
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MEDLINE and which will be linked to online journals from publishers. The
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bibliographic components of the specification have had support for PubMed IDs
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added. These include biblio.asn (objbibli.[ch]), pub.asn (objpub.[ch]),
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medline.asn (objmedli.[ch]).
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2) pub-type - MEDLINE includes strings indicating the type of a publication.
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The medline definition has had the attribute pub-type added to support these
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strings.
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From the 1996 MeSH, here's the list.
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Abstract
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Bibliography
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Classical Article
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Clinical Conference
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Clinical Trial
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Clinical Trial, Phase I
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Clinical Trial, Phase II
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Clinical Trial, Phase III
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Clinical Trial, Phase IV
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Comment
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Consensus Development Conference
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Consensus Development Conference, NIH
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Controlled Clinical Trial
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Corrected and Republished Article
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Current Biog-Obit
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Dictionary
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Directory
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Duplicate Publication
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Editorial
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Festschrift
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Guideline
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Historical Article
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Historical Biography
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Interview
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Journal Article
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Legal Brief
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Letter
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Meeting Report
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Meta-Analysis
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Monograph
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Multicenter Study
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News
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Newspaper Article
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Overall
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Periodical Index
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Practice Guideline
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Published Erratum
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Randomized Controlled Trial
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Retracted Publication
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Retraction of Publication
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Review
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Review Literature
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Review of Reported Cases
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Review, Academic
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Review, Multicase
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Review, Tutorial
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Scientific Integrity Review
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Technical Report
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Twin Study
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3) virion - the attribute virion has been added to BioSource.genome. It just
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complements proviral which was already there. This will map to a /virion
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qualifier in the new GenBank feature table definition.
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4) division - OrgName.div now (optionally) can contain the GenBank division code
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(eg. PRI).
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5) signal-peptide, transit-peptide - were added to Prot-ref, to support
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annotation of protein features on the protein sequence in a way that could be
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mapped to a GenBank feature table.
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That's all. Relevant sections of the asn.1 specification are shown below.
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================================================================================
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biblio.asn
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PubMedId ::= INTEGER -- Id from the PubMed database at NCBI
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and..
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Cit-gen ::= SEQUENCE { -- NOT from ANSI, this is a catchall
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cit VisibleString OPTIONAL , -- anything, not parsable
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authors Auth-list OPTIONAL ,
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muid INTEGER OPTIONAL , -- medline uid
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journal Title OPTIONAL ,
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volume VisibleString OPTIONAL ,
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issue VisibleString OPTIONAL ,
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pages VisibleString OPTIONAL ,
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date Date OPTIONAL ,
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serial-number INTEGER OPTIONAL , -- for GenBank style references
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title VisibleString OPTIONAL , -- eg. cit="unpublished",title="title"
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pmid PubMedId OPTIONAL } -- PubMed Id
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pub.asn
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Pub ::= CHOICE {
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gen Cit-gen , -- general or generic unparsed
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sub Cit-sub , -- submission
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medline Medline-entry ,
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muid INTEGER , -- medline uid
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article Cit-art ,
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journal Cit-jour ,
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book Cit-book ,
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proc Cit-proc , -- proceedings of a meeting
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patent Cit-pat ,
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pat-id Id-pat , -- identify a patent
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man Cit-let , -- manuscript, thesis, or letter
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equiv Pub-equiv, -- to cite a variety of ways
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pmid PubMedId } -- PubMedId
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medline.asn
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-- a MEDLINE or PubMed entry
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Medline-entry ::= SEQUENCE {
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uid INTEGER OPTIONAL , -- MEDLINE UID, sometimes not yet available if
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from PubMed
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em Date , -- Entry Month
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cit Cit-art , -- article citation
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abstract VisibleString OPTIONAL ,
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mesh SET OF Medline-mesh OPTIONAL ,
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substance SET OF Medline-rn OPTIONAL ,
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xref SET OF Medline-si OPTIONAL ,
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idnum SET OF VisibleString OPTIONAL , -- ID Number (grants, contracts)
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gene SET OF VisibleString OPTIONAL ,
