//***************************************************************************************************************
Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : MothurChimera() {
try {
fastafile = filename;
outputDir = o;
templateFileName = temp; templateSeqs = readSeqs(temp);
setMask(mask);
filter = f;
window = win;
numWanted = numW;
distCalc = new eachGapDist();
decalc = new DeCalculator();
mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
ofstream out2;
m->openOutputFile(mapInfo, out2);
out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
out2.close();
}
catch(exception& e) {
m->errorOut(e, "Ccode", "Ccode");
exit(1);
}
}
Bellerophon::Bellerophon(string name, bool filterSeqs, bool c, int win, int inc, int p, string o) : Chimera() {
try {
fastafile = name;
correction = c;
outputDir = o;
window = win;
increment = inc;
processors = p;
//read in sequences
seqs = readSeqs(fastafile);
numSeqs = seqs.size();
if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); }
//do soft filter
if (filterSeqs) {
createFilter(seqs, 0.5);
for (int i = 0; i < seqs.size(); i++) { runFilter(seqs[i]); }
}
distCalculator = new eachGapDist();
//set default window to 25% of sequence length
string seq0 = seqs[0]->getAligned();
if (window == 0) { window = seq0.length() / 4; }
else if (window > (seq0.length() / 2)) {
m->mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); m->mothurOutEndLine();
window = (seq0.length() / 2);
}
if (increment > (seqs[0]->getAlignLength() - (2*window))) {
if (increment != 10) {
m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine();
increment = 10;
if (increment > (seqs[0]->getAlignLength() - (2*window))) { increment = 0; }
}else{ increment = 0; }
}
if (increment == 0) { iters = 1; }
else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
//initialize pref
pref.resize(iters);
for (int i = 0; i < iters; i++) {
Preference temp;
for (int j = 0; j < numSeqs; j++) {
pref[i].push_back(temp);
}
}
}
catch(exception& e) {
m->errorOut(e, "Bellerophon", "Bellerophon");
exit(1);
}
}
AHalfLifeDecoder::AHalfLifeDecoder(const char *fname) : AMeshDecoder(fname)
{
init();
openFile(fname);
readHeader();
if(numbones) readBones();
if(numbonecontrollers) readBoneControllers();
if(numhitboxes) readHitBoxes();
if(numseq) readSeqs();
if(numseqgroups) readSeqGroups();
if(numtextures) readTextures();
if(numskinref*numskinfamilies) readSkins();
if(numbodyparts) readBodyParts();
if(numattachments) readAttachments();
if(soundtable) readSounds();
if(soundgroups) readSoundGroups();
if(numtransitions) readTransitions();
}
