/* objmime.c * =========================================================================== * * 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. * * =========================================================================== * * File Name: objmime.c * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * $Log: objmime.c,v $ * Revision 6.11 2001/11/21 16:38:23 thiessen * move cn3d stuff into bundle * * Revision 6.10 2001/11/21 14:25:41 thiessen * remove BisotrucOrId * * Revision 6.9 2001/11/20 15:59:34 thiessen * add imports to BundleSeqsAligns * * Revision 6.8 2001/11/16 14:54:26 thiessen * add new general type * * Revision 6.7 2001/06/21 14:44:29 thiessen * add new user annotations * * Revision 6.6 2001/06/14 14:21:32 thiessen * add style dictionary to mime blobs * * Revision 6.5 1999/09/16 17:12:02 ywang * use SeqAnnotSetAsnRead/Write to replace AsnGenericUserSeqOfAsnRead/Write to remove problem with seqannotset * * Revision 6.4 1998/12/07 16:29:28 ywang * add object loaded for mime type Biostruc-seqs * * ========================================================================== */ #include #define NLM_GENERATED_CODE_PROTO /* hand change add include --- lyg */ #include #include static Boolean loaded = FALSE; /*hand change from ncbimime.h -- lyg & yanli */ #include #ifndef NLM_EXTERN_LOADS #define NLM_EXTERN_LOADS {} #endif NLM_EXTERN Boolean LIBCALL objmimeAsnLoad(void) { if ( ! loaded) { NLM_EXTERN_LOADS if ( ! AsnLoad ()) return FALSE; loaded = TRUE; } return TRUE; } /************************************************** * Generated object loaders for Module NCBI-Mime * Generated using ASNCODE Revision: 6.5 at Dec 4, 1998 2:11 PM * **************************************************/ /************************************************** * * NcbiMimeAsn1Free() * **************************************************/ NLM_EXTERN NcbiMimeAsn1Ptr LIBCALL NcbiMimeAsn1Free(ValNodePtr anp) { Pointer pnt; if (anp == NULL) { return NULL; } pnt = anp->data.ptrvalue; switch (anp->choice) { default: break; case NcbiMimeAsn1_entrez: EntrezGeneralFree(anp -> data.ptrvalue); break; case NcbiMimeAsn1_alignstruc: BiostrucAlignFree(anp -> data.ptrvalue); break; case NcbiMimeAsn1_alignseq: BiostrucAlignSeqFree(anp -> data.ptrvalue); break; case NcbiMimeAsn1_strucseq: BiostrucSeqFree(anp -> data.ptrvalue); break; case NcbiMimeAsn1_strucseqs: BiostrucSeqsFree(anp -> data.ptrvalue); break; case NcbiMimeAsn1_general: BiostrucSeqsAlignsCddFree(anp -> data.ptrvalue); break; } return MemFree(anp); } /************************************************** * * NcbiMimeAsn1AsnRead() * **************************************************/ NLM_EXTERN NcbiMimeAsn1Ptr LIBCALL NcbiMimeAsn1AsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; ValNodePtr anp; Uint1 choice; Boolean isError = FALSE; Boolean nullIsError = FALSE; AsnReadFunc func; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* NcbiMimeAsn1 ::= (self contained) */ atp = AsnReadId(aip, amp, NCBI_MIME_ASN1); } else { atp = AsnLinkType(orig, NCBI_MIME_ASN1); /* link in local tree */ } if (atp == NULL) { return NULL; } anp = ValNodeNew(NULL); if (anp == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */ goto erret; } func = NULL; atp = AsnReadId(aip, amp, atp); /* find the choice */ if (atp == NULL) { goto erret; } if (atp == NCBI_MIME_ASN1_entrez) { choice = NcbiMimeAsn1_entrez; func = (AsnReadFunc) EntrezGeneralAsnRead; } else if (atp == NCBI_MIME_ASN1_alignstruc) { choice = NcbiMimeAsn1_alignstruc; func = (AsnReadFunc) BiostrucAlignAsnRead; } else if (atp == NCBI_MIME_ASN1_alignseq) { choice = NcbiMimeAsn1_alignseq; func = (AsnReadFunc) BiostrucAlignSeqAsnRead; } else if (atp == NCBI_MIME_ASN1_strucseq) { choice = NcbiMimeAsn1_strucseq; func = (AsnReadFunc) BiostrucSeqAsnRead; } else if (atp == NCBI_MIME_ASN1_strucseqs) { choice = NcbiMimeAsn1_strucseqs; func = (AsnReadFunc) BiostrucSeqsAsnRead; } else if (atp == NCBI_MIME_ASN1_general) { choice = NcbiMimeAsn1_general; func = (AsnReadFunc) BiostrucSeqsAlignsCddAsnRead; } anp->choice = choice; if (func != NULL) { anp->data.ptrvalue = (* func)(aip, atp); if (aip -> io_failure) goto erret; if (nullIsError && anp->data.ptrvalue == NULL) { goto erret; } } ret: AsnUnlinkType(orig); /* unlink local tree */ return anp; erret: anp = MemFree(anp); aip -> io_failure = TRUE; goto ret; } /************************************************** * * NcbiMimeAsn1AsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL NcbiMimeAsn1AsnWrite(NcbiMimeAsn1Ptr anp, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, writetype = NULL; Pointer pnt; AsnWriteFunc func = NULL; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, NCBI_MIME_ASN1); /* link local tree */ if (atp == NULL) { return FALSE; } if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } av.ptrvalue = (Pointer)anp; if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) { goto erret; } pnt = anp->data.ptrvalue; switch (anp->choice) { case NcbiMimeAsn1_entrez: writetype = NCBI_MIME_ASN1_entrez; func = (AsnWriteFunc) EntrezGeneralAsnWrite; break; case NcbiMimeAsn1_alignstruc: writetype = NCBI_MIME_ASN1_alignstruc; func = (AsnWriteFunc) BiostrucAlignAsnWrite; break; case NcbiMimeAsn1_alignseq: writetype = NCBI_MIME_ASN1_alignseq; func = (AsnWriteFunc) BiostrucAlignSeqAsnWrite; break; case NcbiMimeAsn1_strucseq: writetype = NCBI_MIME_ASN1_strucseq; func = (AsnWriteFunc) BiostrucSeqAsnWrite; break; case NcbiMimeAsn1_strucseqs: writetype = NCBI_MIME_ASN1_strucseqs; func = (AsnWriteFunc) BiostrucSeqsAsnWrite; break; case NcbiMimeAsn1_general: writetype = NCBI_MIME_ASN1_general; func = (AsnWriteFunc) BiostrucSeqsAlignsCddAsnWrite; break; } if (writetype != NULL) { retval = (* func)(pnt, aip, writetype); /* write it out */ } if (!retval) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * EntrezGeneralNew() * **************************************************/ NLM_EXTERN EntrezGeneralPtr LIBCALL EntrezGeneralNew(void) { EntrezGeneralPtr ptr = MemNew((size_t) sizeof(EntrezGeneral)); return ptr; } /************************************************** * * EntrezGeneralFree() * **************************************************/ NLM_EXTERN EntrezGeneralPtr LIBCALL EntrezGeneralFree(EntrezGeneralPtr ptr) { if(ptr == NULL) { return NULL; } MemFree(ptr -> title); Data_dataFree(ptr -> Data_data); MemFree(ptr -> location); return MemFree(ptr); } /************************************************** * * Data_dataFree() * **************************************************/ static Data_dataPtr LIBCALL Data_dataFree(ValNodePtr anp) { Pointer pnt; if (anp == NULL) { return NULL; } pnt = anp->data.ptrvalue; switch (anp->choice) { default: break; case Data_data_ml: MedlineEntryFree(anp -> data.ptrvalue); break; case Data_data_prot: SeqEntryFree(anp -> data.ptrvalue); break; case Data_data_nuc: SeqEntryFree(anp -> data.ptrvalue); break; case Data_data_genome: SeqEntryFree(anp -> data.ptrvalue); break; case Data_data_structure: BiostrucFree(anp -> data.ptrvalue); break; case Data_data_strucAnnot: BiostrucAnnotSetFree(anp -> data.ptrvalue); break; } return MemFree(anp); } /************************************************** * * EntrezGeneralAsnRead() * **************************************************/ NLM_EXTERN EntrezGeneralPtr LIBCALL EntrezGeneralAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; EntrezGeneralPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* EntrezGeneral ::= (self contained) */ atp = AsnReadId(aip, amp, ENTREZ_GENERAL); } else { atp = AsnLinkType(orig, ENTREZ_GENERAL); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = EntrezGeneralNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == ENTREZ_GENERAL_title) { if ( AsnReadVal(aip, atp, &av) <= 0) { goto erret; } ptr -> title = av.ptrvalue; atp = AsnReadId(aip,amp, atp); } if (atp == ENTREZ_GENERAL_data) { ptr -> Data_data = Data_dataAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == ENTREZ_GENERAL_style) { if ( AsnReadVal(aip, atp, &av) <= 0) { goto erret; } ptr -> style = av.intvalue; atp = AsnReadId(aip,amp, atp); } if (atp == ENTREZ_GENERAL_location) { if ( AsnReadVal(aip, atp, &av) <= 0) { goto erret; } ptr -> location = av.ptrvalue; atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = EntrezGeneralFree(ptr); goto