Load ncbi (6.1.20031028) into ncbi-tools6/branches/upstream/current.

8 files changed, 765 insertions, 0 deletions

diff --git a/util/tables/raw_scoremat.c b/util/tables/raw_scoremat.c
new file mode 100644
index 00000000..d0c4e47d
--- /dev/null
+++ b/util/tables/raw_scoremat.c
@@ -0,0 +1,122 @@
+/*  $Id: raw_scoremat.c,v 1.2 2003/10/02 15:37:34 ivanov Exp $
+ * ===========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author:  Aaron Ucko
+ *
+ * File Description:
+ *   Protein alignment score matrices; shared between the two toolkits.
+ *
+ */
+
+#include <util/tables/raw_scoremat.h>
+
+#include <ctype.h>
+#include <string.h>
+
+#include "sm_blosum45.c"
+#include "sm_blosum62.c"
+#include "sm_blosum80.c"
+#include "sm_pam30.c"
+#include "sm_pam70.c"
+
+static const char kNCBIstdaa[] = "-ABCDEFGHIKLMNPQRSTVWXYZU*";
+
+
+int NCBISM_GetIndex(const SNCBIPackedScoreMatrix* sm, int aa)
+{
+    const char *p;
+
+    /* Translate to NCBIeaa */
+    if (aa >= 0  &&  aa < sizeof(kNCBIstdaa)) {
+        aa = kNCBIstdaa[aa];
+    } else if (islower(aa)) {
+        aa = toupper(aa);
+    }
+
+    p = strchr(sm->symbols, aa);
+    return p ? p - sm->symbols : -1;
+}
+
+
+TNCBIScore NCBISM_GetScore(const SNCBIPackedScoreMatrix* sm,
+                           int aa1, int aa2)
+{
+    int i1, i2;
+    i1 = NCBISM_GetIndex(sm, aa1);
+    i2 = NCBISM_GetIndex(sm, aa2);
+    if (i1 >=0  &&  i2 >= 0) {
+        return sm->scores[i1 * strlen(sm->symbols) + i2];
+    } else {
+        return sm->defscore;
+    }
+}
+
+
+void NCBISM_Unpack(const SNCBIPackedScoreMatrix* psm,
+                   SNCBIFullScoreMatrix* fsm)
+{
+    const char* sym;
+    int         dim, i, j, aa1, aa2;
+
+    sym = psm->symbols;
+    dim = strlen(sym);
+    /* fill with default */
+    memset(&fsm->s, psm->defscore, NCBI_FSM_DIM * NCBI_FSM_DIM);
+    for (i = 0;  i < dim;  ++i) {
+        aa1 = sym[i];
+        /* get core (NCBIeaa x NCBIeaa) */
+        for (j = 0;  j < dim;  ++j) {
+            aa2 = sym[j];
+            fsm->s[aa1][aa2] = psm->scores[i * dim + j];
+        }
+        /* extend horizontally */
+        for (aa2 = 0;  aa2 < sizeof(kNCBIstdaa);  ++aa2) {
+            fsm->s[aa1][aa2] = fsm->s[aa1][(int)kNCBIstdaa[aa2]];
+        }
+        for (aa2 = 'a';  aa2 <= 'z';  ++aa2) {
+            fsm->s[aa1][aa2] = fsm->s[aa1][toupper(aa2)];
+        }
+    }
+    /* extend vertically */
+    for (aa1 = 0;  aa1 < sizeof(kNCBIstdaa);  ++aa1) {
+        memcpy(fsm->s[aa1], fsm->s[(int)kNCBIstdaa[aa1]], NCBI_FSM_DIM);
+    }
+    for (aa1 = 'a';  aa1 <= 'z';  ++aa1) {
+        memcpy(fsm->s[aa1], fsm->s[toupper(aa1)], NCBI_FSM_DIM);
+    }
+}
+
+
+/*
+ * ===========================================================================
+ * $Log: raw_scoremat.c,v $
+ * Revision 1.2  2003/10/02 15:37:34  ivanov
+ * Get rid of compilation warnings
+ *
+ * Revision 1.1  2003/08/21 19:48:20  ucko
+ * Add tables library (shared with C) for raw score matrices, etc.
+ *
+ * ===========================================================================
+ */
diff --git a/util/tables/raw_scoremat.h b/util/tables/raw_scoremat.h
new file mode 100644
index 00000000..434e4a0a
--- /dev/null
+++ b/util/tables/raw_scoremat.h
@@ -0,0 +1,95 @@
+#ifndef UTIL_TABLES___SCOREMAT__H
+#define UTIL_TABLES___SCOREMAT__H
+
+/*  $Id: raw_scoremat.h,v 1.1 2003/08/21 19:48:19 ucko Exp $
+ * ===========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author:  Aaron Ucko
+ *
+ */
+
+/** @file scoremat.h
+ ** Protein alignment score matrices; shared between the two toolkits.
