std::vector<std::string> ConfigFile::getArray(std::string strAttribute, std::vector<std::string> listDefaults)
{
std::map<std::string, ConfigAttribute>::iterator p;
//Find the uppercase string in the map
std::string lstr = Uppercase(strAttribute);
p = m_mapConfig.find(lstr);
if (p != m_mapConfig.end() && p->second.bIsArray)
{
return p->second.listValues;
}
else
{
std::cout << "Variable " << strAttribute.c_str() << " does not exist in config file or is not an array." << std::endl;
//Store the default value in the config file
if(m_bAddDefaultsToConfig && listDefaults.size() > 0)
{
setArray(strAttribute, listDefaults);
}
return listDefaults;
}
}
BOOL
CALLBACK
EnumNamesProc(
HMODULE Module,
PCWSTR Type,
PWSTR Name,
LONG Param
)
{
if (!EnumResourceLanguagesW(Module, Uppercase(Type), Uppercase(Name), EnumLangProc, 0))
{
DWORD Error = GetLastError();
wprintf(L"EnumResourceLanguages failed %x\n", Error);
}
return TRUE;
}
void ConfigFile::setString(std::string strAttribute, std::string strValue)
{
ConfigAttribute element;
element.strAttribute = strAttribute;
element.strValue = strValue;
m_mapConfig[Uppercase(strAttribute)] = element;
bIsModified = true;
}
LPTSTR lstrfind( LPTSTR pszStr, LPTSTR pszSearchStr )
/************************************************************************/
{
LPTSTR psz, pszSearch, pszStart = NULL;
WORD wChar, wCharSearch;
if( !( psz = Uppercase( pszStr )))
return( NULL );
if( !( pszSearch = Uppercase( pszSearchStr )))
return( NULL );
while( *psz )
{
if( IsDBCSLeadByte(( BYTE )*psz ))
wChar = *(( LPWORD )psz );
else
wChar = *psz;
if( IsDBCSLeadByte(( BYTE )*pszSearch ))
wCharSearch = *(( LPWORD )pszSearch );
else
wCharSearch = *pszSearch;
if( wChar == wCharSearch ) // If a character match...
{
pszSearch = MyCharNext( pszSearch );
if( !pszStart )
pszStart = psz;
}
else // If not a character match...
{
pszSearch = pszSearchStr;
pszStart = NULL;
}
if( !( *pszSearch )) // If at the end of the search string...
break;
psz = MyCharNext( psz );
}
return( pszStart );
}
bool ConfigFile::getBool(std::string strAttribute, bool bDefault)
{
std::string strReturn;
std::string strDefault;
std::ostringstream strStream;
strStream << bDefault;
strDefault = strStream.str();
strReturn = getString(strAttribute, strDefault);
if(strReturn == "1" || Uppercase(strReturn) == "TRUE")
{
return true;
}
return false;
}
BOOL
CALLBACK
EnumTypesProc(
HMODULE Module,
PWSTR Type,
LONG Param
)
{
if (!EnumResourceNamesW(Module, Type = Uppercase(Type), EnumNamesProc, 0))
{
WCHAR Buffer[20];
DWORD Error = GetLastError();
wprintf(L"EnumResourceNames(%p, %x %ls) failed %x\n", Module, Type, IdToString(Type, Buffer, NUMBER_OF(Buffer)), Error);
}
return TRUE;
}
void ConfigFile::setArray(std::string strAttribute, std::vector<std::string> listValues)
{
//Put the string in the map
setString(strAttribute, "Array()");
//Get the ConfigAttribute out of the map
std::map<std::string, ConfigAttribute>::iterator p;
//Find the uppercase string in the map
std::string lstr = Uppercase(strAttribute);
p = m_mapConfig.find(lstr);
if (p != m_mapConfig.end())
{
p->second.bIsArray = true;
p->second.listValues = listValues;
}
}
std::string ConfigFile::getString(std::string strAttribute, std::string strDefault)
{
std::map<std::string, ConfigAttribute>::iterator p;
//Find the uppercase string in the map
std::string lstr = Uppercase(strAttribute);
p = m_mapConfig.find(lstr);
if (p != m_mapConfig.end())
{
return p->second.strValue;
}
else
{
std::cout << "Variable " << strAttribute.c_str() << " does not exist in config file." << std::endl;
//Store the default value in the config file
if(m_bAddDefaultsToConfig)
{
setString(strAttribute, strDefault);
}
return strDefault;
}
}
long ReadLandMarkFile (char filename[], Land_Mark *onelandmark,
long reportlevel)
{
/***
Read in a set of points that define landmarks. These are not just
coronaries, but can also be occlusions, stimulus needles or other
goodies.
Input:
filename name of the coronary artery file to open.
surfnum current surface number
onelandmark pointer to the land mark structure for this surface
Return:
error =1 for successful reading of an old format coronary file.
=2 for success with a new format file.
otherwise, error of some sort.
***/
long i, j_start, pnum, firstpnum;
long error, ncorpts, nnewcorpts, segnum, segnumval;
long pntnum;
double distance, dist_threshold=0;
char instring[80], lmstring[20], *instring_p, *atoken_p;
char newfilename[100];
char sepchars[] = " ,\n";
FILE *luin_p;
/***********************************************************************/
if( reportlevel )
fprintf(stderr,"In ReadLMarkFile\n ");
error = 2;
/* First, open the file. */
if ((luin_p = fopen(filename, "r")) == NULL)
{
strcpy( newfilename, filename );
StripExtension( newfilename );
strcat( newfilename, ".lmarks");
if ((luin_p = fopen(newfilename, "r")) == NULL)
{
fprintf(stderr, "In readlmarkfile.c: error opening landmark file\n"
" Could not open either %s or %s \n",
filename, newfilename);
return ERR_FILE;
}
}
/*** Now, read in the contents of the file. ***/
/*** First line: the number of landmark segments to read ***/
if ( ReadLine( instring, luin_p ) == NULL )
{
fprintf(stderr,"**** Readlmarkfile Error: end of file hit "
" at start of file"
" ***\n");
return -5;
}
if (sscanf(instring, "%i", &onelandmark->numsegs) != 1)
{
fprintf(stderr,"*** In readlmarkfile.c: error in first "
"line of read ***\n");
error = -10;
return error;
}
/*** Set up the memory to hold the segments of the landmark ***/
if (( onelandmark->segs = (LandMarkSeg *)
calloc( (size_t) onelandmark->numsegs, sizeof(LandMarkSeg) ))
== NULL)
{
printf("*** ReadLandMarkfile: error getting memory\n");
return( ERR_MEM );
}
/*** Now the loop that reads all the Landmarks. ***/
for( segnum=0; segnum < onelandmark->numsegs; segnum++ )
{
long optional[4] = {-1, -1, -1, -1};
int optionalIndex = 0;
if ( reportlevel > 2 )
printf(" segnum = %d resetting npts to 0\n", segnum);
onelandmark->segs[segnum].segnum = segnum;
npts = 0;
if( ReadLine( instring, luin_p ) == NULL )
{
fprintf(stderr,"+++ (readlmarkfile.c)\n"
"+++ End of file hit before expected\n"
