Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/squid/stockholm.h b/binaries/src/clustalo/src/squid/stockholm.h
new file mode 100644 (file)
index 0000000..a9cae55
--- /dev/null
+++ b/binaries/src/clustalo/src/squid/stockholm.h
@@ -0,0 +1,51 @@
+#ifndef STOCKHOLM_H_INCLUDED
+#define STOCKHOLM_H_INCLUDED
+
+#include "gki.h"
+
+typedef struct {
+  int   *linetype;             /* e.g. STOCKHOLM_GF_LINE; always valid */
+  int   *featurecode;          /* all markup codes: e.g. STOCKHOLM_GF_ID; 
+                                  nonmarkup: always set to STOCKHOLM_UNPARSED */
+  char **featurename;          /* all unparsed markup codes: string, e.g. "ID";
+                                  all other lines: NULL */
+  int   *seqidx;               /* all GS, GR, GC, sequence lines: which sequence;
+                                  other lines: 0 */
+  int   *len;                  /* all GR, GC, sequence lines: length of text field;
+                                  other lines: 0 */
+  char **text;                 /* all unparsed nonblank lines: rest of data
+                                  other lines: NULL */
+  int    nseqalloc;            /* current nseqs allocated for in aseqs and ainfo */
+  int    nlines;               /* number of lines in this skel */
+  int    nlinealloc;           /* current # of lines allocated for in this skel */
+  int    overall_line;         /* line # in file (important in files w/ >1 ali)*/
+} alifile_skeleton;
+
+#define STOCKHOLM_GF_LINE      0
+#define STOCKHOLM_GS_LINE      1 
+#define STOCKHOLM_GC_LINE      2
+#define STOCKHOLM_GR_LINE      3
+#define STOCKHOLM_SEQ_LINE     4
+#define STOCKHOLM_BLANK_LINE   5
+#define STOCKHOLM_COMMENT_LINE 6
+
+#define STOCKHOLM_UNPARSED  0
+#define STOCKHOLM_GF_ID     1
+#define STOCKHOLM_GF_AC     2
+#define STOCKHOLM_GF_DE     3
+#define STOCKHOLM_GF_AU     4
+#define STOCKHOLM_GF_GA     5
+#define STOCKHOLM_GF_NC     6
+#define STOCKHOLM_GF_TC     7
+#define STOCKHOLM_GS_WT     100
+#define STOCKHOLM_GS_AC     101
+#define STOCKHOLM_GS_DE     102
+#define STOCKHOLM_GC_CS     200
+#define STOCKHOLM_GC_RF     201
+#define STOCKHOLM_GR_SS     300
+#define STOCKHOLM_GR_SA     301
+
+#define SKEL_NSEQLUMP       10    /* allocate for new seqs in blocks of this size */
+#define SKEL_LUMPSIZE       100           /* allocate for new lines in skel in blocks of this size */
+
+#endif /*STOCKHOLM_H_INCLUDED*/