X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=sources%2Fmulticoil%2Fscpos.c;fp=sources%2Fmulticoil%2Fscpos.c;h=389e995c1c40130e0d2d169f1d93ea3aa06fad75;hb=81362e35a140cd040e948b921053e74267f8a6e3;hp=0000000000000000000000000000000000000000;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

diff --git a/sources/multicoil/scpos.c b/sources/multicoil/scpos.c
new file mode 100644
index 0000000..389e995
--- /dev/null
+++ b/sources/multicoil/scpos.c
@@ -0,0 +1,138 @@
+#include <stdio.h>
+#include <math.h>   /** Defines HUGE_VAL. **/
+#include "sc.h"
+#include "scconst.h"
+#include "scio.h"
+#include "scsystem.h"
+
+
+
+
+void add_seq2(long pfreqs[AANUM][POSNUM], 
+	long ptotals[POSNUM],
+	long pfreqp[AANUM][AANUM][POSNUM][POSNUM], 
+	long ptotalp[POSNUM][POSNUM],
+        char reg[MAXSEQLEN],
+	char seq[MAXSEQLEN], int seqlen, int bias)
+/* Temporarily add or remove the sequence under consideration from the 
+   positive data? (bias=-1 removes, bias=1 adds) */ 
+{
+  int i, posi, j, posj;
+
+  for (i = 0; i < seqlen; i++) 
+    if (seq[i] < AANUM && reg[i]!='.') {
+        posi = reg[i];
+	for (j = i+1; j <= i+POSNUM && j < seqlen && (reg[j] == (posj = (posi+j-i)%POSNUM)); j++) 
+	  if (seq[j] < AANUM) {
+	    pfreqp[seq[i]][seq[j]][posi][posj] += bias;
+	    ptotalp[posi][posj] += bias;
+	  }
+	pfreqs[seq[i]][posi] += bias;
+	ptotals[posi] += bias;
+      }
+}
+
+
+
+
+remove_all_input_seq_from_table(long pfreqs[AANUM][POSNUM], 
+	   long ptotals[POSNUM],long pfreqp[AANUM][AANUM][POSNUM][POSNUM], 
+	   long ptotalp[POSNUM][POSNUM], char *testfile_name, int bias)
+{
+  Sequence sequence;
+  char title[MAXLINE],code[MAXLINE];
+  char seq[MAXSEQLEN], reg[MAXSEQLEN];
+  int i, posi, j, posj;
+  FILE *ftest;
+
+ 
+  sequence.title = title;
+  sequence.code = code;
+  sequence.seq = seq;
+  sequence.reg= reg;
+
+  ftest = sopen(testfile_name,"r");
+  while (getseq2(ftest,&sequence)) {
+    for (i = 0; i < sequence.seqlen; i++) 
+      if (seq[i] < AANUM && reg[i]!='.') {
+        posi = reg[i];
+	for (j = i+1; j <= i+POSNUM && j < sequence.seqlen && (reg[j] == (posj = (posi+j-i)%POSNUM)); j++) 
+	  if (seq[j] < AANUM) {
+	    pfreqp[seq[i]][seq[j]][posi][posj] += bias;
+	    ptotalp[posi][posj] += bias;
+	  }
+	pfreqs[seq[i]][posi] += bias;
+	ptotals[posi] += bias;
+      }
+  }
+  sclose(ftest);
+}
+
+
+
+
+
+
+
+int getpos (FILE *fl, Sequence *sequence) 
+/* Read in the next sequence from a .pos file */
+{
+ int c,count=0;
+ char *code = sequence->code;
+ char *title = sequence->title;
+ char *seq = sequence->seq;
+ char *reg = sequence->reg; 
+ 
+
+ c=fgetc(fl);
+ while (c!='>' && c!=EOF)
+  c=fgetc(fl);
+ if (c==EOF)
+  return(0);
+ /* Get the code */
+ c=fgetc(fl);
+ while (c!='\n')
+ {
+  code[count++]=c;
+  c=fgetc(fl);
+ }
+ code[count]=0;
+ count=0;
+ /* Get the title info */
+ c=fgetc(fl);
+ while (c!='\n') {
+   title[count++]=c;
+   c=fgetc(fl);
+ }
+ title[count]=0;
+ count=0;
+ /* Get the sequence */
+ c=fgetc(fl);
+ while (c!='*' && c!=EOF)
+ {
+  if (aanum(c)!=(char) -1)
+   seq[count++]=aanum(c);
+  c=fgetc(fl);
+ }
+ sequence->seqlen=count;
+ count=0;
+ /* Get the register info */
+ c=fgetc(fl);
+ while (c!='*' && c!=EOF)
+ {
+  if (c>='a' && c<='z')
+   reg[count++]=c-'a';
+  else if (c=='.')
+   reg[count++]='.';
+  c=fgetc(fl);
+ }
+ if (sequence->seqlen != count) {
+   fprintf(stderr, "erroneous .pos file!\n");
+   /*exit(-1);*/
+ }
+ if (c==EOF)
+  return(0);
+ else
+  return(1);
+}
+