"+++ Will take the %d landmarks we have already\n",
segnum);
onelandmark->numsegs = segnum;
return error;
}
/*** Read through the line token by token and permit some flexibility
of the contents of this line, allowing the segnumval and setstring
parameters to be optional. ***/
instring_p = instring;
atoken_p = strtok( instring_p, sepchars );
i = strtol( atoken_p, NULL, 10 );
strcpy(lmstring, strtok( NULL, sepchars ) );
if ( lmstring == NULL )
{
ReportError( "ReadLMarkFile", "reading landmark type string",
ERR_FILE, instring);
return( ERR_FILE );
}
if ( ( atoken_p = strtok( NULL, sepchars ) ) == NULL )
{
ReportError( "ReadLMarkFile", "reading number of landmark points",
ERR_FILE, instring);
return( ERR_FILE );
}
ncorpts = strtol( atoken_p, NULL, 10 );
// allow for either segnumval, a color triple, or both
while ( (atoken_p = strtok( NULL, sepchars)) != NULL &&
optionalIndex < 4) {
optional[optionalIndex] = (short) strtol( atoken_p, NULL, 10 );
optionalIndex++;
}
if (optionalIndex == 1 || optionalIndex == 4)
segnumval = optional[0];
else
segnumval = -1;
{
int c;
for (c = 0; c < 3; c++) {
onelandmark->segs[segnum].color[c] =
(short) optional[c + (optionalIndex != 3?1:0)];
}
}
/*
if (sscanf(instring, "%d %s %d %d %s", &i, instring, &ncorpts) != 3)
{
fprintf(stderr,"*** In readlmarkfile.c: error reading number of"
" points and landmark type in coronary #%d ***\n",
segnum+1);
fprintf(stderr,"*** Each landmark must be preceeded by a line"
" that tells the segment number,"
" the type of landmark it is\n"
" and number of points\n");
error = -10;
return error;
}
*/
if ( i != segnum+1 )
fprintf(stderr,"+++ (readlmarkfile.c): the file says this is"
" segment %d\n"
"+++ But I have it as number %d\n", i, segnum+1);
onelandmark->segs[segnum].numpts = ncorpts;
onelandmark->segs[segnum].segnumval = segnumval;
/*** Now some pointer gymnastics to get rid of leading blanks
and terminate the string properly, and convert it to uppercase.***/
/* lmstring_p = &instring[0];
lmstring_p += strspn( lmstring_p, " ");
len = strcspn( lmstring_p, "\n#" );
*(lmstring_p+len) = '\0';
strncpy( lmstring, lmstring_p, (size_t) len+1);
*/
Uppercase( lmstring );
/*** Now see if the string matches the legal values. ***/
if( strncmp( lmstring, "CORONAR", 6 ) == 0 ||
strncmp( lmstring, "ARTER", 5) == 0 )
{
onelandmark->segs[segnum].type = LM_COR;
}
else if ( strncmp( lmstring, "OCCLUS", 3 ) == 0 )
{
onelandmark->segs[segnum].type = LM_OCCLUS;
}
else if ( strncmp( lmstring, "STITCH", 5 ) == 0 ||
strncmp( lmstring, "CLOS", 4 ) == 0 )
{
onelandmark->segs[segnum].type = LM_STITCH;
}
else if ( strncmp( lmstring, "STIM", 3 ) == 0 )
{
onelandmark->segs[segnum].type = LM_STIM;
}
else if ( strncmp( lmstring, "LEAD", 4 ) == 0 )
{
onelandmark->segs[segnum].type = LM_LEAD;
}
else if ( strncmp( lmstring, "PLANE", 5 ) == 0 )
{
onelandmark->segs[segnum].type = LM_PLANE;
}
else if ( strncmp( lmstring, "ROD", 3 ) == 0 )
{
onelandmark->segs[segnum].type = LM_ROD;
}
else if ( strncmp( lmstring, "PACENEEDLE", 6 ) == 0 )
{
onelandmark->segs[segnum].type = LM_PACENEEDLE;
}
else if ( strncmp( lmstring, "CATH", 4 ) == 0 )
{
onelandmark->segs[segnum].type = LM_CATH;
}
else if ( strncmp( lmstring, "FIBER", 4 ) == 0 )
{
onelandmark->segs[segnum].type = LM_FIBER;
}
else if ( strncmp( lmstring, "RECNEEDLE", 6 ) == 0 )
{
onelandmark->segs[segnum].type = LM_RECNEEDLE;
}
else if ( strncmp( lmstring, "CANNULA", 6 ) == 0 )
{
onelandmark->segs[segnum].type = LM_CANNULA;
} else
{
printf("** ReadLMarkfile: With landmark string: %s\n"
"** we cannot set the type\n", lmstring);
onelandmark->segs[segnum].type = -1;
}
/*** Set aside some memory for the coronary points. ***/
if( reportlevel > 2 )
fprintf(stderr," Allocating space for points "
"in landmarks\n"
" We want space for %d points\n",
ncorpts );
if( ( onelandmark->segs[segnum].pts = Alloc_fmatrix( ncorpts, 3 )
) == NULL )
{
printf("*** ReadLandmarkFile: error getting memory for %d pts\n",
ncorpts);
return (ERR_MEM);
}
if( ( onelandmark->segs[segnum].rad = (float *)
calloc((size_t) ncorpts, sizeof(float) ) ) == NULL )
{
fprintf(stderr,"*** Readlmarkfile, error allocating memory\n"
" for rads");
return (ERR_MEM);
}
if ( (onelandmark->segs[segnum].labels = Alloc_cmatrix( ncorpts, 40)
) == NULL )
{
printf("*** ReadLandmarkFile: error getting memory for labels\n");
return (ERR_MEM);
}
/*** Check the first line of the points and see if we have a new
or old coronary file format. ***/
if ( segnum == 0 )
{
if( ReadLine( instring, luin_p ) == NULL )
{
fprintf(stderr,"*** (readlmarkfile.c)\n"
"*** End of file hit while reading landmark %d\n",
segnum+1);
return( ERR_FILE );
}
if (sscanf( instring, "%f %f %f %f %39s",
&onelandmark->segs[segnum].pts[npts][CUTIL_X],
&onelandmark->segs[segnum].pts[npts][CUTIL_Y],
&onelandmark->segs[segnum].pts[npts][CUTIL_Z],
&onelandmark->segs[segnum].rad[npts],
onelandmark->segs[segnum].labels[npts]) >= 4)
{
if (reportlevel > 2)
fprintf(stderr," Landmark file seems to be in "
"proper format\n");
}
else if (sscanf( instring, "%f %f",
&onelandmark->segs[segnum].pts[npts][CUTIL_X],
&onelandmark->segs[segnum].pts[npts][CUTIL_Y]) == 2)
{
printf(" This is old format Coronary file\n"
" Redo the file !!!\n");
onelandmark->numsegs = 0;
return( ERR_FILE );
} else
{
fprintf(stderr,"*** Error in Readlmarkfile since file does not"
" fit a known format ***\n");
fprintf(stderr," Line reads %s", instring);
fprintf(stderr," So problems here\n");
return(-1);
}
j_start = 1;
npts++;
} else
j_start = 0;
/*** Now get on with reading the file. ***/
firstpnum = npts;
nnewcorpts = ncorpts;
for( pntnum=j_start; pntnum<ncorpts; pntnum++ )
{
if( ReadLine( instring, luin_p ) == NULL )
{
fprintf(stderr,"**** (readlmarkfile.c)\n"
"**** End of file hit while reading landmark %d\n"
"**** and point %d\n", segnum+1, pntnum+1);
return( ERR_FILE );
}
if (sscanf( instring, "%f %f %f %f %39s",
&onelandmark->segs[segnum].pts[npts][CUTIL_X],
&onelandmark->segs[segnum].pts[npts][CUTIL_Y],
&onelandmark->segs[segnum].pts[npts][CUTIL_Z],
&onelandmark->segs[segnum].rad[npts],
onelandmark->segs[segnum].labels[npts])
< 4)
{
fprintf(stderr,"*** In readlmarkfile: error reading points"
