c++/compilers/unix/GCC.sh

@@ -3,7 +3,7 @@
 # Setup the local working environment for the "configure" script
 #   Compiler:   GCC
 #
-# $Revision: 491630 $  // by Denis Vakatov, NCBI (vakatov@ncbi.nlm.nih.gov)
+# $Revision: 578209 $  // by Denis Vakatov, NCBI (vakatov@ncbi.nlm.nih.gov)
 #############################################################################
 
 
@@ -51,11 +51,16 @@ case "$1" in
      elif test "`$CXX -V$1 -dumpversion 2>/dev/null`" = "$1"; then
        CXX="$CXX -V$1"
        CC="$CC -V$1"
-     elif test "`$CXX -dumpversion 2>/dev/null`" \!= "$1"; then
+     else
+       case "`$CXX -dumpversion 2>/dev/null`" in
+         "$1" | "$1".* ) ;;
+         * )
            cat <<EOF
 ERROR:  cannot find GCC version $1; you may need to adjust PATH explicitly.
 EOF
            exit 1
+           ;;
+       esac
      fi
      shift
   ;;

c++/compilers/vs2015/datatool.bat

 @echo off
-REM $Id: datatool.bat 532246 2017-04-03 15:48:07Z gouriano $
+REM $Id: datatool.bat 577623 2019-01-07 18:13:55Z ivanov $
 REM ===========================================================================
 REM 
 REM                            PUBLIC DOMAIN NOTICE
@@ -66,8 +66,8 @@ for /f %%a in ('xcopy "%input_asn_path%" "%dest_spec%" /q /d /y') do (set copied
 set copied_def=0
 if not exist "%input_def_path%" echo [-] > "%input_def_path%"
 if exist "%input_def_path%" for /f %%a in ('xcopy "%input_def_path%" "%dest_spec%" /q /d /y') do (set copied_def=%%a)
-if not %copied_asn%==0 goto DOGENERATE
-if not %copied_def%==0 goto DOGENERATE
+if not "%copied_asn%"=="0" goto DOGENERATE
+if not "%copied_def%"=="0" goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%.files"   goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%__.cpp"   goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%___.cpp"  goto DOGENERATE

c++/compilers/vs2015/install.sh

 #! /bin/sh
-# $Id: install.sh 561966 2018-04-16 13:07:35Z ivanov $
+# $Id: install.sh 577506 2019-01-04 18:39:23Z ivanov $
 # Authors:  Denis Vakatov    (vakatov@ncbi.nlm.nih.gov)
 #           Anton Lavrentiev (lavr@ncbi.nlm.nih.gov)
 #
@@ -34,7 +34,6 @@ echo "[`basename $script`] NCBI C++:  \"$builddir\" to \"$target\"..."
 
 
 # Derive the destination dirs
-docdir="$target"/doc
 scriptdir="$target"/scripts
 incdir="$target"/include
 srcdir="$target"/src
@@ -67,10 +66,6 @@ makedir "$target" -p
 makedir "$tmpdir" -p
 
 
-# Documentation
-echo "[`basename $script`] Installing documentation..."
-install "$builddir/doc" "$docdir"
-
 # Scripts
 echo "[`basename $script`] Installing scripts..."
 install "$builddir/scripts" "$scriptdir"

c++/compilers/vs2017/datatool.bat

 @echo off
-REM $Id: datatool.bat 555778 2018-01-23 16:47:32Z gouriano $
+REM $Id: datatool.bat 577623 2019-01-07 18:13:55Z ivanov $
 REM ===========================================================================
 REM 
 REM                            PUBLIC DOMAIN NOTICE
@@ -66,8 +66,8 @@ for /f %%a in ('xcopy "%input_asn_path%" "%dest_spec%" /q /d /y') do (set copied
 set copied_def=0
 if not exist "%input_def_path%" echo [-] > "%input_def_path%"
 if exist "%input_def_path%" for /f %%a in ('xcopy "%input_def_path%" "%dest_spec%" /q /d /y') do (set copied_def=%%a)
-if not %copied_asn%==0 goto DOGENERATE
-if not %copied_def%==0 goto DOGENERATE
+if not "%copied_asn%"=="0" goto DOGENERATE
+if not "%copied_def%"=="0" goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%.files"   goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%__.cpp"   goto DOGENERATE
 if not exist "%src_subtree%%input_asn_name%___.cpp"  goto DOGENERATE

