int CConfigure::GetIntParam(const string& astrKey,const string& astrSection,const string& astrCfgFile){
string lstrValue = GetStrParam(astrKey,astrSection,astrCfgFile);
return atoi(lstrValue.c_str());
}
char* CJPersistFile::Get256CharStrParam( U32 parentId, U32 parentIndex, U32 childId, U32 childIndex) { return GetStrParam(parentId, parentIndex=0, childId=eNONE, childIndex);}
void ReadParams(int argc, char **argv)
{
int i, j, k;
char ch, *P, st[4];
int modelTwoArgs = 0;
model=NONE;
scaleTrees=0;
treeScale=0.0;
scaleBranches=0;
branchScale=0.0;
maxPartitions=1;
numPartitions=1;
userSeed = 0;
numCats=1;
rateHetero=NoRates;
catRate[0]=1.0;
gammaShape=1.0;
invariableSites=0;
proportionInvariable = 0.0;
equalFreqs = 1;
equalTstv = 1;
tstv=0.50002;
for (i = 0; i < NUM_AA_REL_RATES; i++) {
aaRelativeRate[i] = 1.0;
}
for (i = 0; i < NUM_AA; i++) {
aaFreq[i] = 1.0;
}
aaFreqSet = 0;
numSites=-1;
numDatasets=1;
ancestorSeq=0;
writeAncestors=0;
writeRates=0;
verbose=1;
fileFormat = PHYLIPFormat;
quiet=0;
treeFile=0;
textFile=0;
for (i=1; i<argc; i++) {
P=argv[i];
if (*P=='-') {
P++;
ch=toupper(*P);
P++;
switch (ch) {
case 'H':
PrintTitle();
PrintUsage();
exit(0);
break;
case 'M':
k = i;
if (GetStrParam(argc, argv, &i, P, st, 3)) {
fprintf(stderr, "Bad (or missing) Model Code: %s\n\n", argv[i]);
exit(1);
}
P=st;
if (i > k) {
modelTwoArgs = 1;
}
model=-1;
for (j=F84; j<numModels; j++) {
if (strncmp(P, modelNames[j], 3)==0) {
model=j;
if (model <= GTR) {
isNucModel = 1;
numStates = 4;
} else {
isNucModel = 0;
numStates = 20;
}
} else if (strncmp(P, "REV", 3)==0) {
model=GTR;
isNucModel = 1;
numStates = 4;
}
}
if (model==-1) {
fprintf(stderr, "Unknown Model: %s\n\n", argv[i]);
exit(1);
}
break;
}
}
}
if (model==NONE) {
fprintf(stderr, "No model has been specified (use the -m option)\n\n");
PrintUsage();
exit(1);
}
for (i=1; i<argc; i++) {
P=argv[i];
if (*P!='-') {
if (treeFile) {
fprintf(stderr, "Illegal command parameter: %s\n\n", argv[i]);
PrintUsage();
exit(1);
}
treeFile=1;
strcpy(treeFileName, argv[i]);
} else if (*P=='-' && toupper(*(P+1))=='X') {
P++; P++;
if (*P=='\0') {
i++;
P = argv[i];
}
textFile=1;
strcpy(textFileName, P);
} else {
P++;
ch=toupper(*P);
P++;
switch (ch) {
case 'H':
// already delt with
break;
case 'M':
// already delt with
if (modelTwoArgs) {
// the model took two arguments so skip the second one.
i++;
}
break;
case 'L':
if (GetIntParams(argc, argv, &i, P, 1, &numSites) || numSites<1) {
fprintf(stderr, "Bad (or missing) sequence length: %s\n\n", argv[i]);
exit(1);
}
break;
case 'N':
if (GetIntParams(argc, argv, &i, P, 1, &numDatasets) || numDatasets<1) {
fprintf(stderr, "Bad (or missing) number of datasets: %s\n\n", argv[i]);
exit(1);
}
break;
case 'P':
if (GetIntParams(argc, argv, &i, P, 1, &maxPartitions) || maxPartitions < 1) {
fprintf(stderr, "Bad number of partitions: %s\n\n", argv[i]);
exit(1);
}
break;
case 'C':
if (!isNucModel) {
fprintf(stderr, "You can only have codon rates when using nucleotide models\n\n");
exit(1);
}
if (rateHetero==GammaRates) {
fprintf(stderr, "You can only have codon rates or gamma rates not both\n\n");
exit(1);
}
numCats=3;
rateHetero=CodonRates;
if (GetDoubleParams(argc, argv, &i, P, 3, catRate) ||
catRate[0] <= 0.0 || catRate[1] <= 0.0 || catRate[2] <= 0.0 ) {
fprintf(stderr, "Bad Category Rates: %s\n\n", argv[i]);
exit(1);
}
break;
case 'I':
if (GetDoubleParams(argc, argv, &i, P, 1, &proportionInvariable) ||
proportionInvariable < 0.0 || proportionInvariable >= 1.0) {
fprintf(stderr, "Bad Proportion of Invariable Sites: %s\n\n", argv[i]);
exit(1);
}
invariableSites = 1;
break;
case 'A':
if (rateHetero==CodonRates) {
fprintf(stderr, "You can only have codon rates or gamma rates not both\n\n");
