1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
// $Id: molphyFormat.cpp 962 2006-11-07 15:13:34Z privmane $
#include "molphyFormat.h"
#include "someUtil.h"
#include "errorMsg.h"
sequenceContainer molphyFormat::read(istream &infile, const alphabet* alph) {
sequenceContainer mySeqData = readUnAligned(infile, alph);
mySeqData.makeSureAllSeqAreSameLengthAndGetLen();
return mySeqData;
}
sequenceContainer molphyFormat::readUnAligned(istream &infile, const alphabet* alph) {
vector<string> seqFileData;
putFileIntoVectorStringArray(infile,seqFileData);
if (seqFileData.empty()){
errorMsg::reportError("unable to open file, or file is empty in molphy format");
}
vector<string>::iterator currentLinePosition = seqFileData.begin();
string::const_iterator itStr = seqFileData.begin()->begin();
string::const_iterator itStrEnd = seqFileData.begin()->end();
int f_numSeq;
bool readSeqNum= fromStringIterToInt(itStr,itStrEnd,f_numSeq);
if (readSeqNum == false) errorMsg::reportError("Error reading number of sequences while reading MOLPHY sequence format");
int f_seqLength;
bool readSeqLen= fromStringIterToInt(itStr,itStrEnd,f_seqLength);
if (readSeqLen == false) errorMsg::reportError("Error reading the sequences length while reading MOLPHY sequence format");
currentLinePosition++; // we read the first line.
//---------------------------------------------------------------------
sequenceContainer mySeqData;
//---------------------------------------------------------------------
// vector<sequenceContainer::sequenceDatum*> vec;
// seqDataPtr->getSequenceDatumPtrVectorNonConst(vec);
int localID=-1;
vector<string>::const_iterator it1 = seqFileData.begin();
++it1; //skipping the first line that was read already.
while (it1!= seqFileData.end()) {
localID++;
if (it1->empty()) {
it1++;
continue; // empty line continue
}
// read the name.
string name(*it1);
it1++;
string tmpString;
while (it1 != seqFileData.end()) {
if (tmpString.size() < f_seqLength) {
tmpString+=*it1;
++it1;
}
else break;
}
mySeqData.add(sequence(tmpString,name,"",localID,alph));
}
return mySeqData;
}
void molphyFormat::write(ostream &out, const sequenceContainer& sd) {
out<<sd.numberOfSeqs()<<" "<<sd.seqLen()<<endl;
for (sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();it5!=sd.constTaxaEnd();++it5) {
out<<it5->name()<<endl;
string seqString = it5->toString();
int k=0;
for (string::const_iterator cPos=seqString.begin() ; cPos != seqString.end() ; cPos ++,k++ ) {
if (k>0 && ((k%60)==0)) out<<endl;
out<<*cPos;
}
out<<endl;
}
}
|