" at coronary #%d and point #%d ***\n",
segnum+1, pntnum+1);
fprintf(stderr,"*** instring reads %s", instring);
error = -20;
return (error);
}
if ( pntnum == j_start )
dist_threshold = ( onelandmark->segs[segnum].pts[npts][CUTIL_X] *
onelandmark->segs[segnum].pts[npts][CUTIL_X] +
onelandmark->segs[segnum].pts[npts][CUTIL_Y] *
onelandmark->segs[segnum].pts[npts][CUTIL_Y] +
onelandmark->segs[segnum].pts[npts][CUTIL_Z] *
onelandmark->segs[segnum].pts[npts][CUTIL_Z] ) /
10.E8;
npts++;
/*** Check for doubles. ***/
for (pnum=firstpnum; pnum<npts-1; pnum++)
{
if ( ( distance =
VECMAG3((onelandmark->segs[segnum].pts[pnum][CUTIL_X] -
onelandmark->segs[segnum].pts[npts-1][CUTIL_X] ),
(onelandmark->segs[segnum].pts[pnum][CUTIL_Y] -
onelandmark->segs[segnum].pts[npts-1][CUTIL_Y] ),
(onelandmark->segs[segnum].pts[pnum][CUTIL_Z] -
onelandmark->segs[segnum].pts[npts-1][CUTIL_Z] ) ) )
< dist_threshold ) {
fprintf(stderr,"+++ ReadLmarkfile in segment %d"
": You have doubled"
" points dude!\n"
" Point %d has a double"
" %f, %f, %f \n"
" And distance between them is %f\n",
segnum+1, pntnum+1,
onelandmark->segs[segnum].pts[npts-1][CUTIL_X],
onelandmark->segs[segnum].pts[npts-1][CUTIL_Y],
onelandmark->segs[segnum].pts[npts-1][CUTIL_Z],
distance);
npts--;
nnewcorpts--;
}
}
if ( reportlevel > 3 )
{
if ( npts < 50 )
{
fprintf(stderr," Line %d reads %s\n"
" and returns %f %f %f and %f\n",
npts, instring,
onelandmark->segs[segnum].pts[npts-1][CUTIL_X],
onelandmark->segs[segnum].pts[npts-1][CUTIL_Y],
onelandmark->segs[segnum].pts[npts-1][CUTIL_Z],
onelandmark->segs[segnum].rad[npts-1]);
}
}
}
if ( nnewcorpts != ncorpts ) {
onelandmark->segs[segnum].numpts = nnewcorpts;
}
if ( reportlevel > 3 )
{
fprintf(stderr," Coronary points and radii from segment %d\n",
segnum);
for( i=0; i < onelandmark->segs[segnum].numpts; i++ )
{
fprintf(stderr," %d %f %f %f %f \n",
i,
onelandmark->segs[segnum].pts[i][CUTIL_X],
onelandmark->segs[segnum].pts[i][CUTIL_Y],
onelandmark->segs[segnum].pts[i][CUTIL_Z],
onelandmark->segs[segnum].rad[i]);
}
}
}
fclose(luin_p);
return (error);
}
// get the next element in source, returns true no error, bEof will be set to true if eof is hit
bool Elementizer::GetNext(bool& bEof)
{
// update back data
m_backOffsets[m_backIndex&0x03] = m_sourceOffset;
m_backFlags[m_backIndex&0x03] = m_sourceFlags;
m_backIndex++;
// default to type_undefined
m_type = 0;
m_value = 0;
m_value_2 = 0;
m_asm = -1;
m_opType = -1;
m_pSymbolEntry = 0;
// no error, and not end of file
int error = error_none;
bEof = false;
bool bDocComment = false;
int constantBase = 0;
// setup source and symbol pointers
char* pSource = m_pCompilerData->source;
int sourceStart = m_sourceOffset;
m_currentSymbol[0] = 0;
int symbolOffset = 0;
while(1)
{
char currentChar = pSource[m_sourceOffset++];
// parse
if (constantBase > 0)
{
// this handles reading in a constant of base 2, 4, 10, or 16
// the constantBase value is set based on prefix characters handled below
if (currentChar == '_')
{
// skip over _'s
continue;
}
char digitValue;
if (!CheckDigit(currentChar, digitValue, (char)constantBase))
{
char notUsed;
char nextChar = pSource[m_sourceOffset];
bool bNextCharDigit = CheckDigit(nextChar, notUsed, (char)constantBase);
if ((constantBase == 10 &&
(currentChar == '.' && bNextCharDigit)) ||
currentChar == 'e' || currentChar == 'E')
{
// handle float
m_sourceOffset = sourceStart;
if (GetFloat(pSource, m_sourceOffset, m_value))
{
m_sourceOffset--; // back up to point at last digit
m_type = type_con_float;
}
else
{
error = error_fpcmbw;
}
}
else
{
// done with this constant
m_sourceOffset--; // back up to point at last digit
m_type = type_con;
}
constantBase = 0;
break;
}
else
{
// multiply accumulate the constant
m_value *= constantBase;
m_value += digitValue;
}
continue;
}
else if (m_sourceFlags != 0)
{
// old string? (continue parsing a string)
// for strings, m_sourceFlags will start out 0, and then cycle between 1 and 2 for
// each character of the string, when it is 1, a type_comma is returned, when it is
// 2 the next character is returned
// return a comma element between each character of the string
if (m_sourceFlags == 1)
{
m_sourceFlags++;
m_sourceOffset--;
m_type = type_comma;
break;
}
// reset flag
m_sourceFlags = 0;
// check for errors
if (currentChar == '\"')
{
error = error_es;
break;
}
else if (currentChar == 0)
{
m_sourceOffset--; // back up from eof
error = error_eatq;
break;
}
else if (currentChar == 13)
{
error = error_eatq;
break;
}
// return the character
m_value = currentChar;
// check the next character, if it's not a " then setup so the next
// call returns a type_comma, if it is a ", then we are done with this string
// and we leave the offset pointing after the "
currentChar = pSource[m_sourceOffset++];
if (currentChar != '\"')
{
m_sourceOffset--;
m_sourceFlags++;
}
// return the character constant
m_type = type_con;
break;
}
else if (currentChar == '\"')
{
// new string (start parsing a string)
// we got here because m_sourceFlags was 0 and the character is a "
// get first character of string
currentChar = pSource[m_sourceOffset++];
// check for errors
if (currentChar == '\"')
{
error = error_es;
break;
}
else if (currentChar == 0)
{
m_sourceOffset--; // back up from eof
error = error_eatq;
break;
}
else if (currentChar == 13)
{
error = error_eatq;
break;
}
// return the character in value
m_value = currentChar & 0x000000FF;
// check the next character, it's it's not a " then setup so the next
// call returns a type_comma, if it is a " then it means it's a one character
// string and we leave the offset pointing after the "
currentChar = pSource[m_sourceOffset++];
if (currentChar != '\"')
{
m_sourceOffset--; // back up, so this character will be read after the type_comma
m_sourceFlags = 1; // cause the next call to return a type_comma
}
// return the character constant
m_type = type_con;
break;
}
else if (currentChar == 0)
{
// eof
m_type = type_end;
bEof = true;
m_sourceOffset--;
sourceStart = m_sourceOffset;
break;
}
else if (currentChar == 13)
{
// eol
m_type = type_end;
break;
}
else if (currentChar <= ' ')
{
// space or tab?