+ **/
+
+#include <util/tables/tables_export.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/** data types */
+
+typedef signed char TNCBIScore;
+typedef struct SNCBIPackedScoreMatrix {
+    const char*       symbols;  /**< order of residues */
+    const TNCBIScore* scores;   /**< strlen(symbols) x strlen(symbols) */
+    TNCBIScore        defscore; /**< score for unknown residues */
+} SNCBIPackedScoreMatrix;
+
+/** These two functions aren't very fast, but avoid the memory and time
+ ** overhead of unpacking.
+ ** Residues (aa, aa1, aa2) may be either NCBIstdaa, NCBIeaa, or
+ ** lowercase NCBIeaa, though matrices generally don't cover U.
+ **/
+extern NCBI_TABLES_EXPORT
+int        NCBISM_GetIndex(const SNCBIPackedScoreMatrix* sm, int aa);
+extern NCBI_TABLES_EXPORT
+TNCBIScore NCBISM_GetScore(const SNCBIPackedScoreMatrix* sm,
+                           int aa1, int aa2);
+
+/** Recommended approach: unpack and index directly. */
+#define NCBI_FSM_DIM 128
+typedef struct SNCBIFullScoreMatrix {
+    TNCBIScore s[NCBI_FSM_DIM][NCBI_FSM_DIM];
+} SNCBIFullScoreMatrix;
+
+extern NCBI_TABLES_EXPORT
+void NCBISM_Unpack(const SNCBIPackedScoreMatrix* psm,
+                   SNCBIFullScoreMatrix* fsm);
+
+/** The standard matrices. */
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Blosum45;
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Blosum62;
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Blosum80;
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam30;
+extern NCBI_TABLES_EXPORT const SNCBIPackedScoreMatrix NCBISM_Pam70;
+
+#ifdef __cplusplus
+}
+#endif
+
+/*
+* ===========================================================================
+*
+* $Log: raw_scoremat.h,v $
+* Revision 1.1  2003/08/21 19:48:19  ucko
+* Add tables library (shared with C) for raw score matrices, etc.
+*
+*
+* ===========================================================================
+*/
+
+#endif  /* UTIL_TABLES___SCOREMAT__H */
diff --git a/util/tables/sm_blosum45.c b/util/tables/sm_blosum45.c
new file mode 100644
index 00000000..bfa42b59
--- /dev/null
+++ b/util/tables/sm_blosum45.c
@@ -0,0 +1,99 @@
+/*  $Id: sm_blosum45.c,v 1.1 2003/08/21 19:48:20 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* Matrix made by matblas from blosum45.iij */
+/* * column uses minimum score */
+/* BLOSUM Clustered Scoring Matrix in 1/3 Bit Units */
+/* Blocks Database = /data/blocks_5.0/blocks.dat */
+/* Cluster Percentage: >= 45 */
+/* Entropy =   0.3795, Expected =  -0.2789 */
+
+static const TNCBIScore s_Blosum45PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  5, -2, -1, -2, -1, -1, -1,  0, -2, -1, -1, -1,
+            -1, -2, -1,  1,  0, -2, -2,  0, -1, -1,  0, -5 },
+    /*R*/ { -2,  7,  0, -1, -3,  1,  0, -2,  0, -3, -2,  3,
+            -1, -2, -2, -1, -1, -2, -1, -2, -1,  0, -1, -5 },
+    /*N*/ { -1,  0,  6,  2, -2,  0,  0,  0,  1, -2, -3,  0,
+            -2, -2, -2,  1,  0, -4, -2, -3,  4,  0, -1, -5 },
+    /*D*/ { -2, -1,  2,  7, -3,  0,  2, -1,  0, -4, -3,  0,
+            -3, -4, -1,  0, -1, -4, -2, -3,  5,  1, -1, -5 },
+    /*C*/ { -1, -3, -2, -3, 12, -3, -3, -3, -3, -3, -2, -3,
