src/objtools/blast/seqdb_reader/seqdbcommon.cpp File Reference

Detailed Description

Definitions of various helper functions for SeqDB.

Definition in file seqdbcommon.cpp.

#include <ncbi_pch.hpp>
#include <corelib/metareg.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbifile.hpp>
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <util/sequtil/sequtil.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/general/general__.hpp>
#include "seqdbgeneral.hpp"
#include "seqdbatlas.hpp"
#include <algorithm>

Include dependency graph for seqdbcommon.cpp:

Go to the source code of this file.

Classes

class  CSeqDB_FileExistence
 File existence test interface. More...
class  CSeqDB_AtlasAccessor
 Check file existence using CSeqDBAtlas. More...
class  CSeqDB_SimpleAccessor
 Check file existence using CFile. More...
class  CSeqDB_SortOidLessThan
 Compare SGiOid structs by OID. More...
class  CSeqDB_SortGiLessThan
 Compare SGiOid structs by GI. More...
class  CSeqDB_SortTiLessThan
 Compare SGiOid structs by GI. More...
class  CSeqDB_SortSeqIdLessThan
 Compare SSeqIdOid structs by SeqId. More...

Functions

CSeqDB_Substring SeqDB_RemoveDirName (CSeqDB_Substring s)
 Returns a filename minus greedy path.
CSeqDB_Substring SeqDB_RemoveFileName (CSeqDB_Substring s)
 Returns a path minus filename.
CSeqDB_Substring SeqDB_RemoveExtn (CSeqDB_Substring s)
 Returns a filename minus greedy path.
bool SeqDB_SplitString (CSeqDB_Substring &buffer, CSeqDB_Substring &front, char delim)
 Parse a prefix from a substring.
void SeqDB_CombinePath (const CSeqDB_Substring &one, const CSeqDB_Substring &two, const CSeqDB_Substring *extn, string &outp)
 Combine a filesystem path and file name.
static bool s_SeqDB_DBExists (const string &dbname, char dbtype, CSeqDB_FileExistence &access)
 Test whether an index or alias file exists.
static string s_GetPathSplitter ()
 Returns the character used to seperate path components in the current operating system or platform.
void SeqDB_ConvertOSPath (string &dbs)
 Change path delimiters to platform preferred kind in-place.
string SeqDB_MakeOSPath (const string &dbs)
 Return path with delimiters changed to platform preferred kind.
static string s_SeqDB_TryPaths (const string &blast_paths, const string &dbname, char dbtype, bool exact, CSeqDB_FileExistence &access)
 Search for a file in a provided set of paths.
static string s_SeqDB_FindBlastDBPath (const string &dbname, char dbtype, string *sp, bool exact, CSeqDB_FileExistence &access, const string path="")
string SeqDB_FindBlastDBPath (const string &dbname, char dbtype, string *sp, bool exact, CSeqDBAtlas &atlas, CSeqDBLockHold &locked)
 Finds a file in the search path.
string SeqDB_ResolveDbPath (const string &filename)
 Resolve a file path using SeqDB's path algorithms.
void SeqDB_JoinDelim (string &a, const string &b, const string &delim)
 Join two strings with a delimiter.
template<class TCompare, class TVector>
void s_InsureOrder (TVector &v)
void SeqDB_ReadBinaryGiList (const string &fname, vector< int > &gis)
 Read a binary-format GI list from a file.
static bool s_SeqDB_IsBinaryGiList (const char *fbeginp, const char *fendp, bool &has_long_ids)
 This function determines whether a file is a valid binary gi file.
void SeqDB_ReadMemoryGiList (const char *fbeginp, const char *fendp, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order)
 Read a text or binary GI list from an area of memory.
void SeqDB_ReadMemoryTiList (const char *fbeginp, const char *fendp, vector< CSeqDBGiList::STiOid > &tis, bool *in_order)
 Read a text or binary TI list from an area of memory.
bool SeqDB_IsBinaryGiList (const string &fname)
 Returns true if the file name passed contains a binary gi list.
void SeqDB_ReadGiList (const string &fname, vector< CSeqDBGiList::SGiOid > &gis, bool *in_order)
 Read a text or binary GI list from a file.
void SeqDB_ReadTiList (const string &fname, vector< CSeqDBGiList::STiOid > &tis, bool *in_order)
 Read a text or binary TI list from a file.
void SeqDB_ReadGiList (const string &fname, vector< int > &gis, bool *in_order)
 Read a text or binary GI list from a file.
void SeqDB_CombineAndQuote (const vector< string > &dbs, string &dbname)
 Combine and quote list of database names.
void SeqDB_SplitQuoted (const string &dbname, vector< CTempString > &dbs)
 Split a (possibly) quoted list of database names into pieces.
void SeqDB_SplitQuoted (const string &dbname, vector< CSeqDB_Substring > &dbs)
 Combine and quote list of database names.
void SeqDB_FileIntegrityAssert (const string &file, int line, const string &text)
 Report file corruption by throwing an eFile CSeqDBException.

