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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/textfile.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/objscore.h"
#include "libMUSCLE/tree.h"
#include "libMUSCLE/profile.h"
namespace muscle {
void DoSP()
{
TextFile f(g_pstrSPFileName.get());
MSA a;
a.FromFile(f);
ALPHA Alpha = ALPHA_Undefined;
switch (g_SeqType.get())
{
case SEQTYPE_Auto:
Alpha = a.GuessAlpha();
break;
case SEQTYPE_Protein:
Alpha = ALPHA_Amino;
break;
case SEQTYPE_DNA:
Alpha = ALPHA_DNA;
break;
case SEQTYPE_RNA:
Alpha = ALPHA_RNA;
break;
default:
Quit("Invalid SeqType");
}
SetAlpha(Alpha);
a.FixAlpha();
SetPPScore();
const unsigned uSeqCount = a.GetSeqCount();
if (0 == uSeqCount)
Quit("No sequences in input file %s", g_pstrSPFileName.get());
MSA::SetIdCount(uSeqCount);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
a.SetSeqId(uSeqIndex, uSeqIndex);
SetSeqWeightMethod(g_SeqWeight1.get());
Tree tree;
TreeFromMSA(a, tree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get());
SetMuscleTree(tree);
SetMSAWeightsMuscle((MSA &) a);
SCORE SP = ObjScoreSP(a);
Log("File=%s;SP=%.4g\n", g_pstrSPFileName.get(), SP);
fprintf(stderr, "File=%s;SP=%.4g\n", g_pstrSPFileName.get(), SP);
}
}
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