+            -2, -2, -4, -1, -1, -5, -3, -1, -2, -3, -2, -5 },
+    /*Q*/ { -1,  1,  0,  0, -3,  6,  2, -2,  1, -2, -2,  1,
+             0, -4, -1,  0, -1, -2, -1, -3,  0,  4, -1, -5 },
+    /*E*/ { -1,  0,  0,  2, -3,  2,  6, -2,  0, -3, -2,  1,
+            -2, -3,  0,  0, -1, -3, -2, -3,  1,  4, -1, -5 },
+    /*G*/ {  0, -2,  0, -1, -3, -2, -2,  7, -2, -4, -3, -2,
+            -2, -3, -2,  0, -2, -2, -3, -3, -1, -2, -1, -5 },
+    /*H*/ { -2,  0,  1,  0, -3,  1,  0, -2, 10, -3, -2, -1,
+             0, -2, -2, -1, -2, -3,  2, -3,  0,  0, -1, -5 },
+    /*I*/ { -1, -3, -2, -4, -3, -2, -3, -4, -3,  5,  2, -3,
+             2,  0, -2, -2, -1, -2,  0,  3, -3, -3, -1, -5 },
+    /*L*/ { -1, -2, -3, -3, -2, -2, -2, -3, -2,  2,  5, -3,
+             2,  1, -3, -3, -1, -2,  0,  1, -3, -2, -1, -5 },
+    /*K*/ { -1,  3,  0,  0, -3,  1,  1, -2, -1, -3, -3,  5,
+            -1, -3, -1, -1, -1, -2, -1, -2,  0,  1, -1, -5 },
+    /*M*/ { -1, -1, -2, -3, -2,  0, -2, -2,  0,  2,  2, -1,
+             6,  0, -2, -2, -1, -2,  0,  1, -2, -1, -1, -5 },
+    /*F*/ { -2, -2, -2, -4, -2, -4, -3, -3, -2,  0,  1, -3,
+             0,  8, -3, -2, -1,  1,  3,  0, -3, -3, -1, -5 },
+    /*P*/ { -1, -2, -2, -1, -4, -1,  0, -2, -2, -2, -3, -1,
+            -2, -3,  9, -1, -1, -3, -3, -3, -2, -1, -1, -5 },
+    /*S*/ {  1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -3, -1,
+            -2, -2, -1,  4,  2, -4, -2, -1,  0,  0,  0, -5 },
+    /*T*/ {  0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1,
+            -1, -1, -1,  2,  5, -3, -1,  0,  0, -1,  0, -5 },
+    /*W*/ { -2, -2, -4, -4, -5, -2, -3, -2, -3, -2, -2, -2,
+            -2,  1, -3, -4, -3, 15,  3, -3, -4, -2, -2, -5 },
+    /*Y*/ { -2, -1, -2, -2, -3, -1, -2, -3,  2,  0,  0, -1,
+             0,  3, -3, -2, -1,  3,  8, -1, -2, -2, -1, -5 },
+    /*V*/ {  0, -2, -3, -3, -1, -3, -3, -3, -3,  3,  1, -2,
+             1,  0, -3, -1,  0, -3, -1,  5, -3, -3, -1, -5 },
+    /*B*/ { -1, -1,  4,  5, -2,  0,  1, -1,  0, -3, -3,  0,
+            -2, -3, -2,  0,  0, -4, -2, -3,  4,  2, -1, -5 },
+    /*Z*/ { -1,  0,  0,  1, -3,  4,  4, -2,  0, -3, -2,  1,
+            -1, -3, -1,  0, -1, -2, -2, -3,  2,  4, -1, -5 },
+    /*X*/ {  0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1,
+            -1, -1, -1,  0,  0, -2, -1, -1, -1, -1, -1, -5 },
+    /***/ { -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,
+            -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Blosum45 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Blosum45PSM[0],
+    -5
+};
diff --git a/util/tables/sm_blosum62.c b/util/tables/sm_blosum62.c
new file mode 100644
index 00000000..3f356def
--- /dev/null
+++ b/util/tables/sm_blosum62.c
@@ -0,0 +1,99 @@
+/*  $Id: sm_blosum62.c,v 1.1 2003/08/21 19:48:20 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* Matrix made by matblas from blosum62.iij */
+/* * column uses minimum score */
+/* BLOSUM Clustered Scoring Matrix in 1/2 Bit Units */
+/* Blocks Database = /data/blocks_5.0/blocks.dat */
+/* Cluster Percentage: >= 62 */
+/* Entropy =   0.6979, Expected =  -0.5209 */
+