Variables

static char const rcsid [] = "$Id: seqdbcommon.cpp 168560 2009-08-18 12:28:42Z maning $"

Function Documentation

static string s_GetPathSplitter (   )  [static]
 

Returns the character used to seperate path components in the current operating system or platform.

Definition at line 251 of file seqdbcommon.cpp.

Referenced by s_SeqDB_TryPaths().

template<class TCompare, class TVector>
void s_InsureOrder (  TVector &  v  ) 
 

Definition at line 547 of file seqdbcommon.cpp.

static bool s_SeqDB_DBExists (  const string &  dbname,
char  dbtype,
CSeqDB_FileExistence &  access
)  [static]
 

Test whether an index or alias file exists.

The provide filename is combined with both of the extensions appropriate to the database sequence type, and the resulting strings are checked for existence in the file system. The 'access' object defines how to check file existence.

Parameters:
dbname Input path and filename
dbtype Database type, either protein or nucleotide
access The file access object.
Returns:
true if either of the index or alias files is found

Definition at line 223 of file seqdbcommon.cpp.

References CSeqDB_FileExistence::DoesFileExist().

Referenced by s_SeqDB_TryPaths().

static string s_SeqDB_FindBlastDBPath (  const string &  dbname,
char  dbtype,
string *  sp,
bool  exact,
CSeqDB_FileExistence &  access,
const string  path = ""
)  [static]
 

Definition at line 360 of file seqdbcommon.cpp.

References CSeqDBAtlas::GenerateSearchPath(), and s_SeqDB_TryPaths().

Referenced by SeqDB_FindBlastDBPath(), and SeqDB_ResolveDbPath().

static bool s_SeqDB_IsBinaryGiList (  const char *  fbeginp,
const char *  fendp,
bool &  has_long_ids
)  [static]
 

This function determines whether a file is a valid binary gi file.

Parameters:
fbeginp pointer to start of file [in]
fendp pointer to end of file [in]
has_long_ids will be set to true if the gi file contains long IDs [out]
Returns:
true if file is binary
Exceptions:
CSeqDBException if file is empty or invalid gi file

Definition at line 779 of file seqdbcommon.cpp.

References NCBI_THROW.

Referenced by SeqDB_IsBinaryGiList(), SeqDB_ReadMemoryGiList(), and SeqDB_ReadMemoryTiList().

static string s_SeqDB_TryPaths (  const string &  blast_paths,
const string &  dbname,
char  dbtype,
bool  exact,
CSeqDB_FileExistence &  access
)  [static]
 

Search for a file in a provided set of paths.

This function takes a search path as a ":" delimited set of path names, and searches in those paths for the given database component. The component name may include path components. If the exact flag is set, the path is assumed to contain any required extension; otherwise extensions for index and alias files will be tried. Each element of the search path is tried in sequential order for both index or alias files (if exact is not set), before moving to the next element of the search path. The path returned from this function will not contain a file extension unless the provided filename did (in which case, exact is normally set).

Parameters:
blast_paths List of filesystem paths seperated by ":".
dbname Base name of the database index or alias file to search for.
dbtype Type of database, either protein or nucleotide.
exact Set to true if dbname already contains any needed extension.
atlas The memory management layer.
locked The lock holder object for this thread.
Returns:
Full pathname, minus extension, or empty string if none found.

Definition at line 315 of file seqdbcommon.cpp.