c++/compilers/vs2017/install.sh

 #! /bin/sh
-# $Id: install.sh 561966 2018-04-16 13:07:35Z ivanov $
+# $Id: install.sh 577506 2019-01-04 18:39:23Z ivanov $
 # Authors:  Denis Vakatov    (vakatov@ncbi.nlm.nih.gov)
 #           Anton Lavrentiev (lavr@ncbi.nlm.nih.gov)
 #
@@ -34,7 +34,6 @@ echo "[`basename $script`] NCBI C++:  \"$builddir\" to \"$target\"..."
 
 
 # Derive the destination dirs
-docdir="$target"/doc
 scriptdir="$target"/scripts
 incdir="$target"/include
 srcdir="$target"/src
@@ -67,10 +66,6 @@ makedir "$target" -p
 makedir "$tmpdir" -p
 
 
-# Documentation
-echo "[`basename $script`] Installing documentation..."
-install "$builddir/doc" "$docdir"
-
 # Scripts
 echo "[`basename $script`] Installing scripts..."
 install "$builddir/scripts" "$scriptdir"

c++/compilers/vs2017/make.bat

 @ECHO OFF
-REM $Id: make.bat 556795 2018-02-05 16:14:31Z ivanov $
+REM $Id: make.bat 579874 2019-02-07 14:28:45Z ivanov $
 REM ===========================================================================
 REM
 REM                            PUBLIC DOMAIN NOTICE
@@ -58,6 +58,7 @@ rem --- Required parameters
 
 set cmd=%~1%
 set solution=%~2
+set solution_name=%solution:/=_%
 set libdll=%~3
 set arch=%~4
 
@@ -154,7 +155,10 @@ if not "%with_openmp%" == "" (
 
 time /t
 echo INFO: Configure "%libdll%\%solution% [ReleaseDLL|%arch%]"
-%DEVENV% %libdll%\build\%solution%.sln /build "ReleaseDLL|%archwc%" /project "_CONFIGURE_"
+set log=__%libdll%_%solution_name%.configure.log
+echo %DEVENV% %libdll%\build\%solution%.sln /build "ReleaseDLL|%archwc%" /project "_CONFIGURE_" /out %log%
+%DEVENV% %libdll%\build\%solution%.sln /build "ReleaseDLL|%archwc%" /project "_CONFIGURE_" /out %log%
+type %log%
 if errorlevel 1 goto ABORT
 if not _%cmd% == _make goto COMPLETE
 
@@ -186,7 +190,9 @@ rem Subroutines
 
 :build
    echo INFO: Building "%libdll%\%solution% [%1|%arch%]"
-   %DEVENV% %libdll%\build\%solution%.sln /build "%1|%archw%" /project "_BUILD_ALL_"
+   set log=__%libdll%_%solution_name%.build.%1.log
+   %DEVENV% %libdll%\build\%solution%.sln /build "%1|%archw%" /project "_BUILD_ALL_" /out %log%
+   type %log%
    exit /b %errorlevel%
 
 :check

c++/compilers/xcode30_prj/copybin.sh

 #!/bin/sh
-# $Id: copybin.sh 190015 2010-04-27 17:14:13Z gouriano $
+# $Id: copybin.sh 576271 2018-12-12 17:35:52Z ivanov $
 # ===========================================================================
 # 
 #                            PUBLIC DOMAIN NOTICE
@@ -42,8 +42,8 @@ done
 test -d ${BUILD_TREE_BIN} || mkdir -p ${BUILD_TREE_BIN}
 echo ${CONFIGURATION} | grep elease > /dev/null
 if test $? -eq 0 -o "$PTB_NOCOPYBIN" != ""; then
-  mv -f ${TARGET_BUILD_DIR}/${TARGET_NAME}* ${BUILD_TREE_BIN}
+  mv -f ${TARGET_BUILD_DIR}/${PRODUCT_NAME}* ${BUILD_TREE_BIN}
 else
-  cp -f -p -R ${TARGET_BUILD_DIR}/${TARGET_NAME}* ${BUILD_TREE_BIN}
+  cp -f -p -R ${TARGET_BUILD_DIR}/${PRODUCT_NAME}* ${BUILD_TREE_BIN}
 fi
 exit 0

