source: branches/lib/GDE/MUSCLE/src/savebest.cpp

#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);
        }