void Tree::ReadMrBayes(string filename) {
ifstream is(filename.c_str());
mRoot = new PolyNode();
PolyNode* currentNode = mRoot;
char c = ' ';
while ((!is.eof()) && (c != '=')) is >> c;
ReadPhylip(is,currentNode);
// SetLabelOffset(0);
mRoot->SetSuper(this);
}
/* Function: MSAFileRead()
* Date: SRE, Fri May 28 16:01:43 1999 [St. Louis]
*
* Purpose: Read the next msa from an open alignment file.
* This is a wrapper around format-specific calls.
*
* Args: afp - open alignment file
*
* Returns: next alignment, or NULL if out of alignments
*/
MSA *
MSAFileRead(MSAFILE *afp)
{
MSA *msa = NULL;
switch (afp->format) {
case MSAFILE_STOCKHOLM: msa = ReadStockholm(afp); break;
case MSAFILE_MSF: msa = ReadMSF(afp); break;
case MSAFILE_A2M: msa = ReadA2M(afp); break;
case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break;
case MSAFILE_SELEX: msa = ReadSELEX(afp); break;
case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break;
default:
Die("MSAFILE corrupted: bad format index");
}
return msa;
}
int Tree::ReadFromStream(istream& is, int header) {
mRoot = new PolyNode();
PolyNode* currentNode = mRoot;
/*
char c = is.peek();
while (c != '(') {
c = is.get();
if (c == '[') {
do {
c = is.get();
}
while (c != ']');
}
c = is.peek();
}
*/
int ok = ReadPhylip(is,currentNode);
SetLabelOffset(0);
mRoot->SetSuper(this);
return (ok && (GetSize() > 1));
}
/*****************************************************************
* phylip.c test driver:
*
*/
int
main(int argc, char **argv)
{
MSAFILE *afp;
MSA *msa;
char *file;
file = argv[1];
if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL)
Die("Couldn't open %s\n", file);
printf("format %d\n", afp->format);
while ((msa = ReadPhylip(afp)) != NULL)
{
WritePhylip(stdout, msa);
MSAFree(msa);
}
MSAFileClose(afp);
exit(0);
}