c++/include/algo/blast/api/rps_aux.hpp

-/* $Id: rps_aux.hpp 369420 2012-07-19 13:41:19Z boratyng $
+/* $Id: rps_aux.hpp 579190 2019-01-31 13:23:44Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -164,7 +164,7 @@ private:
     
     /// Pointer which contains pointers to data managed by the data members
     /// above
-    BlastRPSInfo* m_RpsInfo;
+    unique_ptr<BlastRPSInfo> m_RpsInfo;
 };
 
 END_SCOPE(blast)

c++/include/algo/blast/blastinput/blast_args.hpp

-/*  $Id: blast_args.hpp 565102 2018-06-06 17:25:02Z rackerst $
+/*  $Id: blast_args.hpp 579216 2019-01-31 16:18:17Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -942,6 +942,10 @@ public:
         return m_Subjects;
     }
 
+    void SetIPGFilteringSupport(bool val) {
+        m_SupportIPGFiltering = val;
+    }
+
 protected:
     CRef<CSearchDatabase> m_SearchDb;/**< Description of the BLAST database */
     bool m_RequestMoleculeType;     /**< Determines whether the database's
@@ -958,6 +962,7 @@ protected:
     CRef<objects::CScope> m_Scope;  /**< CScope object in which all subject
                                       sequences read are kept */
     bool m_SupportsDatabaseMasking; /**< true if it's supported */
+    bool m_SupportIPGFiltering;     /**< true if IPG filtering is supported */
 };
 
 /// Argument class to collect options specific to igBLAST
@@ -1066,7 +1071,9 @@ public:
         m_Html(false),
         m_IsIgBlast(isIgblast),
         m_LineLength(align_format::kDfltLineLength),
-        m_FormatFlags(flag)
+        m_FormatFlags(flag),
+        m_HitsSortOption(-1),
+        m_HspsSortOption(-1)
     {
         if (m_IsIgBlast) {
             m_DfltNumAlignments = m_DfltNumDescriptions = 10;
@@ -1093,7 +1100,8 @@ public:
     virtual void
     ParseFormattingString(const CArgs& args,
                           EOutputFormat& fmt_type,
-                          string& custom_fmt_spec) const;
+                          string& custom_fmt_spec,
+                          string& custom_delim) const;
 
     /// Get the choice of formatted output
     EOutputFormat GetFormattedOutputChoice() const {
@@ -1143,6 +1151,14 @@ public:
     size_t GetLineLength() const {
     	return m_LineLength;
     }
+    int GetHitsSortOption() const {
+        return m_HitsSortOption;
+    }
+    int GetHspsSortOption() const {
+        return m_HspsSortOption;
+    }
+    string GetCustomDelimiter(){return m_CustomDelim;}
+    
 protected:
     EOutputFormat m_OutputFormat;   ///< Choice of formatting output
     bool m_ShowGis;                 ///< Display NCBI GIs?
@@ -1157,6 +1173,9 @@ protected:
     string m_CustomOutputFormatSpec;
     size_t m_LineLength;
     EFormatFlags m_FormatFlags;
+    int m_HitsSortOption;
+    int m_HspsSortOption;
+    string m_CustomDelim;
 };
 
 /// Formatting args for magicblast advertising only SAM and fast tabular
@@ -1242,7 +1261,7 @@ public:
 
     /// Get the number of threads to spawn
     size_t GetNumThreads() const { return m_NumThreads; }
-private:
+protected:
     size_t m_NumThreads;        ///< Number of threads to spawn
 };
 

c++/include/algo/blast/blastinput/cmdline_flags.hpp

-/*  $Id: cmdline_flags.hpp 562577 2018-04-24 15:51:23Z fongah2 $
+/*  $Id: cmdline_flags.hpp 579216 2019-01-31 16:18:17Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -77,6 +77,11 @@ NCBI_BLASTINPUT_EXPORT extern const string kArgNegativeGiList;
 /// argument for gi list to exclude from a BLAST database search
 NCBI_BLASTINPUT_EXPORT extern const string kArgNegativeSeqidList;
 