sourceStart = m_sourceOffset;
continue;
}
else if (currentChar == '\'')
{
// comment
// read until end of line or file, handle doc comment
if (pSource[m_sourceOffset] == '\'')
{
m_sourceOffset++; // skip over second '
bDocComment = true;
g_pCompilerData->doc_flag = true;
}
while(1)
{
currentChar = pSource[m_sourceOffset++];
if (currentChar == 0)
{
m_sourceOffset--; // back up from eof
m_type = type_end;
bEof = true;
break;
}
if (bDocComment)
{
DocPrint(currentChar);
}
if (currentChar == 13)
{
m_type = type_end;
break;
}
}
break;
}
else if (currentChar == '{')
{
// brace comment
// read the whole comment, handling doc comments as needed
int braceCommentLevel = 1;
if (pSource[m_sourceOffset] == '{')
{
m_sourceOffset++; // skip over second {
bDocComment = true;
g_pCompilerData->doc_flag = true;
if (pSource[m_sourceOffset] == 13)
{
m_sourceOffset++; // skip over end if present
}
}
while(1)
{
currentChar = pSource[m_sourceOffset++];
if (currentChar == 0)
{
if (bDocComment)
{
error = error_erbb;
}
else
{
error = error_erb;
}
m_sourceOffset--; // back up from eof
sourceStart = m_sourceOffset;
break;
}
else if (!bDocComment && currentChar == '{')
{
braceCommentLevel++;
}
else if (currentChar == '}')
{
if (bDocComment && pSource[m_sourceOffset] == '}')
{
m_sourceOffset++; // skip over second }
break;
}
else if (!bDocComment)
{
braceCommentLevel--;
if (braceCommentLevel < 1)
{
break;
}
}
}
else if (bDocComment)
{
DocPrint(currentChar);
}
}
if (error == error_none)
{
sourceStart = m_sourceOffset;
continue;
}
else
{
break;
}
}
else if (currentChar == '}')
{
// unmatched brace comment end
error = error_bmbpbb;
break;
}
else if (currentChar == '%')
{
// binary
currentChar = pSource[m_sourceOffset++];
char temp;
if (currentChar == '%')
{
// double binary
currentChar = pSource[m_sourceOffset++];
if (!CheckDigit(currentChar, temp, 4))
{
error = error_idbn;
break;
}
constantBase = 4;
}
else
{
if (!CheckDigit(currentChar, temp, 2))
{
error = error_idbn;
break;
}
constantBase = 2;
}
m_sourceOffset--; // back up to first digit
// constantBase is now set, so loop back around to read in the constant
continue;
}
else if (currentChar == '$')
{
// hex
currentChar = pSource[m_sourceOffset++];
char temp;
if (!CheckDigit(currentChar, temp, 16))
{
m_sourceOffset--;
m_type = type_asm_org;
break;
}
constantBase = 16;
m_sourceOffset--; // back up to first digit
// constantBase is now set, so loop back around to read in the constant
continue;
}
else if (currentChar >= '0' && currentChar <= '9')
{
// dec
constantBase = 10;
m_sourceOffset--; // back up to first digit
// constantBase is now set, so loop back around to read in the constant
continue;
}
else
{
// symbol
currentChar = Uppercase(currentChar);
if (CheckWordChar(currentChar))
{
// do word symbol
while(CheckWordChar(currentChar) && symbolOffset <= symbol_limit)
{
m_currentSymbol[symbolOffset++] = currentChar;
currentChar = Uppercase(pSource[m_sourceOffset++]);
}
if (symbolOffset > symbol_limit)
{
error = error_sexc;
}
else
{
// back up so we point at last char of symbol
m_sourceOffset--;
// terminate symbol
m_currentSymbol[symbolOffset] = 0;
m_pSymbolEntry = m_pSymbolEngine->FindSymbol(m_currentSymbol);
}
}
else
{
// try non-word symbol (one or two char operators)
m_currentSymbol[symbolOffset++] = currentChar;
currentChar = pSource[m_sourceOffset++];
bool bDoOneChar = false;
bool bDoTwoChar = false;
// if the next char is not whitespace or eol
if (currentChar > ' ')
{
// three char symbol
// assign second char into symbol
m_currentSymbol[symbolOffset++] = currentChar;
// read third char into symbol
m_currentSymbol[symbolOffset++] = pSource[m_sourceOffset++];
// terminate symbol
m_currentSymbol[symbolOffset] = 0;
m_pSymbolEntry = m_pSymbolEngine->FindSymbol(m_currentSymbol);
if (m_pSymbolEntry == 0)
{
bDoTwoChar = true;
symbolOffset--;
}
}
if (bDoTwoChar)
{
// two char symbol
// back up so we point at last char of symbol
m_sourceOffset--;
// terminate symbol
m_currentSymbol[symbolOffset] = 0;
m_pSymbolEntry = m_pSymbolEngine->FindSymbol(m_currentSymbol);
if (m_pSymbolEntry == 0)
{
bDoOneChar = true;
symbolOffset--;
}
}
if (bDoOneChar || currentChar <= ' ')
{
// one char symbol
// back up so we point at last char of symbol
m_sourceOffset--;
// terminate symbol
m_currentSymbol[symbolOffset] = 0;
m_pSymbolEntry = m_pSymbolEngine->FindSymbol(m_currentSymbol);
if (m_pSymbolEntry == 0)
{
error = error_uc;
}
}
}
break;
}
}
// update pointers
m_pCompilerData->source_start = sourceStart;
m_pCompilerData->source_finish = m_sourceOffset;
// if we got a symbol, then set the type, value, etc.
if (m_type == 0 && m_pSymbolEntry)
{
SetFromSymbolEntry();
}
if (error != error_none)
{
m_pCompilerData->error = true;
m_pCompilerData->error_msg = g_pErrorStrings[error];
return false;
}
return true;
}
bool strieql(const std::string s1, const std::string s2)
{
std::string cs1 = s1, cs2 = s2;
Uppercase(cs1); Uppercase(cs2);
return (cs1 == cs2);
}
bool ConfigFile::ImportXML(std::string strXML)
{
TiXmlDocument doc;
//Load document from strXML using streams
std::istringstream strIStream;
strIStream.str(strXML);
strIStream >> doc;
if ( doc.NoChildren() )
{
std::cout << "Could not parse xml string. Error='" << doc.ErrorDesc() << "'. Using Default Data" << std::endl;
m_strLastError = doc.ErrorDesc();
//Use already loaded defaults
return false;
}
TiXmlNode* parent = 0;
TiXmlNode* child = 0;
TiXmlNode* tempChild = 0;
TiXmlElement* configElement = 0;
TiXmlElement* itemElement = 0;
TiXmlElement* tempElement = 0;
// Get the "configData" element.
parent = doc.FirstChild( m_strIdentifier.c_str() );
assert( parent );
configElement =parent->ToElement();
assert( configElement );
//Read all the configuration data
for( child = configElement->FirstChild(); child; child = child->NextSibling() )
{
itemElement = child->ToElement();
assert( itemElement );
//convert to uppercase
std::string strElement = itemElement->Value();
//replace underscore with whitespace
std::replace(strElement.begin(), strElement.end(), '_', ' ');
ConfigAttribute element;
element.strAttribute = strElement;
element.strValue = itemElement->Attribute( "value");
//Read the sub items from the file and store as an array
if(!itemElement->NoChildren() || element.strValue == "Array()")
{
element.bIsArray = true;
for( tempChild = itemElement->FirstChild(); tempChild; tempChild = tempChild->NextSibling() )
{
tempElement = tempChild->ToElement();
assert( tempElement );
element.listValues.push_back(tempElement->Attribute( "value"));
}
}
m_mapConfig[Uppercase(strElement)] = element;
}
return true;
return true;
}
/**
* Fill the Option fields, with the argc array
*/
int Read_Command_Line(option *io, int argc, char **argv)
{
int c;
int idx;
int i;
int writemode;
PhyML_Printf("\n. command-line: ");
For(i,argc) PhyML_Printf("%s ",argv[i]);
if(argc == 1) Exit("\n. No argument was passed to the program. Please check the documentation. \n");
struct option longopts[] =
{
{"n_rgrft", required_argument,NULL,0},
{"n_globl", required_argument,NULL,1},
{"max_dist", required_argument,NULL,2},
{"n_optim", required_argument,NULL,3},
{"n_best", required_argument,NULL,4},
{"model", required_argument,NULL,5},
{"search", required_argument,NULL,6},
{"datatype", required_argument,NULL,7},
{"multiple", required_argument,NULL,8},
{"input", required_argument,NULL,9},
{"bootstrap", required_argument,NULL,10},
{"ts/tv", required_argument,NULL,11},
{"nclasses", required_argument,NULL,12},
{"pinv", required_argument,NULL,13},
{"alpha", required_argument,NULL,14},
{"inputtree", required_argument,NULL,15},
{"min_diff_lk_local", required_argument,NULL,16},
{"min_diff_lk_global",required_argument,NULL,17},
{"steph_spr", no_argument,NULL,18},
{"brent_it_max", required_argument,NULL,19},
{"rand_start", no_argument,NULL,20},
{"n_rand_starts", required_argument,NULL,21},
{"sequential", no_argument,NULL,22},
{"inside_opt", no_argument,NULL,23},
{"p_moves", required_argument,NULL,24},
{"fast_nni", no_argument,NULL,25},
{"g_pars", no_argument,NULL,26},
{"r_seed", required_argument,NULL,27},
{"collapse_boot", required_argument,NULL,28},
{"random_boot", required_argument,NULL,29},
{"print_trace", no_argument,NULL,30},
{"print_site_lnl", no_argument,NULL,31},
{"print_site_lk", no_argument,NULL,31},
{"cov", no_argument,NULL,32},
{"cov_delta", required_argument,NULL,33},
{"cov_alpha", required_argument,NULL,34},
{"cov_ncats", required_argument,NULL,35},
{"ps", no_argument,NULL,36},
{"cov_free", no_argument,NULL,37},
{"no_gap", no_argument,NULL,38},
{"n_rr_branch", required_argument,NULL,39},
{"append", no_argument,NULL,40},
{"no_five_branch", no_argument,NULL,41},
{"pars_thresh", required_argument,NULL,42},
{"min_diff_lk_move", required_argument,NULL,43},
{"hybrid", no_argument,NULL,44},
{"use_median", no_argument,NULL,45},
{"run_id", required_argument,NULL,46},
{"pars", no_argument,NULL,47},
{"quiet", no_argument,NULL,48},
{"version", no_argument,NULL,49},
{"calibration_file", required_argument,NULL,50},
{"calibration", required_argument,NULL,50},
{"clade_file", required_argument,NULL,50},
{"boot_progress_every", required_argument,NULL,51},
{"aa_rate_file", required_argument,NULL,52},
{"chain_len", required_argument,NULL,53},
{"sample_freq", required_argument,NULL,54},
{"burnin", required_argument,NULL,55},
{"no_memory_check", no_argument,NULL,56},
{"no_colalias", no_argument,NULL,57},
{"alias_subpatt", no_argument,NULL,58},
{"no_sequences", no_argument,NULL,59},
{"prior", no_argument,NULL,59},
{"fastlk", no_argument,NULL,60},
{"free_rates", no_argument,NULL,61},
{"freerates", no_argument,NULL,61},
{"freerate", no_argument,NULL,61},
{"free_rate", no_argument,NULL,61},
{"is", no_argument,NULL,62},
// no 63 since it corresponds to character '?'
