Imported Upstream version 6.1.20100808

5 files changed, 174 insertions, 15 deletions

diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
index 1ab48ed0..1f51ee3c 100644
--- a/network/id2arch/id2.asn
+++ b/network/id2arch/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 1.22 $
+--$Revision: 1.23 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -70,7 +70,10 @@ ID2-Request-Get-Seq-id ::= SEQUENCE {
                 text    (2),    -- text Seq-id (accession etc) is preferred
                 general (4),    -- general Seq-id is preferred
                 all     (127),  -- return all qualified Seq-ids of the sequence
-                label   (128)   -- return a sequence string label as general id
+                label   (128),  -- return a sequence string label as string
+                                -- in general id with db "LABEL"
+                taxid   (256)   -- return a sequence taxonomy ID as integer
+                                -- in general id with db "TAXID"
         } DEFAULT any
 }
 
diff --git a/network/id2arch/id2.c b/network/id2arch/id2.c
index 13fd3160..a0f8cbb0 100644
--- a/network/id2arch/id2.c
+++ b/network/id2arch/id2.c
@@ -2766,7 +2766,7 @@ ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       if ( AsnReadVal(aip, atp, &av) <= 0) {
          goto erret;
       }
-      ptr -> end_of_reply = av.boolvalue;
+      ptr -> end_of_reply = TRUE;
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == ID2_REPLY_reply) {
@@ -2782,6 +2782,8 @@ ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       ptr -> discard = av.intvalue;
       atp = AsnReadId(aip,amp, atp);
+   } else {
+      ptr -> discard = -1;
    }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
@@ -2961,15 +2963,19 @@ ID2ReplyAsnWrite(ID2ReplyPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
       }
    }
    AsnGenericUserSeqOfAsnWrite(ptr -> error, (AsnWriteFunc) ID2ErrorAsnWrite, aip, ID2_REPLY_error, ID2_REPLY_error_E);
-   av.boolvalue = ptr -> end_of_reply;
-   retval = AsnWrite(aip, ID2_REPLY_end_of_reply,  &av);
+   if (ptr -> end_of_reply) {
+      av.boolvalue = ptr -> end_of_reply;
+      retval = AsnWrite(aip, ID2_REPLY_end_of_reply,  &av);
+   }
    if (ptr -> Reply_reply != NULL) {
       if ( ! Reply_replyAsnWrite(ptr -> Reply_reply, aip, ID2_REPLY_reply)) {
          goto erret;
       }
    }
-   av.intvalue = ptr -> discard;
-   retval = AsnWrite(aip, ID2_REPLY_discard,  &av);
+   if (ptr -> discard != -1) {
+      av.intvalue = ptr -> discard;
+      retval = AsnWrite(aip, ID2_REPLY_discard,  &av);
+   }
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -3517,7 +3523,7 @@ ID2ReplyGetSeqIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       if ( AsnReadVal(aip, atp, &av) <= 0) {
          goto erret;
       }
-      ptr -> end_of_reply = av.boolvalue;
+      ptr -> end_of_reply = TRUE;
       atp = AsnReadId(aip,amp, atp);
    }
 
