Creation of OpenFOAM-dev repository 15/04/2008

applications/utilities/parallelProcessing/decompositionMethods/metis-5.0pre2/GKlib/trunk/seq.c

@@ -0,0 +1,171 @@
+/*
+ *
+ * Sequence handler library by Huzefa Rangwala
+ * Date : 03.01.2007
+ *
+ *
+ *
+ */
+
+
+#include<GKlib.h>
+
+
+
+
+/*********************************************************/
+/* ! \brief Initializes the <tt>gk_seq_t</tt> variable
+
+
+
+
+\param A pointer to gk_seq_t itself
+\returns null
+*/
+/***********************************************************************/
+
+void gk_seq_init(gk_seq_t *seq)
+{
+    
+    seq->len = 0;
+    seq->sequence = NULL;
+        
+    seq->pssm = NULL;
+    seq->psfm = NULL;
+    
+    seq->name = NULL;
+    
+}
+
+/***********************************************************************/
+/*! \brief This function creates the localizations for the various sequences
+
+\param    string i.e amino acids, nucleotides, sequences
+\returns  gk_i2cc2i_t variable
+*/
+/*********************************************************************/
+
+gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet)
+{
+    
+    
+    int nsymbols;
+    gk_loop_t i;
+    gk_i2cc2i_t *t;
+
+    nsymbols = strlen(alphabet);
+    t        = gk_malloc(sizeof(gk_i2cc2i_t),"gk_i2c_create_common");
+    t->n     = nsymbols;
+    t->i2c   = gk_cmalloc(256, "gk_i2c_create_common");
+    t->c2i   = gk_imalloc(256, "gk_i2c_create_common");
+    
+
+    gk_cset(256, -1, t->i2c);
+    gk_iset(256, -1, t->c2i);
+    
+    for(i=0;i<nsymbols;i++){
+	t->i2c[i] = alphabet[i];
+	t->c2i[(int)alphabet[i]] = i;
+    }
+
+    return t;
+
+}
+
+
+/*********************************************************************/
+/*! \brief This function reads a pssm in the format of gkmod pssm
+
+\param file_name is the name of the pssm file
+\returns gk_seq_t
+*/
+/********************************************************************/
+gk_seq_t *gk_seq_ReadGKMODPSSM(char *filename)
+{
+    
+    gk_seq_t *seq;
+    gk_loop_t i, j, ii;
+    int ntokens,nbytes,len;
+    FILE *fpin;
+    
+    
+    gk_Tokens_t tokens;
+    static char *AAORDER = "ARNDCQEGHILKMFPSTWYVBZX*";
+    static int PSSMWIDTH = 20;
+    char header[PSSMWIDTH], line[MAXLINELEN];
+    gk_i2cc2i_t *converter;
+
+    
+    converter = gk_i2cc2i_create_common(AAORDER);
+    
+    gk_getfilestats(filename, &len, &ntokens, &nbytes);
+    len --;
+
+    seq = gk_malloc(sizeof(gk_seq_t),"gk_seq_ReadGKMODPSSM");
+    gk_seq_init(seq);
+    
+    seq->len = len;
+    seq->sequence = gk_imalloc(len, "gk_seq_ReadGKMODPSSM");
+    seq->pssm     = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM");
+    seq->psfm     = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM");
+    
+    seq->nsymbols = PSSMWIDTH;
+    seq->name     = gk_getbasename(filename);
+    
+    fpin = gk_fopen(filename,"r","gk_seq_ReadGKMODPSSM");
+
+
+    /* Read the header line */
+    fgets(line, MAXLINELEN-1, fpin);
+    gk_strtoupper(line);
+    gk_strtokenize(line, " \t\n", &tokens);
+
+    for (i=0; i<PSSMWIDTH; i++)
+	header[i] = tokens.list[i][0];
+    
+    gk_freetokenslist(&tokens);
+    
+
+    /* Read the rest of the lines */
+    for (i=0, ii=0; ii<len; ii++) {
+	fgets(line, MAXLINELEN-1, fpin);
+	gk_strtoupper(line);
+	gk_strtokenize(line, " \t\n", &tokens);
+	
+	seq->sequence[i] = converter->c2i[(int)tokens.list[1][0]];
+	
+	for (j=0; j<PSSMWIDTH; j++) {
+	    seq->pssm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+j]);
+	    seq->psfm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+PSSMWIDTH+j]);
+	}
+	
+      
+	
+	gk_freetokenslist(&tokens);
+	i++;
+    }
+    
+    seq->len = i; /* Reset the length if certain characters were skipped */
+    
+    gk_fclose(fpin);
+
+    return seq;
+}
+
+
+/**************************************************************************/
+/*! \brief This function frees the memory allocated to the seq structure.
+ 
+\param   gk_seq_t
+\returns nothing
+*/
+/**************************************************************************/
+void gk_seq_free(gk_seq_t *seq)
+{
+    gk_iFreeMatrix(&seq->pssm, seq->len, seq->nsymbols);
+    gk_iFreeMatrix(&seq->psfm, seq->len, seq->nsymbols);
+    gk_free((void **)&seq->name, &seq->sequence, LTERM);
+    //gk_free((void **)&seq, LTERM);
+    gk_free((void **) &seq, LTERM);
+
+}