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pmid PubMedId OPTIONAL , -- MEDLINE records may include
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the PubMedId
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pub-type SET OF VisibleString OPTIONAL } -- may show publication types
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(review, etc)
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seqfeat.asn
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OrgName ::= SEQUENCE {
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name CHOICE {
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binomial BinomialOrgName , -- genus/species type name
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virus VisibleString , -- virus names are different
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hybrid MultiOrgName , -- hybrid between organisms
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namedhybrid BinomialOrgName , -- some hybrids have genus x species
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name
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partial PartialOrgName } OPTIONAL , -- when genus not known
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attrib VisibleString OPTIONAL , -- attribution of name
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mod SEQUENCE OF OrgMod OPTIONAL ,
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lineage VisibleString OPTIONAL , -- lineage with semicolon separators
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gcode INTEGER OPTIONAL , -- genetic code (see CdRegion)
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mgcode INTEGER OPTIONAL , -- mitochondrial genetic code
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div VisibleString OPTIONAL } -- GenBank division code
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BioSource ::= SEQUENCE {
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genome INTEGER { -- biological context
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unknown (0) ,
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genomic (1) ,
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chloroplast (2) ,
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chromoplast (3) ,
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kinetoplast (4) ,
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mitochondrion (5) ,
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plastid (6) ,
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macronuclear (7) ,
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extrachrom (8) ,
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plasmid (9) ,
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transposon (10) ,
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insertion-seq (11) ,
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cyanelle (12) ,
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proviral (13) ,
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virion (14) } DEFAULT unknown ,
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origin INTEGER {
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unknown (0) ,
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natural (1) , -- normal biological entity
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natmut (2) , -- naturally occurring mutant
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mut (3) , -- artificially mutagenized
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artificial (4) , -- artificially engineered
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synthetic (5) , -- purely synthetic
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other (255) } DEFAULT unknown ,
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org Org-ref ,
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subtype SEQUENCE OF SubSource OPTIONAL }
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Prot-ref ::= SEQUENCE {
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name SET OF VisibleString OPTIONAL , -- protein name
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desc VisibleString OPTIONAL , -- description (instead of name)
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ec SET OF VisibleString OPTIONAL , -- E.C. number(s)
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activity SET OF VisibleString OPTIONAL , -- activities
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db SET OF Dbtag OPTIONAL , -- ids in other dbases
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processed ENUMERATED { -- processing status
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not-set (0) ,
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preprotein (1) ,
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mature (2) ,
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signal-peptide (3) ,
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transit-peptide (4) } DEFAULT not-set }
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|
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|
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=============================================================================
|
|
Notes from Previous Releases
|
|
=============================================================================
|
|
|
|
New Functions in Version 4.0
|
|
|
|
There are a host of new functions in this release, but as usual we have not
|
|
managed to make time to document them all. Large parts of Sequin are present
|
|
which will be announced and described more fully in the fall. However,
|
|
specific tools of immediate interest are:
|
|
|
|
blast2 - this is the long awaited BLAST client/server which permits structured
|
|
interaction with BLAST over the internet. We have provided a basic client
|
|
that produces the traditional blast output. In addition, the function call
|
|
interface can be used in more elaborate clients. For more information
|
|
contact Tom Madden, madden@ncbi.nlm.nih.gov
|
|
|
|
WARNING!!! blast2 is the client we plan to support on the longer term.
|
|
The blast1 client we included for those of you who wanted a head start
|
|
will NOT be supported in future. Please shift any blast1 clients to the
|
|
(very similar) blast2 interface as soon as possible.
|
|
|
|
sim, sim2 - protein and DNA sequence alignments in linear space. This is
|
|
the function call interface to these valuable tools. Applications have
|
|
been written which are available by ftp as are published papers. For more
|
|
information contact Jinghui Zhang, zjing@ncbi.nlm.nih.gov
|
|
|
|
|
|
|
|
|
|
Changes in ASN.1 spec 4.0 from 3.0
|
|
|
|
|
|
Affil - biblio.asn
|
|
added the field "postal-code" for Zip code finally.
|
|
|
|
Contact-info - submit.asn
|
|
added the field "contact" which is type "Author". The contact info has
|
|
evolved into a fully structured form, so I just took Author which has
|
|
structured names and structured address (Affil). We will eventually
|
|
phase out all the less structured ones in Contact-info.
|
|
|
|
OrgName - sefeat.asn
|
|
added "lineage", "gcode", "mgcode" for the lineage, genetic code, and
|
|
mitochondrial genetic code. This is part of Org-ref, and consolidates
|
|
all the organism info (except original SOURCE line) out of the
|
|
GenBank block... and enables us to deliver it nicely from Taxon.
|
|
|
|
Seq-descr - seq.asn
|
|
removed the Seq-descr "neighbors" and replaced it with "dbxref", since
|
|
neighbors has never been used. This is used to add cross-references to
|
|
the whole entry.
|
|
|
|
Pubdesc - seq.asn
|
|
has an added slot, "reftype" which is an integer and is used to
|
|
indicate the GenBank usage of a reference.
|
|
|
|
0 - seq - applies to the sequence. This is default and they way it is
|
|
used now.
|
|
1 - sites - applies to (unspecified) features. Equivalent to a GenBank
|
|
SITES feature. We could switch to this from using the
|
|
Imp-feat we do now.
|
|
2 - feats - applies to specific features. The idea here is provide a
|
|
place for the full citation, so features nead only reference
|
|
it. If now features reference it should be removed. This
|
|
would work for checking content when only a part of a sequence
|
|
is copied or pasted. A "sites" ref could not have this check
|
|
since we do not know which features it goes to.
|
|
|
|
Seq-feat - seqfeat.asn
|
|
added a slot called "dbxref" to Seq-feat. This is a SET OF Dbtag. It will
|
|
be for adding the new db_xref qualifiers to features. We already have some
|
|
of these in the xref slots of Gene-ref, Prot-ref, Org-ref. It means we ahve
|
|
to check two places in these cases. I do not want to retire the slots
|
|
since these were meant to be used in other contexts besides features.. and
|
|
Org-ref already is.
|
|
|
|
|
|
added a slot called "anticodon" to the tRNA extension of the RNA feature.
|
|
This is a Seq-loc that points to the location of the anticodon in a tRNA.
|
|
We have been populating this data in a User-object, and will have to do
|
|
a retro to convert it.
|
|
|
|
EXPORTED Genetic-code
|
|
|
|
|
|
Seq-align - seqalign.asn
|
|
|
|
added "bounds" to Seq-align so you can record the regions over which
|
|
an alignment was computed.. not always included in the resulting alignment
|
|
itself.