@@ -3577,8 +3583,10 @@ ID2ReplyGetSeqIdAsnWrite(ID2ReplyGetSeqIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
       }
    }
    AsnGenericChoiceSeqOfAsnWrite(ptr -> seq_id, (AsnWriteFunc) SeqIdAsnWrite, aip, ID2_REPLY_GET_SEQ_ID_seq_id, ID2_REPLY_GET_SEQ_ID_seq_id_E);
-   av.boolvalue = ptr -> end_of_reply;
-   retval = AsnWrite(aip, REPLY_GET_SEQ_ID_end_of_reply,  &av);
+   if (ptr -> end_of_reply) {
+      av.boolvalue = ptr -> end_of_reply;
+      retval = AsnWrite(aip, REPLY_GET_SEQ_ID_end_of_reply,  &av);
+   }
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -3707,7 +3715,7 @@ ID2ReplyGetBlobIdAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       if ( AsnReadVal(aip, atp, &av) <= 0) {
          goto erret;
       }
-      ptr -> end_of_reply = av.boolvalue;
+      ptr -> end_of_reply = TRUE;
       atp = AsnReadId(aip,amp, atp);
    }
    if (atp == REPLY_GET_BLOB_ID_blob_state) {
@@ -3781,8 +3789,10 @@ ID2ReplyGetBlobIdAsnWrite(ID2ReplyGetBlobIdPtr ptr, AsnIoPtr aip, AsnTypePtr ori
    av.intvalue = ptr -> split_version;
    retval = AsnWrite(aip, GET_BLOB_ID_split_version,  &av);
    AsnGenericUserSeqOfAsnWrite(ptr -> annot_info, (AsnWriteFunc) ID2SSeqAnnotInfoAsnWrite, aip, REPLY_GET_BLOB_ID_annot_info, REPLY_GET_BLOB_ID_annot_info_E);
-   av.boolvalue = ptr -> end_of_reply;
-   retval = AsnWrite(aip, REPLY_GET_BLOB_ID_end_of_reply,  &av);
+   if (ptr -> end_of_reply) {
+      av.boolvalue = ptr -> end_of_reply;
+      retval = AsnWrite(aip, REPLY_GET_BLOB_ID_end_of_reply,  &av);
+   }
    av.intvalue = ptr -> blob_state;
    retval = AsnWrite(aip, REPLY_GET_BLOB_ID_blob_state,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
diff --git a/network/id2arch/id2.patch b/network/id2arch/id2.patch
new file mode 100644
index 00000000..069fb0e2
--- /dev/null
+++ b/network/id2arch/id2.patch
@@ -0,0 +1,143 @@
+*** id2.c	Thu Jan  7 15:08:05 2010
+--- id2.c.new	Thu Jan  7 13:58:12 2010
+*************** ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr
+*** 2766,2772 ****
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = av.boolvalue;
+        atp = AsnReadId(aip,amp, atp);
+     }
+     if (atp == ID2_REPLY_reply) {
+--- 2766,2772 ----
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = TRUE;
+        atp = AsnReadId(aip,amp, atp);
+     }
+     if (atp == ID2_REPLY_reply) {
+*************** ID2ReplyAsnRead(AsnIoPtr aip, AsnTypePtr
+*** 2782,2787 ****
+--- 2782,2789 ----
+        }
+        ptr -> discard = av.intvalue;
+        atp = AsnReadId(aip,amp, atp);
++    } else {
++       ptr -> discard = -1;
+     }
+  
+     if (AsnReadVal(aip, atp, &av) <= 0) {
+*************** ID2ReplyAsnWrite(ID2ReplyPtr ptr, AsnIoP
+*** 2961,2975 ****
+        }
+     }
+     AsnGenericUserSeqOfAsnWrite(ptr -> error, (AsnWriteFunc) ID2ErrorAsnWrite, aip, ID2_REPLY_error, ID2_REPLY_error_E);
+!    av.boolvalue = ptr -> end_of_reply;
+!    retval = AsnWrite(aip, ID2_REPLY_end_of_reply,  &av);
+     if (ptr -> Reply_reply != NULL) {
+        if ( ! Reply_replyAsnWrite(ptr -> Reply_reply, aip, ID2_REPLY_reply)) {
+           goto erret;
+        }
+     }
+!    av.intvalue = ptr -> discard;
+!    retval = AsnWrite(aip, ID2_REPLY_discard,  &av);
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+        goto erret;
+     }
+--- 2963,2981 ----
+        }
+     }
+     AsnGenericUserSeqOfAsnWrite(ptr -> error, (AsnWriteFunc) ID2ErrorAsnWrite, aip, ID2_REPLY_error, ID2_REPLY_error_E);
+!    if (ptr -> end_of_reply) {
+!       av.boolvalue = ptr -> end_of_reply;
+!       retval = AsnWrite(aip, ID2_REPLY_end_of_reply,  &av);
+!    }
+     if (ptr -> Reply_reply != NULL) {
+        if ( ! Reply_replyAsnWrite(ptr -> Reply_reply, aip, ID2_REPLY_reply)) {
+           goto erret;
+        }
+     }
+!    if (ptr -> discard != -1) {
+!       av.intvalue = ptr -> discard;
+!       retval = AsnWrite(aip, ID2_REPLY_discard,  &av);
+!    }
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+        goto erret;
+     }
+*************** ID2ReplyGetSeqIdAsnRead(AsnIoPtr aip, As
+*** 3517,3523 ****
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = av.boolvalue;
+        atp = AsnReadId(aip,amp, atp);
+     }
+  
+--- 3523,3529 ----
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = TRUE;
+        atp = AsnReadId(aip,amp, atp);
+     }
+  
+*************** ID2ReplyGetSeqIdAsnWrite(ID2ReplyGetSeqI
+*** 3577,3584 ****
+        }
+     }
+     AsnGenericChoiceSeqOfAsnWrite(ptr -> seq_id, (AsnWriteFunc) SeqIdAsnWrite, aip, ID2_REPLY_GET_SEQ_ID_seq_id, ID2_REPLY_GET_SEQ_ID_seq_id_E);
+!    av.boolvalue = ptr -> end_of_reply;
+!    retval = AsnWrite(aip, REPLY_GET_SEQ_ID_end_of_reply,  &av);
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+        goto erret;
+     }
+--- 3583,3592 ----
+        }
+     }
+     AsnGenericChoiceSeqOfAsnWrite(ptr -> seq_id, (AsnWriteFunc) SeqIdAsnWrite, aip, ID2_REPLY_GET_SEQ_ID_seq_id, ID2_REPLY_GET_SEQ_ID_seq_id_E);
+!    if (ptr -> end_of_reply) {
+!       av.boolvalue = ptr -> end_of_reply;
+!       retval = AsnWrite(aip, REPLY_GET_SEQ_ID_end_of_reply,  &av);
+!    }
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+        goto erret;
+     }
+*************** ID2ReplyGetBlobIdAsnRead(AsnIoPtr aip, A
+*** 3707,3713 ****
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = av.boolvalue;
+        atp = AsnReadId(aip,amp, atp);
+     }
+     if (atp == REPLY_GET_BLOB_ID_blob_state) {
+--- 3715,3721 ----
+        if ( AsnReadVal(aip, atp, &av) <= 0) {
+           goto erret;
+        }
+!       ptr -> end_of_reply = TRUE;
+        atp = AsnReadId(aip,amp, atp);
+     }
+     if (atp == REPLY_GET_BLOB_ID_blob_state) {
+*************** ID2ReplyGetBlobIdAsnWrite(ID2ReplyGetBlo
+*** 3781,3788 ****
+     av.intvalue = ptr -> split_version;
+     retval = AsnWrite(aip, GET_BLOB_ID_split_version,  &av);
+     AsnGenericUserSeqOfAsnWrite(ptr -> annot_info, (AsnWriteFunc) ID2SSeqAnnotInfoAsnWrite, aip, REPLY_GET_BLOB_ID_annot_info, REPLY_GET_BLOB_ID_annot_info_E);
+!    av.boolvalue = ptr -> end_of_reply;
+!    retval = AsnWrite(aip, REPLY_GET_BLOB_ID_end_of_reply,  &av);
+     av.intvalue = ptr -> blob_state;
+     retval = AsnWrite(aip, REPLY_GET_BLOB_ID_blob_state,  &av);
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+--- 3789,3798 ----
+     av.intvalue = ptr -> split_version;
+     retval = AsnWrite(aip, GET_BLOB_ID_split_version,  &av);
+     AsnGenericUserSeqOfAsnWrite(ptr -> annot_info, (AsnWriteFunc) ID2SSeqAnnotInfoAsnWrite, aip, REPLY_GET_BLOB_ID_annot_info, REPLY_GET_BLOB_ID_annot_info_E);
+!    if (ptr -> end_of_reply) {
+!       av.boolvalue = ptr -> end_of_reply;
+!       retval = AsnWrite(aip, REPLY_GET_BLOB_ID_end_of_reply,  &av);
+!    }
+     av.intvalue = ptr -> blob_state;
+     retval = AsnWrite(aip, REPLY_GET_BLOB_ID_blob_state,  &av);
+     if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
diff --git a/network/id2arch/makefile b/network/id2arch/makefile
index 8e095f75..26df2322 100644
--- a/network/id2arch/makefile
+++ b/network/id2arch/makefile
@@ -32,6 +32,7 @@ id2.c id2gen.h: id2.l id2.h all.l seqsplit.l
 	$(CODEGEN) -i id2map.h -l id2.l,seqsplit.l,all.l -o id2gen -d .
 	cat id2gen.c | grep -v "^ *\* *Generated" > id2.c && rm -f id2gen.c
 	cat id2gen.h | grep -v "^ *\* *Generated" > x     && mv x id2gen.h
+	@patch id2.c <id2.patch
 
