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<TITLE> [C++ Toolkit ANNOUNCE] NCBI C++ Toolkit Release (April 2, 2003)
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<H1>[C++ Toolkit ANNOUNCE] NCBI C++ Toolkit Release (April 2, 2003)</H1>
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<!--htdig_noindex-->
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<B>Denis Vakatov</B>
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<A HREF="mailto:cpp-announce%40ncbi.nlm.nih.gov?Subject=%5BC%2B%2B%20Toolkit%20ANNOUNCE%5D%20NCBI%20C%2B%2B%20Toolkit%20Release%20%28April%202%2C%202003%29&In-Reply-To="
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TITLE="[C++ Toolkit ANNOUNCE] NCBI C++ Toolkit Release (April 2, 2003)">vakatov at ncbi.nlm.nih.gov
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</A><BR>
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<I>Wed Apr 16 17:08:26 EDT 2003</I>
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<P><UL>
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<LI>Previous message: <A HREF="000079.html">[C++ Toolkit ANNOUNCE]
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Public pre-Release of the C++ Toolkit sources (More on the topic)
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<!--beginarticle-->
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<PRE>The newest release of the NCBI C++ Toolkit is available at:
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<A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/">ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/</A>
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It includes tarballs for UNIX, MS-Window and Darwin.
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A large (and yet incomplete) list of significant changes in the
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Toolkit's API and functionality can be found in:
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<A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/RELEASE_NOTES">ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/RELEASE_NOTES</A>
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The current version of RELEASE_NOTES goes here:
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#############################################################################
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NCBI C++ Toolkit Release (April 2, 2003)
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#############################################################################
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*** DOWNLOAD
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<A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/Apr_2_2003/">ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/Apr_2_2003/</A>
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#############################################################################
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*** CONTENT
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Source code archives:
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ncbi_cxx_unix.tar.gz -- for UNIX'es (see the list of UNIX flavors below)
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ncbi_cxx_mac_cw.sit -- for MacOS 10.X / CodeWarrior 8.0 Update 8.3
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ncbi_cxx_macosx.tar.gz -- for MacOS 10.X / GCC 3.1
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ncbi_cxx_win.exe -- for MS-Windows / MSVC++ 6.0 (self-extracting)
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ncbi_cxx_win.zip -- for MS-Windows / MSVC++ 6.0
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Other:
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RELEASE_NOTES -- this file
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timestamp -- when the sources were checked out of the CVS
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#############################################################################
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*** NEW DEVELOPMENTS -- LIBRARIES
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------------------------------------------------------------------
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+++++ CoreLib +++++ (corelib)
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1. Redesigned CRef<>:
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A) constructor made explicit,
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B) const CRef<> now returns const reference to the object.
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2. Remplemented CPipe, enabled it for "windows" subsystem under MS-Windows.
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3. Multiple fixes and extentions in the NStr:: string manipulation functions.
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------------------------------------------------------------------
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+++++ Data streaming, Networking, and Dispatching +++++ (connect)
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1. Implemented C++ API for sockets (based on the "C" SOCK API).
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2. "C" SOCK API to support UDP (datagram) sockets.
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3. Put in a draft implementation of C++ datagram socket API.
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4. These two went to the 'util' library:
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A) CStreamUtils::Readsome() -- a portable substitute to
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'istream::readsome' method, which also tries its best to
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behave reasonably when reading from a non-blocking source.
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B) CStreamUtils::Pushback() -- to put an arbitrary block of data
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"back" to the standard C++ 'istream'.
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------------------------------------------------------------------
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+++++ Database Connectivity (DBAPI) +++++ (dbapi)
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1. Adapted FreeTDS version 8 (see LICENSE file to use it) to be built
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as a part of the Toolkit (FreeTDS driver -- on UNIX only).
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2. Added projects to build DBAPI drivers as DLLs on MS-Win/MSVC++:
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CTLib, DBLib, MSDBLib, and ODBC.
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------------------------------------------------------------------
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+++++ CGI/FastCGI Framework +++++ (dbapi)
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1. Improved and extended logging and statistics.
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2. Added "Cookie affinity" support.
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3. Allow for a graceful break of FastCGI loop using a "watch file".
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4. CCgiApp -- added new methods GetFCgiIteration() and IsFastCGI().
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------------------------------------------------------------------
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+++++ Data Serialization +++++ (serial)
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1. XML streams now support serialization of objects which are generated by
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a DTD specification (see also +Datatool+ below).
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2. Added type-info structures and functions for CTime.
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------------------------------------------------------------------
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+++++ Object Manager +++++ (objects/objmgr)
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1. Reimplemented CSeqMap class for working with sequence maps.
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A) Performance improved significantly for large segmented sequences.