+/// IPG list file name to restrict BLAST database
+NCBI_BLASTINPUT_EXPORT extern const string kArgIpgList;
+
+/// argument for IPG list to exclude from a BLAST database search
+NCBI_BLASTINPUT_EXPORT extern const string kArgNegativeIpgList;
 
 /// List of filtering algorithms to apply to subjects as soft masking
 extern const string kArgDbSoftMask;

c++/include/algo/blast/core/blast_options.h

-/* $Id: blast_options.h 562577 2018-04-24 15:51:23Z fongah2 $
+/* $Id: blast_options.h 577682 2019-01-08 12:49:31Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -167,7 +167,13 @@ extern "C" {
 
 /** Default max frequency for a database word. Words with higher frequency
     will be masked in the lookup table. */
-#define MAX_DB_WORD_COUNT_MAPPER 60
+#define MAX_DB_WORD_COUNT_MAPPER 30
+
+/** Default maximum insert size: distance on the subject between reads that
+    belong to a pair, for spliced and non-spliced alignments */
+#define MAGICBLAST_MAX_INSERT_SIZE_SPLICED 1000000
+#define MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED 100000
+
 
 /** Value used to indicate that no IMPALA-style scaling should be performed
  * when scaling a PSSM */

c++/include/algo/blast/format/blast_format.hpp

-/* $Id: blast_format.hpp 556289 2018-01-29 17:33:51Z jianye $
+/* $Id: blast_format.hpp 577762 2019-01-08 18:10:19Z ivanov $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -79,13 +79,19 @@ public:
         string productive;
     };
         
-    
     enum {
         /// The line length of pairwise blast output
         kFormatLineLength = 68,
         kMinTaxFormatLineLength = 100
     };
 
+    ///Display options for blast_report
+    enum DisplayOption {
+        eDescriptions,
+        eAlignments,
+        eMetadata,
+        eDescriptionsWithTemplates // this option is not implemented in blast_report
+    };
     /// Constructor
     /// @param opts BLAST options used in the search [in]
     /// @param db_adapter Adapter object representing a BLAST database or
@@ -249,6 +255,15 @@ public:
                            blast::CPsiBlastIterationState::TSeqIds prev_seqids =
                            blast::CPsiBlastIterationState::TSeqIds());
 
+    ///Print Metadata in json format or descriptions in html format or alignments in html format
+    ///app.ini file with template info must be present
+    /// @param results Object containing alignments, mask regions, and
+    ///                ancillary data to be output [in]
+    /// @param displayOption indicates what info to display
+    void PrintReport(const blast::CSearchResults& results,              
+                        CBlastFormat::DisplayOption displayOption);
+
+
     /// Writes out the query and results as an "archive" format
     /// @param queries Query factory to provide queries
     /// @param options_handle BLAST options
@@ -299,6 +314,12 @@ public:
 
     /// Set Alignment Length
     void SetLineLength(size_t len) {m_LineLength = len;}    
+    void SetAlignSeqList(string alignSeqList) {m_AlignSeqList = alignSeqList;}
+    void SetHitsSortOption(int hitsSortOption) {m_HitsSortOption = hitsSortOption;}
+    void SetHspsSortOption(int hspsSortOption) {m_HspsSortOption = hspsSortOption;}
+    void SetCustomDelimiter(string customDelim) {m_CustomDelim = customDelim;}
+    
+    
 
     static void PrintArchive(CRef<objects::CBlast4_archive> archive,
             					  CNcbiOstream& out);
@@ -390,6 +411,15 @@ private:
     /// If true, print long sequence ids (database|accession)
     bool m_LongSeqId;
     