|
|
|
|
added two new types:
|
|
A) Packed-seg -- a denser representation from Colombe and Jinghui
|
|
B) disc - discontinuous alignments as a SEQUENCE OF Seq-align
|
|
|
|
|
|
Seq-annot - seq.asn
|
|
|
|
added a field to Seq-annot, Align-def, to discriminate types of
|
|
alignment sets. This has the advantage of minimal changes as well as
|
|
separating sets of alignments from conceptually single alignments. I am
|
|
not sure it is necessary to distinguish "alt" from "blocks" though. Also
|
|
it means you can attach more info, with other Seq-annot fields and/or by
|
|
expanding the Align-def. I put in "ids" in Align-def specifically to put
|
|
the one Seq-id that is the "master" for type "ref". I made it a SET OF
|
|
so we could use it for other collections where we might want to list
|
|
more than one.
|
|
|
|
added "ids" and "locs" as allowed types within Seq-annot. This would
|
|
enable us to pass lists like this around between tools with all the
|
|
addtional descriptive information in Annotdesc. I know this will be
|
|
useful.
|
|
|
|
added "general" to Annot-id for tracking 3rd party annotations.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Introduction
|
|
|
|
This distribution is release 5.0 of the NCBI core library for building
|
|
portable software, and AsnLib, a collection of routines for handling ASN.1
|
|
data and developing ASN.1 software applications. AsnLib and the asntool
|
|
application are built using the CoreLib routines. In the \doc directory is an
|
|
MS Word file which details the information given below. It is also available
|
|
as hardcopy. See the README in \doc.
|
|
|
|
The lowest layer of code is the CoreLib. These are multi-
|
|
platform functions for memory allocation (including byte stores), string
|
|
manipulation, file input and output, error and general messages, and
|
|
time and date notification. These functions have been written only
|
|
where we found that the existing ANSI functions were not sufficiently
|
|
multi-platform or well- behaved among all of the platforms that we
|
|
support. For each platform (a combination of processor, operating
|
|
system, compiler, and windowing system), we supply a specific ncbilcl.h
|
|
file, which contains typedefs and defines for multi-platform symbols,
|
|
and includes a number of standard header files. (For example,
|
|
ncbilcl.msw is used for the Microsoft C compiler under Microsoft Windows
|
|
on the PC.) Use of these symbols, and of the functions in the CoreLib,
|
|
allow us to write multi-platform source code for a variety of disparate
|
|
platforms.
|
|
|
|
The next layer of code is the AsnLib stream reader. This is
|
|
used in conjunction with a header file and a parse table loader file,
|
|
both of which are produced by processing the formal ASN.1 specification
|
|
with the AsnTool application. The symbolic defines in the
|
|
header file are pointers into the parse table, in which the ASN.1
|
|
specification is represented. To read at the stream reader level, a
|
|
program alternates between calls to AsnReadId and AsnReadVal. AsnReadId
|
|
returns a pointer into the parse table, which can be compared against
|
|
the defines in the AsnTool-generated header. For example, in the
|
|
specification for MEDLINE records, the Medline-entry section has an item
|
|
called "uid", for the unique ID of the record. This is symbolized in
|
|
the header file as MEDLINE_ENTRY_uid. When AsnReadId returns this
|
|
symbol, the program calls AsnReadVal to obtain the uid for that record.
|
|
AsnKillValue is also needed to free any memory allocated by AsnReadVal,
|
|
which occurs when the value is a string and not an integer. The entire
|
|
set of records on the Entrez CD-ROM can be read as a single stream with
|
|
the AsnLib functions.
|
|
|
|
The ASN.1 records may be accessed at a higher level through the object
|
|
loaders, which utilize the stream processing functions to
|
|
load C memory structures with the contents of the ASN.1 objects. For
|
|
each ASN.1 object we specify, we also define an equivalent C memory
|
|
structure. The object loader level of code contains functions to read
|
|
and write each ASN.1 object. These are hierarchical, as are the ASN.1
|
|
specifications. Calling the top level loader, SeqEntryAsnRead, will
|
|
load an entire SeqEntry from an open AsnIo channel, and will return a
|
|
pointer to the loaded memory structure. The read function for an AsnIo
|
|
channel can be swapped to refer to a normal disk file, a network socket,
|
|
or to compressed data, which it automatically decompresses. The object
|
|
loader code can interconvert between the highly-branched memory object
|
|
and a linear ASN.1 message with complete fidelity. The object loaders
|
|
have additional functions, including the ability to explore the
|
|
structure and notify the program when particular data elements are
|
|
encountered. The entire contents of the Entrez CD-ROM can also be
|
|
streamed through the object loaders. However, most calls to the object
|
|
loaders for simply reading a particular record are done via the data
|
|
access functions (see below).
|
|
|
|
The data access functions allow a program to call the object loaders on
|
|
a sequence or MEDLINE record given the uid of the record.
|
|
This will get the data into memory regardless of whether the data are
|
|
compressed on the Entrez CD-ROM or are obtained through a service over
|
|
the Internet. This means that a detailed understanding of the files and
|
|
formats on the Entrez disc is not needed by application programmers. The
|
|
function to load a sequence record, SeqEntryGet, needs the uid to
|
|
retrieve and a complexity code parameter. A sequence record is in the
|
|
form of a NucProt set. This contains a nucleotide (which may itself be
|
|
composed of segments) and all of the proteins it is known to encode.
|
|
The set of segments is called a SegSet, and the individual sequences are
|
|
called BioSeqs. We have taken the liberty of producing this integrated
|
|
view, but the complexity code parameter allows the record to be easily
|
|
loaded in a simpler, more traditional form, if desired. The accession
|
|
number term list is built to supply the proper uids to support this
|
|
facility. This access library is compatible with Entrez release 1.0 or
|
|
later only.