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B) Sequence map iterator CSeqMap_CI implemented for efficient browsing
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and iteration of sequence map segments.
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2. Reimplemented CSeqVector class for working with sequence data.
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A) Sequence map iterator CSeqMap_CI was used for efficient access to
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data segments.
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B) Performance improved significantly by efficient use of inlined methods.
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3. Rewrote several inefficient methods of CHandleRange and
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CHandleRangeMap classes.
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4. Changed in CScope:
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A) Optimized communication with CDataSource by adding several
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data/index caches.
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B) Added priorities to data sources.
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5. Rewrote CFeat_CI, CAlign_CI and CGraph_CI:
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A) Performance of feature iterator increased more then order of magnitude:
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a) CFeat_CI and CGraph_CI return temporary objects instead of mapped
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CSeq_feat or CSeq_graph,
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b) Feature gathering and location mapping is performed in one pass,
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c) Added several cached indexes,
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d) Soring of features is performed at the end of feature gathering
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inside resulting vector<>,
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e) Highly optimized feature sorting function.
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B) Implemented lots of addditional tuning flags for feature iterator like:
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a) Several level of sequence map selection for features gathering,
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b) Several level of restriction of feature source location,
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c) Different sorting methods.
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6. Added top level Seq-entry iterator to CScope (CTSE_CI).
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7. Added possibility to remove or replace annotations in seq-entries indexed
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by CDataSource.
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8. Added CBioseq_Handle::GetComplexityLevel() method returning Seq-entry of
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required complexity.
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9. Renamed test applications and adjusted makefiles to match the source
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file names. Added a script and adjusted makefiles to run loader-related
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tests through different database interfaces (ID1 and PubSeq).
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------------------------------------------------------------------
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+++++ Alignment Manager +++++ (objects/alnmgr)
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1. Classes for fast and easy access to the segments or chunks of an
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alignment (CAlnMap and related) and the the base pairs of each sequence
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(CAlnVec).
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2. Classes (CAlnMix and related) for constructing a virtual multiple
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alignment out of a set of input alignments.
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NOTE:
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All AlnMgr functionality is based upon the Seq-align and
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Dense-seg ASN.1 specifications.
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------------------------------------------------------------------
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+++++ Alignment Algorithms +++++ (algo)
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A new library called `algo' has been introduced with a purpose to
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facilitate computationally intensive tasks. The library resides in a
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top-level Toolkit tree branch and is built with speed optimization on.
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This first release of the library includes several alignment algorithms
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widely used by biologists:
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- CNWAligner:
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The Needleman-Wunsch algorithm producing pairwise global alignments of
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nucleotide or protein sequences. The implementation uses affine penalty
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model and optionally supports end space free alignments.
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- CMMAligner:
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Derived from CNWAligner, this class encapsulates the Hirschberg's
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divide-and-conquer algorithm (also credited to Myers and Miller) under
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which the amount of space required to run the NW becomes a linear
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function of sequence's lengths. While the latter is achieved at a
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cost of lower performance, a parallel version of the algorithm which
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is also provided can run even faster than the classical NW in a
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multiple-CPU environment.
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- CNWAlignerMrna2Dna:
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As it is apparent from its name, this sort of algorithm is specifically
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designed for making spliced alignments. The algorithm calculates global
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alignment specially accounting for splice signals in its dynamic
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programming recurrences resulting in better alignments for these
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particular types of sequences.
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A sample program is provided to demonstrate the usage of the library,
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though it is also profound enough to be used as a standalone application.
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------------------------------------------------------------------
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+++++ Object Validator +++++ (objects/validator)
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A complete implementation of a C++ Validator is now available (excluding
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validation of alignments). The test_validator application can validate
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Seq-entry, Seq-submit and standalone annotation records. It can run in a
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batch mode to handle NCBI release files.
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------------------------------------------------------------------
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+++++ Flat-File Generator +++++ (objects/flat)
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There is a new version of flat-file generator, with support for some
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additional output formats (EMBL, GBSeq, and tabular as well as GenBank).
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NOTE: neither version produces canonical output; use the C Toolkit for that.
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------------------------------------------------------------------
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+++++ Miscellaneous Libs (additions and improvements) +++++
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1. `seqset' (objects/seqset)
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-- [CSeq_entry] Code to read sequences from FASTA files.
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2. `seqloc' (objects/seqloc)
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-- [CSeq_loc] Caching of heavily used CSeq_loc::GetTotalRange() method.
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3. `seqfeat' (objects/??????)
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-- [CSeq_feat] Optimized feature sorting methods.
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4. `util' (util)
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-- [logrotate] Class for automatically-rotated log files.
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-- [strsearch] Fast string search utilities using Boyer-Moore algorithm
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and a finite state automat search.