{"rate_model", required_argument,NULL,64},
{"ratemodel", required_argument,NULL,64},
{"log_l", no_argument,NULL,65},
{"gamma_lens", no_argument,NULL,66},
{"il", no_argument,NULL,66},
{"codpos", required_argument,NULL,67},
{"constraint_file", required_argument,NULL,68},
{"constraint_tree", required_argument,NULL,68},
{"help", no_argument,NULL,69},
{"mutmap", no_argument,NULL,70},
{"parvals", required_argument,NULL,71},
{"constrained_lens", no_argument,NULL,72},
{"xml", required_argument,NULL,73},
{"l_var", required_argument,NULL,74},
#ifdef BEAGLE
{"beagle_resource", required_argument,NULL,75},
#endif
{"ancestral", no_argument,NULL,76},
{"anc", no_argument,NULL,76},
{"coord_file", required_argument,NULL,77},
{0,0,0,0}
};
io->datatype = UNDEFINED;
#ifndef PHYML
int open_ps_file = 0;
#endif
idx=-1;
do
{
c = getopt_long(argc,argv,"qi:d:m:b:n:t:f:zk:v:c:a:u:ho:s:x:g:l:ep",longopts,&idx);
switch(c)
{
case 77:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_coord_file, optarg);
io->fp_in_coord = Openfile(io->in_coord_file,READ);
}
Free(tmp);
break;
}
case 76:
{
io->ancestral = YES;
break;
}
#ifdef BEAGLE
case 75:
{
io->beagle_resource = (int)atoi(optarg);
break;
}
#endif
case 74:
{
io->mod->l_var_sigma = String_To_Dbl(optarg);
break;
}
case 73:
{
#ifdef INVITEE
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
PhyTime_XML(optarg);
return 0;
#elif defined(PHYML)
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
PhyML_XML(optarg);
return 0;
#elif defined(DATE)
Free_Optimiz(io->mod->s_opt);
M4_Free_M4_Model(io->mod->m4mod);
Free_Model_Basic(io->mod);
Free_Input(io);
DATE_XML(optarg);
return 0;
#endif
break;
}
case 72:
{
io->mod->s_opt->constrained_br_len = YES;
break;
}
case 71:
{
io->mcmc->in_fp_par = fopen(optarg,"r");
io->mcmc->randomize = NO;
break;
}
case 70:
{
io->mutmap = YES;
break;
}
case 68:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_constraint_tree_file, optarg);
io->fp_in_constraint_tree = Openfile(io->in_constraint_tree_file,0);
}
Free(tmp);
break;
}
case 67:
{
phydbl pos;
pos = atof(optarg);
io->codpos = (int)pos;
if(io->codpos < 1 || io->codpos > 3)
{
char choix;
PhyML_Printf("\n. Coding position must be set to 1, 2 or 3.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
break;
}
case 66:
{
io->mod->gamma_mgf_bl = YES;
io->mod->s_opt->opt_gamma_br_len = YES;
break;
}
case 65:
{
io->mod->log_l = YES;
break;
}
case 64:
{
char *s;
int i;
s = (char *)mCalloc(T_MAX_NAME,sizeof(char));
i = 0;
while(optarg[i++]) s[i]=tolower(optarg[i]);
if(!strcmp(optarg,"gbd")) io->rates->model = THORNE;
else if(!strcmp(optarg,"gbs")) io->rates->model = GUINDON;
else if(!strcmp(optarg,"gamma")) io->rates->model = GAMMA;
else if(!strcmp(optarg,"clock")) io->rates->model = STRICTCLOCK;
else if(!strcmp(optarg,"strictclock")) io->rates->model = STRICTCLOCK;
else if(!strcmp(optarg,"strict_clock")) io->rates->model = STRICTCLOCK;
else
{
PhyML_Printf("\n. rate_model should be 'gbs', 'gbd', 'gamma' or 'clock'.");
Exit("\n");
}
Free(s);
break;
}
case 62:
{
io->mcmc->is = YES;
break;
}
case 61:
{
io->mod->ras->free_mixt_rates = YES;
io->mod->s_opt->opt_free_mixt_rates = YES;
break;
}
case 60:
{
io->lk_approx = NORMAL;
break;
}
case 59:
{
io->mcmc->use_data = NO;
break;
}
case 58:
{
io->do_alias_subpatt = YES;
break;
}
case 57:
{
io->colalias = NO;
break;
}
case 56:
{
io->mem_question = NO;
break;
}
case 55:
{
phydbl len;
len = atof(optarg);
io->mcmc->chain_len_burnin = (int)len;
if(io->mcmc->chain_len_burnin < 1)
{
char choix;
PhyML_Printf("\n. chain_len_burnin must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 54:
{
phydbl len;
len = atof(optarg);
io->mcmc->sample_interval = (int)len;
if(io->mcmc->sample_interval < 1)
{
char choix;
PhyML_Printf("\n. sample_interval must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 53:
{
phydbl len;
len = atof(optarg);
io->mcmc->chain_len = (int)len;
if(io->mcmc->chain_len < 1)
{
char choix;
PhyML_Printf("\n. chain_len must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 52:
{
char *s;
s = (char *)mCalloc(T_MAX_FILE, sizeof(char));
strcpy(s,optarg);
io->mod->fp_aa_rate_mat = Openfile(s,0);
strcpy(io->mod->aa_rate_mat_file->s,s);
Free(s);
break;
}
case 51:
{
io->boot_prog_every = atoi(optarg);
if(io->boot_prog_every < 1)
{
char choix;
PhyML_Printf("\n. boot_progress_every must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 50:
{
strcpy(io->clade_list_file,optarg);
break;
}
case 49:
{
PhyML_Printf("\n. This is PhyML version %s.\n\n",VERSION);
Exit("");
break;
}
case 48 :
{
io->quiet = 1;
break;
}
case 'p' : case 47 :
{
io->in_tree = 1;
break;
}
case 46 :
{
io->append_run_ID = YES;
strcpy(io->run_id_string,optarg);
break;
}
case 45 :
{
io->mod->ras->gamma_median = 1;
break;
}
case 44 :
{
io->mod->s_opt->hybrid_thresh = 0;
break;
}
case 43 :
{
io->mod->s_opt->min_diff_lk_move = atof(optarg);
if(io->mod->s_opt->min_diff_lk_move < 0)
{
char choix;
PhyML_Printf("\n. Min_diff_lk_move must be a double greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 42 :
{
io->mod->s_opt->pars_thresh = (int)atoi(optarg);
if(io->mod->s_opt->pars_thresh < 0)
{
PhyML_Printf("\n. The parsimony threshold must be an integer greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
Exit("\n");
}
break;
}
case 41 :
{
io->mod->s_opt->opt_five_branch = 0;
break;
}
case 40 :
{
writemode = 2;
break;
}
case 39 :
{
break;
}
case 38 :
{
io->rm_ambigu = 1;
break;
}
case 37 :
{
io->mod->s_opt->opt_cov_free_rates = YES;
io->mod->m4mod->use_cov_alpha = NO;
io->mod->m4mod->use_cov_free = YES;
break;
}
case 36 :
{
#ifndef PHYML
open_ps_file = 1;
#endif
break;
}
case 35 :
{
io->mod->m4mod->n_h = (int)atoi(optarg);
if(io->mod->m4mod->n_h < 1)
{
char choix;
PhyML_Printf("\n. The number of classes must be greater than 0.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 34 :
{
io->mod->m4mod->use_cov_alpha = YES;
io->mod->m4mod->use_cov_free = NO;
if(!strcmp(optarg,"e") || !strcmp(optarg,"E") ||
!strcmp(optarg,"estimated") || !strcmp(optarg,"ESTIMATED"))
{
io->mod->s_opt->opt_cov_alpha = YES;
io->mod->m4mod->alpha = 1.0;
}
else
{
io->mod->m4mod->alpha = (phydbl)atof(optarg);
if(io->mod->m4mod->alpha < 1.E-5)
{
char choix;
PhyML_Printf("\n. The value of alpha must be greater than 1.E-5.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
