Load ncbi (6.1.20040202) into ncbi-tools6/branches/upstream/current.

5 files changed, 62 insertions, 15 deletions

diff --git a/asnlib/asn.h b/asnlib/asn.h
index aecb424e..1f3179a1 100644
--- a/asnlib/asn.h
+++ b/asnlib/asn.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 1/1/91
 *
-* $Revision: 6.10 $
+* $Revision: 6.11 $
 *
 * File Description:
 *   This header the interface to all the routines in the ASN.1 libraries
@@ -48,6 +48,9 @@
 * 02-24-94 Schuler     AsnTypeStringToHex moved here (from asntypes.h)
 *
 * $Log: asn.h,v $
+* Revision 6.11  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
 * Revision 6.10  2003/09/15 16:16:32  kans
 * added AsnWriteEx, AsnTxtWriteEx, and AsnPrintStream
 *
@@ -390,6 +393,7 @@ NLM_EXTERN AsnTypePtr LIBCALL AsnTypeFind PROTO((AsnModulePtr amp, CharPtr str))
 #define AsnFind(x) AsnTypeFind(NULL,x)    /* find type (all) */
 NLM_EXTERN CharPtr LIBCALL AsnFindPrimName PROTO((AsnTypePtr atp));
 NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseType PROTO((AsnTypePtr atp));
+NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseTypeDTD PROTO((AsnTypePtr atp));
 NLM_EXTERN CharPtr LIBCALL AsnFindBaseName PROTO((AsnTypePtr atp));
 NLM_EXTERN Int2 LIBCALL AsnFindBaseIsa PROTO((AsnTypePtr atp));
 NLM_EXTERN AsnTypePtr LIBCALL AsnLinkType PROTO((AsnTypePtr type, AsnTypePtr localtype));
diff --git a/asnlib/asndebin.c b/asnlib/asndebin.c
index 124b32e4..86e1c4f6 100644
--- a/asnlib/asndebin.c
+++ b/asnlib/asndebin.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.5 $
+* $Revision: 6.6 $
 *
 * File Description:
 *   Special binary form (BER) decoder for ASN.1
@@ -45,6 +45,9 @@
 * 08-01-93 Gish        AsnDeBinReadString calls MemGet instead of MemNew
 *
 * $Log: asndebin.c,v $
+* Revision 6.6  2003/12/10 15:41:19  sirotkin
+* As per toolkit RT request 15030485 and Jim Ostell, afety checks after ato2=AsnFindBaseIsa(atp) were added.
+*
 * Revision 6.5  2002/10/09 19:16:31  ivanov
 * Fixed buffer overrun in the AsnDeBinReadReal()
 *
@@ -118,9 +121,15 @@ NLM_EXTERN AsnTypePtr LIBCALL  AsnBinReadId (AsnIoPtr aip, AsnTypePtr atp)
 
 		if (used == ASNDEBIN_EOF)      /* end of file */
 			return NULL;
+                /* see RT toolbox ticket 15030485 for the below fix */
 
 		atp2 = AsnFindBaseType(atp);   /* find the base type */
-		if (atp2 == NULL) return NULL;
+		if (atp2 == NULL)
+			return atp2;
+		if (atp2->type == NULL)
+			return atp2->type;
+		isa = atp2->type->isa;
+
 
 		if (atp2->type->isa != CHOICE_TYPE)
 		{
diff --git a/asnlib/asnenbin.c b/asnlib/asnenbin.c
index 1c34be40..afcf1432 100644
--- a/asnlib/asnenbin.c
+++ b/asnlib/asnenbin.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.5 $
+* $Revision: 6.6 $
 *
 * File Description:
 *   Special binary (BER) encoder for ASN.1
@@ -42,6 +42,9 @@
 * 04-20-93 Schuler     LIBCALL calling convention
 *
 * $Log: asnenbin.c,v $
+* Revision 6.6  2003/11/07 20:57:02  beloslyu
+* fix the c++ style comments to a C ones
+*
 * Revision 6.5  2003/08/01 16:55:24  gouriano
 * workaround MSVC++.NET optimization bug
 *
@@ -360,7 +363,7 @@ NLM_EXTERN void AsnEnBinInteger (Int4 theInt, AsnIoPtr aip, AsnTypePtr atp)
 	{
 		for (i = 0; i < 3; i++)
 			octets[i] = octets[i+1];
-// dirty workaround of an optimization bug of MSVC++.NET compiler
+/* dirty workaround of an optimization bug of MSVC++.NET compiler */
 #if defined(_MSC_VER) 
 #  if _MSC_VER < 1300
 		octets[3] = 0;
@@ -424,7 +427,7 @@ NLM_EXTERN void AsnEnBinBigInt (Int8 theInt, AsnIoPtr aip, AsnTypePtr atp)
 	{
 		for (i = 0; i < 7; i++)
 			octets[i] = octets[i+1];
-// dirty workaround of an optimization bug of MSVC++.NET compiler
+/* dirty workaround of an optimization bug of MSVC++.NET compiler */
 #if defined(_MSC_VER) 
 #  if _MSC_VER < 1300
 		octets[7] = 0;
diff --git a/asnlib/asnprint.c b/asnlib/asnprint.c
index 5328c5c4..5d142c66 100644
--- a/asnlib/asnprint.c
+++ b/asnlib/asnprint.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.18 $
+* $Revision: 6.20 $
 *
 * File Description:
 *   Routines for printing ASN.1 value notation (text) messages and
@@ -42,6 +42,12 @@
 * 3/4/91   Kans        Stricter typecasting for GNU C and C++
 *
 * $Log: asnprint.c,v $
+* Revision 6.20  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
+* Revision 6.19  2003/12/02 19:52:48  gouriano
+* Corrected DTD generation
+*
 * Revision 6.18  2003/09/15 16:16:32  kans
 * added AsnWriteEx, AsnTxtWriteEx, and AsnPrintStream
 *
@@ -1901,7 +1907,7 @@ static void AsnXMLElementStart(AsnTypePtr atp, AsnIoPtr aip)
 
