/*}}}*/
int main(int argc, char** argv)/*{{{*/
{
if (argc < 2)
{
PrintHelp();
return -1;
}
int i = 0;
int j = 0;
char outpath[MAX_PATH+1] = "./";
char listfile[MAX_PATH+1] = "";
char outAlphabet[NUM_BLOSUM+1] = ""; //if outAlphabet not set, using the default BLOSUM alphabet
double scale = 100.0;
//char **filenamelist = NULL;
bool isOutputLast2Col = false;
bool isQuietMode = false;
set <string> filenamelist_set;
set <string> ::iterator iss;
int numfile = 0;
int errmsg = 0;
i = 1;
while(i < argc)/*{{{*/
{
if(strcmp(argv[i], "-h") == 0|| strcmp(argv[i], "--help") == 0)
{
PrintHelp();
errmsg = 1;
break;
}
else if (strcmp(argv[i], "-d") == 0)
{
my_strcpy(outpath,argv[i+1], MAX_PATH);
i += 2;
}
else if (strcmp(argv[i], "-s") == 0)
{
scale = atof(argv[i+1]);
i += 2;
}
else if (strcmp(argv[i], "-i") == 0)
{
isOutputInteger = true;
i ++;
}
else if (strcmp(argv[i], "-l") == 0 || strcmp(argv[i], "--list") == 0)
{
my_strcpy(listfile,argv[i+1], MAX_PATH);
i += 2;
}
else if (strcmp(argv[i], "--alphabet") == 0 || strcmp(argv[i], "-a") == 0)
{
my_strcpy(outAlphabet,argv[i+1], NUM_BLOSUM);
if(!IsValidAlphabet(outAlphabet))
{
errmsg = -1;
break;
}
i += 2;
}
else if (strcmp(argv[i], "-q") == 0)
{
isQuietMode = true;
i ++;
}
else if (strcmp(argv[i], "--pssm") == 0)
{
isOutputLast2Col = true;
i ++;
}
else
{
filenamelist_set.insert(argv[i]);
i ++;
}
}/*}}}*/
numfile = filenamelist_set.size();
if(errmsg != 0)
{
return errmsg;
}
if(strcmp(listfile,"") == 0 && filenamelist_set.size() == 0)
{
fprintf(stderr,"Error! neither listfile nor mtx file in the argument list are set\n");
return -1;
}
else if(strcmp(listfile,"") != 0)
{
FILE *fpin;
fpin = fopen(listfile,"r");
checkfilestream(fpin,listfile,"r");
int linesize;
int maxline = 300;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
while((linesize = fgetline(fpin, line , maxline)) != EOF)
{
if(linesize > 0) filenamelist_set.insert(line);
}
fclose(fpin);
}
VerifyFolder(outpath);
Array1D <char> aaSeq_1darray(LONGEST_SEQ+1);
Array2D <double> profile_2darray(LONGEST_SEQ, NUM_BLOSUM);
Array1D <double> parameter_1darray(NUM_PARAMETER);
char *aaSeq = aaSeq_1darray.array1D;
double **profile = profile_2darray.array2D;
double *parameter = parameter_1darray.array1D;
double *score1 = NULL;
double *score2 = NULL;
char modmfile[MAX_PATH+1] = "";
char pssmfile[MAX_PATH+1] = "";
char mtxfile[MAX_PATH+1] = "";
char rtname[MAX_PATH+1] = "";
char filepath[MAX_PATH+1] = "";
int length;
int lengthpssm;
int cntfile = 0;
for(iss = filenamelist_set.begin() ; iss != filenamelist_set.end(); iss ++)
{
score1 = NULL;
score2 = NULL;
my_strcpy(mtxfile, (*iss).c_str(), MAX_PATH);
rootname(mtxfile, rtname);
getfilepath(mtxfile, filepath);
if(getmtx(mtxfile, length, aaSeq, parameter, profile, scale) <= 0)
