// OnOK() calls wxWindow::Validate, then wxWindow::TransferDataFromWindow.
// If this returns TRUE, the function either calls EndModal(wxID_OK) if the
// dialog is modal, or sets the return value to wxID_OK and calls Show(FALSE)
// if the dialog is modeless.
void COutputFilenameDlg::OnOK(wxCommandEvent& event)
{
// ensure there are no illegal characters in the filename
//TransferDataFromWindow(); // whm removed 21Nov11
m_strFilename = pEdit->GetValue(); // whm added 21Nov11
wxString fn = m_strFilename;
wxString illegals = wxFileName::GetForbiddenChars(); //_T(":?*\"\\/|<>");
wxString scanned = SpanExcluding(fn, illegals);
if (scanned == fn)
{
// BW added 22July08; check for a name clash
bool bNamesClash = gpApp->GetDocument()->FilenameClash(fn);
if (bNamesClash)
{
// IDS_TYPED_DOCNAME_CLASHES
wxMessageBox(_("The name you typed clashes with an existing document name. Please type a different name.")
,_T(""), wxICON_EXCLAMATION | wxOK);
return; // leave user in the dialog, to fix the name
}
}
else
{
// there is at least one illegal character, replace each such
// by a space, beep, and show the modified string to the user
//int nFound = -1;
// whm Note: Since different platforms have slightly differing illegal characters for file
// names, etc., we will not hard code the search for characters as does the MFC version.
// Instead, we'll scan the file name char by char and change any that are illegal to spaces.
int ct;
int foundPos;
for (ct = 0; ct < (int)fn.Length(); ct++)
{
foundPos = FindOneOf(fn, illegals);
if (foundPos != -1)
fn[foundPos] = _T(' ');
}
m_strFilename = fn;
//TransferDataFromWindow(); // whm removed 21Nov11
// whm note 21Nov11 the TransferDataFromWindow() call above would defeat the preceding code
// that replaces any illegal char with a space, so I've removed it entirely.
::wxBell();
// if we decide to verbally tell the user what the beep means:
//wxString message;
//message = message.Format(_("Names cannot include these characters: %s (Note: An .xml extension will be automatically added.) Please try the New... command again."),illegals.c_str());
//wxMessageBox(message, _("Bad characters found in name"), wxICON_INFORMATION | wxOK); }
}
event.Skip(); //EndModal(wxID_OK); //AIModalDialog::OnOK(event); // not virtual in wxDialog
}
int main(int argc, char** argv)/*{{{*/
{
bool isNonOptionArg = false;
if(argc < 2)
{
PrintHelp();
return 0;
}
int i,j;
char modmfile[MAX_PATH+1] = "";
char modmfilelist[MAX_PATH+1] = "";
char outfile[MAX_PATH+1] = "";
char suppliedAlphabet[SIZE_ALPHABET+1] = ""; /*force supplied alphabet to the alphabet in the output binary file*/
char outpath[MAX_PATH+1] = ""; /*default output path for the binary file is the same as the ascii file*/
double value = 0.0;
int mode = 0;
const char control_option[] = "bp"; //options which control the program, and does not take parameters
char tmpfile[MAX_PATH+1] = "/tmp/fileXXXXXX";
if (mkstemp(tmpfile) == -1)
{
fprintf(stderr, "Error! No temporary file can be created\n");
return -1;
}
FILE *fptmp = fopen(tmpfile,"w");
bool isIDsSet = false;
bool isOutputTimeInfo = true;
i = 1;
while(i < argc)/*{{{*/
{
if(argv[i][0] == '-' && !isNonOptionArg) //options
{
isNonOptionArg = false;
if(IsInCharSet(argv[i][1], control_option))//if argv[i][1] is in control_option, it might be used as -aqs
{
for(j = 1 ; j < strlen(argv[i]); j++)
{
switch (argv[i][j])
{
case 'b': isWriteBinaryFile = true; break;
case 'p': isPrintOut = true; break;
default : fprintf(stderr,"Invalid option, non-control option '%c' can be used together with contorl-option\n", argv[j]); return -1;
}
}
i ++;
}
