int main(int argc, Char *argv[])
{ /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
argc = 1; /* macsetup("SeqBoot",""); */
argv[0] = "SeqBoot";
#endif
init(argc,argv);
openfile(&infile, INFILE, "input file", "r", argv[0], infilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
doinput(argc, argv);
bootwrite();
freenewer();
freenew();
freerest();
if (nodep)
matrix_char_delete(nodep, spp);
if (nodef)
matrix_double_delete(nodef, spp);
FClose(infile);
if (factors) {
FClose(factfile);
FClose(outfactfile);
}
if (weights)
FClose(weightfile);
if (categories) {
FClose(catfile);
FClose(outcatfile);
}
if(mixture)
FClose(outmixfile);
if(ancvar)
FClose(outancfile);
if (justwts && !permute) {
FClose(outweightfile);
}
else
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
if (justwts && !permute)
fixmacfile(outweightfilename);
if (categories)
fixmacfile(outcatfilename);
if (mixture)
fixmacfile(outmixfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
int main(int argc, Char *argv[])
{
int i;
#ifdef MAC
argc = 1; /* macsetup("Fitch",""); */
argv[0]="Fitch";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
strcpy(progname,argv[0]);
openfile(&infile,INFILE,"input file","r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
firstset = true;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file","w",argv[0],outtreename);
for (i=0;i<spp;++i){
enterorder[i]=0;}
for (ith = 1; ith <= datasets; ith++) {
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n",ith);
if (progress)
printf("\nData set # %ld:\n\n",ith);
}
fitch_getinput();
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
firstset = false;
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
}
if (trout)
FClose(outtree);
FClose(outfile);
FClose(infile);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
long i;
#ifdef MAC
argc = 1; /* macsetup("Contml",""); */
argv[0] = "Contml";
#endif
init(argc, argv);
emboss_getoptions("fcontml", argc, argv);
progname = argv[0];
ibmpc = IBMCRT;
ansi = ANSICRT;
firstset = true;
doinit();
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n", ith);
if (progress)
printf("\nData set # %ld:\n", ith);
}
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
free(l0gf[i]);
}
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("\nDone.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
ajPhyloFreqDel(&phylofreq);
ajPhyloTreeDelarray(&phylotrees);
ajFileClose(&embossoutfile);
ajFileClose(&embossouttree);
embExit();
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
long i;
#ifdef MAC
argc = 1; /* macsetup("Contml",""); */
argv[0] = "Contml";
#endif
init(argc, argv);
progname = argv[0];
openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
firstset = true;
datasets = 1;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n", ith);
if (progress)
printf("\nData set # %ld:\n", ith);
}
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
free(l0gf[i]);
}
FClose(outfile);
FClose(outtree);
FClose(infile);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("\nDone.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
char *ReadFileBuf(char *name, int *size)
{
FILE *fp;
char *buf, *ext;
int txt = 1;
int n;
ext = GetExt(name);
if (!StrCmp(ext, ".txt")) {
txt = 1;
} else {
txt = 0;
}
fp = FOpen(name, "rb");
if (fp == NULL) {
return NULL;
}
fseek(fp, 0, SEEK_END);
