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Use Resize() to set number of items in CEntrez2_id_list. JIRA CXX-12361
Replaced auto_ptr with unique_ptr. JIRA CXX-11620
Fixed TGi usage. JIRA CXX-10489, CXX-8347
Deprecated old THROW*_TRACE macros, added new set with clearer names and behavior. JIRA CXX-11288
Minimize usage of GI_FROM/GI_TO. Use IntId command line arguments for GIs. JIRA CXX-8347
NStr::Split() - replace usages of legacy deprecated flags. JIRA:CXX-7754
Reset diag stream only when using custom log file.
Removed SetDiagStream(0) call.
Always allow dead entries. JIRA CXX-9169
Added flag to allow fetching dead entries. JIRA CXX-9169
Replaced GI_FROM with GI_CONST. JIRA CXX-8347
Replaced deprecated Tokenize() calls.
Substitute NStr::Split with modern flags (or NStr::fSplit_NoMergeDelims in a couple of cases) for deprecated usages of NStr::Split and NStr::Truncate. JIRA: CXX-5600.
Use ERR_FATAL macro for correct no-return info. JIRA: CXX-5700
Added Abort() after ERR_POST(Fatal) that does not return anyway. JIRA: CXX-5700
id1_fetch: Accommodate more sequence ID formats. * Allow "-in" files to list bare accessions (though it's still best practice to use either GIs or FASTA-style tagged accessions). JIRA: CXX-5521. * In the historical ad-hoc parenthesized format, make version numbers optional, so that the official example of 5(HUMHBB) actually works.
When building with LLVM libc++ (the standard C++ library on Mac OS X 10.9
and FreeBSD 10), have CNcbiOstrstream be modern ostringstream rather than
legacy ostrstream to avoid a bug that resulted in memory corruption when
going past the initial allocation. To that end:
* Conditionally introduce an NCBI_SHUN_OSTRSTREAM macro to facilitate
eventually using ostringstream in at least some GNU libstdc++ builds too.
* Introduce a helper NCBI_STRSTREAM_INIT macro for giving CNcbiStrstream an
initial buffer, as strstream's and stringstream's constructors take
different arguments.
* Consistently use CNcbiOstrstream and CNcbiOstrstreamToString throughout;
when only the output length is of interest, use tellp (in conjunction
with NcbiStreamposToInt8) rather than pcount. NB: stringstream does NOT
derive from {i,o}stringstream, but all uses of CNcbiStrstream with
CNcbiOstrstreamToString were in contexts in which CNcbiOstrstream
sufficed.
* Explicitly DO use ostrstream when deliberately populating a fixed-length
buffer (specifically, when formulating PubSeqOS requests).
Leave CNcbiIstrstream as is for now, as it has no such bug and changing it
would necessitate touching a lot of constructor calls. Also, don't worry
about CNcbiStrstreambuf, whose only explicit usage is in the form of an
unused variable.
JIRA: CXX-3820, CXX-4913.
Switched most of the toolkit to TGi. JIRA CXX-3431
Some formatting modes require CBioseq_Handle. JIRA: CXX-2399
Implemented -extfeat option.
Honor maxplex option. Added timeout option.
Add flag to instantiate gaps in FASTA output
Various improvements to CFastaOstream, mostly per Christiam Camacho's feedback: * Rename flags from eFlagName to fFlagName; update in-tree usage, but continue to support the historical names for now. * Add a new fSuppressRange flag to gloss over the distinction between excerpts and full sequences. * Add a new fReverseStrand flag to flip the (typically implicit) location. * Add a new fKeepGTSigns flag to allow titles to contain embedded '>' characters, to accommodate listing further equivalent deflines. * Throw CObjmgrUtilException with subtype eBadLocation when passed an out-of-range location. (JIRA: CXX-306)
Fixed svn properties in trunk/c++.
CVS $Log$ keyword clean-up: everything except "internal".
Increase the -gi (and -ent) limit to kMax_Int.
Rename ff to ffg due to Mac-specific namespace pollution.
Use the new flat file generator
When parsing exotic ID formats, parse versions ourself rather than requiring CSeq_id to have an extra constructor.