else if(strcmp(argv[i],"-h") == 0 ||strcmp(argv[i],"--help")==0 )
{
PrintHelp();
return 0;
}
else if(strcmp(argv[i],"-H") == 0 )
{
PrintVerboseHelp();
return 0;
}
else if(strcmp(argv[i],"-a") == 0 )
{
my_strcpy(suppliedAlphabet, argv[i+1], SIZE_ALPHABET);
i += 2;
}
else if( (strcmp(argv[i],"-o") == 0) || (strcmp(argv[i], "--out") == 0))
{
if( ( i = option_parser_filename(argc, argv, i, outfile)) == -1)
return -1;
}
else if( (strcmp(argv[i], "--outpath") == 0))
{
if( ( i = option_parser_filename(argc, argv, i, outpath)) == -1)
return -1;
}
else if( (strcmp(argv[i],"-l") == 0) )
{
if( ( i = option_parser_filename(argc, argv, i, modmfilelist)) == -1)
return -1;
}
else if( (strcmp(argv[i], "--mode") == 0))
{
if( ( i = option_parser_numeric(argc, argv, i, mode, true, 0, 1)) == -1)
return -1;
}
else if (strcmp(argv[i], "--sad") == 0)/*indicating the modm file contains SAD information*/
{
isHaveSAD = true;
i ++;
}
else if (strcmp(argv[i], "--notime") == 0)/*do not output time info*/
{
isOutputTimeInfo = false;
i ++;
}
else if (strcmp(argv[i], "--") == 0)//next item is non option argument
{
isNonOptionArg = true;
i ++;
continue;
}
else
{
fprintf(stderr,"Error! Invalid argument '%s'\n", argv[i]);
return -1;
}
}
else //non-option argument
{
if(!isIDsSet)
{
fptmp = fopen(tmpfile,"w");
if(fptmp == NULL)
{
fprintf(stderr,"can not open file '%s' for write\n", tmpfile);
assert( fptmp != NULL);
}
}
fprintf(fptmp,"%s\n",argv[i]);
isIDsSet = true;
i ++;
}
}/*}}}*/
if(isIDsSet) fclose(fptmp);
if(!isIDsSet && strcmp(modmfilelist, "") == 0)
{
fprintf(stderr,"Error! neither ids and idListFile set\n");
PrintHelp();
return -1;
}
else if(isIDsSet && strcmp(modmfilelist,"") == 0)
{
my_strcpy(modmfilelist,tmpfile,MAX_PATH);
}
FILE *fpout = NULL;
if(strcmp(outfile,"") == 0 || strcasecmp(outfile, "stdout") == 0)
{
fpout = stdout;
}
else
{
fpout = fopen(outfile, "w");
checkfilestream(fpout, outfile,"w");
}
clock_t start, finish;
double duration;
int tmp;
start = clock();
FILE *fpFileList = fopen(modmfilelist, "r");
checkfilestream(fpFileList, modmfilelist, "r");
int linesize;
int maxline = 300;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
int sizeAlphabet = 0;
char alphabet[SIZE_ALPHABET+1] = "";
int numRes = 0;
Array1D <Profile> profile_1darray(2000);
Profile *profile = profile_1darray.array1D;
Array1D <ProfileSAD> profileSAD_1darray(2000);
ProfileSAD *profileSAD = profileSAD_1darray.array1D;
double parameter[8];
int status_sscanf = 0;
int cntFile = 0;
while((linesize = fgetline(fpFileList,line, maxline)) != EOF)
{
my_strcpy(modmfile, line, MAX_PATH);
for(j = 0; j < 8; j ++)
{
parameter[j] = 0.0;
}
strcpy(alphabet,"");
if(mode == 0) /*read text file*/
{
FILE *fpin = fopen(modmfile,"r");
checkfilestream(fpin,modmfile,"r");
char str[100] = "";
char first_non_blank_char = ' ';
int cntRes = 0;
while((linesize = fgetline(fpin, line, maxline)) != EOF)
{
if(line[0] == '#' || linesize <=0 )
{
continue;
}
sscanf(line, " %c", &first_non_blank_char);
if (first_non_blank_char == 'N')/*alphabet line*/
{
SpanExcluding(line, str);
if(!isHaveSAD)
{
my_strcpy(alphabet, str+5, SIZE_ALPHABET);
}
else
{
my_strcpy(alphabet, str+8, SIZE_ALPHABET);
}
}
else if (isdigit(first_non_blank_char))
{
if(!isHaveSAD)
{
profile[cntRes].score1 = 0.0;
profile[cntRes].score2 = 0.0;
status_sscanf = sscanf(line,"%d %c %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",/*{{{*/
&profile[cntRes].aaSeqIndex,
&profile[cntRes].aa,
&profile[cntRes].p[0],
&profile[cntRes].p[1],
&profile[cntRes].p[2],
&profile[cntRes].p[3],
&profile[cntRes].p[4],
&profile[cntRes].p[5],
&profile[cntRes].p[6],
&profile[cntRes].p[7],
&profile[cntRes].p[8],