n = ftell(fp);
fseek(fp, 0, SEEK_SET);
buf = (char *)Malloc(sizeof(char) * n);
fread(buf, sizeof(char), n, fp);
if (txt) {
buf[n - 1] = '\0';
}
FClose(fp);
*size = n;
return buf;
}
/* IsWave: check config parms to see if target is a waveform */
Boolean IsWave(char *srcFile)
{
FILE *f;
long nSamp,sampP, hdrS;
short sampS,kind;
Boolean isPipe,bSwap,isWave;
isWave = tgtPK == WAVEFORM;
if (tgtPK == ANON){
if ((srcFF == HTK || srcFF == ESIG) && srcFile != NULL){
if ((f=FOpen(srcFile,WaveFilter,&isPipe)) == NULL)
HError(1011,"IsWave: cannot open File %s",srcFile);
switch (srcFF) {
case HTK:
if (!ReadHTKHeader(f,&nSamp,&sampP,&sampS,&kind,&bSwap))
HError(1013, "IsWave: cannot read HTK Header in File %s",
srcFile);
break;
case ESIG:
if (!ReadEsignalHeader(f, &nSamp, &sampP, &sampS,
&kind, &bSwap, &hdrS, isPipe))
HError(1013, "IsWave: cannot read Esignal Header in File %s",
srcFile);
break;
}
isWave = kind == WAVEFORM;
FClose(f,isPipe);
} else
isWave = TRUE;
}
return isWave;
}
static PackFile *PackOpenFromFile(char *name)
{
FILE *fp;
PackFile *pack;
int num, i;
int packPtr = 0;
fp = FOpen(name, "rb");
if (fp == NULL) {
EngineError("not find %s\n", name);
}
pack = (PackFile *)Malloc(sizeof(PackFile));
fread(&num, sizeof(int), 1, fp);
packPtr += sizeof(int);
pack->file = (struct Data *)Malloc(sizeof(struct Data) * num);
pack->num = num;
for (i = 0; i < pack->num; i++) {
struct Data *file = &pack->file[i];
fread(file->name, sizeof(char), MAX_PATH, fp);
EncodeName(file->name, 0);
packPtr += sizeof(char) * MAX_PATH;
fread(&file->size, sizeof(int), 1, fp);
packPtr += sizeof(int);
file->ptr = packPtr;
fseek(fp, file->ptr + file->size, SEEK_SET);
packPtr += file->size;
file->data = NULL;
}
FClose(fp);
return pack;
}
/* ProcessText: read text files line by line and count ngrams */
void ProcessText(char *fn, bool lastFile)
{
FILE *f;
LabId id;
bool isPipe;
char word[256];
if (trace&T_TOP)
printf("Reading source text file %s\n",(fn==NULL) ? "<stdin>" : fn);
if ((fn!=NULL) && (strcmp(fn,"-")!=0)) {
if ((f = FOpen(fn,LMTextFilter,&isPipe))==NULL)
HError(16410,"ProcessText: unable to open text file %s", fn);
} else {
f = stdin;
}
while (fscanf(f,"%255s",word)==1) {
if (pruneWords) {
if ((id = GetLabId(word,FALSE))==NULL && (id = unkId)==NULL) {
stdBuf.used=0;
continue;
}
} else {
id = GetLabId(word,TRUE);
}
if (trace&T_INP) printf("[%s]\n",id->name);
PutShiftRegister(id,&stdBuf);
}
if (fn!=NULL) {
FClose(f,isPipe);
if (lastFile)
CompressBuffer(stdBuf.ngb,TRUE);
} else {
CompressBuffer(stdBuf.ngb,TRUE);
}
}
void sendmesg(per_request* reqInfo, char *url, FILE *fp)
{
char *loc, *furl;
loc = newString(HUGE_STRING_LEN,STR_REQ);
furl = newString(HUGE_STRING_LEN,STR_REQ);
FClose(fp);
if (!strstr(url, "://")) { /*** If not a full URL ***/
if (url[0] != '/') { /*** Relative URL ***/
char *last = strrchr(reqInfo->url,'/');
int x = 0, y = 0;
while (((reqInfo->url+x) <= last) && (y < HUGE_STRING_LEN)) {
loc[y] = *(reqInfo->url+x);
x++; y++;
}
loc[y] = '\0';
strncat(loc,url,HUGE_STRING_LEN - y);
} else {
strncpy(loc,url,HUGE_STRING_LEN);
}
construct_url(furl, reqInfo->hostInfo, loc);
die(reqInfo,SC_REDIRECT_TEMP,furl);
} else {
die(reqInfo,SC_REDIRECT_TEMP,url);
}
}
/*
* Saves the list of parameters to file.
*
* The given file_format is a hint to the file's format.
*
* Returns non-zero on error.