Explicit (unsigned char) casts in ctype routines
Removed deprecated methods
CObjectManager made singleton, GetInstance() added. CXXXXDataLoader constructors made private, added static RegisterInObjectManager() and GetLoaderNameFromArgs() methods.
Added PCH ncbi_pch.hpp
Fix typo that accidentally introduced an implicit temporary CSeq_id.
Don't try to pass temporary CSeq_id objects, even by const reference, as CSeq_id has no public copy constructor.
Moved genbank loader and its readers sources to new location in objtools. Genbank is now in library libncbi_xloader_genbank. Id1 reader is now in library libncbi_xreader_id1. OBJMGR_LIBS macro updated correspondingly. Old headers temporarily will contain redirection to new location for compatibility: objmgr/gbloader.hpp > objtools/data_loaders/genbank/gbloader.hpp objmgr/reader_id1.hpp > objtools/data_loaders/genbank/readers/id1/reader_id1.hpp
Redesigned type aliases in serialization library. Fixed the code (removed CRef-s, added explicit initializers etc.)
Rearranged src/objects/ subtree. This includes the following shifts:
- src/objects/asn2asn --> arc/app/asn2asn
- src/objects/testmedline --> src/objects/ncbimime/test
- src/objects/objmgr --> src/objmgr
- src/objects/util --> src/objmgr/util
- src/objects/alnmgr --> src/objtools/alnmgr
- src/objects/flat --> src/objtools/flat
- src/objects/validator --> src/objtools/validator
- src/objects/cddalignview --> src/objtools/cddalignview
In addition, libseq now includes six of the objects/seq... libs, and libmmdb
replaces the three libmmdb? libs.
Direct flat output to *m_OutputFile rather than hard-coding cout.
Added '-repeat' option. Updated includes.
Give all RPC clients unique basenames.
Switch to new (differently buggy ;-)) flat-file generator. Drop s_SplitString, as NStr::Tokenize does the same thing.
iterate->ITERATE
Rework to take advantage of new ID1 and Entrez2 client classes generated by datatool
Use CFastaOstream rather than custom code. Fix spelling of NONEXISTENT.
Fix behavior when given a list of IDs.
exceptions replaced by CNcbiException-type ones
+Error message if a GI was not found
Take advantage of CONNECT_Init()
GetTitle() is now in sequence::.
Use GetTitle() from <objects/util/sequence.hpp>
Merge in Andrei Gourianov's changes to use the new OM (thanks!) Remove some dead code. Don't automatically turn on tracing, even when building with _DEBUG; it is always possible to set DIAG_TRACE in the environment instead. Move CVS log to end.
OM/OM1 renaming
Print complete debug and trace information when compiled with _DEBUG
Removed CRef<> argument from choice variant setter, updated sources to use references instead of CRef<>s
Remove duplicate includes.
Fixed includes to work with the updated datatool
Add #includes required by new datatool version.
Handle new Entrez docsum interface properly.
Restructured to avoid CRefs as arguments.
Request ASCII from CSeq_vector.
Seq_vector now properly starts from zero rather than one; adjust code that uses it accordingly.
move BREAK to a central location; move CBioseq::GetTitle to object manager
Edit in-source version of CVS log to avoid end-of-comment marker. (Oops.)
Drop */util/asciiseqdata.* in favor of CSeq_vector. Rewrite GenBank output code to take fuller advantage of the object manager.
Clean up includes.
Centralize (rudimentary) code to get a sequence's title.
Work around bug in Workshop's handling of declarations in for-loop initializers.
More cleanups from Denis.
Put utility code in the objects namespace.
Moved utility code to {src,include}/objects/util (to become libxobjutil).
Moved static members of CGenbankWriter to above their first use.
CConn_ServiceStream() - arguments adjusted
Un-#include <cstdlib> and <cctype> which break IRIX/MIPSpro compilation and apparently are not needed after all
Cope with new Entrez interface; fix MSVC build.
Adapted to latest revision of object manager interface.
Use NStr::IntToString instead of Stringify.
Dramatically fleshed out id1_fetch
Typo fixed
Comment out excessive debug/trace printout
Redesigned support for non-blocking sream read operations
Added support for non-blocking stream reading
The first working revision
Next debug version, still not working
Initial revision. Compiles and links, but apparently is not working yet.
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