|
|
|
|
The sequence utilities and application programmer interface layer
|
|
allows exploration of the loaded memory structures and
|
|
generation of standard literature or sequence reports from those
|
|
objects. For example, a BioSeq can be converted to FASTA or GenBank
|
|
flat file formats and saved to a file, and a MEDLINE record can be saved
|
|
in MEDLARS format, which is suitable for entry into personal
|
|
bibliographic database programs. A sequence port can be opened that
|
|
gives a simple, linear view of a segmented sequence, converting
|
|
alphabets, merging exon segments, and dealing with information on both
|
|
strands of the DNA. This layer also includes some functions to explore
|
|
the NucProt set. The explore functions visit each individual BioSeq in
|
|
the set, calling a callback function for each sequence node so that a
|
|
program can examine feature tables and other information that are
|
|
associated with the NucProt or SegSets or with the individual sequences.
|
|
|
|
Vibrant is a multi-platform user interface development library that runs
|
|
on the Macintosh, Microsoft Windows on the PC, or X11 and OSF/Motif on
|
|
UNIX and VAX computers [separate documentation]. It is used to build
|
|
the graphical interface for the Entrez application (whose source code is
|
|
in the browser directory). The philosophy behind Vibrant is that
|
|
everything in the published user interface guidelines (the generic
|
|
behavior of windows, menus, buttons, etc.), as well as positioning and
|
|
sizing of graphical control objects, is taken care of automatically.
|
|
The program provides callback functions that are notified when the user
|
|
has manipulated an object. Vibrant and Entrez code are not supported,
|
|
but are provided on an as-is basis.
|
|
|
|
The advantage of using AsnLib and the object loaders, as they are
|
|
implemented, is that application program developers merely need to
|
|
recompile their programs with the new (AsnTool-generated) header files
|
|
and load the new parse tables (included with the Entrez software) in
|
|
order to be able to read the new data. This process is straightforward,
|
|
and will not break existing program code. The application is free to
|
|
ignore new fields if it does not choose to take advantage of the new
|
|
kinds of information.
|
|
|
|
When developing new ASN.1 specifications, as of June 1994 it is possible to
|
|
automatically generate the object loaders and header files for those
|
|
specifications, using the AsnCode utility. For some complex ASN.1
|
|
specifications, however, AsnCode may fail to generate the correct source code.
|
|
|
|
The documentation is currently being brought up to date. The programs
|
|
in the demo directory are designed to teach the proper use of many of
|
|
the functions discussed above. Many of these programs are not yet
|
|
documented. The simplest is testcore.c, which tests various functions
|
|
in the CoreLib. The most complex is getfeat.c, which takes an accession
|
|
number of locus name, determines the unique seq ID, retrieves the entry
|
|
from the Entrez CD-ROM using the data access library, locates all coding
|
|
region features using the explore functions, and prints the DNA
|
|
sequences of all exons using sequence port functions. If you cannot
|
|
extract and print the doc.tar.Z file, please send an email message with
|
|
your land mailing address and phone number to toolbox@ncbi.nlm.nih.gov,
|
|
and we will mail a copy to you.
|
|
|
|
The contents of the ncbi directory (the highest level, containing the
|
|
NCBI Software Development Kit source code in several subdirectories) is
|
|
shown below. The readme file contains instructions on copying the
|
|
appropriate make files to be built in the build directory. The makeall
|
|
file copies headers to the include directory builds four libraries
|
|
(ncbi, ncbiobj, ncbicdr and vibrant), copying them to the lib directory.
|
|
The makedemo file builds the demo programs and the Entrez application:
|
|
|
|
api Application Programmer Interface, Sequence Utilities
|
|
asn ASN.1 specifications for publications and sequences
|
|
asnlib Source code for AsnLib and asntool
|
|
asnload AsnLib headers and dynamic parse tables (Mac and PC)
|
|
asnstat AsnLib headers that use static memory (UNIX and VMS)
|
|
bin Asntool executable copied here
|
|
biostruc Source code for Molecular Modelling DataBase functions
|
|
browser Source code for Entrez application
|
|
build Empty directory for building tools and libraries
|
|
cdromlib Access routines for data on the Entrez CD-ROM
|
|
cn3d Source code for Vibrant-based 3D structure viewer
|
|
config Configuration files for NCBI software:
|
|
mac
|
|
unix
|
|
vms
|
|
win
|
|
corelib Source code for NCBI Core Software Library
|
|
data Data files used for sequence conversion
|
|
demo AsnLib and sequence utility demonstration programs
|
|
desktop Source code for Vibrant-based viewers and editors
|
|
doc Documentation in Microsoft Word file
|
|
include Include files required by applications are copied here
|
|
lib Libraries copied here
|
|
link Contains several subdirectories with build accessory files:
|
|
macmet Macintosh Metrowerks/CodeWarrior
|
|
macmpw Macintosh MPW C
|
|
mswin Microsoft C and Borland C for Windows
|
|
make Make files for various systems
|
|
network Network version of data access
|
|
apple
|
|
blast2
|
|
encrypt
|
|
entrez
|
|
netmanag
|
|
nsclilib
|
|
object Functions for reading and writing complex objects
|
|
sequin Source code for Sequin application
|
|
tools Source code for alignment and other contributed utilities
|
|
readme File that contains important building instructions
|
|
vibrant Source code for Vibrant portable interface package
|
|
|
|
The platforms that are supported (as indicated by the suffix on the
|
|
relevant ncbilcl.h file) are shown below. Those marked with an asterisk
|
|
(*) are available as-is:
|
|
|
|
370* IBM 370
|
|
acc SUN acc compiler
|
|
alf DEC Alpha under OSF/1
|
|
aov DEC Alpha under AXP/OpenVMS
|
|
aux* Macintosh A/UX
|
|
bor Borland for DOS
|
|
bwn Borland for Microsoft Windows
|
|
ccr CenterLine CodeCenter
|
|
cpp SUN C++
|
|
cra* Cray
|
|
cvx* Convex
|
|
gcc Gnu gcc (under SunOS, not Solaris)
|
|
hp * Hewlett Packard
|
|
lna* Linux on DEC Alpha
|
|
lnx Linux (RedHat Linux release 5.2 with kernel 2.0.36)
|
|
met Macintosh Metrowerks compiler
|
|
mpw Macintosh Programmer's Workshop
|
|
msc Microsoft C for DOS
|
|
msw Microsoft for Windows
|
|
nxt* NeXT
|
|
r6k* IBM RS 6000
|
|
scr CodeCenter under Sun Solaris
|
|
sgi Silicon Graphics
|
|
sin Sun Solaris on Intel processors
|
|
sol Sun Solaris (for cc and gcc)
|
|
thc THINK C on Macintosh
|
|
ult DEC ULTRIX
|
|
vms DEC VAX/VMS
|
|
|
|
Questions or comments can be directed to toolbox@ncbi.nlm.nih.gov.