*/
int SARParmSaveToFile(
const char *filename, int file_format,
void **parm, int total_parms,
void *client_data,
int (*progress_func)(void *, long, long)
)
{
int status = -1;
FILE *fp;
if(filename == NULL)
return(status);
/* Open file for writing. */
fp = FOpen(filename, "wb");
if(fp == NULL)
return(status);
/* Save by file format type. */
if(1)
{
status = SARParmSaveToFileAny(
filename, fp,
parm, total_parms,
client_data, progress_func
);
}
/* Close file. */
FClose(fp);
return(status);
}
BOOL CMFile::FDeleteFile()
{
if(bDontClose) return FALSE;
if (FileOpen)
FClose();
return DeleteFile(File->GetFilePath());
}
int main(int argc, Char *argv[])
{ /* main program */
#ifdef MAC
argc = 1; /* macsetup("Neighbor",""); */
argv[0] = "Neighbor";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
ith = 1;
while (ith <= datasets) {
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n",ith);
if (progress)
printf("Data set # %ld:\n",ith);
}
getinput();
maketree();
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
ith++;
}
FClose(infile);
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
CMFile::~CMFile()
{
if(!bDontClose)
{
FClose();
if ( File != NULL) delete File;
}
}
/* Export number of frames, mean, var to a given directory */
void ExportNMV(SpkrAccListItem *sal, char *OutDirName, char *tgtPKStr)
{
FILE *oFile;
Boolean isPipe;
char oFileName[MAXSTRLEN];
char pathBuffer1[MAXSTRLEN];
char pathBuffer2[MAXSTRLEN];
SpkrAccListItem *p;
int i;
p = sal;
while(p != NULL){
/* create output file name for current spkr index */
if ( pathPattern[0] != '\0'){
if ( MaskMatch(pathPattern,pathBuffer1,p->sa->SpkrName) != TRUE ){
HError(2039,"HCompV: ExportNMV: path pattern matching failure on speaker: %s\n",p->sa->SpkrName);
}
MakeFN(pathBuffer1,OutDirName,NULL,pathBuffer2);
MakeFN(p->sa->SpkrName,pathBuffer2,NULL,oFileName);
}
else
MakeFN(p->sa->SpkrName,OutDirName,NULL,oFileName);
/* open and write */
oFile = FOpen(oFileName,NoOFilter,&isPipe);
if (oFile == NULL){
HError(2011,"HCompV: ExportNMV: output file creation error %s",oFileName);
}
/* write header */
fprintf(oFile,"<CEPSNORM> <%s>",tgtPKStr);
/* write number frames */
if (strchr(oflags,'n')){
fprintf(oFile,"\n<NFRAMES> %d",p->sa->NumFrame);
}
/* write mean */
if (strchr(oflags,'m')){
fprintf(oFile,"\n<MEAN> %d\n",vSize);
for (i=1;i<=vSize;i++){
fprintf(oFile," %e",(p->sa->meanSum[i]));
}
}
/* write variance */
if (strchr(oflags,'v')){
fprintf(oFile,"\n<VARIANCE> %d\n",vSize);
for (i=1;i<=vSize;i++){
fprintf(oFile," %e",(p->sa->squareSum[i]));
}
}
fprintf(oFile,"\n");
FClose(oFile,isPipe);
p = p->nextSpkr;
}
}
static void gui_download_window_done(struct gui_download_window *dw)
{
struct dlnode *dln,*dln2 = NULL;
struct browser_window *bw;
bool queuedl = false;
if(!dw) return;
bw = dw->bw;
if((nsoption_bool(download_notify)) && (dw->result == AMINS_DLOAD_OK))
{
Notify(ami_gui_get_app_id(), APPNOTIFY_Title, messages_get("amiDownloadComplete"),
APPNOTIFY_PubScreenName, "FRONT",
APPNOTIFY_BackMsg, dw->fname,
APPNOTIFY_CloseOnDC, TRUE,
APPNOTIFY_Text, dw->fname,
TAG_DONE);