References CSeqDB_FileExistence::DoesFileExist(), NStr::eMergeDelims, ITERATE, s_GetPathSplitter(), s_SeqDB_DBExists(), SeqDB_CombinePath(), SeqDB_MakeOSPath(), and NStr::Tokenize().

Referenced by s_SeqDB_FindBlastDBPath().

void SeqDB_CombineAndQuote (  const vector< string > &  dbs,
string &  dbname
) 
 

Combine and quote list of database names.

SeqDB permits multiple databases to be opened by a single CSeqDB instance, by passing the database names as a space-delimited list to the CSeqDB constructor. To support paths and filenames with embedded spaces, surround any space-containing names with double quotes ('"'). Filenames not containing spaces may be quoted safely with no effect. (This solution prevents the use of names containing embedded double quotes.)

This method combines a list of database names into a string encoded in this way.

Parameters:
dbname Combined database name.
dbs Database names to combine.

Definition at line 1313 of file seqdbcommon.cpp.

References size.

void SeqDB_CombinePath (  const CSeqDB_Substring &  path,
const CSeqDB_Substring &  file,
const CSeqDB_Substring *  extn,
string &  outp
) 
 

Combine a filesystem path and file name.

Combine a provided filesystem path and a file name. This function tries to avoid duplicated delimiters. If either string is empty, the other is returned. Conceptually, the first path might be the current working directory and the second path is a filename. So, if the second path starts with "/", the first path is ignored. Also, care is taken to avoid duplicated delimiters. If the first path ends with the delimiter character, another delimiter will not be added between the strings. The delimiter used will vary from operating system to operating system, and is adjusted accordingly. If a file extension is specified, it will also be appended.

Parameters:
path The filesystem path to use
file The name of the file (may include path components)
extn The file extension (without the "."), or NULL if none.
outp A returned string containing the combined path and file name

Definition at line 133 of file seqdbcommon.cpp.

References CDirEntry::GetPathSeparator(), one, CSeqDB_Substring::Size(), and two.

Referenced by CSeqDB_BasePath::CSeqDB_BasePath(), CSeqDB_Path::CSeqDB_Path(), CSeqDB_Path::ReplaceFilename(), and s_SeqDB_TryPaths().

void SeqDB_ConvertOSPath (  string &  dbs  ) 
 

Change path delimiters to platform preferred kind in-place.

The path is modified in place. The 'Convert' interface is more efficient for cases where the new path would be assigned to the same string object. Delimiter conversion should be called by SeqDB at least once on any path received from the user, or via filesystem sources such as alias files.

Parameters:
dbs This string will be changed in-place.

Definition at line 265 of file seqdbcommon.cpp.

References CDirEntry::GetPathSeparator().

Referenced by CSeqDB_BasePath::FixDelimiters(), CSeqDB_FileName::FixDelimiters(), CSeqDB_BaseName::FixDelimiters(), and SeqDB_MakeOSPath().

void SeqDB_FileIntegrityAssert (  const string &  file,
int  line,
const string &  text
) 
 

Report file corruption by throwing an eFile CSeqDBException.

This function is only called in the case of validation failure, and is used in code paths where the validation failure may be related to file corruption or filesystem problems. File data is considered a user input, so checks for corrupt file are treated as input validation. This means that (1) checks that may be caused by file corruption scenarios are not disabled in debug mode, and (2) an exception (rather than an abort) is used. Note that this function does not check the assert, so it should only be called in case of failure.

Parameters:
file Name of the file containing the assert.
line The line the assert in on.
text The text version of the asserted condition.

Definition at line 1789 of file seqdbcommon.cpp.

References CSeqDBException::eFileErr, NStr::IntToString(), and SeqDB_ThrowException().

string SeqDB_FindBlastDBPath (  const string &  file_name,
char  dbtype,
string *  sp,
bool  exact,
CSeqDBAtlas &  atlas,
CSeqDBLockHold &  locked
) 
 

Finds a file in the search path.