{
fprintf(stderr, "%d \t %s getting mtx file error!",cntfile+1, mtxfile);
continue;
}
lengthpssm = length ;
int profileIndex[NUM_BLOSUM]; //order the profile according to the outAlphabet
for(j = 0; j < NUM_BLOSUM; j ++) profileIndex[j] = j;
if(strcmp(outAlphabet,"") != 0)
{
for(i = 0 ; i < NUM_AA; i++)
{
profileIndex[i] = Char2Digit(outAlphabet[i], BLOSUM1D_alphabet);
}
}
else
{
my_strcpy(outAlphabet, BLOSUM1D_alphabet, NUM_BLOSUM);
}
if(isOutputLast2Col)
{
score1 = new double [LONGEST_SEQ];
score2 = new double [LONGEST_SEQ];
sprintf(pssmfile, "%s/%s.pssm", filepath, rtname);
lengthpssm = GetPSSM(pssmfile, lengthpssm, NULL, NULL, NULL, score1, score2);
}
if ( length != lengthpssm)
{
fprintf(stderr,"Error! length of mtx file and pssm not the same for %s", rtname);
}
else
{
sprintf(modmfile, "%s/%s.modm", outpath, rtname);
WriteMODMFile(modmfile, aaSeq, length, profile, profileIndex, outAlphabet, score1, score2, parameter, isOutputInteger);
if(!isQuietMode) fprintf(stdout,"%d %s output\n", cntfile+1, modmfile);
}
if (score1 != NULL) delete [] score1;
if (score2 != NULL) delete [] score2;
}
//
return 0;
}
void KeyPad::ProcessKey()
{
char K=ReadKey();
KD = Char2Digit(K);
// if (K!=NoKeyChar)
{
switch (CurrState)
{
case 0:
LCDRow1 = "A-Sch/B-SetUp";
switch (K)
{
case FKeySetCurrSched:
CurrState = KSTATE_SETCURRSCHED;
break;
case FKeySetUpSched:
CurrState = KSTATE_SETUPSCHED;
CurrSubState = 0;
break;
}
break;
case KSTATE_SETCURRSCHED :
LCDRow1 = "Choose Schedule";
if (KD>=0 && KD < ScheduleSets)
{
//Set Current Schedule KD
(*mFeedSch).ActiveSet=KD;
CurrState = 0;
}
break;
case KSTATE_SETUPSCHED :
LCDRow1 = "S"+String((*mFeedSch).ActiveSet,DEC)+"~";
switch (CurrSubState)
{
case 0: //Choose Sched Type - Cyclic (1) or OnTime (2),
//Cyclic : 1 / OnTime : 4
LCDRow1 += "1Cycl/2OnTime";
CurrNumber = 0;
CurrSubState = KD==1 ? 1 : (KD==2 ? 4 : 0) ;
P1 = 0;
P2 = 0;
P3 = 0;
break;
case 1: //Cyclic Chosen, Choose FeedsCount
LCDRow1 += "Count";
NumbEntering (K,2,0,&P1);
break;
case 2: //Cyclic Chosen, Choose FeedsInterval
LCDRow1 += "Interval";
NumbEntering (K,3,1,&P2);
break;
case 3: //Cyclic Chosen, Choose FeedDur
LCDRow1 += "Duration";
NumbEntering (K,0,2,&P3);
if (CurrSubState == 0)
{
InitCyclicSchedule(P1,P2*60,P3);
CurrState = 0;
}
break;
// case 4: //OnTime Chosen, Choose FeedN
//
// case 5: //OnTime Chosen, Choose FeedTime
//
// case 6: //OnTime Chosen, Choose FeedDur
}
break;
default :
break;
}
}
if (CurrState == KSTATE_SETUPSCHED)
{
LCDRow2="";
if (CurrSubState >= 1)
LCDRow2 = "C";
if (CurrSubState >= 2)
LCDRow2 += String(P1,DEC) + "|I";
if (CurrSubState >= 3)
LCDRow2 += String(P2,DEC) + "|D";
LCDRow2 += CurrString;
// LCDRow2 +=".";
}
else
LCDRow2= ""; //CurrString;
}