alloc.c

C-package of "Long Short-Term Memory" for Protein classification

  /* Memory allocation for Input/Target Arrays etc 
  * 
  * 
  * $Id: alloc.c 1272 2007-05-09 16:26:20Z mhe $ 
  */

#include <stdlib.h>
#include <stdio.h>
#include "lstm.h"
#include "roc.h"
#include "alloc.h"

void alloc () {
    
  /* AA symbols train */
  fprintf(stderr, "alloc mem for AA symbols training %d MB\n", training_size * maxseqlentrain * sizeof(char) / 1024 / 1024); 
  aaSym = alloc2DimCharArray(aaSym, training_size, maxseqlentrain);
 
  
  /* AA symbols test */
  fprintf(stderr, "alloc mem for AA symbols test %d MB\n", test_size * maxseqlentest * sizeof(char) / 1024 / 1024);
  aaSym_t = alloc2DimCharArray(aaSym_t, test_size, maxseqlentest);
  
   
  /* input train */
  fprintf(stderr, "alloc mem for inp training %d KB\n", maxseqlentrain * (windowsize) * sizeof(double) / 1024);
  inp = alloc2DimDoubleArray(inp, maxseqlentrain, windowsize);
  
  /* input index train */
  fprintf(stderr, "alloc mem for inp_idx training %d KB\n", maxseqlentrain * (windowsize)  * sizeof(int) / 1024);
  inp_idx = alloc2DimIntArray(inp_idx, maxseqlentrain, windowsize);

  /* fasta description train */
  //fprintf(stderr, "alloc mem for fasta description training %d KB\n", MAXCHARSFASTADESC * training_size  * sizeof(char) / 1024);
  //fasta_desc = alloc2DimCharArray(fasta_desc, training_size, MAXCHARSFASTADESC);
  
  /* input test */
  fprintf(stderr, "alloc mem for inp test %d KB\n", maxseqlentest * (windowsize) * sizeof(double) / 1024);
  inp_t = alloc2DimDoubleArray(inp_t, maxseqlentest, windowsize);
    
  /* input index test */
  fprintf(stderr, "alloc mem for inp_idx test %d KB\n", maxseqlentest * (windowsize) * sizeof(int) / 1024);
  inp_idx_t = alloc2DimIntArray(inp_idx_t, maxseqlentest, windowsize);
  
  /* fasta description test */
  //fprintf(stderr, "alloc mem for fasta description test %d KB\n", MAXCHARSFASTADESC * test_size  * sizeof(char) / 1024);
  //fasta_desc_t = alloc2DimCharArray(fasta_desc_t, test_size, MAXCHARSFASTADESC);
  
  
  
  /* target train */
  fprintf(stderr, "alloc mem for tar Train %.1f kB\n", (double)training_size * sizeof(int) / 1024);
  tar = allocIntArray(tar, training_size);
  
  /* target test */
  fprintf(stderr, "alloc mem for tar Test %.1f kB\n", (double)test_size * sizeof(int) / 1024);
  tar_t = allocIntArray(tar_t, test_size);
  fprintf(stderr, "\n");
  
  length = allocIntArray(length, training_size);
  length_t = allocIntArray(length_t, test_size);
  
  Y_in = allocDoubleArray(Y_in, num_blocks);
  Y_out = allocDoubleArray(Y_out, num_blocks);
  G = alloc2DimDoubleArray(G, num_blocks, MAXBLOCKSIZE);
  H = alloc2DimDoubleArray(H, num_blocks, MAXBLOCKSIZE);
  S = alloc2DimDoubleArray(S, num_blocks, MAXBLOCKSIZE);
  Yc = alloc2DimDoubleArray(Yc, num_blocks, MAXBLOCKSIZE);
  
}

void alloc2(int num_prot, int num_prot_t) {
    prand = allocIntArray(prand, num_prot);
    sptrain = (struct seqperf*)malloc(sizeof(struct seqperf) * num_prot);
    sptest = (struct seqperf*)malloc(sizeof(struct seqperf) * num_prot_t);
}

void alloc3(int numunits) {
  W = alloc2DimDoubleArray(W, numunits, numunits);
  DW = alloc2DimDoubleArray(DW, numunits, numunits);
  DWold = alloc2DimDoubleArray(DWold, numunits, numunits);
  Yk_new = allocDoubleArray(Yk_new, numunits);
  Yk_old = allocDoubleArray(Yk_old, numunits);
  SI = alloc3DimDoubleArray(SI, num_blocks, MAXBLOCKSIZE, numunits);
  SC = alloc3DimDoubleArray(SC, num_blocks, MAXBLOCKSIZE, numunits);
  
  e  = allocDoubleArray(e, numunits);
  ec = alloc2DimDoubleArray(ec, num_blocks, MAXBLOCKS);
  eo = allocDoubleArray(eo, num_blocks);
  es = alloc2DimDoubleArray(es, num_blocks, MAXBLOCKS);
  
}