|
|
|
|
ANSI C:
|
|
|
|
This software requires an ANSI C compiler. This will be no problem at
|
|
all except to people on Sun machines, where the bundled C compiler, cc, is
|
|
non-ansi. However, you can use the Sun unbundled compiler, acc, or the Gnu
|
|
compiler, gcc (which is free) and that works just fine. If you have written
|
|
applications on the Sun with non-ANSI functions, the ANSI compilers will
|
|
complain. See the notes below if this is a problem.
|
|
|
|
|
|
Installation
|
|
|
|
To build the NCBI toolkit you need to look for platform-dependent instructions:
|
|
For UNIX:
|
|
look at the file make/readme.unx
|
|
For Mac:
|
|
look at the file make/readme.mac
|
|
For Microsoft Windows95/98/NT:
|
|
look at the file make/readme.dos
|
|
|
|
There is some information which may be useful for NCBI tookit building
|
|
in the file doc/FAQ.txt
|
|
|
|
ALL -
|
|
change to the directory above ncbi subdirectory
|
|
|
|
Unix
|
|
tested on Sun Sparc (Solaris 2.6, Sunos 4.1.3),
|
|
Silicon Graphics IRIX 5.* and 6.*, DEC Alpha with OSF/1 V5.1,
|
|
Linux (Red Hat Linux release 6.2 with kernel 2.2.16) on Intel,
|
|
Sun Solaris for Intel (Solaris 2.7).
|
|
|
|
Run the script ncbi/make/makedis.csh keeping it's output in the
|
|
separate file:
|
|
for sh or bash:
|
|
ncbi/make/makedis.csh 2>&1 | tee out.makedis.csh
|
|
for csh or tcsh:
|
|
ncbi/make/makedis.csh |& tee out.makedis.csh
|
|
If that script gives you an error like this:
|
|
Your platform is not supported.
|
|
To port ncbi toolkit to your platform consult
|
|
the files platform/*.ncbi.mk
|
|
then you should check the script ncbi/make/makedis.csh and
|
|
add proper platform-dependent ncbi.mk file in ncbi/platform
|
|
directory.
|
|
|
|
Other UNIX: AIX, ULTRIX, NeXt, Sun acc,
|
|
Follows models above. Read header in makeall.unx and makedemo.unx
|
|
for details.
|
|
|
|
for all UNIX, edit .ncbirc as described in section "CONFIGURATION OR
|
|
SETTINGS FILES".
|
|
optional edit .login to "setenv NCBI=[path to .ncbirc file]"
|
|
|
|
MS-DOS
|
|
look at the file make/readme.dos
|
|
|
|
Mac
|
|
tested on CodeWarrior IDE 2.1, MacOS 8.0
|
|
All - copy config:mac:ncbi.cnf to your System Folder, or to the
|
|
System Folder:Preferences subfolder
|
|
edit the "ASNLOAD" line in "ncbi.cnf" to point to the
|
|
ncbi:asnload directory in this release
|
|
edit the "DATA" line to point to the ncbi/data directory
|
|
CodeWarrior - raise Preferred Size of Script Editor from 700 to 3000,
|
|
and raise Preferred Size of CodeWarrior IDE 2.1 by
|
|
2000 (e.g., from 8206 to 10206), using Get Info from
|
|
the Finder.
|
|
to compile for MC680x0 platform (default is PowerPC),
|
|
change property MASTER from "PPC" to "68K".
|
|
run copyhdrs.met
|
|
run makeall.met
|
|
run makenet.met
|
|
run makedemo.met
|
|
Think C - no longer supported
|
|
MPW C - no longer supported
|
|
|
|
Changes to VMS make file naming conventions:
|
|
|
|
The old .dcl prefix (last character is a lower case L) was changed
|
|
to .dc1 (last character is the numeral 1) to allow for different make files
|
|
for DecWindows 1.1 and DecWindows 1.2. Several new .dc2 files were
|
|
contributed by David Mathog of CalTech. A synopsis of his additional
|
|
instructions:
|
|
|
|
VAX C DecWindows 1.1 Use .dcl1 files.
|
|
DEC C DecWindows 1.1 Use .dcl1 files,
|
|
but change cc to cc/standard=vaxc
|
|
VAX C DecWindows 1.2 This combination has not been tested.
