int sh2reg(char *str)
{
char *p,*p1;
int flg=0;
if(!str) return flg;
strins(str,'^');
for(p1=p=str; *p ; p++) {
p=stptok(p,0,0,"?*.[\\");
if(!*p) break;
if(*p=='\\') {
++p;
continue;
}
if(*p=='[') {
p1=strchr(p,']');
if(p1) {
flg=1;
p=p1;
continue;
}
}
switch(*p) {
case '?':
*p='.';
flg=1;
break;
case '*':
p=strins(p,'.');
flg=1;
break;
case '.':
p=strins(p,'\\');
break;
default:
break;
}
}
strcat(str,"$");
return flg;
}
char* expndcoef(char* expr)
{
if (expr == NULL || *expr == '\0')
return expr;
//find indep var
char* tok1;
char* indeppos = (char*)memchr(expr, indep_var, strlen(expr));
if(indeppos == NULL)
return expr;
//check for coef where indep var is found and then add the rest.
tok1 = strsub(expr,0,indeppos-expr);
if(strpbrk(tok1+strlen(tok1)-2,"0123456789") != NULL)
tok1 = strins(tok1, "*", indeppos-expr);
char* tok2 = expndcoef(indeppos+1);
strcat(tok1,tok2);
return tok1;
}
//#ifdef TEST
int
main (int argc, char **argv)
{
#define MAXBUFSIZE 32768
char buf[MAXBUFSIZE];
#if 0
const char *b = "123(123.32.21.44)214";
const char *s = "(xxx.xx.xx.xx)";
// const char *p = memmem2 (b, strlen (b), s, strlen (s), MEMCMP2_WCARD('*', 'x'));
const char *p = memmem2 (b, strlen (b), s, strlen (s), MEMCMP2_WCARD('x'));
printf ("%s\n", p);
strcpy (buf, "1234567890");
strins (buf + 2, 6, "abc");
printf ("%s\n", buf);
#else
strcpy (buf, "12434akjgkjh56453fdsg");
stritrim_s (buf, "sg", "xx");
printf (buf);
#endif
return 0;
}
char* inspare(char* expr)
{
//insert at begining and end of string
char* newexpr;
newexpr = strins(expr,"(",0);
newexpr = strins(newexpr,")",strlen(newexpr));
//insert around pre-existing parenthesis
int para_flag = ((char*)memchr(newexpr+1,'(',strlen(newexpr)))-newexpr;
int epara_flag = 0;
while(para_flag >= 0 )
{
newexpr = strins(newexpr,"(",para_flag);
epara_flag = ((char*)memchr(newexpr+para_flag,')',strlen(newexpr+para_flag+1)))-newexpr;
if(epara_flag >= 0)
newexpr = strins(newexpr,")",epara_flag);
para_flag = ((char*)memchr(newexpr+epara_flag,'(',strlen(newexpr)))-newexpr;
}
//insert before and after '+' and/or '-'
int p_flag = strpbrk(newexpr,"+-")-newexpr;
while(p_flag >= 0)
{
newexpr = strins(newexpr,")",p_flag);
newexpr = strins(newexpr,"(",p_flag+2);
p_flag = strpbrk(newexpr+p_flag+2,"+-")-newexpr;
}
return newexpr;
}
int main( int argc, char **argv )
{
int i, j;
FILE *fp, *infp;
char **seq;
int *grpseq;
char *tmpseq;
int **pointt;
static char name[M][B];
static int nlen[M];
double **mtx;
double **mtx2;
double score, score0;
static short *table1;
char b[B];
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
#if 0
PreRead( stdin, &njob, &nlenmax );
#else
getnumlen( infp );
#endif
rewind( infp );
if( njob < 2 )
{
fprintf( stderr, "At least 2 sequences should be input!\n"
"Only %d sequence found.\n", njob );
exit( 1 );
}
tmpseq = AllocateCharVec( nlenmax+1 );
seq = AllocateCharMtx( njob, nlenmax+1 );
grpseq = AllocateIntVec( nlenmax+1 );
pointt = AllocateIntMtx( njob, nlenmax+1 );
mtx = AllocateDoubleMtx( njob, njob );
mtx2 = AllocateDoubleMtx( njob, njob );
pamN = NOTSPECIFIED;
#if 0
FRead( infp, name, nlen, seq );
#else
readData( infp, name, nlen, seq );
#endif
fclose( infp );
constants( njob, seq );
if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
else tsize = (int)pow( 6, 6 );
maxl = 0;
for( i=0; i<njob; i++ )
{
gappick0( tmpseq, seq[i] );
nlen[i] = strlen( tmpseq );
if( nlen[i] < 6 )
{
fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
exit( 1 );
}
if( nlen[i] > maxl ) maxl = nlen[i];
if( dorp == 'd' ) /* nuc */
{
seq_grp_nuc( grpseq, tmpseq );
makepointtable_nuc( pointt[i], grpseq );
}
else /* amino */
{
seq_grp( grpseq, tmpseq );
makepointtable( pointt[i], grpseq );
}
}
for( i=0; i<njob; i++ )
{
table1 = (short *)calloc( tsize, sizeof( short ) );