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-- [range] Optimized CRange<> and CRangeMap<> classes.
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5. `xobjutil' (objects/util)
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-- [sequence] a) Converting coordinates between corresponding source and
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product locations on a feature, and generally determining
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one location's position relative to another.
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b) Class CCdregion_translate for rapid translation
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from a given genetic code, allowing all of the iupac
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nucleotide ambiguity characters.
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c) Added TestForOverlap() and GetBestOverlappingFeat().
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-- [genbank] Optimized GenBank formatter.
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6. `regexp' (util/regexp)
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-- PCRE library (see LICENSE) has been embedded into the Toolkit.
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7. `html' (html)
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-- Added code to support Sergey Kurdin's popup menu.
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#############################################################################
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*** NEW DEVELOPMENTS -- APPLICATIONS and TOOLS
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------------------------------------------------------------------
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+++++ NCBI Genome Workbench (GBench) +++++ (gui/gbench, gui/core, etc)
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There is a fledgling GBench project which matures rapidly; it
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however has its own release schedule so far (although it is a part of
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the Toolkit). To get more info about the GBench:
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<A HREF="http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/tools/gbench/gbench.html">http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/tools/gbench/gbench.html</A>
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or contact GBench project leader, Mike DiCuccio.
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"GBench: NCBI Genome Workbench is an application for visualization of
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molecule information (sequences, alignment, molecule features, etc)."
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------------------------------------------------------------------
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+++++ Datatool +++++ (serial/datatool)
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1. Can now generate serialization code based on a DTD specification.
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While it does not yet support all of DTD features, the most
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widely used features are implemented, and new can be added upon request.
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2. Can now generate simple clients for RPC-style ASN.1- or XML-based
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network services, and has been configured to do so for
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NCBI's ID1, Entrez2, and Medline Archive services.
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#############################################################################
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*** BUILD FRAMEWORK
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------------------------------------------------------------------
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+++++ Parallel build w/GMAKE +++++
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gmake -jN should now work properly (though the build system still
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doesn't support cross-project parallelization with any version of
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make).
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------------------------------------------------------------------
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+++++ MacOS 10.X / CodeWarrior 8.0 Update 8.3 +++++
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Projects include targets to compile with BSD/Apple headers and libraries or
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with MSL headers and libraries.
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------------------------------------------------------------------
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+++++ MS-Win/MSVC project tree +++++
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1. Added project "all_objects_generation" to auto-generate
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serialization source code "on-the-fly" during the build.
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NOTE: so, we do not have to pack pre-generated serialization code
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to the MS-Win/MSVC distribution archive anymore.
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2. Amended the code to be built as DLLs.
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3. Created new workspace (and underlying projects) to build "cluster DLLs"
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(i.e. DLLs which implement APIs corresponding to several static libs).
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#############################################################################
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*** DOCUMENTATION
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It has been mostly frozen lately due to its conversion from HTML to
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XML format. The reformatted version of the docs will replace the old
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one soon.
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There is also an interesting development underway -- to use the
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DOXYGEN source browser to complement the traditional docs with
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structured DOXIGEN-generated "Library Reference" ones based
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on the in-source comments.
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#############################################################################
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*** BACKWARD COMPATIBILITY
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There have been quite a lot of API changes since the October release,
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mostly in the code generation for serializable objects and in the
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ObjectManager related APIs since the October release.
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------------------------------------------------------------------
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+++++ Exceptions +++++
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There is an effort underway to back-fit the Toolkit with
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hierarchically organized exception classes, so now some parts of
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the code throw these new exceptions rather than e.g. "runtime_error".
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Still, the new exception class hierarchy is derived from "std::exception".
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For more details, see APPENDIX "BACKWARD_COMPATIBILITY.Exception" attached.
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------------------------------------------------------------------
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+++++ "External" packages used +++++
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The code has been adapted to work with the newer version of
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the NCBI C Toolkit and some 3rd party packages:
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FLTK -- 1.1.3
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wxWin -- 2.4.0
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FCGI -- 2.2.0
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------------------------------------------------------------------
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+++++ Miscellaneous +++++
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1. Changed names for the static-lib versions DBAPI drivers on MS Windows
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(added suffix "_static", like: dbapi_driver_odbc_static.lib)
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------------------------------------------------------------------
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+++++
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So, be prepared to encounter and fight code backward-compatibility issues.
