JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

[jabaws.git] / binaries / src / clustalo / src / squid / squid.h

diff --git a/binaries/src/clustalo/src/squid/squid.h b/binaries/src/clustalo/src/squid/squid.h
index 72b97d2..a987bfb 100644 (file)
--- a/binaries/src/clustalo/src/squid/squid.h
+++ b/binaries/src/clustalo/src/squid/squid.h
@@ -131,7 +131,7 @@ extern int  squid_errno;    /* error codes     */
 /****************************************************
  * Single sequence information
  ****************************************************/ 
-#define SQINFO_NAMELEN 64
+#define SQINFO_NAMELEN 128 /* increased 64 -> 128, FS, r274 -> */
 #define SQINFO_DESCLEN 128
 
 struct seqinfo_s {
@@ -147,6 +147,7 @@ struct seqinfo_s {
   int      type;                /* kRNA, kDNA, kAmino, or kOther         */
   char    *ss;                  /* 0..len-1 secondary structure string   */
   char    *sa;                 /* 0..len-1 % side chain surface access. */
+  char    *co;                 /* 0..len-1 secondary struct confidence  */
 };
 typedef struct seqinfo_s SQINFO;
 
@@ -161,6 +162,7 @@ typedef struct seqinfo_s SQINFO;
 #define SQINFO_OLEN  (1 << 8)
 #define SQINFO_SS    (1 << 9)
 #define SQINFO_SA    (1 << 10)
+#define SQINFO_CO    (1 << 11)
 
 
 /****************************************************
@@ -244,6 +246,7 @@ extern int      aa_index[];     /* convert 0..19 indices to 0..26       */
                                /* 17 was Clustal. Now alignment format*/
 #ifdef CLUSTALO
 #define SQFILE_VIENNA   18     /* Vienna format: concatenated fasta           */
+#define SQFILE_DUBLIN   19      /* unaligned version of Stockholm */
 #endif
 #define IsUnalignedFormat(fmt)  ((fmt) && (fmt) < 100)