+    
+    CShowBlastDefline::SDeflineTemplates *m_DeflineTemplates;
+    CDisplaySeqalign::SAlignTemplates *m_AlignTemplates;
+    string m_AlignSeqList;
+
+    int m_HitsSortOption;
+    int m_HspsSortOption;
+    string m_CustomDelim;
+
     /// Output the ancillary data for one query that was searched
     /// @param summary The ancillary data to report [in]
     void x_PrintOneQueryFooter(const blast::CBlastAncillaryData& summary);
@@ -492,6 +522,13 @@ private:
 
    void x_InitSAMFormatter();
    void x_PrintTaxReport(const blast::CSearchResults& results);
+   void x_InitDeflineTemplates(void);
+   void x_InitAlignTemplates(void);
+   void x_DisplayDeflinesWithTemplates(CConstRef<CSeq_align_set> aln_set);
+   void x_SetAlignParameters(CDisplaySeqalign& cds);
+   void x_DisplayAlignsWithTemplates(CConstRef<CSeq_align_set> aln_set,const blast::CSearchResults& results);
+   //Creates json object array of info for each defline to display
+   void x_CreateDeflinesJson(CConstRef<CSeq_align_set> aln_set);
 };
 
 END_NCBI_SCOPE

c++/include/cgi/cgi_exception.hpp

 #ifndef CGI___CGI_EXCEPTION__HPP
 #define CGI___CGI_EXCEPTION__HPP
 
-/*  $Id: cgi_exception.hpp 540924 2017-07-12 15:06:18Z grichenk $
+/*  $Id: cgi_exception.hpp 578930 2019-01-28 18:18:04Z ivanov $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -132,10 +132,10 @@ protected:
     virtual void x_Init(const CDiagCompileInfo& info,
                         const string& message,
                         const CException* prev_exception,
-                        EDiagSev severity);
+                        EDiagSev severity) override;
 
     /// Override method for copying exception data.
-    virtual void x_Assign(const CException& src);
+    virtual void x_Assign(const CException& src) override;
 
 private:
     EStatusCode m_StatusCode;
@@ -165,7 +165,7 @@ public:
         eValue,     //< Bad cookie value
         eString     //< Bad cookie string (Set-Cookie:) format
     };
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch (GetErrCode()) {
         case eValue:   return "Bad cookie";
@@ -205,7 +205,7 @@ public:
         eData        //< Syntaxically correct but contains odd data (from the
                      //< point of view of particular CGI application)
     };
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch ( GetErrCode() ) {
         case eCookie:    return "Malformed HTTP Cookie";
@@ -265,7 +265,7 @@ public:
         eErrno,   //< Generic system call failure
         eModTime  //< File modification time cannot be obtained
     };
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch (GetErrCode()) {
         case eErrno:    return "System error";
@@ -292,7 +292,7 @@ public:
         eDoubleHeader,          ///< Header has already been written
         eBadHeaderValue         ///< Invalid header value
     };
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch ( GetErrCode() ) {
         case eDoubleHeader:   return "Header has already been written";
@@ -320,7 +320,7 @@ public:
         eHeaderSent          ///< Header has been written
     };
 
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch ( GetErrCode() ) {
         case eHeaderSent:  return "Header has been written";
@@ -350,7 +350,7 @@ public:
         eAttrNotFound,         ///< Attribute not found
         eNotLoaded             ///< Session not loaded
     };
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch ( GetErrCode() ) {
         case eSessionId:            return "SessionId not specified";
@@ -381,7 +381,7 @@ public:
         eApp     //< Other error
     };
 
-    virtual const char* GetErrCodeString(void) const
+    virtual const char* GetErrCodeString(void) const override
     {
         switch (GetErrCode()) {
         case eApp:   return "CGI application error";

c++/include/common/ncbi_package_ver.h

@@ -7,8 +7,8 @@
 #define NCBI_PACKAGE                       1
 #define NCBI_PACKAGE_NAME                  "blast"
 #define NCBI_PACKAGE_VERSION_MAJOR         2
-#define NCBI_PACKAGE_VERSION_MINOR         8
-#define NCBI_PACKAGE_VERSION_PATCH         1
+#define NCBI_PACKAGE_VERSION_MINOR         9
+#define NCBI_PACKAGE_VERSION_PATCH         0
 #define NCBI_PACKAGE_CONFIG                ""
 