+static const TNCBIScore s_Blosum62PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  4, -1, -2, -2,  0, -1, -1,  0, -2, -1, -1, -1,
+            -1, -2, -1,  1,  0, -3, -2,  0, -2, -1,  0, -4 },
+    /*R*/ { -1,  5,  0, -2, -3,  1,  0, -2,  0, -3, -2,  2,
+            -1, -3, -2, -1, -1, -3, -2, -3, -1,  0, -1, -4 },
+    /*N*/ { -2,  0,  6,  1, -3,  0,  0,  0,  1, -3, -3,  0,
+            -2, -3, -2,  1,  0, -4, -2, -3,  3,  0, -1, -4 },
+    /*D*/ { -2, -2,  1,  6, -3,  0,  2, -1, -1, -3, -4, -1,
+            -3, -3, -1,  0, -1, -4, -3, -3,  4,  1, -1, -4 },
+    /*C*/ {  0, -3, -3, -3,  9, -3, -4, -3, -3, -1, -1, -3,
+            -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4 },
+    /*Q*/ { -1,  1,  0,  0, -3,  5,  2, -2,  0, -3, -2,  1,
+             0, -3, -1,  0, -1, -2, -1, -2,  0,  3, -1, -4 },
+    /*E*/ { -1,  0,  0,  2, -4,  2,  5, -2,  0, -3, -3,  1,
+            -2, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4 },
+    /*G*/ {  0, -2,  0, -1, -3, -2, -2,  6, -2, -4, -4, -2,
+            -3, -3, -2,  0, -2, -2, -3, -3, -1, -2, -1, -4 },
+    /*H*/ { -2,  0,  1, -1, -3,  0,  0, -2,  8, -3, -3, -1,
+            -2, -1, -2, -1, -2, -2,  2, -3,  0,  0, -1, -4 },
+    /*I*/ { -1, -3, -3, -3, -1, -3, -3, -4, -3,  4,  2, -3,
+             1,  0, -3, -2, -1, -3, -1,  3, -3, -3, -1, -4 },
+    /*L*/ { -1, -2, -3, -4, -1, -2, -3, -4, -3,  2,  4, -2,
+             2,  0, -3, -2, -1, -2, -1,  1, -4, -3, -1, -4 },
+    /*K*/ { -1,  2,  0, -1, -3,  1,  1, -2, -1, -3, -2,  5,
+            -1, -3, -1,  0, -1, -3, -2, -2,  0,  1, -1, -4 },
+    /*M*/ { -1, -1, -2, -3, -1,  0, -2, -3, -2,  1,  2, -1,
+             5,  0, -2, -1, -1, -1, -1,  1, -3, -1, -1, -4 },
+    /*F*/ { -2, -3, -3, -3, -2, -3, -3, -3, -1,  0,  0, -3,
+             0,  6, -4, -2, -2,  1,  3, -1, -3, -3, -1, -4 },
+    /*P*/ { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1,
+            -2, -4,  7, -1, -1, -4, -3, -2, -2, -1, -2, -4 },
+    /*S*/ {  1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -2,  0,
+            -1, -2, -1,  4,  1, -3, -2, -2,  0,  0,  0, -4 },
+    /*T*/ {  0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1,
+            -1, -2, -1,  1,  5, -2, -2,  0, -1, -1,  0, -4 },
+    /*W*/ { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3,
+            -1,  1, -4, -3, -2, 11,  2, -3, -4, -3, -2, -4 },
+    /*Y*/ { -2, -2, -2, -3, -2, -1, -2, -3,  2, -1, -1, -2,
+            -1,  3, -3, -2, -2,  2,  7, -1, -3, -2, -1, -4 },
+    /*V*/ {  0, -3, -3, -3, -1, -2, -2, -3, -3,  3,  1, -2,
+             1, -1, -2, -2,  0, -3, -1,  4, -3, -2, -1, -4 },
+    /*B*/ { -2, -1,  3,  4, -3,  0,  1, -1,  0, -3, -4,  0,
+            -3, -3, -2,  0, -1, -4, -3, -3,  4,  1, -1, -4 },
+    /*Z*/ { -1,  0,  0,  1, -3,  3,  4, -2,  0, -3, -3,  1,
+            -1, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4 },
+    /*X*/ {  0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1,
+            -1, -1, -2,  0,  0, -2, -1, -1, -1, -1, -1, -4 },
+    /***/ { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
+            -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Blosum62 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Blosum62PSM[0],