}
download_context_destroy(dw->ctx);
if((dln = dw->dln))
{
dln2 = (struct dlnode *)GetSucc((struct Node *)dln);
if((dln!=dln2) && (dln2)) queuedl = true;
free(dln->filename);
Remove((struct Node *)dln);
FreeVec(dln);
}
FClose(dw->fh);
SetComment(dw->fname, dw->url);
downloads_in_progress--;
DisposeObject(dw->objects[OID_MAIN]);
DelObject(dw->node);
if(queuedl) {
nsurl *url;
if (nsurl_create(dln2->node.ln_Name, &url) != NSERROR_OK) {
amiga_warn_user("NoMemory", 0);
} else {
browser_window_navigate(bw,
url,
NULL,
BW_NAVIGATE_DOWNLOAD,
NULL,
NULL,
NULL);
nsurl_unref(url);
}
}
ami_try_quit(); /* In case the only window open was this download */
}
void ami_fetch_file_free(void *vf)
{
struct ami_file_fetch_info *fetch = (struct ami_file_fetch_info*)vf;
/* LOG(("ami file fetcher free %lx",fetch)); */
if(fetch->fh) FClose(fetch->fh);
if(fetch->mimetype) free(fetch->mimetype);
if(fetch->path) free(fetch->path);
DelObject(fetch->obj); // delobject frees fetch
}
void ami_fetch_file_abort(void *vf)
{
struct ami_file_fetch_info *fetch = (struct ami_file_fetch_info*)vf;
/* LOG(("ami file fetcher abort")); */
if (fetch->fh) {
FClose(fetch->fh);
fetch->fh = 0;
}
fetch->aborted = true;
}
/* WriteMatBigram: write out old HVite format bigram */
static void WriteMatBigram(LModel *lm,char *fn,int flags)
{
const float epsilon = 0.000001;
MatBiLM *matbi;
FILE *file;
Boolean isPipe;
Vector v;
double x,y;
int i,j,rep;
if (trace&T_TIO)
printf("\nMB "),fflush(stdout);
matbi = lm->data.matbi;
file=FOpen(fn,LangModOFilter,&isPipe);
for (i=1;i<=matbi->numWords;i++) {
if (trace&T_TIO) {
if ((i%25)==0)
printf(". "),fflush(stdout);
if ((i%800)==0)
printf("\n "),fflush(stdout);
}
fprintf(file,"%-8s ",ReWriteString(matbi->wdlist[i]->name,
NULL,ESCAPE_CHAR));
v=matbi->bigMat[i];rep=0;x=-1.0;
for (j=1;j<=matbi->numWords;j++){
y = L2F(v[j]);
if (fabs(y - x) <= epsilon) rep++;
else {
if (rep>0) {
fprintf(file,"*%d",rep+1);
rep=0;
}
x = y;
if (x == 0.0)
fprintf(file," 0");
else if (x == 1.0)
fprintf(file," 1");
else
fprintf(file," %e",x);
}
}
if (rep>0)
fprintf(file,"*%d",rep+1);
fprintf(file,"\n");
}
FClose(file,isPipe);
if (trace&T_TIO)
printf("\n"),fflush(stdout);
}
/*
Debug_DumpNet
*/
void Debug_DumpNet (LexNet *net)
{
int i, j, k, N;
LexNode *ln;
LexNodeInst *inst;
TokenSet *ts;
RelToken *rtok;
FILE *debugFile;
Boolean isPipe;
static char *debug_net_fn = "net.dump";
debugFile = FOpen (debug_net_fn, NoOFilter, &isPipe);
if (!debugFile) {
printf ("fopen failed\n");
return;
}
fprintf (debugFile, "(LexNet *) %p\n", net);
fprintf (debugFile, "nNodes %d\n", net->nNodes);
for (i = 0; i < net->nNodes; ++i) {
ln = &net->node[i];
inst = ln->inst;
if (inst) {
fprintf (debugFile, "node %d (LexNode *) %p", i, ln);
fprintf (debugFile, " type %d nfoll %d", ln->type, ln->nfoll);
if (ln->type == LN_MODEL)
fprintf (debugFile, " name %s",
FindMacroStruct (net->hset, 'h', ln->data.hmm)->id->name);
fprintf (debugFile, "\n");
assert (inst->node == ln);
fprintf (debugFile, " (LexNodeInst *) %p", inst);
fprintf (debugFile, " best %f\n", inst->best);