if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
if( i % 10 == 0 )
{
fprintf( stderr, "%4d / %4d\r", i+1, njob );
}
makecompositiontable_p( table1, pointt[i] );
for( j=i; j<njob; j++ )
{
score = (double)commonsextet_p( table1, pointt[j] );
mtx[i][j] = score;
}
free( table1 );
}
for( i=0; i<njob; i++ )
{
score0 = mtx[i][i];
for( j=0; j<njob; j++ )
mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0;
}
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
{
#if TEST
double jscore;
jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 );
fprintf( stdout, "jscore = %f\n", jscore );
fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] );
#endif
mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
#if TEST
fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] );
#endif
}
if( disopt )
{
for( i=0; i<njob; i++ )
{
sprintf( b, "=lgth = %04d", nlen[i] );
strins( b, name[i] );
}
}
fp = fopen( "hat2", "w" );
if( !fp ) ErrorExit( "Cannot open hat2." );
WriteHat2( fp, njob, name, mtx2 );
fclose( fp );
fprintf( stderr, "\n" );
SHOWVERSION;
exit( 0 );
}
// add a variable to the environment or alias to the alias list
int add_list( char *envstr, PCH pchList )
{
char *line;
PCH feptr, env_arg, env_end, last_var;
unsigned int length;
int rval = 0;
ULONG size; // size of environment or alias blocks
// OS/2 & NT need semaphores to keep processes from simultaneously
// writing the alias list
HMTX SemHandle = 0;
char szVarName[32];
if ( pchList == 0L )
pchList = glpEnvironment;
line = envstr;
if ( *line == '=' ) {
return ( error( ERROR_4DOS_BAD_SYNTAX, envstr ));
}
for ( ; (( *line ) && ( *line != '=' )); line++ ) {
if ( pchList == glpAliasList ) {
if ( iswhite( *line )) {
strcpy( line, skipspace( line ) );
break;
}
}
else // ensure environment entry is in upper case
*line = (unsigned char)_ctoupper( *line );
}
if ( *line == '=' ) {
// point to the first char of the argument
line++;
// collapse whitespace around '=' in aliases, but not in env
// variables, for COMMAND.COM compatibility (set abc def= ghi)
if ( pchList == glpAliasList )
strcpy( line, skipspace( line ));
} else if ( *line ) {
// add the missing '='
strins( line, "=" );
line++;
}
// removing single back quotes at the beginning and end of an alias
// argument (they're illegal there; the user is probably making a
// mistake with ALIAS /R)
if (( *line == SINGLE_QUOTE ) && ( pchList == glpAliasList )) {
// remove leading single quote
strcpy( line, line + 1 );
// remove trailing single quote
if ((( length = strlen( line )) != 0 ) && ( line[--length] == SINGLE_QUOTE ))
line[length] = '\0';
}
// block other processes & threads while updating alias list
if ( pchList == glpAliasList ) {
// disable signals temporarily
HoldSignals();
// get & lock a semaphore
RequestSemaphore( &SemHandle, SEMAPHORE_NAME );
}
// get pointers to beginning & end of alias/environment space
size = QueryMemSize( pchList );
env_end = pchList + ( size - 4 );
// get pointer to end of environment or alias variables
last_var = end_of_env( pchList );
length = strlen( envstr ) + 1;
// special case for BeginLIBPATH and EndLIBPATH
sscanf( envstr, "%31[^=]", szVarName );
if (stricmp( szVarName, BEGINLIBPATH ) == 0) {
if ((DosSetExtLIBPATH( line, BEGIN_LIBPATH ) == NO_ERROR))
return 0;
return ERROR_EXIT;
}
if (stricmp( szVarName, ENDLIBPATH ) == 0) {
if ((DosSetExtLIBPATH( line, END_LIBPATH ) == NO_ERROR))
return 0;
return ERROR_EXIT;
}
// check for modification or deletion of existing entry
if (( env_arg = get_list( envstr, pchList )) != 0L ) {
// get the start of the alias or variable name
for ( feptr = env_arg; (( feptr > pchList ) && ( feptr[-1] != '\0' )); feptr-- )
;
if ( *line == '\0' ) {
// delete an alias or environment variable
