fixed too many partial CDS bug

Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1
Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984

detectors/cds/tools/lib/libnws.awk

@@ -0,0 +1,146 @@
+#
+# NWS alignment
+#
+
+# -----------------------
+# make identity substitution matrix for given alphabet
+#
+function IdentityMatrix(alpha, mat, diag, ndiag, _local_, n, i, j, ci, cj) {
+  if (diag == "")  diag  = 0
+  if (ndiag == "") ndiag = 1
+  alpha = toupper(alpha)
+  delete mat
+  n = length(alpha)
+  for (i = 1 ; i <= n ; i++) {
+    ci = substr(alpha, i, 1)
+    for (j = 1 ; j <= n ; j++) {
+      cj = substr(alpha, j, 1)
+      mat[ci][cj] = (i == j) ? diag : ndiag
+    }
+  }
+}
+
+# -----------------------
+# internal utility : reverse string
+#
+  function _Reverse(s, _local_, i, n, rs) {
+    rs = "";
+    n = length(s);
+    for (i = n ; i >= 1 ; i--)
+      rs = rs "" substr(s, i, 1)
+    return rs;
+  }
+
+# -----------------------
+# internal utility : alignment traceback for NWS
+#
+  function _Traceback(dir, s1, s2, n1, n2, align, _local_, i, c1, c2, c3) {
+    delete align
+    while (dir[n1][n2] != 0) {
+      if (dir[n1][n2] == "s") {
+        c1 = substr(s1, n1--, 1)
+        c2 = substr(s2, n2--, 1)
+        c3 = (c1 == c2) ? tolower(c1) : "*"
+      }
+      else if (dir[n1][n2] == "i") {
+        c1 = "-"
+        c2 = substr(s2, n2--, 1)
+        c3 = "-"
+      }
+      else {
+        c1 = substr(s1, n1--, 1)
+        c2 = "-"
+        c3 = "-"
+      }
+      align[1] = align[1] "" c1
+      align[2] = align[2] "" c2
+      align[3] = align[3] "" c3
+    }
+    for (i = 1 ; i <= 3 ; i++)
+      align[i] = _Reverse(align[i])
+  }
+
+# -----------------------
+# internal utility : min
+#
+  function _Min(a, b) {
+    return (a < b ? a : b)
+  }
+
+# -----------------------
+# sequence alignment NWS
+#
+# todo : check alphabet
+#
+#   --> i
+#  |
+#  v d
+#
+function AlignNWS(s1, s2, subst, indel, local, align,
+                     _local_, rev, n1, n2, i, j, c1, c2, m2,
+                           ws, wi, wd, w,
+                           mat, dir) {
+                           
+   s1 = toupper(s1) ; s2 = toupper(s2)
+   n1 = length(s1)  ; n2 = length(s2)
+   if (local && (n2 < n1)) {
+     rev = s1 ; s1 = s2 ; s2 = rev
+     rev = n1 ; n1 = n2 ; n2 = rev
+   }
+
+   if (indel == "") indel = 1
+
+   #
+   # nws alignment
+   #
+   for (i = 0 ; i <= n1 ; i++) {
+     c1 = substr(s1, i, 1)
+     for (j = 0 ; j <= n2 ; j++) {
+       c2 = substr(s2, j, 1)
+       if (i && j) {
+         ws = mat[i-1][j-1] + subst[c1][c2]
+         wd = mat[i-1][j] + indel
+         wi = mat[i][j-1] + indel
+         w  = _Min(ws, _Min(wi, wd))
+         mat[i][j] = w
+         dir[i][j] = (w == ws) ? "s" : (w == wi) ? "i" : "d"
+       } else if (i) {
+         mat[i][j] = mat[i-1][j] + indel
+         dir[i][j] = "d"
+       } else if (j) {
+         mat[i][j] = mat[i][j-1] + (local ? 0 : indel)
+         dir[i][j] = "i"
+       } else {
+         mat[i][j] = 0
+         dir[i][j] = 0
+       }
+     }
+     # delete mat[i-1]
+   }
+
+   #
+   # adjust last line in local mode
+   #
+   if (local) {
+     m2 = n2
+     for (j = m2 ; j >= 0 ; j--) {
+       if (mat[n1][j] < mat[n1][m2])
+         m2 = j
+     }
+     mat[n1][n2] = mat[n1][m2]
+     for (j = m2 + 1 ; j <= n2 ; j++) {
+       dir[n1][j] = "i"
+     }
+   }
+
+   #
+   # traceback
+   #
+   _Traceback(dir, s1, s2, n1, n2, align)
+   
+   if (rev) {
+     rev = align[1] ; align[1] = align[2]; align[2] = rev
+   }
+   
+   return mat[n1][n2]
+}