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#include "muscle.h"
#include "msa.h"
#include "params.h"
#include "textfile.h"
static void DoOutput(MSA &msa)
{
bool AnyOutput = false;
// Flag options, at most one used (because only one -out filename)
TextFile fileOut(g_pstrOutFileName, true);
if (g_bFASTA)
{
msa.ToFASTAFile(fileOut);
AnyOutput = true;
}
else if (g_bMSF)
{
msa.ToMSFFile(fileOut);
AnyOutput = true;
}
else if (g_bAln)
{
msa.ToAlnFile(fileOut);
AnyOutput = true;
}
else if (g_bHTML)
{
msa.ToHTMLFile(fileOut);
AnyOutput = true;
}
else if (g_bPHYI)
{
msa.ToPhyInterleavedFile(fileOut);
AnyOutput = true;
}
else if (g_bPHYS)
{
msa.ToPhySequentialFile(fileOut);
AnyOutput = true;
}
// If -out option was given but no flags, output as FASTA
if (!AnyOutput && strcmp(g_pstrOutFileName, "-") != 0)
msa.ToFASTAFile(fileOut);
fileOut.Close();
// Value options
if (g_pstrFASTAOutFileName)
{
TextFile File(g_pstrFASTAOutFileName, true);
msa.ToFASTAFile(File);
}
if (g_pstrMSFOutFileName)
{
TextFile File(g_pstrMSFOutFileName, true);
msa.ToMSFFile(File);
}
if (g_pstrClwOutFileName)
{
TextFile File(g_pstrClwOutFileName, true);
msa.ToAlnFile(File);
}
if (g_pstrClwStrictOutFileName)
{
g_bClwStrict = true;
TextFile File(g_pstrClwStrictOutFileName, true);
msa.ToAlnFile(File);
}
if (g_pstrHTMLOutFileName)
{
TextFile File(g_pstrHTMLOutFileName, true);
msa.ToHTMLFile(File);
}
if (g_pstrPHYIOutFileName)
{
TextFile File(g_pstrPHYIOutFileName, true);
msa.ToPhySequentialFile(File);
}
if (g_pstrPHYSOutFileName)
{
TextFile File(g_pstrPHYSOutFileName, true);
msa.ToPhySequentialFile(File);
}
if (0 != g_pstrScoreFileName)
WriteScoreFile(msa);
}
void MuscleOutput(MSA &msa)
{
MHackEnd(msa);
if (g_bStable)
{
MSA msaStable;
Stabilize(msa, msaStable);
msa.Clear(); // save memory
DoOutput(msaStable);
}
else
DoOutput(msa);
}
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