JPRED-2 Add alscript to the Git repository

[jpred.git] / sources / alscript / src / array.h

diff --git a/sources/alscript/src/array.h b/sources/alscript/src/array.h
new file mode 100644 (file)
index 0000000..8eaebc6
--- /dev/null
+++ b/sources/alscript/src/array.h
@@ -0,0 +1,73 @@
+/* Matrix file structure - eg. Dayhoffs matrix */
+
+struct pmatrix {
+    char *title;    /* title of matrix */
+    char *indx;            /* Index to matrix - ie amino acid codes */
+    int  inlen;            /* number of residues per line */
+    int **array;    /* the actual pair score array */
+};
+
+/* Standard structure for storing protein sequence data */
+
+struct seqdat {        /* all lengths include char terminator and [0] */
+    int ilen;  /* length of identifier*/
+    char *id;  /* identifier */
+    int tlen;  /* length of title */
+    char *title;       /* title */
+    int slen;  /* length of sequence*/
+    char *seq; /* sequence */
+};
+
+/* smseq Structure to store the details of an alignment - the alignment
+itself is stored in an array of seqdat structures
+*/
+
+struct smseq {
+       int nseq;               /* number of seqs in the alignment */
+       int blen;               /* length of the alignment = no of residues +2 */
+       char *title;            /* a name for the alignment */
+       int ninfo;              /* number of lines of info */
+       char **info;            /* optional information about the alignment */
+       char *gapchars;         /* string of valid gap-characters */
+};
+
+
+/*  mseq Structure for storing multiply aligned sequence data - 
+    arranged so that
+    aligned positions in different sequences are adjacent 
+    This structure could easily be extended to include additional annotations
+    (eg. the name of the alignment, its history, etc. etc.) can be added
+    without having to modify existing code (I hope..)
+    */
+
+struct sident {
+    char *id;      /* sequence id */
+    char *title;    /* sequence title */
+    int uid;       /* unique identifier number for sequence */
+};
+
+struct alseq {
+    char *line;            /* one position in the sequence alignment */
+};
+
+struct mseq {
+    int nseq;          /* number of sequences in this aligned bloc */
+    int blen;          /* overall aligned length of the bloc */
+    struct sident *itd;        /* list of id,title,uid structures */
+    struct alseq *bloc;        /* pointer to list of blen lines of the alignment
+                          structure used to allow future expansion of info
+                          on a per-aligned line basis (eg. presence of 
+                          flexible gap, etc)*/
+};
+
+/* structure to hold default values for id lengths etc. */
+struct defstr {
+       int maxilen;    /* max id len */
+       int maxtlen;    /* max title len */
+       int maxslen;    /* max sequence length */
+};
+
+
+
+
+