break;
}
case 33 :
{
if(!strcmp(optarg,"e") || !strcmp(optarg,"E") ||
!strcmp(optarg,"estimated") || !strcmp(optarg,"ESTIMATED"))
{
io->mod->s_opt->opt_cov_delta = YES;
io->mod->m4mod->delta = 1.0;
}
else
{
io->mod->m4mod->delta = (phydbl)atof(optarg);
if(atof(optarg) < 1.E-10)
{
char choix;
PhyML_Printf("\n. The value of delta must be larger than 1.E-10.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
break;
}
case 32 :
{
io->mod->use_m4mod = YES;
break;
}
case 31 :
{
io->print_site_lnl = YES;
break;
}
case 30 :
{
io->print_trace = YES;
break;
}
case 29 :
{
io->random_boot_seq_order = (int)atoi(optarg);
break;
}
case 28 :
{
io->collapse_boot = (int)atoi(optarg);
break;
}
case 27 :
{
io->r_seed = (int)atoi(optarg);
break;
}
case 26 :
{
io->mod->s_opt->general_pars = YES;
break;
}
case 25 :
{
io->mod->s_opt->fast_nni = YES;
break;
}
case 24 :
{
io->mod->s_opt->p_moves_to_examine = (phydbl)atof(optarg);
break;
}
case 23 :
{
io->mod->s_opt->wim_inside_opt = 1;
break;
}
case 0 :
{
io->mod->s_opt->wim_n_rgrft = atoi(optarg);
break;
}
case 1 :
{
io->mod->s_opt->wim_n_globl = atoi(optarg);
break;
}
case 2 :
{
io->mod->s_opt->wim_max_dist = atoi(optarg);
break;
}
case 3 :
{
io->mod->s_opt->wim_n_optim = atoi(optarg);
break;
}
case 4 :
{
io->mod->s_opt->wim_n_best = atoi(optarg);
break;
}
case 16 :
{
io->mod->s_opt->min_diff_lk_local = atof(optarg);
break;
}
case 17 :
{
io->mod->s_opt->min_diff_lk_global = atof(optarg);
break;
}
case 18 :
{
io->mod->s_opt->steph_spr = 0;
io->mod->s_opt->greedy = 1;
break;
}
case 19 :
{
io->mod->s_opt->brent_it_max = atoi(optarg);
break;
}
case 20 :
{
io->mod->s_opt->random_input_tree = 1;
break;
}
case 21 :
{
io->mod->s_opt->random_input_tree = 1;
io->mod->s_opt->n_rand_starts = atoi(optarg);
if(io->mod->s_opt->n_rand_starts < 1) Exit("\n== Number of random starting trees must be > 0.\n\n");
}
case 's':case 6:
{
if((!strcmp(optarg,"spr")) || (!strcmp(optarg,"SPR")))
{
io->mod->s_opt->topo_search = SPR_MOVE;
io->mod->s_opt->greedy = (io->mod->s_opt->steph_spr)?(0):(1);
}
else if((!strcmp(optarg,"nni")) || (!strcmp(optarg,"NNI")))
{
io->mod->s_opt->topo_search = NNI_MOVE;
io->mod->s_opt->random_input_tree = 0;
}
else if((!strcmp(optarg,"best")) || (!strcmp(optarg,"BEST")))
{
io->mod->s_opt->topo_search = BEST_OF_NNI_AND_SPR;
io->mod->s_opt->greedy = (io->mod->s_opt->steph_spr)?(0):(1);
}
break;
}
case 'd':case 7:
{
if(!strcmp(optarg,"nt"))
{
io->datatype = NT;
io->mod->ns = 4;
io->mod->m4mod->n_o = 4;
if((io->mod->whichmodel == LG) ||
(io->mod->whichmodel == WAG) ||
(io->mod->whichmodel == DAYHOFF) ||
(io->mod->whichmodel == JTT) ||
(io->mod->whichmodel == BLOSUM62) ||
(io->mod->whichmodel == MTREV) ||
(io->mod->whichmodel == RTREV) ||
(io->mod->whichmodel == CPREV) ||
(io->mod->whichmodel == DCMUT) ||
(io->mod->whichmodel == VT) ||
(io->mod->whichmodel == MTMAM) ||
(io->mod->whichmodel == MTART) ||
(io->mod->whichmodel == HIVW) ||
(io->mod->whichmodel == HIVB) ||
(io->mod->whichmodel == AB) ||
(io->mod->whichmodel == CUSTOMAA)
)
{
io->mod->whichmodel = HKY85;
strcpy(io->mod->modelname->s, "HKY85\0");
}
}
else if (!strcmp(optarg,"aa"))
{
io->datatype = AA;
io->mod->s_opt->opt_kappa = NO;
io->mod->ns = 20;
io->mod->m4mod->n_o = 20;
if(
(io->mod->whichmodel == JC69) ||
(io->mod->whichmodel == K80) ||
(io->mod->whichmodel == F81) ||
(io->mod->whichmodel == HKY85) ||
(io->mod->whichmodel == F84) ||
(io->mod->whichmodel == TN93) ||
(io->mod->whichmodel == GTR) ||
(io->mod->whichmodel == CUSTOM)
)
{
io->mod->whichmodel = LG;
strcpy(io->mod->modelname->s, "LG\0");
}
}
else if ((!strcmp(optarg,"generic")) || (!strcmp(optarg,"gen")))
{
io->datatype = GENERIC;
}
else
{
char choix;
PhyML_Printf("\n. Unknown argument to -d option: please use `nt' for DNA or `aa' for Amino-Acids\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case 'm': case 5 :
{
int i;
For(i,strlen(optarg)) Uppercase(optarg+i);
if(!isalpha(optarg[0]))
{
strcpy(io->mod->custom_mod_string->s,optarg);
if(strlen(io->mod->custom_mod_string->s) != 6)
{
Warn_And_Exit("\n. The string should be of length 6.\n");
}
else
{
/* Make_Custom_Model(io->mod); */
/* Translate_Custom_Mod_String(io->mod); */
}
io->datatype = NT;
io->mod->whichmodel = CUSTOM;
strcpy(io->mod->modelname->s, "custom");
io->mod->s_opt->opt_kappa = NO;
io->mod->s_opt->opt_rr = YES;
}
else if (strcmp(optarg, "JC69") == 0)
{
io->datatype = NT;
io->mod->whichmodel = JC69;
}
else if(strcmp(optarg, "K80") == 0)
{
io->datatype = NT;
io->mod->whichmodel = K80;
}
else if(strcmp(optarg, "F81") == 0)
{
io->datatype = NT;
io->mod->whichmodel = F81;
}
else if (strcmp(optarg, "HKY85") == 0)
{
io->datatype = NT;
io->mod->whichmodel = HKY85;
}
else if(strcmp(optarg, "F84") == 0)
{
io->datatype = NT;
io->mod->whichmodel = F84;
}
else if (strcmp (optarg,"TN93") == 0)
{
io->datatype = NT;
io->mod->whichmodel = TN93;
}
else if(strcmp (optarg, "GTR") == 0)
{
io->datatype = NT;
io->mod->whichmodel = GTR;
}
else if(strcmp(optarg, "DAYHOFF") == 0)
{
io->datatype = AA;
io->mod->whichmodel = DAYHOFF;
}
else if(strcmp (optarg, "JTT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = JTT;
}
else if(strcmp(optarg, "MTREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTREV;
}
else if(strcmp (optarg, "LG") == 0)
{
io->datatype = AA;
io->mod->whichmodel = LG;
}
else if(strcmp (optarg, "WAG") == 0)
{
io->datatype = AA;
io->mod->whichmodel = WAG;
}
else if(strcmp(optarg, "DCMUT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = DCMUT;
}
else if(strcmp (optarg, "RTREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = RTREV;
}
else if(strcmp(optarg, "CPREV") == 0)
{
io->datatype = AA;
io->mod->whichmodel = CPREV;
}
else if(strcmp(optarg, "VT") == 0)
{
io->datatype = AA;
io->mod->whichmodel = VT;
}
else if(strcmp(optarg, "BLOSUM62") == 0)
{
io->datatype = AA;
io->mod->whichmodel = BLOSUM62;
}
else if(strcmp(optarg, "MTMAM") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTMAM;
}
else if (strcmp(optarg,"MTART") == 0)
{
io->datatype = AA;
io->mod->whichmodel = MTART;
}
else if (strcmp(optarg,"HIVW") == 0)
{
io->datatype = AA;
io->mod->whichmodel = HIVW;
}
else if(strcmp(optarg, "HIVB") == 0)
{
io->datatype = AA;