This function resolves the full name of a file. It searches for a file of the provided base name and returns the provided name with the full path attached. If the exact_name flag is set, the file is assumed to have any extension it may need, and none is added for searching or stripped from the return value. If exact_name is not set, the file is assumed to end in ".pin", ".nin", ".pal", or ".nal", and if such a file is found, that extension is stripped from the returned string. Furthermore, in the exact_name == false case, only file extensions relevant to the dbtype are considered. Thus, if dbtype is set to 'p' for protein, only ".pin" and ".pal" are checked for; if it is set to nucleotide, only ".nin" and ".nal" are considered. The places where the file may be found are dependant on the search path. The search path consists of the current working directory, the contents of the BLASTDB environment variable, the BLASTDB member of the BLAST group of settings in the NCBI meta-registry. This registry is an interface to settings found in (for example) a ".ncbirc" file found in the user's home directory (but several paths are usually checked). Finally, if the provided file_name starts with the default path delimiter (which is OS dependant, but for example, "/" on Linux), the path will be taken to be absolute, and the search path will not affect the results.

Parameters:
file_name File base name for which to search
dbtype Input file base name
sp If non-null, the ":" delimited search path is returned here
exact If true, the file_name already includes any needed extension
atlas The memory management layer.
locked The lock holder object for this thread.
Returns:
Fully qualified filename and path, minus extension

Definition at line 401 of file seqdbcommon.cpp.

References CSeqDBAtlas::GetSearchPath(), and s_SeqDB_FindBlastDBPath().

Referenced by CSeqDBTaxInfo::CSeqDBTaxInfo(), and CSeqDBAliasSets::x_FindBlastDBPath().

bool SeqDB_IsBinaryGiList (  const string &  fname  ) 
 

Returns true if the file name passed contains a binary gi list.

Parameters:
fname The name of the GI list file. [in]
Exceptions:
CSeqDBException if file is invalid or empty

Definition at line 1157 of file seqdbcommon.cpp.

References CMemoryFile::GetPtr(), CMemoryFile::GetSize(), s_SeqDB_IsBinaryGiList(), and SeqDB_MakeOSPath().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastDBAliasApp::CreateAliasFile().

void SeqDB_JoinDelim (  string &  a,
const string &  b,
const string &  delim
) 
 

Join two strings with a delimiter.

This function returns whichever of two provided strings is non-empty. If both are non-empty, they are joined with a delimiter placed between them. It is intended for use when combining strings, such as a space delimited list of database volumes. It is probably not suitable for joining file system paths with filenames (use something like SeqDB_CombinePaths).

Parameters:
a First component and returned path
b Second component
delim The delimiter to use when joining elements

Definition at line 451 of file seqdbcommon.cpp.

Referenced by CSeqDB_TitleWalker::AddString().

string SeqDB_MakeOSPath (  const string &  dbs  ) 
 

Return path with delimiters changed to platform preferred kind.

The path is modified and returned. The 'Make' interface is more convenient for cases where the input path and output path are different objects. Delimiter conversion should be called by SeqDB at least once on any path received from the user, or via filesystem sources such as alias files.

Parameters:
dbs This is the input path.
Returns:
The modified path is returned.

Definition at line 279 of file seqdbcommon.cpp.

References SeqDB_ConvertOSPath().

Referenced by CSeqDB_SimpleAccessor::DoesFileExist(), s_SeqDB_TryPaths(), SeqDB_IsBinaryGiList(), SeqDB_ReadBinaryGiList(), SeqDB_ReadGiList(), and SeqDB_ReadTiList().

void SeqDB_ReadBinaryGiList (  const string &  name,
vector< int > &  gis
) 
 

Read a binary-format GI list from a file.

Parameters:
name The name of the file containing GIs. [in]
gis The GIs returned by this function. [out]

Definition at line 746 of file seqdbcommon.cpp.

References CMemoryFile::GetPtr(), CMemoryFile::GetSize(), NCBI_THROW, SeqDB_GetStdOrd(), and SeqDB_MakeOSPath().

void SeqDB_ReadGiList (  const string &  fname,
vector< int > &  gis,
bool *  in_order = 0
) 
 

Read a text or binary GI list from a file.

The GIs in a file are read into the provided vector<int>. If the in_order parameter is not null, the function will test the GIs for orderedness. It will set the bool to which in_order points to true if so, false if not.