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#############################################################################
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*** PLATFORMS (OS's, compilers used inside NCBI)
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------------------------------------------------------------------
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+++++ UNIX +++++
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Linux, INTEL, GCC 3.0.4
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Linux, INTEL, ICC 7.0
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Solaris, SPARC, WorkShop 6 update 2 C++ 5.3 Patch 111685-13
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Solaris, SPARC, GCC 2.95.2
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Solaris, SPARC, GCC 3.0.4
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Solaris, INTEL, WorkShop 6 update 2 C++ 5.3 Patch 111686-13
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Solaris, INTEL, GCC 2.95.2
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IRIX64, SGI-Mips, MIPSpro 7.3.1.2m
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FreeBSD, INTEL, GCC 3.0.4
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Tru64, ALPHA, GCC 2.95.3
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Tru64, ALPHA, Compaq C V6.3-029 / Compaq C++ V6.5-014
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------------------------------------------------------------------
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+++++ MS Windows +++++
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MSVC++ 6.0 Service Pack 5.....
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------------------------------------------------------------------
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+++++ MacOSX +++++
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MacOS 10.1, GCC 3.1 (patched, see "doc/config_darwin.html)
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MacOS 10.2, GCC 3.1 (patched, see "doc/config_darwin.html)
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MacOS 10.X, CodeWarrior 8.0 Update 8.3
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#############################################################################
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*** CAVEATS
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------------------------------------------------------------------
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+++++ MacOS 10.2 / GCC 3.1 +++++
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Toolkit builds okay in all modes, but it runs okay only in Debug, non-DLL mode.
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Also, GBench requires DYLD_BIND_AT_LAUNCH to be set. Otherwise it will not
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run (will hang at startup waiting for semaphore).
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These are GCC-related issues and Apple aware of them. The next OS release
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(expected in September, with a preview available in June) is supposed to
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address most of them and introduce many others, since they will be switching
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to 64 bit hardware.
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------------------------------------------------------------------
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+++++ MacOS 10.X / CodeWarrior 8.0 Update 8.3 +++++
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1. Not all of the applications are built.
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2. GUI-related projects are not built.
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------------------------------------------------------------------
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+++++ GCC 3.2 +++++
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This version has a bug (fixed in 3.2.1) in the C++ iostream implementation,
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so some of the code that relies on C++ iostreams (such as serialization
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and iostream wrappers for network and other types of connections, as
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well as ObjectManager GenBank loader) would not work. Advice: upgrade.
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#############################################################################
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*** ETC
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1. The GCC/X11 configuration on MacOS X behaves (builds and runs)
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just like a regular UNIX:
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ncbi_cxx_macosx.tar.gz -> ncbi_cxx_unix.tar.gz
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=============================================================================
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=============================================================================
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APPENDIX
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#############################################################################
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BACKWARD_COMPATIBILITY: Exceptions
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1.
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We are continuing with the effort to make the C++ Toolkit exceptions
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more structured -- creating a library/module based hierarchy of
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exceptions, such as:
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CException
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CCoreException
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CFileException
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CMutexException
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CStringException
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..........
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CConnectException
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..........
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..........
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CXxxException
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..........
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..........
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..........
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..........
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..........
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1.A) One reason to do this is to allow upper-level user to easily
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identify (in his code) which exactly library or module has
|
|
thrown the exception, and what was the particular reason for throwing it.
|
|
This is really necessary sometimes.
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|
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1.B) Another reason to do this is to make all exceptions used
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|
(and thrown from) inside the C++ Toolkit to have more common
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|
functionality (as described and implemented in the base "CException"
|
|
class).
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|
|
|
|
|
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2.
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As a consequence of this development, "C{Errno,Parse}Exception" will be
|
|
eliminated whatsoever. We realize that it may create some backward
|
|
compatibility problems for some of your code which relies on these,
|
|
but:
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|
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2.A) All problems related to the elimination of "C{Errno,Parse}Exception"
|
|
will show up early (during the code compilation), and they can be fixed
|
|
rather quickly -- you just start catching the new, lib/mod-specific
|
|
exceptions (which BTW, still provide the "C{Errno,Parse}Exception" API,
|
|
see [2.C] below).
|
|
|
|
2.B) Having such generic, library/module-independent
|
|
"C{Errno,Parse}Exception" around does not do one any good service
|
|
as they provide no information on their origin and specific error
|
|
(except in the err.message, but it's neither reliable nor easy or
|
|
obvious to extract the needed info from the messages as they are
|
|
intended to be used for logging, and not to be parsed by some
|
|
wild-guessing ad hoc message-parsing code).
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|
|
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2.C) There are templates CErrnoTemplException<> and CParseTemplException<>
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|
to allow the creation of exceptions which would have this specific
|
|
("errno" and "parse" oriented) APIs, and yet belong to the right
|
|
place in the C++ Toolkit hierarchy.
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|
|
|
|
|
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#############################################################################
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$Date: 2003/04/16 20:57:20 $
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#############################################################################
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</PRE>
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