N = (ln->type == LN_MODEL) ? ln->data.hmm->numStates : 1;
for (j = 0; j < N; ++j) {
ts = &inst->ts[j];
if (ts->n > 0) {
fprintf (debugFile, " state %d (TokenSet *) %p", j+1, ts);
fprintf (debugFile, " score %f\n", ts->score);
for (k = 0; k < ts->n; ++k) {
rtok = &ts->relTok[k];
fprintf (debugFile, " (RelToken *) %p", rtok);
fprintf (debugFile, " delta %f lmstate %p lmscore %f\n",
rtok->delta, rtok->lmState, rtok->lmscore);
}
}
}
}
}
FClose (debugFile, isPipe);
}
nserror
gui_window_save_link(struct gui_window *g, nsurl *url, const char *title)
{
char fname[1024];
STRPTR openurlstring,linkname;
struct DiskObject *dobj = NULL;
linkname = ASPrintf("Link_to_%s",FilePart(nsurl_access(url)));
if(AslRequestTags(savereq,
ASLFR_Window, g->shared->win,
ASLFR_SleepWindow, TRUE,
ASLFR_TitleText,messages_get("NetSurf"),
ASLFR_Screen,scrn,
ASLFR_InitialFile,linkname,
TAG_DONE))
{
strlcpy(fname, savereq->fr_Drawer, 1024);
AddPart(fname,savereq->fr_File,1024);
ami_set_pointer(g->shared, GUI_POINTER_WAIT, false);
if(ami_download_check_overwrite(fname, g->shared->win, 0))
{
BPTR fh;
if((fh = FOpen(fname,MODE_NEWFILE,0)))
{
/* \todo Should be URLOpen on OS4.1 */
openurlstring = ASPrintf("openurl \"%s\"\n",nsurl_access(url));
FWrite(fh,openurlstring,1,strlen(openurlstring));
FClose(fh);
FreeVec(openurlstring);
SetComment(fname, nsurl_access(url));
dobj = GetIconTags(NULL,ICONGETA_GetDefaultName,"url",
ICONGETA_GetDefaultType,WBPROJECT,
TAG_DONE);
dobj->do_DefaultTool = "IconX";
PutIconTags(fname,dobj,
ICONPUTA_NotifyWorkbench,TRUE,
TAG_DONE);
FreeDiskObject(dobj);
}
FreeVec(linkname);
}
ami_reset_pointer(g->shared);
}
return NSERROR_OK;
}
int main(int argc, Char *argv[])
{ /* distances from restriction sites or fragments */
#ifdef MAC
argc = 1; /* macsetup("Restdist",""); */
argv[0] = "Restdist";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
strcpy(progname,argv[0]);
openfile(&infile,INFILE,"input data file","r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
firstset = true;
doinit();
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1 && progress)
printf("\nData set # %ld:\n\n",ith);
makedists();
writedists();
}
FClose(infile);
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
} /* distances from restriction sites or fragments */
enterId=GetLabId("!ENTER",TRUE); /* All sentences should or are coerced */
exitId=GetLabId("!EXIT",TRUE); /* to start enterId and end exitId */
unknownId=GetLabId("!NULL",TRUE); /* Name for words not in list */
while (NextArg() == SWITCHARG) {
s = GetSwtArg();
if (strlen(s)!=1)
static void PackClose(PackFile *pack)
{
if (!pack) {
WriteLog("free pack file\n");
return;
}
Free(pack->file);
Free(pack);
if (packFile != NULL) {
FClose(packFile);
}
WriteLog("free pack file\n");
}
void buildtree()
{
long i, j, nextnode;
node *p;
changed = false;
newtree = false;
switch (how) {
case arb:
arbitree();
break;
case use:
/* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */
openfile(&intree,INTREE,"input tree file", "rb",progname,intreename);
names = (boolean *)Malloc(spp*sizeof(boolean));
firsttree = true; /**/