+    -4
+};
diff --git a/util/tables/sm_blosum80.c b/util/tables/sm_blosum80.c
new file mode 100644
index 00000000..dad0d652
--- /dev/null
+++ b/util/tables/sm_blosum80.c
@@ -0,0 +1,99 @@
+/*  $Id: sm_blosum80.c,v 1.1 2003/08/21 19:48:20 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* Matrix made by matblas from blosum80.iij */
+/* * column uses minimum score */
+/* BLOSUM Clustered Scoring Matrix in 1/2 Bit Units */
+/* Blocks Database = /data/blocks_5.0/blocks.dat */
+/* Cluster Percentage: >= 80 */
+/* Entropy =   0.9868, Expected =  -0.7442 */
+
+static const TNCBIScore s_Blosum80PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  5, -2, -2, -2, -1, -1, -1,  0, -2, -2, -2, -1,
+            -1, -3, -1,  1,  0, -3, -2,  0, -2, -1, -1, -6 },
+    /*R*/ { -2,  6, -1, -2, -4,  1, -1, -3,  0, -3, -3,  2,
+            -2, -4, -2, -1, -1, -4, -3, -3, -2,  0, -1, -6 },
+    /*N*/ { -2, -1,  6,  1, -3,  0, -1, -1,  0, -4, -4,  0,
+            -3, -4, -3,  0,  0, -4, -3, -4,  4,  0, -1, -6 },
+    /*D*/ { -2, -2,  1,  6, -4, -1,  1, -2, -2, -4, -5, -1,
+            -4, -4, -2, -1, -1, -6, -4, -4,  4,  1, -2, -6 },
+    /*C*/ { -1, -4, -3, -4,  9, -4, -5, -4, -4, -2, -2, -4,
+            -2, -3, -4, -2, -1, -3, -3, -1, -4, -4, -3, -6 },
+    /*Q*/ { -1,  1,  0, -1, -4,  6,  2, -2,  1, -3, -3,  1,
+             0, -4, -2,  0, -1, -3, -2, -3,  0,  3, -1, -6 },
+    /*E*/ { -1, -1, -1,  1, -5,  2,  6, -3,  0, -4, -4,  1,
+            -2, -4, -2,  0, -1, -4, -3, -3,  1,  4, -1, -6 },
+    /*G*/ {  0, -3, -1, -2, -4, -2, -3,  6, -3, -5, -4, -2,
+            -4, -4, -3, -1, -2, -4, -4, -4, -1, -3, -2, -6 },
+    /*H*/ { -2,  0,  0, -2, -4,  1,  0, -3,  8, -4, -3, -1,
+            -2, -2, -3, -1, -2, -3,  2, -4, -1,  0, -2, -6 },
+    /*I*/ { -2, -3, -4, -4, -2, -3, -4, -5, -4,  5,  1, -3,
+             1, -1, -4, -3, -1, -3, -2,  3, -4, -4, -2, -6 },
+    /*L*/ { -2, -3, -4, -5, -2, -3, -4, -4, -3,  1,  4, -3,
+             2,  0, -3, -3, -2, -2, -2,  1, -4, -3, -2, -6 },
+    /*K*/ { -1,  2,  0, -1, -4,  1,  1, -2, -1, -3, -3,  5,
+            -2, -4, -1, -1, -1, -4, -3, -3, -1,  1, -1, -6 },
+    /*M*/ { -1, -2, -3, -4, -2,  0, -2, -4, -2,  1,  2, -2,
+             6,  0, -3, -2, -1, -2, -2,  1, -3, -2, -1, -6 },
+    /*F*/ { -3, -4, -4, -4, -3, -4, -4, -4, -2, -1,  0, -4,
+             0,  6, -4, -3, -2,  0,  3, -1, -4, -4, -2, -6 },
+    /*P*/ { -1, -2, -3, -2, -4, -2, -2, -3, -3, -4, -3, -1,
+            -3, -4,  8, -1, -2, -5, -4, -3, -2, -2, -2, -6 },
+    /*S*/ {  1, -1,  0, -1, -2,  0,  0, -1, -1, -3, -3, -1,
+            -2, -3, -1,  5,  1, -4, -2, -2,  0,  0, -1, -6 },
+    /*T*/ {  0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -2, -1,
+            -1, -2, -2,  1,  5, -4, -2,  0, -1, -1, -1, -6 },
+    /*W*/ { -3, -4, -4, -6, -3, -3, -4, -4, -3, -3, -2, -4,
+            -2,  0, -5, -4, -4, 11,  2, -3, -5, -4, -3, -6 },
+    /*Y*/ { -2, -3, -3, -4, -3, -2, -3, -4,  2, -2, -2, -3,
+            -2,  3, -4, -2, -2,  2,  7, -2, -3, -3, -2, -6 },
+    /*V*/ {  0, -3, -4, -4, -1, -3, -3, -4, -4,  3,  1, -3,