&profile[cntRes].p[9],
&profile[cntRes].p[10],
&profile[cntRes].p[11],
&profile[cntRes].p[12],
&profile[cntRes].p[13],
&profile[cntRes].p[14],
&profile[cntRes].p[15],
&profile[cntRes].p[16],
&profile[cntRes].p[17],
&profile[cntRes].p[18],
&profile[cntRes].p[19],
&profile[cntRes].score1,
&profile[cntRes].score2
);/*}}}*/
if(status_sscanf < 22)
{
fprintf(stderr,"current line=%s\n!", line );
fprintf(stderr,"The profile maybe incomplete, status_sscanf = %d, number %d, file %s\n!", status_sscanf, cntRes+1, modmfile );
assert (status_sscanf >= 22);
}
}
else
{
profileSAD[cntRes].score1 = 0.0;
profileSAD[cntRes].score2 = 0.0;
status_sscanf = sscanf(line,"%d %c %1c%1d%1c %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",/*{{{*/
&profileSAD[cntRes].aaSeqIndex,
&profileSAD[cntRes].aa,
&profileSAD[cntRes].shape,
&profileSAD[cntRes].waterAcc,
&profileSAD[cntRes].dsspSec,
&profileSAD[cntRes].p[0],
&profileSAD[cntRes].p[1],
&profileSAD[cntRes].p[2],
&profileSAD[cntRes].p[3],
&profileSAD[cntRes].p[4],
&profileSAD[cntRes].p[5],
&profileSAD[cntRes].p[6],
&profileSAD[cntRes].p[7],
&profileSAD[cntRes].p[8],
&profileSAD[cntRes].p[9],
&profileSAD[cntRes].p[10],
&profileSAD[cntRes].p[11],
&profileSAD[cntRes].p[12],
&profileSAD[cntRes].p[13],
&profileSAD[cntRes].p[14],
&profileSAD[cntRes].p[15],
&profileSAD[cntRes].p[16],
&profileSAD[cntRes].p[17],
&profileSAD[cntRes].p[18],
&profileSAD[cntRes].p[19],
&profileSAD[cntRes].score1,
&profileSAD[cntRes].score2
);/*}}}*/
if(status_sscanf < 25)
{
fprintf(stderr,"current line=%s\n!", line );
fprintf(stderr,"The profile maybe incomplete, status_sscanf = %d, number %d, file %s\n!", status_sscanf, cntRes+1, modmfile );
assert (status_sscanf >= 25);
}
}
cntRes ++;
}
else if (first_non_blank_char == 'K')
{
int j = 0 ;
while((linesize = fgetline(fpin, line, maxline)) != EOF)
{
status_sscanf = sscanf(line,"%s %s %lf %lf", str, str, ¶meter[j], ¶meter[j+1]);
if(status_sscanf < 4)
{
fprintf(stderr,"Warning, file %s may not have psi-blast parameters\n", modmfile);
}
j += 2;
if (j >= 8 ) break;
}
}
}
fclose(fpin);
numRes = cntRes;
if (isWriteBinaryFile)
{
char binaryfile[MAX_PATH+1] = "";
if(strcmp(outpath, "") == 0) /*if outpath is not set, output to the same folder as the ascii file*/
{
sprintf(binaryfile, "%sbin", modmfile); /*if outpath is set*/
}
else
{
char rtname[MAX_PATH+1] = "";
char fileext[MAX_PATH+1] = "";
rootname(modmfile, rtname);
getfileext(modmfile, fileext);
sprintf(binaryfile, "%s/%s.%sbin", outpath, rtname, fileext);
}
// fprintf(stdout,"%d \t write out binary file to %s\n", cntFile, binaryfile) ;
if(strcmp(suppliedAlphabet,"") != 0)
{
my_strcpy(alphabet, suppliedAlphabet, SIZE_ALPHABET);
}
if(!isHaveSAD)
{
WriteBinaryMODM(binaryfile, alphabet, numRes, profile, parameter);
}
else
{
WriteBinaryMODM(binaryfile, alphabet, numRes, profileSAD, parameter);
}
}
}
else if(mode == 1)
{
if(!isHaveSAD)
{
GetBinaryMODM(modmfile, alphabet, numRes, profile, parameter);
if (isPrintOut)
{
WriteMODM(alphabet, profile, numRes, parameter, fpout);
}
}
else
{
GetBinaryMODM(modmfile, alphabet, numRes, profileSAD, parameter);
if (isPrintOut)
{
WriteMODM(alphabet, profileSAD, numRes, parameter, fpout);
}
}
}
cntFile ++;
}
finish = clock();
duration = double(finish-start) /double(CLOCKS_PER_SEC);
//printf("CLOCKS_PER_SEC=%d, start=%lf, finish=%lf\n", CLOCKS_PER_SEC, start, finish);
if (isOutputTimeInfo)
{
if(mode == 0)
{
fprintf(stdout,"reading text file cost %lf seconds\n", duration);
}
else if(mode == 1)
{
fprintf(stdout,"reading bindary file cost %lf seconds\n", duration);
}
}
if(fpout != NULL && fpout != stdout) fclose(fpout);
return 0;
}
