rsem v1.1.16

[rsem.git] / Buffer.h

diff --git a/Buffer.h b/Buffer.h
new file mode 100644 (file)
index 0000000..1ce28bc
--- /dev/null
+++ b/Buffer.h
@@ -0,0 +1,81 @@
+#ifndef BUFFER_H_
+#define BUFFER_H_
+
+#include<cstdio>
+#include<fstream>
+#include<pthread.h>
+
+#include "my_assert.h"
+
+typedef unsigned long long bufsize_type;
+const int FLOATSIZE = sizeof(float);
+
+class Buffer {
+public:
+       Buffer(int nMB, int nSamples, int cvlen, const char* tmpF) {
+               cpos = 0;
+               size = bufsize_type(nMB) * 1024 * 1024 / FLOATSIZE / cvlen;
+               if (size > (bufsize_type)nSamples) size = nSamples;
+               general_assert(size > 0, "Memory allocated for credibility intervals is not enough!");
+               size *= cvlen;
+
+               buffer = new float[size];
+               ftmpOut.open(tmpF, std::ios::binary);
+               pthread_mutex_init(&lock, NULL);
+
+               fr = to = 0;
+               this->nSamples = nSamples;
+               this->cvlen = cvlen;
+       }
+
+       ~Buffer() {
+               if (fr < to) flushToTempFile();
+
+               delete[] buffer;
+               pthread_mutex_destroy(&lock);
+               ftmpOut.close();
+       }
+
+       void write(int n, float **vecs) {
+               pthread_assert(pthread_mutex_lock(&lock), "pthread_mutex_lock", "Error occurred while acquiring the lock!");
+               for (int i = 0; i < n; i++) {
+                       if (size - cpos < bufsize_type(cvlen)) flushToTempFile();
+                       memcpy(buffer + cpos, vecs[i], FLOATSIZE * cvlen);
+                       cpos += cvlen;
+                       ++to;
+               }
+               pthread_assert(pthread_mutex_unlock(&lock), "pthread_mutex_unlock", "Error occurred while releasing the lock!");
+       }
+
+private:
+       bufsize_type size, cpos; // cpos : current position
+
+       float *buffer;
+       std::ofstream ftmpOut;
+       pthread_mutex_t lock;
+
+       int fr, to; // each flush, sample fr .. to - 1
+       int nSamples, cvlen;
+
+       void flushToTempFile() {
+               std::streampos gap1 = std::streampos(fr) * FLOATSIZE;
+               std::streampos gap2 = std::streampos(nSamples - to) * FLOATSIZE;
+               float *p = NULL;
+
+               ftmpOut.seekp(0, std::ios_base::beg);
+               for (int i = 0; i < cvlen; i++) {
+                       p = buffer + i;
+                       ftmpOut.seekp(gap1, std::ios_base::cur);
+                       for (int j = fr; j < to; j++) {
+                               ftmpOut.write((char*)p, FLOATSIZE);
+                               p += cvlen;
+                       }
+                       ftmpOut.seekp(gap2, std::ios_base::cur);
+               }
+
+               cpos = 0;
+               fr = to;
+       }
+};
+
+#endif /* BUFFER_H_ */