+             1, -1, -3, -2,  0, -3, -2,  4, -4, -3, -1, -6 },
+    /*B*/ { -2, -2,  4,  4, -4,  0,  1, -1, -1, -4, -4, -1,
+            -3, -4, -2,  0, -1, -5, -3, -4,  4,  0, -2, -6 },
+    /*Z*/ { -1,  0,  0,  1, -4,  3,  4, -3,  0, -4, -3,  1,
+            -2, -4, -2,  0, -1, -4, -3, -3,  0,  4, -1, -6 },
+    /*X*/ { -1, -1, -1, -2, -3, -1, -1, -2, -2, -2, -2, -1,
+            -1, -2, -2, -1, -1, -3, -2, -1, -2, -1, -1, -6 },
+    /***/ { -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,
+            -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Blosum80 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Blosum80PSM[0],
+    -6
+};
diff --git a/util/tables/sm_pam30.c b/util/tables/sm_pam30.c
new file mode 100644
index 00000000..3b62f8ad
--- /dev/null
+++ b/util/tables/sm_pam30.c
@@ -0,0 +1,97 @@
+/*  $Id: sm_pam30.c,v 1.1 2003/08/21 19:48:20 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] */
+/* PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574 */
+/* Expected score = -5.06, Entropy = 2.57 bits */
+/* Lowest score = -17, Highest score = 13 */
+
+static const TNCBIScore s_Pam30PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  6, -7, -4, -3, -6, -4, -2, -2, -7, -5, -6, -7,
+            -5, -8, -2,  0, -1,-13, -8, -2, -3, -3, -3,-17 },
+    /*R*/ { -7,  8, -6,-10, -8, -2, -9, -9, -2, -5, -8,  0,
+            -4, -9, -4, -3, -6, -2,-10, -8, -7, -4, -6,-17 },
+    /*N*/ { -4, -6,  8,  2,-11, -3, -2, -3,  0, -5, -7, -1,
+            -9, -9, -6,  0, -2, -8, -4, -8,  6, -3, -3,-17 },
+    /*D*/ { -3,-10,  2,  8,-14, -2,  2, -3, -4, -7,-12, -4,
+           -11,-15, -8, -4, -5,-15,-11, -8,  6,  1, -5,-17 },
+    /*C*/ { -6, -8,-11,-14, 10,-14,-14, -9, -7, -6,-15,-14,
+           -13,-13, -8, -3, -8,-15, -4, -6,-12,-14, -9,-17 },
+    /*Q*/ { -4, -2, -3, -2,-14,  8,  1, -7,  1, -8, -5, -3,
+            -4,-13, -3, -5, -5,-13,-12, -7, -3,  6, -5,-17 },
+    /*E*/ { -2, -9, -2,  2,-14,  1,  8, -4, -5, -5, -9, -4,
+            -7,-14, -5, -4, -6,-17, -8, -6,  1,  6, -5,-17 },
+    /*G*/ { -2, -9, -3, -3, -9, -7, -4,  6, -9,-11,-10, -7,
+            -8, -9, -6, -2, -6,-15,-14, -5, -3, -5, -5,-17 },
+    /*H*/ { -7, -2,  0, -4, -7,  1, -5, -9,  9, -9, -6, -6,
+           -10, -6, -4, -6, -7, -7, -3, -6, -1, -1, -5,-17 },
+    /*I*/ { -5, -5, -5, -7, -6, -8, -5,-11, -9,  8, -1, -6,
+            -1, -2, -8, -7, -2,-14, -6,  2, -6, -6, -5,-17 },
+    /*L*/ { -6, -8, -7,-12,-15, -5, -9,-10, -6, -1,  7, -8,
+             1, -3, -7, -8, -7, -6, -7, -2, -9, -7, -6,-17 },
+    /*K*/ { -7,  0, -1, -4,-14, -3, -4, -7, -6, -6, -8,  7,
+            -2,-14, -6, -4, -3,-12, -9, -9, -2, -4, -5,-17 },
+    /*M*/ { -5, -4, -9,-11,-13, -4, -7, -8,-10, -1,  1, -2,
+            11, -4, -8, -5, -4,-13,-11, -1,-10, -5, -5,-17 },
+    /*F*/ { -8, -9, -9,-15,-13,-13,-14, -9, -6, -2, -3,-14,
+            -4,  9,-10, -6, -9, -4,  2, -8,-10,-13, -8,-17 },
+    /*P*/ { -2, -4, -6, -8, -8, -3, -5, -6, -4, -8, -7, -6,
+            -8,-10,  8, -2, -4,-14,-13, -6, -7, -4, -5,-17 },
+    /*S*/ {  0, -3,  0, -4, -3, -5, -4, -2, -6, -7, -8, -4,
+            -5, -6, -2,  6,  0, -5, -7, -6, -1, -5, -3,-17 },
