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#include "muscle.h"
#include "msa.h"
#include "textfile.h"
#include <time.h>
MSA *ptrBestMSA;
static const char *pstrOutputFileName;
void SetOutputFileName(const char *out)
{
pstrOutputFileName = out;
}
void SetCurrentAlignment(MSA &msa)
{
ptrBestMSA = &msa;
}
void SaveCurrentAlignment()
{
static bool bCalled = false;
if (bCalled)
{
fprintf(stderr,
"\nRecursive call to SaveCurrentAlignment, giving up attempt to save.\n");
exit(EXIT_FatalError);
}
if (0 == ptrBestMSA)
{
fprintf(stderr, "\nAlignment not completed, cannot save.\n");
Log("Alignment not completed, cannot save.\n");
exit(EXIT_FatalError);
}
if (0 == pstrOutputFileName)
{
fprintf(stderr, "\nOutput file name not specified, cannot save.\n");
exit(EXIT_FatalError);
}
fprintf(stderr, "\nSaving current alignment ...\n");
TextFile fileOut(pstrOutputFileName, true);
ptrBestMSA->ToFASTAFile(fileOut);
fprintf(stderr, "Current alignment saved to \"%s\".\n", pstrOutputFileName);
Log("Current alignment saved to \"%s\".\n", pstrOutputFileName);
}
void CheckMaxTime()
{
if (0 == g_ulMaxSecs)
return;
time_t Now = time(0);
time_t ElapsedSecs = Now - GetStartTime();
if (ElapsedSecs <= (time_t) g_ulMaxSecs)
return;
Log("Max time %s exceeded, elapsed seconds = %ul\n",
MaxSecsToStr(), ElapsedSecs);
SaveCurrentAlignment();
exit(EXIT_Success);
}
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