 	AsnPrintString(GetXMLname(atp), aip);
 
-	atp2 = AsnFindBaseType(atp);
+	atp2 = AsnFindBaseTypeDTD(atp);
 	if (atp2 == atp)
 	{
 		if ((isa == ENUM_TYPE) || (isa == BOOLEAN_TYPE) ||
@@ -2351,7 +2357,8 @@ static Boolean AsnPrintTypeXML (AsnTypePtr atp, AsnIoPtr aip)
 				if ((atp->optional) || (atp->hasdefault))
 					repeat = "*";
 				else
-					repeat = "+";
+					repeat = "*";
+//					repeat = "+";
 				AsnXMLElementAdd(NULL, atp->branch, repeat, aip, FALSE);
 				break;
 			case INTEGER_TYPE:
@@ -2483,7 +2490,7 @@ static Boolean AsnPrintTypeXML (AsnTypePtr atp, AsnIoPtr aip)
 	}
 	else  /* primitive.. all text */
 	{
-		atp2 = AsnFindBaseType(atp);
+		atp2 = AsnFindBaseTypeDTD(atp);
 		if (atp2 != NULL)
 		{
 			isa = AsnFindBaseIsa(atp);
diff --git a/asnlib/asntypes.c b/asnlib/asntypes.c
index 11015913..cfce072c 100644
--- a/asnlib/asntypes.c
+++ b/asnlib/asntypes.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.6 $
+* $Revision: 6.9 $
 *
 * File Description:
 *   Routines to deal with internal operations on AsnType objects.
@@ -43,6 +43,15 @@
 * 02-24-94 Schuler     Make AsnTypeStringToHex LIBCALL too
 *
 * $Log: asntypes.c,v $
+* Revision 6.9  2003/12/03 19:31:09  gouriano
+* Corrected DTD generation (a different approach)
+*
+* Revision 6.8  2003/12/02 21:40:17  gouriano
+* Revert back to rev 6.6
+*
+* Revision 6.7  2003/12/02 19:52:49  gouriano
+* Corrected DTD generation
+*
 * Revision 6.6  2000/07/25 20:30:58  ostell
 * added support for printing multiple ASN.1 modules as multiple XML DTD and .mod files
 *
@@ -233,6 +242,21 @@ NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseType (AsnTypePtr atp)
 	return atp;
 }
 
+NLM_EXTERN AsnTypePtr LIBCALL AsnFindBaseTypeDTD (AsnTypePtr atp)
+{
+	if (atp == NULL) return NULL;
+
+	if (atp->type == NULL) return NULL;
+
+	if (! ISA_BASETYPE(atp->type->isa))
+	{
+		atp = atp->type;
+		if (atp->type == NULL)   /* not found */
+			return atp;
+	}
+	return atp;
+}
+
 /*****************************************************************************
 *
 *   Int2 AsnFindBaseIsa(atp)
@@ -906,7 +930,7 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 			isa = AsnFindBaseIsa(atp2);
 			if ((doitem) && ((isa == SEQOF_TYPE) || (isa == SETOF_TYPE)))
 			{
-				atp2 = AsnFindBaseType(atp);
+				atp2 = AsnFindBaseTypeDTD(atp);
 				if (atp2 != NULL)
 				{
 				if (atp2->name == NULL)
@@ -957,12 +981,12 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 
 				for (i = (stackptr - 1); (i >= 0) && (! found); i--)
 				{
-					atp2 = AsnFindBaseType(typestack[i]);
+					atp2 = AsnFindBaseTypeDTD(typestack[i]);
 					if ((atp2 != NULL) && (atp2->name != NULL) && (IS_UPPER(*(atp2->name))))
 					{
 						while (i < stackptr)
 						{
-							atp2 = AsnFindBaseType(typestack[i]);
+							atp2 = AsnFindBaseTypeDTD(typestack[i]);
 							if (atp2->name == NULL)
 								tmp = StringMove(tmp, "E");
 							else
@@ -991,7 +1015,7 @@ static void AddXMLname(AsnTypePtr atp, AsnTypePtr PNTR typestack, Int2 stackptr)
 		}
 	}
 
-	atp2 = AsnFindBaseType(atp);
+	atp2 = AsnFindBaseTypeDTD(atp);
 	if ((! atp->imported) && (atp2 != NULL) && (atp2->type != NULL))
 	{
 		isa = atp2->type->isa;