io->mod->whichmodel = HIVB;
}
else if(strcmp(optarg, "AB") == 0)
{
io->datatype = AA;
io->mod->whichmodel = AB;
}
else if (strcmp(optarg, "CUSTOM") == 0)
{
io->datatype = AA;
io->mod->whichmodel = CUSTOMAA;
}
else
{
PhyML_Printf("\n. The model name is incorrect. Please see the documentation.\n");
Exit("\n");
}
Set_Model_Name(io->mod);
break;
}
case 'a':case 14 :
{
if ((strcmp (optarg, "e") == 0) ||
(strcmp (optarg, "E") == 0) ||
(strcmp (optarg, "estimated") == 0) ||
(strcmp (optarg, "ESTIMATED") == 0))
{
io->mod->s_opt->opt_alpha = YES;
}
else if (atof(optarg) < 1.E-10)
{
char choix;
PhyML_Printf("\n. Alpha must be > 1.E-10.\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->alpha->v = (phydbl)atof(optarg);
io->mod->s_opt->opt_alpha = 0;
}
break;
}
case 'b':case 10:
{
if ((int)String_To_Dbl(optarg) < -5)
{
char choix;
PhyML_Printf("\n. Branch test value must be a positive integer for bootstrap, or between -1 and -4 for aLRT branch test\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
if((int)String_To_Dbl(optarg) > 0)
{
io->ratio_test = 0;
io->mod->bootstrap = (int)atoi(optarg);
io->print_boot_trees = 1;
if(io->n_data_sets > 1)
{
char choix;
PhyML_Printf("\n. Bootstrap option is not allowed with multiple data sets\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
}
else if (atoi(optarg)==0)
{
io->mod->bootstrap = 0;
io->ratio_test = 0;
}
else
{
io->mod->bootstrap = 0;
io->ratio_test = -(int)atoi(optarg);
}
}
break;
}
case 'c':case 12:
{
if ((!atoi(optarg)) || (atoi(optarg) < 0))
{
char choix;
PhyML_Printf("\n. Unknown argument to -c option: the number of rate categories must be a positive integer\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->n_catg = atoi(optarg);
if(io->mod->ras->n_catg < 1)
{
PhyML_Printf("\n. The number of rate categories must be a positive integer\n");
Exit("\n");
}
}
break;
}
case 'f':
{
if(!strcmp(optarg,"e"))
{
if(io->datatype == NT)
io->mod->s_opt->opt_state_freq = NO;
else if (io->datatype == AA)
io->mod->s_opt->opt_state_freq = YES;
else
{
PhyML_Printf("\n. Please define the data type (nt or aa) before setting the -f option\n");
Exit("\n");
}
}
else if(!strcmp(optarg,"m"))
{
if (io->datatype == NT)
io->mod->s_opt->opt_state_freq = YES;
else if (io->datatype == AA)
io->mod->s_opt->opt_state_freq = NO;
else
{
PhyML_Printf("\n. Please define the data type (nt or aa) before setting the -f option\n");
Exit("\n");
}
}
else if(!isalpha(optarg[0]))
{
phydbl sum;
double val1,val2,val3,val4;
io->mod->s_opt->opt_state_freq = 0;
io->mod->s_opt->user_state_freq = 1;
/* sscanf(optarg,"%lf,%lf,%lf,%lf", */
/* io->mod->user_b_freq, */
/* io->mod->user_b_freq+1, */
/* io->mod->user_b_freq+2, */
/* io->mod->user_b_freq+3); */
sscanf(optarg,"%lf,%lf,%lf,%lf",&val1,&val2,&val3,&val4);
io->mod->user_b_freq->v[0] = (phydbl)val1;
io->mod->user_b_freq->v[1] = (phydbl)val2;
io->mod->user_b_freq->v[2] = (phydbl)val3;
io->mod->user_b_freq->v[3] = (phydbl)val4;
sum =
(io->mod->user_b_freq->v[0] +
io->mod->user_b_freq->v[1] +
io->mod->user_b_freq->v[2] +
io->mod->user_b_freq->v[3]);
io->mod->user_b_freq->v[0] /= sum;
io->mod->user_b_freq->v[1] /= sum;
io->mod->user_b_freq->v[2] /= sum;
io->mod->user_b_freq->v[3] /= sum;
if(io->mod->user_b_freq->v[0] < .0 ||
io->mod->user_b_freq->v[1] < .0 ||
io->mod->user_b_freq->v[2] < .0 ||
io->mod->user_b_freq->v[3] < .0 ||
io->mod->user_b_freq->v[0] > 1. ||
io->mod->user_b_freq->v[1] > 1. ||
io->mod->user_b_freq->v[2] > 1. ||
io->mod->user_b_freq->v[3] > 1.)
{
Warn_And_Exit("\n. Invalid base frequencies.\n");
}
}
break;
}
case 'h':case 69:
{
Usage();
break;
}
case 'i':case 9:
{
char *tmp;
tmp = (char *) mCalloc (T_MAX_FILE, sizeof(char));
if (strlen (optarg) > T_MAX_FILE -16)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (!Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' does not exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_align_file, optarg);
io->fp_in_align = Openfile(io->in_align_file,0);
strcpy(io->out_file, optarg);
strcpy(io->out_tree_file,optarg);
#ifdef PHYML
strcat(io->out_tree_file,"_phyml_tree");
#elif M4
strcat(io->out_tree_file,"_m4_tree");
#elif PHYREX
strcat(io->out_tree_file,"_phyrex_tree");
#endif
strcpy(io->out_stats_file,optarg);
#ifdef PHYML
strcat(io->out_stats_file,"_phyml_stats");
#elif M4
strcat(io->out_stats_file,"_m4_stats");
#elif PHYREX
strcat(io->out_stats_file,"_phyrex_stats");
#endif
#ifdef PHYREX
strcpy(io->out_summary_file,optarg);
strcat(io->out_summary_file,"_phyrex_summary");
#endif
}
Free (tmp);
break;
}
case 't':case 11:
{
if ((io->mod->whichmodel != JC69) &&
(io->mod->whichmodel != F81) &&
(io->mod->whichmodel != GTR))
{
if ((strcmp(optarg, "e") == 0) ||
(strcmp(optarg, "E") == 0) ||
(strcmp(optarg, "estimated") == 0) ||
(strcmp(optarg, "ESTIMATED") == 0))
{
io->mod->kappa->v = 4.0;
io->mod->s_opt->opt_kappa = YES;
if (io->mod->whichmodel == TN93)
io->mod->s_opt->opt_lambda = YES;
}
else
{
if (atof(optarg) < .0)
{
char choix;
PhyML_Printf("\n. The ts/tv ratio must be a positive number\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->kappa->v = (phydbl)atof(optarg);
io->mod->s_opt->opt_kappa = 0;
io->mod->s_opt->opt_lambda = 0;
}
}
}
break;
}
case 'n':case 8:
{
if ((!atoi(optarg)) || (atoi(optarg) < 0))
{
char choix;
PhyML_Printf("\n. The number of alignments must be a positive integer\n");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else io->n_data_sets = atoi (optarg);
break;
}
case 'q':case 22:
{
io->interleaved = NO;
break;
}
case 'u':case 15:
{
char *tmp;
tmp = (char *)mCalloc(T_MAX_FILE, sizeof(char));
if(strlen(optarg) > T_MAX_FILE -11)
{
char choix;
strcpy (tmp, "\n. The file name'");
strcat (tmp, optarg);
strcat (tmp, "' is too long.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else if (! Filexists (optarg))
{
char choix;
strcpy (tmp, "\n. The file '");
strcat (tmp, optarg);
strcat (tmp, "' doesn't exist.\n");
PhyML_Printf("%s",tmp);
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
strcpy(io->in_tree_file, optarg);
io->in_tree = 2;
io->fp_in_tree = Openfile(io->in_tree_file,READ);
}
Free(tmp);
break;
}
case 'v':case 13:
{
if ((strcmp (optarg, "e") == 0) ||
(strcmp (optarg, "E") == 0) ||
(strcmp (optarg, "estimated") == 0) ||
(strcmp (optarg, "ESTIMATED") == 0))
