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