Parameters:
fname The name of the GI list file. [in]
gis The GIs returned by this function. [out]
in_order If non-null, returns true iff the GIs were in order. [out]

Definition at line 1193 of file seqdbcommon.cpp.

References ITERATE, and SeqDB_ReadGiList().

void SeqDB_ReadGiList (  const string &  fname,
vector< CSeqDBGiList::SGiOid > &  gis,
bool *  in_order = 0
) 
 

Read a text or binary GI list from a file.

The GIs in a file are read into the provided SGiOid vector. The GI half of each element of the vector is assigned, but the OID half will be left as -1. If the in_order parameter is not null, the function will test the GIs for orderedness. It will set the bool to which in_order points to true if so, false if not.

Parameters:
fname The name of the GI list file. [in]
gis The GIs returned by this function. [out]
in_order If non-null, returns true iff the GIs were in order. [out]

Definition at line 1169 of file seqdbcommon.cpp.

References CMemoryFile::GetPtr(), CMemoryFile::GetSize(), SeqDB_MakeOSPath(), and SeqDB_ReadMemoryGiList().

void SeqDB_ReadMemoryGiList (  const char *  fbeginp,
const char *  fendp,
vector< CSeqDBGiList::SGiOid > &  gis,
bool *  in_order = 0
) 
 

Read a text or binary GI list from an area of memory.

The GIs in a memory region are read into the provided SGiOid vector. The GI half of each element of the vector is assigned, but the OID half will be left as -1. If the in_order parameter is not null, the function will test the GIs for orderedness. It will set the bool to which in_order points to true if so, false if not.

Parameters:
fbeginp The start of the memory region holding the GI list. [in]
fendp The end of the memory region holding the GI list. [in]
gis The GIs returned by this function. [out]
in_order If non-null, returns true iff the GIs were in order. [out]

Definition at line 809 of file seqdbcommon.cpp.

References _ASSERT, NCBI_THROW, s_SeqDB_IsBinaryGiList(), and SeqDB_GetStdOrd().

Referenced by CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), and SeqDB_ReadGiList().

void SeqDB_ReadMemoryTiList (  const char *  fbeginp,
const char *  fendp,
vector< CSeqDBGiList::STiOid > &  tis,
bool *  in_order = 0
) 
 

Read a text or binary TI list from an area of memory.

The TIs in a memory region are read into the provided STiOid vector. The TI half of each element of the vector is assigned, but the OID half will be left as -1. If the in_order parameter is not null, the function will test the TIs for orderedness. It will set the bool to which in_order points to true if so, false if not.

Parameters:
fbeginp The start of the memory region holding the TI list. [in]
fendp The end of the memory region holding the TI list. [in]
tis The TIs returned by this function. [out]
in_order If non-null, returns true iff the TIs were in order. [out]

Definition at line 969 of file seqdbcommon.cpp.

References NCBI_THROW, s_SeqDB_IsBinaryGiList(), and SeqDB_GetStdOrd().

Referenced by CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), and SeqDB_ReadTiList().

void SeqDB_ReadTiList (  const string &  fname,
vector< CSeqDBGiList::STiOid > &  tis,
bool *  in_order = 0
) 
 

Read a text or binary TI list from a file.

The TIs in a file are read into the provided STiOid vector. The TI half of each element of the vector is assigned, but the OID half will be left as -1. If the in_order parameter is not null, the function will test the TIs for orderedness. It will set the bool to which in_order points to true if so, false if not.

Parameters:
fname The name of the TI list file. [in]
tis The TIs returned by this function. [out]
in_order If non-null, returns true iff the TIs were in order. [out]

Definition at line 1181 of file seqdbcommon.cpp.

References CMemoryFile::GetPtr(), CMemoryFile::GetSize(), SeqDB_MakeOSPath(), and SeqDB_ReadMemoryTiList().

CSeqDB_Substring SeqDB_RemoveDirName (  CSeqDB_Substring  s  ) 
 

Returns a filename minus greedy path.

Substring version. This returns the part of a file name after the last path delimiter, or the whole path if no delimiter was found.

Parameters:
s Input path
Returns:
Filename portion of path

Definition at line 52 of file seqdbcommon.cpp.

References CSeqDB_Substring::EraseFront(), CSeqDB_Substring::FindLastOf(), and CDirEntry::GetPathSeparator().