 #define NCBI_PACKAGE_VERSION_STRINGIFY(x)  #x

c++/include/common/ncbi_source_ver.h

-/*  $Id: ncbi_source_ver.h 569379 2018-08-21 04:03:03Z syncbot $
+/*  $Id: ncbi_source_ver.h 577239 2019-01-03 05:03:08Z syncbot $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -27,7 +27,7 @@
 #include <ncbiconf.h>
 #include <common/ncbi_build_info.h>
 
-/* #undef NCBI_PRODUCTION_VER */
+#define NCBI_PRODUCTION_VER 20190103
 #define NCBI_DEVELOPMENT_VER 20180821
 
 #if defined(NCBI_PRODUCTION_VER)

c++/include/connect/ncbi_http_session.hpp

 #ifndef CONNECT___NCBI_HTTP_SESSION__HPP
 #define CONNECT___NCBI_HTTP_SESSION__HPP
 
-/* $Id: ncbi_http_session.hpp 567636 2018-07-21 15:53:54Z mcelhany $
+/* $Id: ncbi_http_session.hpp 576759 2018-12-20 14:37:49Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -586,6 +586,7 @@ public:
         eGet        = eReqMethod_Get,
         ePost       = eReqMethod_Post,
         ePut        = eReqMethod_Put,
+		ePatch		= eReqMethod_Patch,
         eDelete     = eReqMethod_Delete
     };
 

c++/include/corelib/ncbiapp.hpp

 #ifndef CORELIB___NCBIAPP__HPP
 #define CORELIB___NCBIAPP__HPP
 
-/*  $Id: ncbiapp.hpp 561402 2018-04-06 16:45:41Z gouriano $
+/*  $Id: ncbiapp.hpp 576975 2018-12-27 12:53:02Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -416,14 +416,16 @@ protected:
 
     /// Flags to adjust standard I/O streams' behaviour.
     enum EStdioSetup {
-        fDefault_SyncWithStdio  = 0x01,
-        ///< Use compiler-specific default as pertains to the synchronizing
-        ///< of "C++" Cin/Cout/Cerr streams with their "C" counterparts.
+        fNoSyncWithStdio  = 0x01,
+        ///< Turn off synchronizing of "C++" cin/cout/cerr streams with
+        ///< their "C" counterparts, possibly making the former not thread-safe.
 
         fDefault_CinBufferSize  = 0x02,
         ///< Use compiler-specific default of Cin buffer size.
         fBinaryCin   = 0x04,  ///< treat standard  input as binary
-        fBinaryCout  = 0x08   ///< treat standard output as binary
+        fBinaryCout  = 0x08,  ///< treat standard output as binary
+
+        fDefault_SyncWithStdio  = 0x00, ///< @deprecated @sa fNoSyncWithStdio
     };
     typedef int TStdioSetupFlags;  ///< Binary OR of "EStdioSetup"
 

c++/include/corelib/ncbimisc.hpp

 #ifndef CORELIB___NCBIMISC__HPP
 #define CORELIB___NCBIMISC__HPP
 
-/*  $Id: ncbimisc.hpp 563123 2018-05-02 17:08:47Z lavr $
+/*  $Id: ncbimisc.hpp 580817 2019-02-21 14:01:24Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -1025,6 +1025,10 @@ public:
 #define GI_TO(T, gi) (static_cast<T>(TIntId(gi)))
 #define GI_FROM(T, value) (TGi(static_cast<TIntId>(value)))
 
+/// Temporary macros to convert TEntrezId to other types (int, unsigned etc.).
+#define ENTREZ_ID_TO(T, entrez_id) (static_cast<T>(TIntId(entrez_id)))
+#define ENTREZ_ID_FROM(T, value) (TGi(static_cast<TIntId>(value)))
+
 /// Convert gi-compatible int to/from other types.
 #define INT_ID_TO(T, id) (static_cast<T>(id))
 #define INT_ID_FROM(T, value) (static_cast<TIntId>(value))