|
|
DEC C DecWindows 1.2 Use .dcl2 files.
|
|
|
|
VMS (without Vibrant) on VAX
|
|
$set def [ncbi.build]
|
|
$copy [-.make]*.dc1 *.com
|
|
$@makeall
|
|
|
|
check ncbi.cfg as described in section "CONFIGURATION OR SETTINGS FILES".
|
|
edit LOGIN.COM to "define NCBI [path to ncbi.cfg file]"
|
|
|
|
To make demos:
|
|
$@makedemo
|
|
|
|
VMS (with Vibrant) on VAX
|
|
$set def [ncbi.build]
|
|
$copy [-.make]*.dc1 *.com
|
|
$@viball
|
|
|
|
check ncbi.cfg as described in section "CONFIGURATION OR SETTINGS FILES".
|
|
edit LOGIN.COM to "define NCBI [path to ncbi.cfg file]"
|
|
|
|
To make demos:
|
|
$@vibdemo
|
|
|
|
Testing
|
|
|
|
VMS only: look in rundemo.dc1 in [make] to see how to give command
|
|
line arguments. Not all demo programs are shown. Run at least testcore.
|
|
|
|
All else:
|
|
|
|
In build should be a program called testcore. Type "testcore -" and
|
|
it should show you some default arguments. Type "testcore" and it will
|
|
run through a variety of functions in CoreLib, prompting you for responses
|
|
along the way. It should run without a crash or error report. If you made
|
|
Vibrant versions all demos will have startup dialog boxes. If not, they
|
|
take command line arguments.
|
|
|
|
If testcore runs, read the documentation for CoreLib and for AsnLib.
|
|
In the AsnLib documentation are instructions for running asntool itself.
|
|
for running a few of the demo programs. There are a large number of demo
|
|
programs now (including Entrez itself, if you made the Vibrant versions).
|
|
|
|
|
|
|
|
CONFIGURATION OR SETTINGS FILES:
|
|
|
|
One of the fundamental problems in writing portable software concerns
|
|
configuration issues. Each individual user's computer will have its own
|
|
particular hardware and software environment, and each machine will have
|
|
its disk file hierarchy set up in a unique manner. A program that needs
|
|
accessory information, such as help files, parse tables, or format
|
|
converters, must be given a means of finding the data regardless of where
|
|
the user has placed the files. The difficulty is compounded by the different
|
|
conventions for naming files and specifying paths on each class of machine.
|
|
For example, the name of a CD-ROM on the Macintosh is fixed, determined by
|
|
information on the CD itself, whereas on the PC it is addressed by a drive
|
|
letter, which can be assigned by the user, but which cannot be reconciled
|
|
with the name the Macintosh sees.
|
|
|
|
An associated problem is that many programs will want to allow the user
|
|
to make persistent changes to parameters. These parameters typically involve
|
|
numbers or font specifications, but may also include paths to data files.
|
|
Some platforms supply such configuration information in preferences files,
|
|
others in environment variables. Manipulating these settings is platform
|
|
dependent, as is the format in which the preference is specified.
|
|
|
|
The NCBI Software Toolkit core library addresses these problems by
|
|
providing configuration or settings files. These are modeled after the .INI
|
|
files used by Microsoft Windows. Settings files are plain ASCII text files
|
|
that may be edited by the user or modified by the program. They are divided
|
|
into sections, each of which is headed by the section name enclosed in square
|
|
brackets. Below each section heading is a series of key=value strings, somewhat
|
|
analogous to the environment variables that are used on many platforms.
|
|
|
|
The ncbi configuration file supplies general purpose configuration
|
|
information on paths for commonly used data files. The typical file set up for
|
|
the Entrez application running on the PC under Microsoft Windows is shown below:
|
|
|
|
[NCBI]
|
|
ROOT=D:
|
|
ASNLOAD=C:\ENTREZ\ASNLOAD\
|
|
DATA=C:\ENTREZ\DATA
|
|
|
|
The only section is entitled NCBI. The ROOT entry refers to the path to
|
|
the Entrez CD-ROM. In this example, the user has configured the machine to
|
|
use drive letter D. (On the Macintosh, the name of the disc is SEQDATA, which
|
|
cannot be changed by the user.) The ASNLOAD specifies the path to the ASN.1
|
|
parse tables. These files are required by the AsnLib functions, and all
|
|
higher-level procedures that call them, including the Object Loader, Sequence
|
|
Utility, and Data Access functions. Files pointed to by the DATA entry contain
|
|
information necessary to convert biomolecule sequence data into different
|
|
alphabets (e.g., unpacking the 2-bit nucleotide code stored on the Entrez CD
|
|
into standard IUPAC letters).
|
|
|
|
Although the contents of a configuration file is similar regardless of
|
|
platform, the name of the file and its location is platform dependent. If the
|
|
base name of the configuration file is xxx, then the actual file name is shown
|
|
below for each platform:
|
|
|
|
Macintosh xxx.cnf
|
|
Microsoft Windows xxx.INI
|
|
MS-DOS (without Windows) xxx.CFG
|
|
UNIX .xxxrc
|
|
VMS xxx.cfg
|
|
|
|
Samples of such files are in subdirectories of \config. The UNIX version
|
|
does not have the leading '.' in filename so you can see it.
|
|
|
|
The location in which these files must reside is also platform dependent,
|
|
and the functions that manipulate the contents may look in several places to
|
|
find these files.