Referenced by CSeqDB_Path::FindBaseName(), CSeqDB_BasePath::FindBaseName(), and CSeqDB_Path::FindFileName().

CSeqDB_Substring SeqDB_RemoveExtn (  CSeqDB_Substring  s  ) 
 

Returns a filename minus greedy path.

This returns the part of a file name after the last path delimiter, or the whole path if no delimiter was found.

Parameters:
s Input path
Returns:
Path minus file extension

Definition at line 78 of file seqdbcommon.cpp.

References CSeqDB_Substring::GetEnd(), CSeqDB_Substring::Resize(), and CSeqDB_Substring::Size().

Referenced by CSeqDB_Path::FindBaseName(), and CSeqDB_Path::FindBasePath().

CSeqDB_Substring SeqDB_RemoveFileName (  CSeqDB_Substring  s  ) 
 

Returns a path minus filename.

Substring version of the above. This returns the part of a file path before the last path delimiter, or the whole path if no delimiter was found.

Parameters:
s Input path
Returns:
Path minus file extension

Definition at line 64 of file seqdbcommon.cpp.

References CSeqDB_Substring::Clear(), CSeqDB_Substring::FindLastOf(), CDirEntry::GetPathSeparator(), and CSeqDB_Substring::Resize().

Referenced by CSeqDB_Path::FindDirName(), and CSeqDB_BasePath::FindDirName().

string SeqDB_ResolveDbPath (  const string &  filename  ) 
 

Resolve a file path using SeqDB's path algorithms.

This finds a file using the same algorithm used by SeqDB to find blast database filenames. The filename must include the extension if any. Paths which start with '/', '\', or a drive letter (depending on operating system) will be treated as absolute paths. If the file is not found an empty string will be returned.

Parameters:
filename Name of file to find.
Returns:
Resolved path or empty string if not found.

Definition at line 439 of file seqdbcommon.cpp.

References s_SeqDB_FindBlastDBPath().

Referenced by BOOST_AUTO_TEST_CASE(), and s_ReadGiList().

void SeqDB_SplitQuoted (  const string &  dbname,
vector< CSeqDB_Substring > &  dbs
) 
 

Combine and quote list of database names.

Parameters:
dbname Combined database name.
dbs Database names to combine.

Definition at line 1357 of file seqdbcommon.cpp.

void SeqDB_SplitQuoted (  const string &  dbname,
vector< CTempString > &  dbs
) 
 

Split a (possibly) quoted list of database names into pieces.

SeqDB permits multiple databases to be opened by a single CSeqDB instance, by passing the database names as a space-delimited list to the CSeqDB constructor. To support paths and filenames with embedded spaces, surround any space-containing names with double quotes ('"'). Filenames not containing spaces may be quoted safely with no effect. (This solution prevents the use of names containing embedded double quotes.)

This method splits a string encoded in this way into individual database names. Note that the resulting vector's objects are CTempString "slice" objects, and are only valid while the original (encoded) string is unchanged.

Parameters:
dbname Combined database name.
dbs Database names to combine.

Definition at line 1340 of file seqdbcommon.cpp.

References ITERATE, and SeqDB_SplitQuoted().

bool SeqDB_SplitString (  CSeqDB_Substring &  buffer,
CSeqDB_Substring &  front,
char  delim
) 
 

Parse a prefix from a substring.

The `buffer' argument is searched for a character. If found, the region before the delimiter is returned in `front' and the region after the delimiter is returned in `buffer', and true is returned. If not found, neither argument changes and false is returned.

Parameters:
buffer Source data to search and remainder if found. [in|out]
front Region before delim if found. [out]
delim Character for which to search. [in]
Returns:
true if the character was found, false otherwise.

Definition at line 115 of file seqdbcommon.cpp.

References buffer, and CSeqDB_Substring::Resize().

Variable Documentation

char const rcsid[] = "$Id: seqdbcommon.cpp 168560 2009-08-18 12:28:42Z maning $" [static]
 

Definition at line 34 of file seqdbcommon.cpp.

Generated on Wed Dec 9 07:47:33 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:18:39 2009 by modify_doxy.py rev. 173732