{
io->mod->s_opt->opt_pinvar = YES;
io->mod->ras->invar = YES;
}
else if ((atof(optarg) < 0.0) || (atof(optarg) > 1.0))
{
char choix;
PhyML_Printf("\n. The proportion of invariable site must be a number between 0.0 and 1.0\n");
PhyML_Printf("\n. Type any key to exit.");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
else
{
io->mod->ras->pinvar->v = (phydbl)atof(optarg);
if (io->mod->ras->pinvar->v > 0.0+SMALL)
io->mod->ras->invar = 1;
else
io->mod->ras->invar = 0;
io->mod->s_opt->opt_pinvar = 0;
}
break;
}
case 'o':
{
if(!strcmp(optarg,"tlr"))
{
io->mod->s_opt->opt_topo = YES;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"tl"))
{
io->mod->s_opt->opt_topo = YES;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = NO;
}
else if(!strcmp(optarg,"t"))
{
Warn_And_Exit("\n. You can't optimize the topology without adjusting branch length too...\n");
}
else if(!strcmp(optarg,"lr"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"l"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = YES;
io->mod->s_opt->opt_subst_param = NO;
}
else if(!strcmp(optarg,"r"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = NO;
io->mod->s_opt->opt_subst_param = YES;
}
else if(!strcmp(optarg,"none") || !strcmp(optarg,"n"))
{
io->mod->s_opt->opt_topo = NO;
io->mod->s_opt->opt_bl = NO;
io->mod->s_opt->opt_subst_param = NO;
}
else
{
char choix;
PhyML_Printf ("\n. The optimization parameter must be 'tlr' or 'tl' or 'lr' or 'l' or 'r' or ''.");
PhyML_Printf("\n. Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
break;
}
case '?':
{
Exit("\n");
break;
}
case -1:
{
break;
}
default:
{
Usage();
break;
}
}
}while(c != -1);
/* if((io->mod->whichmodel == K80) || (io->mod->whichmodel == JC69)) */
/* { */
/* if(io->mod->s_opt->opt_state_freq) */
/* { */
/* char c; */
/* PhyML_Printf("\n. WARNING: nucleotide frequencies must be set to 1/4 with this model.\n"); */
/* PhyML_Printf("\n. Type the enter key to resume the analysis.\n"); */
/* scanf("%c",&c); */
/* } */
/* io->mod->s_opt->opt_state_freq = 0; */
/* } */
if(io->mod->s_opt->constrained_br_len == YES)
{
io->mod->s_opt->opt_topo = NO;
/* io->mod->s_opt->opt_bl = NO; */
}
#ifndef PHYML
if((open_ps_file) || (io->m4_model == YES))
{
strcpy(io->out_ps_file,io->in_align_file);
strcat(io->out_ps_file, "_mc_tree.ps");
io->fp_out_ps = Openfile(io->out_ps_file,WRITE);
}
#endif
if(io->datatype == UNDEFINED) io->datatype = NT;
if((io->mod->s_opt->n_rand_starts) &&
(io->mod->s_opt->topo_search == NNI_MOVE) &&
(io->mod->s_opt->random_input_tree))
{
Warn_And_Exit("\n== The random starting tree option is only compatible with SPR based search options.\n");
}
if ((io->datatype == NT) && (io->mod->whichmodel > 10))
{
char choix;
PhyML_Printf("\n== Err.: model incompatible with the data type. Please use JC69, K80, F81, HKY, F84, TN93 or GTR\n");
PhyML_Printf("\n== Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Warn_And_Exit("\n");
}
else if ((io->datatype == AA) && (io->mod->whichmodel < 11))
{
char choix;
PhyML_Printf("\n== Err.: model incompatible with the data type. Please use LG, Dayhoff, JTT, MtREV, WAG, DCMut, RtREV, CpREV, VT, Blosum62, MtMam, MtArt, HIVw, HIVb or AB.\n");
PhyML_Printf("\n== Type any key to exit.\n");
if(!scanf("%c",&choix)) Exit("\n");
Exit("\n");
}
if(io->mod->use_m4mod == NO)
{
io->mod->s_opt->opt_cov_delta = 0;
io->mod->s_opt->opt_cov_alpha = 0;
io->mod->s_opt->opt_cov_free_rates = 0;
}
if((io->mod->s_opt->opt_cov_free_rates) && (io->mod->s_opt->opt_cov_alpha))
{
io->mod->s_opt->opt_cov_free_rates = 1;
io->mod->m4mod->use_cov_alpha = 0;
io->mod->m4mod->use_cov_free = 1;
}
if(io->print_site_lnl)
{
strcpy(io->out_lk_file,io->in_align_file);
strcat(io->out_lk_file, "_phyml_lk");
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
io->fp_out_lk = Openfile(io->out_lk_file,1);
}
if(io->print_trace)
{
strcpy(io->out_trace_file,io->in_align_file);
strcat(io->out_trace_file,"_phyml_trace");
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
io->fp_out_trace = Openfile(io->out_trace_file,1);
}
if(io->mod->s_opt->random_input_tree)
{
strcpy(io->out_trees_file,io->in_align_file);
strcat(io->out_trees_file,"_phyml_rand_trees");
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
io->fp_out_trees = Openfile(io->out_trees_file,1);
}
if((io->print_boot_trees) && (io->mod->bootstrap > 0))
{
strcpy(io->out_boot_tree_file,io->in_align_file);
strcat(io->out_boot_tree_file,"_phyml_boot_trees");
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
io->fp_out_boot_tree = Openfile(io->out_boot_tree_file,1);
strcpy(io->out_boot_stats_file,io->in_align_file);
strcat(io->out_boot_stats_file,"_phyml_boot_stats");
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
io->fp_out_boot_stats = Openfile(io->out_boot_stats_file,1);
}
if(io->append_run_ID)
{
strcat(io->out_tree_file,"_");
strcat(io->out_stats_file,"_");
strcat(io->out_tree_file,io->run_id_string);
strcat(io->out_stats_file,io->run_id_string);
}
if(io->mod->ras->n_catg == 1) io->mod->s_opt->opt_alpha = 0;
if(!io->mod->s_opt->opt_subst_param)
{
io->mod->s_opt->opt_alpha = 0;
io->mod->s_opt->opt_kappa = 0;
io->mod->s_opt->opt_lambda = 0;
io->mod->s_opt->opt_pinvar = 0;
io->mod->s_opt->opt_rr = 0;
}
if(io->mod->whichmodel != K80 &&
io->mod->whichmodel != HKY85 &&
io->mod->whichmodel != F84 &&
io->mod->whichmodel != TN93)
{
io->mod->s_opt->opt_kappa = 0;
}
if(io->datatype == AA && io->mod->whichmodel == CUSTOMAA && !io->mod->fp_aa_rate_mat)
{
PhyML_Printf("\n== Custom model option with amino-acid requires you to specify a rate matrix file through the '--aa_rate_file' option.\n");
Exit("\n");
}
#if !defined(PHYTIME)
// Make sure you don't erase the input file...
if(!strcmp(io->out_tree_file,io->in_align_file) ||
!strcmp(io->out_stats_file,io->in_align_file)) Generic_Exit(__FILE__,__LINE__,__FUNCTION__);
writemode = WRITE;
io->fp_out_tree = Openfile(io->out_tree_file,writemode);
io->fp_out_stats = Openfile(io->out_stats_file,writemode);
#endif
#if defined(PHYREX)
io->fp_out_summary = Openfile(io->out_summary_file,writemode);
#endif
writemode++; // just to silence a warning message at compilation
if(io->mod->whichmodel == GTR)
{
/* Make_Custom_Model(io->mod); */
io->mod->s_opt->opt_rr = 1;
}
return 1;
}