exit(1);
}
if (rateHetero==NoRates)
rateHetero=GammaRates;
if (GetDoubleParams(argc, argv, &i, P, 1, &gammaShape) || gammaShape<=0.0) {
fprintf(stderr, "Bad Gamma Shape: %s\n\n", argv[i]);
exit(1);
}
break;
case 'G':
if (rateHetero==CodonRates) {
fprintf(stderr, "You can only have codon rates or gamma rates not both\n\n");
exit(1);
}
rateHetero=DiscreteGammaRates;
if (GetIntParams(argc, argv, &i, P, 1, &numCats) || numCats<2 || numCats>MAX_RATE_CATS) {
fprintf(stderr, "Bad number of Gamma Categories: %s\n\n", argv[i]);
exit(1);
}
break;
case 'F':
if (isNucModel) {
if (toupper(*P)=='E'){
/* do nothing - equal freqs is default for nucleotides */
} else {
equalFreqs = 0;
if (GetDoubleParams(argc, argv, &i, P, NUM_NUC, nucFreq)) {
fprintf(stderr, "Bad Nucleotide Frequencies: %s\n\n", argv[i]);
exit(1);
}
}
} else {
aaFreqSet = 1;
if (toupper(*P)=='E'){
equalFreqs = 1;
for(j=0;j<NUM_AA;j++) {
aaFreq[j]=0.05;
}
} else {
equalFreqs = 0;
if (GetDoubleParams(argc, argv, &i, P, NUM_AA, aaFreq)) {
fprintf(stderr, "Bad Amino Acid Frequencies: %s\n\n", argv[i]);
exit(1);
}
}
}
break;
case 'T':
if (model != HKY && model != F84) {
fprintf(stderr, "You can only have a transition/transversion ratio when using HKY or F84 models\n\n");
exit(1);
}
equalTstv = 0;
if (GetDoubleParams(argc, argv, &i, P, 1, &tstv)) {
fprintf(stderr, "Bad Transition-Transversion Ratio: %s\n\n", argv[i]);
exit(1);
}
break;
case 'R':
if (model == GTR) {
if (GetDoubleParams(argc, argv, &i, P, NUM_NUC_REL_RATES, nucRelativeRates)) {
fprintf(stderr, "Bad General Nucleotide Rate Matrix: %s\n\n", argv[i]);
exit(1);
}
if (nucRelativeRates[NUM_NUC_REL_RATES - 1]!=1.0) {
for (j=0; j < NUM_NUC_REL_RATES - 1; j++)
nucRelativeRates[j] /= nucRelativeRates[NUM_NUC_REL_RATES - 1];
nucRelativeRates[NUM_NUC_REL_RATES - 1] = 1.0;
}
} else if ( model == GENERAL) {
if (GetDoubleParams(argc, argv, &i, P, NUM_AA_REL_RATES, aaRelativeRate)) {
fprintf(stderr, "Bad General Amino Acid Rate Matrix: %s\n\n", argv[i]);
exit(1);
}
} else {
fprintf(stderr, "You can only have a general rate matrix when using GTR or GENERAL models\n\n");
exit(1);
}
break;
case 'D':
scaleTrees=1;
if (GetDoubleParams(argc, argv, &i, P, 1, &treeScale) || treeScale<=0.0) {
fprintf(stderr, "Bad Total Tree Scale: %s\n\n", argv[i]);
exit(1);
}
if (scaleBranches) {
fprintf(stderr, "You can't specify both the -d and -s options\n\n");
exit(1);
}
break;
case 'S':
scaleBranches=1;
if (GetDoubleParams(argc, argv, &i, P, 1, &branchScale) || branchScale<=0.0) {
fprintf(stderr, "Bad Branch Length Scale: %s\n\n", argv[i]);
exit(1);
}
if (scaleTrees) {
fprintf(stderr, "You can't specify both the -d and -s options\n\n");
exit(1);
}
break;
case 'K':
if (GetIntParams(argc, argv, &i, P, 1, &ancestorSeq) || ancestorSeq<1) {
fprintf(stderr, "Bad ancestral sequence number: %s\n\n", argv[i]);
exit(1);
}
break;
case 'Z':
userSeed = 1;
if (GetUnsignedLongParams(argc, argv, &i, P, 1, &randomSeed)) {
fprintf(stderr, "Bad random number generator seed: %s\n\n", argv[i]);
exit(1);
}
break;
case 'O':
switch (toupper(*P)) {
case 'P': fileFormat=PHYLIPFormat; break;
case 'R': fileFormat=RelaxedFormat; break;
case 'N': fileFormat=NEXUSFormat; break;
case 'F': fileFormat=FASTAFormat; break;
default:
fprintf(stderr, "Unknown output format: %s\n\n", argv[i]);
PrintUsage();
exit(1);
}
break;
case 'W':
switch (toupper(*P)) {
case 'A': writeAncestors=1; break;
case 'R': writeRates=1; break;
default:
fprintf(stderr, "Unknown write mode: %s\n\n", argv[i]);
PrintUsage();
exit(1);
}
break;
case 'Q':
quiet=1;
break;
default:
fprintf(stderr, "Illegal command parameter: %s\n\n", argv[i]);
PrintUsage();
exit(1);
break;
}
}
}
}