memmove( feptr, next_env( feptr ), (unsigned int)( last_var - next_env(feptr)) + 1);
} else {
// get the relative length (vs. the old variable)
length = strlen( line ) - strlen( env_arg );
}
}
if ( *line != '\0' ) {
// check for out of environment space
if (( last_var + length ) >= env_end ) {
// boost environment or alias list size
if ( ReallocMem( pchList, size + ENVIRONMENT_SIZE ) == NULL) {
rval = error((( pchList == glpAliasList ) ? ERROR_4DOS_OUT_OF_ALIAS : ERROR_4DOS_OUT_OF_ENVIRONMENT), NULL);
goto add_bye;
}
// adjust the environment / alias list size
size = QueryMemSize( pchList );
if ( pchList == glpEnvironment )
gpIniptr->EnvSize = (unsigned int)size;
else if ( pchList == glpAliasList )
gpIniptr->AliasSize = (unsigned int)size;
}
if ( env_arg != 0L ) {
// modify an existing alias or environment variable
// adjust the space & insert new value
feptr = next_env( feptr );
memmove(( feptr + length ), feptr, (unsigned int)( last_var - feptr) + 1 );
strcpy( env_arg, line );
} else {
// put it at the end & add an extra null
strcpy( last_var, envstr );
last_var[length] = '\0';
}
}
add_bye:
if ( pchList == glpAliasList ) {
// clear the semaphore
FreeSemaphore( SemHandle );
EnableSignals();
}
return rval;
}
// add a variable to the environment or alias to the alias list
int PASCAL add_list( LPTSTR pszVariable, TCHAR _far *pchList )
{
LPTSTR pszLine;
TCHAR _far *pszVarName, _far *pszArgument, _far *pszEndOfList, _far *pszLastVariable;
unsigned int uLength;
int nError = 0;
if ( pchList == 0L )
pchList = glpEnvironment;
pszLine = pszVariable;
if ( *pszLine == _TEXT('=') ) {
return ( error( ERROR_4DOS_BAD_SYNTAX, pszVariable ));
}
for ( ; (( *pszLine ) && ( *pszLine != _TEXT('=') )); pszLine++ ) {
if ( pchList != glpEnvironment ) {
if ( iswhite( *pszLine )) {
strcpy( pszLine, skipspace( pszLine ) );
break;
}
}
else // ensure environment entry is in upper case
*pszLine = (unsigned char)_ctoupper( *pszLine );
}
// stupid kludge to strip quotes from PATH for compatibility with
// COMMAND.COM
if (( fWin95 ) && ( pchList == glpEnvironment )) {
char szVarName[8];
if (( uLength = ( pszLine - pszVariable )) > 7 )
uLength = 7;
sprintf( szVarName, "%.*s", uLength, pszVariable );
if ( stricmp( szVarName, PATH_VAR ) == 0 )
StripQuotes( pszLine );
}
if ( *pszLine == _TEXT('=') ) {
// point to the first char of the argument
pszLine++;
// collapse whitespace around '=' in aliases, but not in env
// variables, for COMMAND.COM compatibility (set abc def= ghi)
if ( pchList != glpEnvironment )
strcpy( pszLine, skipspace( pszLine ));
} else if ( *pszLine ) {
// add the missing '='
strins( pszLine, _TEXT("=") );
pszLine++;
}
// removing single back quotes at the beginning and end of an alias
// argument (they're illegal there; the user is probably making a
// mistake with ALIAS /R)
if (( *pszLine == SINGLE_QUOTE ) && ( pchList != glpEnvironment )) {
// remove leading single quote
strcpy( pszLine, pszLine + 1 );
// remove trailing single quote
if ((( uLength = strlen( pszLine )) != 0 ) && ( pszLine[--uLength] == SINGLE_QUOTE ))
pszLine[uLength] = _TEXT('\0');
}
// block other processes & threads while updating list
if ( pchList != glpEnvironment ) {
// disable task switches under Windows and DESQview
CriticalSection( 1 );
}
// get pointers to beginning & end of list space
pszEndOfList = pchList + ((( pchList == glpAliasList ) ? gpIniptr->AliasSize : gpIniptr->EnvSize ) - 4 );
// get pointer to end of environment or alias variables
pszLastVariable = end_of_env( pchList );
uLength = strlen( pszVariable ) + 1;
// check for modification or deletion of existing entry
if (( pszArgument = get_list( pszVariable, pchList )) != 0L ) {
// get the start of the alias or variable name