|
|
|
|
On the Macintosh, the function first looks in the System Folder, then in the
|
|
Preferences folder within the System Folder. (See the Mac OS X addendum in the
|
|
next paragraph). Under Microsoft Windows, the file must be in the Windows
|
|
directory, along with all of the other .INI files. Under DOS without Windows,
|
|
the function first looks in the current working directory, then in the directory
|
|
whose path is specified in the NCBI environment variable. Under UNIX and VMS,
|
|
the current working directory is first checked, then the user's home directory,
|
|
and finally the directory specified by the NCBI environment variable. (Under
|
|
UNIX, when it uses the environment variable, it will check for configuration
|
|
files first without and then with the initial dot.) On the multi- user
|
|
platforms (UNIX and VMS), the use of the NCBI environment variable allows a
|
|
common settings file to be used as the default by multiple users. If such a
|
|
settings file is changed under program control, it is copied over into the
|
|
user's home directory, and the new copy is modified. The order of searching
|
|
for settings files ensures that this new copy is used in all subsequent
|
|
operations.
|
|
|
|
On Mac OS X, it first looks for xxx.cnf in username/Library/Preferences,
|
|
then in package/Contents/Resources, where username is the user's home directory
|
|
and package is the application package. If it does not find the configuration
|
|
file, it then switches to UNIX style, looking for .xxxrc in the home directory
|
|
and then in the current directory. This way Mac OS X applications retain the
|
|
traditional Mac behavior but can also UNIX style configuration files.
|
|
|
|
|
|
contents of ASNLOAD are in ncbi/asnload
|
|
contents of DATA are in ncbi/data
|
|
|
|
Automatic Generation of code to read and write new ASN.1 messages.
|
|
(Previously, ASNCODE USAGE)
|
|
|
|
'asntool' can now generate code for use as ASN.1 readers and writers.
|
|
This functionality used to be in the program called 'asncode'. There
|
|
is thus no longer any need for the *.l* files. An example of how
|
|
to generate this code follows:
|
|
|
|
|
|
asntool -m YOURSPEC.asn -G -B genYOURSPEC
|
|
|
|
Both genYOURSPEC.h and genYOURSPEC.c will be generated.
|
|
|
|
Within asn ASN.1 definitions, types can be EXPORTed and IMPORTed.
|
|
If YOURSPEC.asn imports definitions from otherspec.asn then it has
|
|
to be added to the -m parameter as below. Note that code is only
|
|
generated for the first file.
|
|
|
|
asntool -m YOURSPEC.asn,otherspec.asn -G -B genYOURSPEC
|
|
^
|
|
|
|
Notice the lack of a blank at the caret (^), above. This is important.
|
|
|
|
|
|
MAJOR CHANGES FROM DOCUMENTATION:
|
|
|
|
AsnNode structures have proved to be generally useful and moved from AsnLib
|
|
to ncbimisc. In addition, some elements of structs used in the object loaders
|
|
were called "class" to match the ASN.1 names. Class is a C++ reserved word,
|
|
so all instances of "class" have been changed to "_class".
|
|
|
|
To conform to our naming conventions, we have changed the names appropriately:
|
|
|
|
AsnValue = DataVal
|
|
AsnNode = ValNode
|
|
class = _class
|
|
|
|
A global search and replace of your code with these strings (not restricted
|
|
to words... we want to change AsnNodePtr = ValNodePtr as well) should fix
|
|
any problems. Field names within structures have not been changed. If your
|
|
code uses only the object loaders, you may not find these strings in your
|
|
code at all.
|
|
|
|
DATA ACCESS LIBRARIES
|
|
|
|
cdromlib contains data access routines compatible with release 1.0-6.0
|
|
of the Entrez CDROM. The documentation for these functions are out of
|
|
date. The routines in cdromlib have been split into entrez, sequence, and
|
|
medline access functions. The interface you should normally program to is
|
|
defined in accentr.[ch]. The form of this calls has been changed to make
|
|
them compatible with the NCBI network server, a client/server version of
|
|
data access. A program written to use these calls can access the the cdrom
|
|
data, the network data, a combination, or that plus a local database by just
|
|
fiddling with defines. The form of the api for these functions has also
|
|
been changed to hide the details of storage and caching more so that the
|
|
different optimizations done to support cdrom and network access are
|
|
transparent to the application programmer. The end user tool called
|
|
"Entrez" now uses these libraries as it's only means of data access (i.e.,
|
|
you can write an application of your own with any or all of Entrez's
|
|
functionality using just these routines).
|
|
|
|
NETWORK LIBRARIES
|
|
|
|
The toolbox now includes NCBI "Network Services". This includes
|
|
everything which you need to build your own "Network Entrez" client software.
|
|
The network libraries include a generic network services library (nsclilib),
|
|
which is used to contact the network services dispatcher and connect to a
|
|
desired server. Note that some development platforms require that you obtain
|
|
a few source modules from external vendors. Look at the README files
|
|
contained in the network directory (network/*/README) for more details.
|
|
|
|
|
|
DOCUMENTATION
|
|
|
|
We are rewriting the documentation to conform with all the new features
|
|
contained in this software. We will add it to the package as soon as possible.