c++/include/corelib/ncbithr.hpp

 #ifndef CORELIB___NCBITHR__HPP
 #define CORELIB___NCBITHR__HPP
 
-/*  $Id: ncbithr.hpp 545414 2017-09-06 15:40:16Z grichenk $
+/*  $Id: ncbithr.hpp 579979 2019-02-08 14:16:50Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE

c++/include/dbapi/driver/exception.hpp

 #ifndef DBAPI_DRIVER___EXCEPTION__HPP
 #define DBAPI_DRIVER___EXCEPTION__HPP
 
-/* $Id: exception.hpp 563975 2018-05-17 18:33:33Z ucko $
+/* $Id: exception.hpp 578927 2019-01-28 18:17:52Z ivanov $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -69,21 +69,21 @@ END_SCOPE(impl)
     } \
 public: \
     virtual ~exception_class(void) throw() {} \
-    virtual const char* GetType(void) const {return #exception_class;} \
+    const char* GetType(void) const override {return #exception_class;} \
     typedef int TErrCode; \
     TErrCode GetErrCode(void) const \
     { \
         return typeid(*this) == typeid(exception_class) ? \
             (TErrCode)x_GetErrCode() : (TErrCode)CException::eInvalid; \
     } \
-    virtual CDB_Exception* Clone(void) const \
+    virtual CDB_Exception* Clone(void) const override \
     { \
         return new exception_class(*this); \
     } \
     NCBI_EXCEPTION_DEFAULT_THROW(exception_class) \
 protected: \
     exception_class(void) {} \
-    virtual const CException* x_Clone(void) const \
+    virtual const CException* x_Clone(void) const override \
     { \
         return new exception_class(*this); \
     } \
@@ -187,7 +187,7 @@ public:
     // DEPRECATED, Will be removed soon.
     NCBI_DEPRECATED
     static const char*  SeverityString(EDB_Severity sev);
-    virtual const char* GetErrCodeString(void) const;
+    virtual const char* GetErrCodeString(void) const override;
 
 public:
     // Duplicate methods. We need them to support the old interface.
@@ -231,7 +231,7 @@ public:
     int GetSybaseSeverity(void) const { return m_SybaseSeverity;       }
 
 public:
-    virtual void ReportExtra(ostream& out) const;
+    virtual void ReportExtra(ostream& out) const override;
     virtual CDB_Exception* Clone(void) const;
 
 public:
@@ -261,8 +261,8 @@ protected:
     void x_StartOfWhat(ostream& out) const;
     void x_EndOfWhat  (ostream& out) const;
     void x_Init(const CDiagCompileInfo& info, const string& message,
-                const CException* prev_exception, EDiagSev severity);
-    virtual void x_Assign(const CException& src);
+                const CException* prev_exception, EDiagSev severity) override;
+    virtual void x_Assign(const CException& src) override;
     void x_InitCDB(int db_error_code) { m_DBErrCode = db_error_code; }
     SContext& x_SetContext(void);
 
@@ -338,10 +338,10 @@ public:
     const string& ProcName()  const { return m_ProcName; }
     int           ProcLine()  const { return m_ProcLine; }
 
-    virtual void ReportExtra(ostream& out) const;
+    virtual void ReportExtra(ostream& out) const override;
 
 protected:
-    virtual void x_Assign(const CException& src);
+    virtual void x_Assign(const CException& src) override;
 
 private:
     string m_ProcName;
@@ -376,10 +376,10 @@ public:
     const string& SqlState()   const { return m_SqlState;  }
     int           BatchLine()  const { return m_BatchLine; }
 
-    virtual void ReportExtra(ostream& out) const;
+    virtual void ReportExtra(ostream& out) const override;
 
 protected:
-    virtual void x_Assign(const CException& src);
+    virtual void x_Assign(const CException& src) override;
 
 private:
     string m_SqlState;
@@ -516,11 +516,11 @@ public:
 
     string WhatThis(void) const;
 
-    virtual void ReportExtra(ostream& out) const;
+    virtual void ReportExtra(ostream& out) const override;
 
 protected:
     void ReportErrorStack(ostream& out) const;
-    virtual void x_Assign(const CException& src);
+    virtual void x_Assign(const CException& src) override;
 
 private:
     // We use "deque" instead of "stack" here we need to iterate over all