 id2.l : id2.asn
 	$(ASNTOOL) -m id2.asn -l x.h
@@ -52,6 +53,7 @@ all.l :
 id2.h : id2.asn
 	$(ASNTOOL) -m id2.asn -o id2.h
 	cat id2.h | grep -v "^ *\* *Generated" >x && mv x id2.h
+
 seqsplit.h : seqsplit.asn
 	$(ASNTOOL) -m seqsplit.asn -o seqsplit.h
 
diff --git a/network/id2arch/seqsplit.asn b/network/id2arch/seqsplit.asn
index e64745f8..d1b24322 100644
--- a/network/id2arch/seqsplit.asn
+++ b/network/id2arch/seqsplit.asn
@@ -1,4 +1,4 @@
---$Revision: 1.9 $
+--$Revision: 1.10 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -114,7 +114,8 @@ ID2S-Seq-annot-place-Info ::= SEQUENCE {
 ID2S-Seq-feat-Ids-Info ::= SEQUENCE {
         feat-types      SET OF ID2S-Feat-type-Info OPTIONAL,
         xref-types      SET OF ID2S-Feat-type-Info OPTIONAL,
-        local-ids       SET OF INTEGER OPTIONAL
+        local-ids       SET OF INTEGER OPTIONAL,
+        local-str-ids   SET OF VisibleString OPTIONAL
 }