|
|
|
|
DEMO PROGRAMS
|
|
|
|
As in the tools, there are a number of undocumented programs in the demo
|
|
directory as well, that use a number of the utility functions in api. There
|
|
is also a demo program called "getseq" in the cdromlib directory which
|
|
retrieves a sequence from the cdrom given any valid sequence id. These will
|
|
be described in more detail in the next set of documentation. Briefly:
|
|
|
|
asn2ff.c converts ASN.1 to GenBank flatfile
|
|
asn2rpt.c converts ASN.1 to human readable report
|
|
dosimple.c converts ASN.1 to a "simple sequence"
|
|
getseq.c gets sequence from Entrez Cdrom using data access library,
|
|
writes to disk
|
|
getfeat.c ditto, but writes sequence of any CdRegion features to
|
|
"test.out"
|
|
getmesh.c documented
|
|
getpub.c documented
|
|
indexpub.c documented
|
|
seqtest.c reads ASN.1 sequence, converts to iupac, reports segmented
|
|
sequences, outputs fasta format to seqtest.out
|
|
testcore.c documented
|
|
testobj.c tests Medline object loader, demonstrates error checking using
|
|
NULL asnio stream.
|
|
entrez If Vibrant is installed, the full Entrez program is made.
|
|
asndhuff Demonstrates streaming ASN.1 data from the huffman compressed
|
|
Entrez CDROM (only works on release 1.0 or later).
|
|
entrcmd Standalone non-interactive tool for accessing Entrez data.
|
|
Entrcmd is the search engine used for NCBI's Entrez WWW server.
|
|
asncode Tool for generating object loader source code given a .l
|
|
file which is the output of AsnTool.
|
|
cdscan scans entrez cdrom, makes GenBank, GenPept, or FASTA format
|
|
output. Also has a slot for a replaceable CustomRoutine
|
|
supplied by you. Has two examples of such routines.
|
|
|
|
CALLBACK CONVENTIONS
|
|
|
|
The CoreLib, AsnLib, and Object Loader routines have been converted to use
|
|
the LIBCALL and LIBCALLBACK symbols (FAR PASCAL) on the PC for Windows. This will
|
|
allow us to build dynamic link libraries (DLLs) so that the code can be accessed
|
|
from languages other than C. Callback functions you write that are of types
|
|
AsnOptFreeFunc, AsnExpOptFunc, IoFuncType, AsnReadFunc, AsnWriteFunc, and
|
|
SeqEntryFunc, should be declared using the LIBCALLBACK macro. For example, a
|
|
callback used as an AsnOptFreeFunc should be declared as follows:
|
|
|
|
static Pointer LIBCALLBACK MyOptFreeFunc (Pointer);
|
|
|
|
The SeqEntryFunc callback used by SeqEntryExplore has not yet been modified to
|
|
use the LIBCALLBACK type. This will be added in the near future.
|
|
|
|
</pre>
|
|
<pre class="filecontent-num">
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0001" name="0001">0001</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0002" name="0002">0002</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0003" name="0003">0003</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0004" name="0004">0004</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0005" name="0005">0005</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0006" name="0006">0006</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0007" name="0007">0007</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0008" name="0008">0008</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0009" name="0009">0009</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0010" name="0010">0010</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0011" name="0011">0011</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0012" name="0012">0012</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0013" name="0013">0013</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0014" name="0014">0014</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0015" name="0015">0015</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0016" name="0016">0016</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0017" name="0017">0017</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0018" name="0018">0018</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0019" name="0019">0019</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0020" name="0020">0020</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0021" name="0021">0021</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0022" name="0022">0022</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0023" name="0023">0023</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0024" name="0024">0024</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0025" name="0025">0025</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0026" name="0026">0026</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0027" name="0027">0027</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0028" name="0028">0028</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0029" name="0029">0029</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0030" name="0030">0030</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0031" name="0031">0031</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0032" name="0032">0032</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0033" name="0033">0033</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0034" name="0034">0034</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0035" name="0035">0035</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0036" name="0036">0036</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0037" name="0037">0037</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0038" name="0038">0038</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0039" name="0039">0039</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0040" name="0040">0040</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0041" name="0041">0041</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0042" name="0042">0042</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0043" name="0043">0043</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0044" name="0044">0044</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0045" name="0045">0045</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0046" name="0046">0046</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0047" name="0047">0047</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0048" name="0048">0048</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0049" name="0049">0049</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0050" name="0050">0050</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0051" name="0051">0051</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0052" name="0052">0052</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0053" name="0053">0053</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0054" name="0054">0054</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0055" name="0055">0055</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0056" name="0056">0056</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0057" name="0057">0057</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0058" name="0058">0058</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0059" name="0059">0059</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0060" name="0060">0060</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0061" name="0061">0061</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0062" name="0062">0062</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0063" name="0063">0063</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0064" name="0064">0064</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0065" name="0065">0065</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0066" name="0066">0066</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0067" name="0067">0067</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0068" name="0068">0068</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0069" name="0069">0069</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0070" name="0070">0070</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0071" name="0071">0071</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0072" name="0072">0072</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0073" name="0073">0073</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0074" name="0074">0074</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0075" name="0075">0075</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0076" name="0076">0076</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0077" name="0077">0077</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0078" name="0078">0078</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0079" name="0079">0079</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0080" name="0080">0080</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0081" name="0081">0081</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0082" name="0082">0082</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0083" name="0083">0083</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0084" name="0084">0084</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0085" name="0085">0085</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0086" name="0086">0086</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0087" name="0087">0087</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0088" name="0088">0088</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0089" name="0089">0089</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#0090" name="0090">0090</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1112" name="1112">1112</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1113" name="1113">1113</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1114" name="1114">1114</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1115" name="1115">1115</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1116" name="1116">1116</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1117" name="1117">1117</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1118" name="1118">1118</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1119" name="1119">1119</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1120" name="1120">1120</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1121" name="1121">1121</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1122" name="1122">1122</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1123" name="1123">1123</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1124" name="1124">1124</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1125" name="1125">1125</a>
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<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/readme#1126" name="1126">1126</a>
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