+    /*T*/ { -1, -6, -2, -5, -8, -5, -6, -6, -7, -2, -7, -3,
+            -4, -9, -4,  0,  7,-13, -6, -3, -3, -6, -4,-17 },
+    /*W*/ {-13, -2, -8,-15,-15,-13,-17,-15, -7,-14, -6,-12,
+           -13, -4,-14, -5,-13, 13, -5,-15,-10,-14,-11,-17 },
+    /*Y*/ { -8,-10, -4,-11, -4,-12, -8,-14, -3, -6, -7, -9,
+           -11,  2,-13, -7, -6, -5, 10, -7, -6, -9, -7,-17 },
+    /*V*/ { -2, -8, -8, -8, -6, -7, -6, -5, -6,  2, -2, -9,
+            -1, -8, -6, -6, -3,-15, -7,  7, -8, -6, -5,-17 },
+    /*B*/ { -3, -7,  6,  6,-12, -3,  1, -3, -1, -6, -9, -2,
+           -10,-10, -7, -1, -3,-10, -6, -8,  6,  0, -5,-17 },
+    /*Z*/ { -3, -4, -3,  1,-14,  6,  6, -5, -1, -6, -7, -4,
+            -5,-13, -4, -5, -6,-14, -9, -6,  0,  6, -5,-17 },
+    /*X*/ { -3, -6, -3, -5, -9, -5, -5, -5, -5, -5, -6, -5,
+            -5, -8, -5, -3, -4,-11, -7, -5, -5, -5, -5,-17 },
+    /***/ {-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,
+           -17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Pam30 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Pam30PSM[0],
+    -17
+};
diff --git a/util/tables/sm_pam70.c b/util/tables/sm_pam70.c
new file mode 100644
index 00000000..900398b0
--- /dev/null
+++ b/util/tables/sm_pam70.c
@@ -0,0 +1,97 @@
+/*  $Id: sm_pam70.c,v 1.1 2003/08/21 19:48:20 ucko Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* Author:  Aaron Ucko (via ./convert_scoremat.pl)
+*
+* File Description:
+*   Protein alignment score matrices; shared between the two toolkits.
+*
+* ===========================================================================
+*/
+
+#include <util/tables/raw_scoremat.h>
+
+/* This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] */
+/* PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574 */
+/* Expected score = -2.77, Entropy = 1.60 bits */
+/* Lowest score = -11, Highest score = 13 */
+
+static const TNCBIScore s_Pam70PSM[24][24] = {
+    /*       A,  R,  N,  D,  C,  Q,  E,  G,  H,  I,  L,  K,
+             M,  F,  P,  S,  T,  W,  Y,  V,  B,  Z,  X,  * */
+    /*A*/ {  5, -4, -2, -1, -4, -2, -1,  0, -4, -2, -4, -4,
+            -3, -6,  0,  1,  1, -9, -5, -1, -1, -1, -2,-11 },
+    /*R*/ { -4,  8, -3, -6, -5,  0, -5, -6,  0, -3, -6,  2,
+            -2, -7, -2, -1, -4,  0, -7, -5, -4, -2, -3,-11 },
+    /*N*/ { -2, -3,  6,  3, -7, -1,  0, -1,  1, -3, -5,  0,
+            -5, -6, -3,  1,  0, -6, -3, -5,  5, -1, -2,-11 },
+    /*D*/ { -1, -6,  3,  6, -9,  0,  3, -1, -1, -5, -8, -2,
+            -7,-10, -4, -1, -2,-10, -7, -5,  5,  2, -3,-11 },
+    /*C*/ { -4, -5, -7, -9,  9, -9, -9, -6, -5, -4,-10, -9,
+            -9, -8, -5, -1, -5,-11, -2, -4, -8, -9, -6,-11 },
+    /*Q*/ { -2,  0, -1,  0, -9,  7,  2, -4,  2, -5, -3, -1,
+            -2, -9, -1, -3, -3, -8, -8, -4, -1,  5, -2,-11 },
+    /*E*/ { -1, -5,  0,  3, -9,  2,  6, -2, -2, -4, -6, -2,
+            -4, -9, -3, -2, -3,-11, -6, -4,  2,  5, -3,-11 },
+    /*G*/ {  0, -6, -1, -1, -6, -4, -2,  6, -6, -6, -7, -5,
+            -6, -7, -3,  0, -3,-10, -9, -3, -1, -3, -3,-11 },
+    /*H*/ { -4,  0,  1, -1, -5,  2, -2, -6,  8, -6, -4, -3,