for ( pszVarName = pszArgument; (( pszVarName > pchList ) && ( pszVarName[-1] != _TEXT('\0') )); pszVarName-- )
;
if ( *pszLine == _TEXT('\0') ) {
// delete an alias or environment variable
_fmemmove( pszVarName, next_env( pszVarName ), (unsigned int)( (ULONG_PTR)pszLastVariable - (ULONG_PTR)next_env(pszVarName)) + sizeof(TCHAR));
} else {
// get the relative length (vs. the old variable)
uLength = strlen( pszLine ) - _fstrlen( pszArgument );
}
}
if ( *pszLine != _TEXT('\0') ) {
// check for out of space
if (( pszLastVariable + ( uLength * sizeof(TCHAR) )) >= pszEndOfList ) {
if ( pchList == glpAliasList )
nError = error( ERROR_4DOS_OUT_OF_ALIAS, NULL );
else if ( pchList == glpEnvironment )
nError = error( ERROR_4DOS_OUT_OF_ENVIRONMENT, NULL);
else
nError = error( ERROR_NOT_ENOUGH_MEMORY, NULL );
goto add_bye;
}
if ( pszArgument != 0L ) {
// modify an existing value
// adjust the space & insert new value
pszVarName = next_env( pszVarName );
_fmemmove(( pszVarName + uLength ), pszVarName, (unsigned int)(( (ULONG_PTR)pszLastVariable - (ULONG_PTR)pszVarName ) + sizeof(TCHAR) ));
_fstrcpy( pszArgument, pszLine );
} else {
// put it at the end & add an extra null
_fstrcpy( pszLastVariable, pszVariable );
pszLastVariable[uLength] = _TEXT('\0');
}
}
add_bye:
if ( pchList != glpEnvironment ) {
// re-enable task switches under Windows and DESQview
CriticalSection( 0 );
}
return nError;
}
// create or display environment variables or aliases
static int _fastcall __Set( LPTSTR pszCmdLine, TCHAR _far * pchList )
{
LPTSTR pszArg;
long fSet = 0L;
TCHAR _far *lpszVars;
init_page_size();
// set the pointer to the environment, alias, or function list
// strip leading switches
if (( pszCmdLine != NULL ) && ( *pszCmdLine == gpIniptr->SwChr )) {
if ( GetSwitches( pszCmdLine, "AMPR", &fSet, 1 ) != 0 )
return USAGE_ERR;
}
// check for master environment set
if (( pchList == glpEnvironment ) && ( fSet & SET_MASTER ))
pchList = glpMasterEnvironment;
// read environment or alias file(s)
if ( fSet & SET_READ )
return ( SetFromFile( pszCmdLine, pchList, fSet & ( SET_DEFAULT | SET_SYSTEM | SET_USER | SET_VOLATILE )));
if ( setjmp( cv.env ) == -1 )
return CTRLC;
// pause after each page
if ( fSet & SET_PAUSE ) {
gnPageLength = GetScrRows();
}
if (( pszCmdLine == NULL ) || ( *(pszCmdLine = skipspace( pszCmdLine )) == _TEXT('\0'))) {
// print all the variables or aliases
for ( lpszVars = pchList; ( *lpszVars != _TEXT('\0') ); lpszVars = next_env( lpszVars ) ) {
more_page( lpszVars, 0 );
}
// return an error if no entries exist
return (( lpszVars == pchList ) ? ERROR_LIST_EMPTY : 0 );
}
if ( fSet & SET_EXPRESSION ) {
if (( pszArg = strchr( pszCmdLine, _TEXT('=') )) != NULL ) {
if (( pszArg > pszCmdLine ) && ( strchr( _TEXT("+-*/%&^|><"), pszArg[-1] ) != NULL )) {
TCHAR szBuf[256];
// it's an assignment operator ("set /a test+=2")
sscanf( pszCmdLine, _TEXT(" %[^ +-*/%&^|><=]"), szBuf );
strcpy( pszArg, pszArg+1 );
strins( pszCmdLine, _TEXT("=") );
strins( pszCmdLine, szBuf );
pszArg = pszCmdLine + strlen( szBuf ) + 1;
} else
pszArg = skipspace( pszArg+1 );
} else
pszArg = pszCmdLine;
StripQuotes( pszArg );
evaluate( pszArg );
if ( cv.bn < 0 ) {
qputs( pszArg );
crlf();
}
// create/modify/delete a variable
return (( pszArg == pszCmdLine ) ? 0 : add_list( pszCmdLine, pchList ));
}
// display the current variable or alias argument?
// (setting environment vars requires a '='; it's optional with aliases)
if ((( pszArg = strchr( pszCmdLine, _TEXT('=') )) == NULL ) && (( pchList == 0L ) || ( ntharg( pszCmdLine, 0x8001 ) == NULL ))) {
if (( lpszVars = get_list( pszCmdLine, pchList )) == 0L ) {
return ERROR_NOT_IN_LIST;
}
printf( FMT_FAR_STR_CRLF, lpszVars );
return 0;
}
// create/modify/delete a variable or alias
return ( add_list( pszCmdLine, pchList ));
}