nodep = NULL; /**/
nextnode = 0; /**/
haslengths = 0; /**/
zeros = (long *)Malloc(chars*sizeof(long)); /**/
for (i = 0; i < chars; i++) /**/
zeros[i] = 0; /**/
treeread(intree, &root, treenode, &goteof, &firsttree, nodep, &nextnode,
&haslengths, &grbg, initdolmovenode,false,nonodes);
for (i = spp; i < (nonodes); i++) {
p = treenode[i];
for (j = 1; j <= 3; j++) {
p->stateone = (bitptr)Malloc(words*sizeof(long));
p->statezero = (bitptr)Malloc(words*sizeof(long));
p = p->next;
}
} /* debug: see comment at initdolmovenode() */
/*treeread(which, ch, &root, treenode, names);*/
for (i = 0; i < (spp); i++)
in_tree[i] = names[i];
free(names);
FClose(intree);
break;
case spec:
yourtree();
break;
}
outgrno = root->next->back->index;
if (in_tree[outgrno - 1])
reroot(treenode[outgrno - 1]);
} /* buildtree */
switch(s[0]){
case 'b':
saveLatBin = TRUE; break;
case 'm':
if (bType != unknown)
HError(3019,"HBuild: Can only specifiy one of -m, -n, -w, -x");
bType = matBiGram;
void SetFileTime2(const String & fn, const FILETIME * creationTime,
const FILETIME * lastAccessTime, const FILETIME * lastWriteTime)
{
HANDLE h = FOpen(fn, OPEN_WRITE_BUF, 0);
if (!h)
{
Error2(LOC(L"Error.FileOpen"), fn, ::GetLastError());
}
else
{
SetFileTime2(h, creationTime, lastAccessTime, lastWriteTime);
FClose(h);
}
}
void WriteLog(PCHAR buf, WORD len)
{
WORD F;
if (LogPath != NULL)
{
F = FOpen((PCHARFAR)&LogPath);
if (F == 0xffff)
{
F = FCreate((PCHARFAR)&LogPath);
}
FSize(F);
FWrite(F, (PCHARFAR)buf, len);
FClose(F);
}
}
int main(int argc, Char *argv[])
{ /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
argc = 1; /* macsetup("SeqBoot",""); */
argv[0] = "SeqBoot";
#endif
init(argc,argv);
emboss_getoptions("ffreqboot", argc, argv);
ibmpc = IBMCRT;
ansi = ANSICRT;
doinput(argc, argv);
bootwrite();
FClose(infile);
if (weights)
FClose(weightfile);
if (categories) {
FClose(catfile);
FClose(outcatfile);
}
if(mixture)
FClose(outmixfile);
if(ancvar)
FClose(outancfile);
if (justwts && !permute) {
FClose(outweightfile);
}
else
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
if (justwts && !permute)
fixmacfile(outweightfilename);
if (categories)
fixmacfile(outcatfilename);
if (mixture)
fixmacfile(outmixfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
embExit();
return 0;
}
static PackFile *PackOpen(char *name)
{
FILE *fp;
char tmp[MAX_PATH];
RemoveExt(tmp, name);
StrCat(tmp, MAX_PATH, ".txt");
fp = FOpen(tmp, "r");
if (fp) {
fgets(tmp, MAX_PATH, fp);
FClose(fp);
packFile = FOpen(tmp, "rb");
return PackOpenFromFile(tmp);
}
packFile = FOpen(name, "rb");
return PackOpenFromFile(name);
}
frcDisc = TRUE; break;
case 'e':
gen = GetChkedLong(gst,LONG_MAX,s); break;
case 'h':
srcHdr = TRUE; break;
case 'i':
nItems = GetChkedInt(1,100,s); break;
case 'n':
numS = GetChkedInt(1,SMAX-1,s); break;
case 'o':
obsFmt = TRUE; break;
case 'p':
replay = TRUE; break;
case 'r':
rawOut = TRUE; break;
case 's':
gst = GetChkedLong(0,LONG_MAX,s); break;
case 't':
tgtHdr = TRUE; break;
case 'z':
prData = FALSE; break;
case 'F':
if (NextArg() != STRINGARG)
