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