seqdbgeneral.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: seqdbgeneral.hpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:46:42 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef CORELIB__SEQDB__SEQDBGENERAL_HPP
- #define CORELIB__SEQDB__SEQDBGENERAL_HPP
- /* $Id: seqdbgeneral.hpp,v 1000.1 2004/06/01 19:46:42 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Author: Kevin Bealer
- *
- */
- #include <objtools/readers/seqdb/seqdbcommon.hpp>
- BEGIN_NCBI_SCOPE
- // Temporary development tools/tricks
- extern int seqdb_debug_class;
- enum seqdb_debug_bits {
- debug_rh = 1,
- debug_rhsum = 2,
- debug_mvol = 4,
- debug_alias = 8,
- debug_oid = 16
- };
- #define ifdebug_rh if (seqdb_debug_class & debug_rh) cerr
- #define ifdebug_rhsum if (seqdb_debug_class & debug_rhsum) cerr
- #define ifdebug_mvol if (seqdb_debug_class & debug_mvol) cerr
- #define ifdebug_alias if (seqdb_debug_class & debug_alias) cerr
- #define ifdebug_oid if (seqdb_debug_class & debug_oid) cerr
- // Byte-order-nonspecific (long) versions
- template<typename T>
- inline T SeqDB_GetStdOrdUnaligned(const T * stdord_obj)
- {
- unsigned char * stdord =
- (unsigned char*)(stdord_obj);
-
- unsigned char * pend = stdord + sizeof(T) - 1;
- unsigned char * pcur = stdord;
-
- T retval = *pcur;
-
- while(pcur < pend) {
- retval <<= 8;
- retval += *++pcur;
- }
-
- return retval;
- }
- template<typename T>
- inline T SeqDB_GetBrokenUnaligned(const T * stdord_obj)
- {
- unsigned char * stdord =
- (unsigned char*)(stdord_obj);
-
- unsigned char * pend = stdord;
- unsigned char * pcur = stdord + sizeof(T) - 1;
-
- T retval = *pcur;
-
- while(pcur > pend) {
- retval <<= 8;
- retval += *--pcur;
- }
-
- return retval;
- }
- // Macro Predicates for binary qualities
- #define IS_POWER_OF_TWO(x) ((x) & ((x)-1))
- #define ALIGNED_TO_POW2(x,y) (! ((x) & (-y)))
- #define PTR_ALIGNED_TO_SELF_SIZE(x)
- (IS_POWER_OF_TWO(sizeof(*x)) && ALIGNED_TO_POW2(size_t(x), sizeof(*x)))
- // Portable byte swapping from marshalled version
- #ifdef WORDS_BIGENDIAN
- template<typename T>
- inline T SeqDB_GetStdOrd(const T * stdord_obj)
- {
- if (PTR_ALIGNED_TO_SELF_SIZE(stdord_obj)) {
- return *stdord_obj;
- } else {
- return SeqDB_GetStdOrdUnaligned(stdord_obj);
- }
- }
- template<typename T>
- inline T SeqDB_GetBroken(const T * stdord_obj)
- {
- return SeqDB_GetBrokenUnaligned(stdord_obj);
- }
- #else
- template<typename T>
- inline T SeqDB_GetStdOrd(const T * stdord_obj)
- {
- return SeqDB_GetStdOrdUnaligned(stdord_obj);
- }
- template<typename T>
- inline T SeqDB_GetBroken(const T * stdord_obj)
- {
- if (PTR_ALIGNED_TO_SELF_SIZE(stdord_obj)) {
- return *stdord_obj;
- } else {
- return SeqDB_GetBrokenUnaligned(stdord_obj);
- }
- }
- #endif
- // Combine two paths, trying a little to avoid duplicated delimiters.
- // If either string is empty, the other is returned. Conceptually,
- // the first path is "cwd" and the second path is the filename. So,
- // if the second path starts with "/", the first path is ignored.
- string SeqDB_CombinePath(const string & path, const string & file);
- // Returns a path minus filename (actually, last component).
- string SeqDB_GetDirName (string s);
- // Returns a filename minus greedy path.
- string SeqDB_GetFileName(string s);
- // Returns a filename minus non-greedy extension.
- string SeqDB_GetBasePath(string s);
- // Composition of the above two functions; returns a filename minus
- // greedy path and non-greedy extension.
- string SeqDB_GetBaseName(string s);
- // Find the full name, minus extension, of a ".?al" or ".?in" file,
- // and return it. If not found, return null.
- string SeqDB_FindBlastDBPath(const string & file_name, char dbtype);
- END_NCBI_SCOPE
- #endif // CORELIB__SEQDB__SEQDBGENERAL_HPP