+            -6, -4, -2, -3, -4, -5, -1, -4,  0,  1, -3,-11 },
+    /*I*/ { -2, -3, -3, -5, -4, -5, -4, -6, -6,  7,  1, -4,
+             1,  0, -5, -4, -1, -9, -4,  3, -4, -4, -3,-11 },
+    /*L*/ { -4, -6, -5, -8,-10, -3, -6, -7, -4,  1,  6, -5,
+             2, -1, -5, -6, -4, -4, -4,  0, -6, -4, -4,-11 },
+    /*K*/ { -4,  2,  0, -2, -9, -1, -2, -5, -3, -4, -5,  6,
+             0, -9, -4, -2, -1, -7, -7, -6, -1, -2, -3,-11 },
+    /*M*/ { -3, -2, -5, -7, -9, -2, -4, -6, -6,  1,  2,  0,
+            10, -2, -5, -3, -2, -8, -7,  0, -6, -3, -3,-11 },
+    /*F*/ { -6, -7, -6,-10, -8, -9, -9, -7, -4,  0, -1, -9,
+            -2,  8, -7, -4, -6, -2,  4, -5, -7, -9, -5,-11 },
+    /*P*/ {  0, -2, -3, -4, -5, -1, -3, -3, -2, -5, -5, -4,
+            -5, -7,  7,  0, -2, -9, -9, -3, -4, -2, -3,-11 },
+    /*S*/ {  1, -1,  1, -1, -1, -3, -2,  0, -3, -4, -6, -2,
+            -3, -4,  0,  5,  2, -3, -5, -3,  0, -2, -1,-11 },
+    /*T*/ {  1, -4,  0, -2, -5, -3, -3, -3, -4, -1, -4, -1,
+            -2, -6, -2,  2,  6, -8, -4, -1, -1, -3, -2,-11 },
+    /*W*/ { -9,  0, -6,-10,-11, -8,-11,-10, -5, -9, -4, -7,
+            -8, -2, -9, -3, -8, 13, -3,-10, -7,-10, -7,-11 },
+    /*Y*/ { -5, -7, -3, -7, -2, -8, -6, -9, -1, -4, -4, -7,
+            -7,  4, -9, -5, -4, -3,  9, -5, -4, -7, -5,-11 },
+    /*V*/ { -1, -5, -5, -5, -4, -4, -4, -3, -4,  3,  0, -6,
+             0, -5, -3, -3, -1,-10, -5,  6, -5, -4, -2,-11 },
+    /*B*/ { -1, -4,  5,  5, -8, -1,  2, -1,  0, -4, -6, -1,
+            -6, -7, -4,  0, -1, -7, -4, -5,  5,  1, -2,-11 },
+    /*Z*/ { -1, -2, -1,  2, -9,  5,  5, -3,  1, -4, -4, -2,
+            -3, -9, -2, -2, -3,-10, -7, -4,  1,  5, -3,-11 },
+    /*X*/ { -2, -3, -2, -3, -6, -2, -3, -3, -3, -3, -4, -3,
+            -3, -5, -3, -1, -2, -7, -5, -2, -2, -3, -3,-11 },
+    /***/ {-11,-11,-11,-11,-11,-11,-11,-11,-11,-11,-11,-11,
+           -11,-11,-11,-11,-11,-11,-11,-11,-11,-11,-11,  1 }
+};
+const SNCBIPackedScoreMatrix NCBISM_Pam70 = {
+    "ARNDCQEGHILKMFPSTWYVBZX*",
+    s_Pam70PSM[0],
+    -11
+};
diff --git a/util/tables/tables_export.h b/util/tables/tables_export.h
new file mode 100644
index 00000000..6fdf43c4
--- /dev/null
+++ b/util/tables/tables_export.h
@@ -0,0 +1,57 @@
+#ifndef UTIL_TABLES___TABLES_EXPORT__H
+#define UTIL_TABLES___TABLES_EXPORT__H
+
+/*  $Id: tables_export.h,v 1.1 2003/08/21 19:50:51 ucko Exp $
+ * ===========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Author:  Anatoliy Kuznetsov, Mike DiCuccio
+ *
+ * File Description:
+ *    Defines to provide correct exporting from TABLES DLL in Windows.
+ *    These are necessary to compile DLLs with Visual C++ - exports must be
+ *    explicitly labeled as such.
+ */
+
+
+/*
+ * NULL operations for other cases (C Toolkit)
+ */
+
+#  define NCBI_TABLES_EXPORT
+
+
+
+/*
+ * ==========================================================================
+ *
+ * $Log: tables_export.h,v $
+ * Revision 1.1  2003/08/21 19:50:51  ucko
+ * Add C-Toolkit-specific export setup for tables library
+ *
+ *
+ * ==========================================================================
+ */
+
+#endif  /*  UTIL_TABLES___TABLES_EXPORT__H  */