diff clustalomega/clustal-omega-0.2.0/src/squid/stockholm.h @ 0:ff1768533a07

Migrated tool version 0.2 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalomega/clustal-omega-0.2.0/src/squid/stockholm.h	Tue Jun 07 17:04:25 2011 -0400
@@ -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*/