ret; } /************************************************** * * Data_dataAsnRead() * **************************************************/ static Data_dataPtr LIBCALL Data_dataAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; ValNodePtr anp; Uint1 choice; Boolean isError = FALSE; Boolean nullIsError = FALSE; AsnReadFunc func; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* Data_data ::= (self contained) */ atp = AsnReadId(aip, amp, ENTREZ_GENERAL_data); } else { atp = AsnLinkType(orig, ENTREZ_GENERAL_data); /* link in local tree */ } if (atp == NULL) { return NULL; } anp = ValNodeNew(NULL); if (anp == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */ goto erret; } func = NULL; atp = AsnReadId(aip, amp, atp); /* find the choice */ if (atp == NULL) { goto erret; } if (atp == ENTREZ_GENERAL_data_ml) { choice = Data_data_ml; func = (AsnReadFunc) MedlineEntryAsnRead; } else if (atp == ENTREZ_GENERAL_data_prot) { choice = Data_data_prot; func = (AsnReadFunc) SeqEntryAsnRead; } else if (atp == ENTREZ_GENERAL_data_nuc) { choice = Data_data_nuc; func = (AsnReadFunc) SeqEntryAsnRead; } else if (atp == ENTREZ_GENERAL_data_genome) { choice = Data_data_genome; func = (AsnReadFunc) SeqEntryAsnRead; } else if (atp == ENTREZ_GENERAL_data_structure) { choice = Data_data_structure; func = (AsnReadFunc) BiostrucAsnRead; } else if (atp == ENTREZ_GENERAL_data_strucAnnot) { choice = Data_data_strucAnnot; func = (AsnReadFunc) BiostrucAnnotSetAsnRead; } anp->choice = choice; if (func != NULL) { anp->data.ptrvalue = (* func)(aip, atp); if (aip -> io_failure) goto erret; if (nullIsError && anp->data.ptrvalue == NULL) { goto erret; } } ret: AsnUnlinkType(orig); /* unlink local tree */ return anp; erret: anp = MemFree(anp); aip -> io_failure = TRUE; goto ret; } /************************************************** * * EntrezGeneralAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL EntrezGeneralAsnWrite(EntrezGeneralPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, ENTREZ_GENERAL); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } if (ptr -> title != NULL) { av.ptrvalue = ptr -> title; retval = AsnWrite(aip, ENTREZ_GENERAL_title, &av); } if (ptr -> Data_data != NULL) { if ( ! Data_dataAsnWrite(ptr -> Data_data, aip, ENTREZ_GENERAL_data)) { goto erret; } } av.intvalue = ptr -> style; retval = AsnWrite(aip, ENTREZ_GENERAL_style, &av); if (ptr -> location != NULL) { av.ptrvalue = ptr -> location; retval = AsnWrite(aip, ENTREZ_GENERAL_location, &av); } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * Data_dataAsnWrite() * **************************************************/ static Boolean LIBCALL Data_dataAsnWrite(Data_dataPtr anp, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, writetype = NULL; Pointer pnt; AsnWriteFunc func = NULL; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, ENTREZ_GENERAL_data); /* link local tree */ if (atp == NULL) { return FALSE; } if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } av.ptrvalue = (Pointer)anp; if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) { goto erret; } pnt = anp->data.ptrvalue; switch (anp->choice) { case Data_data_ml: writetype = ENTREZ_GENERAL_data_ml; func = (AsnWriteFunc) MedlineEntryAsnWrite; break; case Data_data_prot: writetype = ENTREZ_GENERAL_data_prot; func = (AsnWriteFunc) SeqEntryAsnWrite; break; case Data_data_nuc: writetype = ENTREZ_GENERAL_data_nuc; func = (AsnWriteFunc) SeqEntryAsnWrite; break; case Data_data_genome: writetype = ENTREZ_GENERAL_data_genome; func = (AsnWriteFunc) SeqEntryAsnWrite; break; case Data_data_structure: writetype = ENTREZ_GENERAL_data_structure; func = (AsnWriteFunc) BiostrucAsnWrite; break; case Data_data_strucAnnot: writetype = ENTREZ_GENERAL_data_strucAnnot; func = (AsnWriteFunc) BiostrucAnnotSetAsnWrite; break; } if (writetype != NULL) { retval = (* func)(pnt, aip, writetype); /* write it out */ } if (!retval) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BiostrucAlignNew() * **************************************************/ NLM_EXTERN BiostrucAlignPtr LIBCALL BiostrucAlignNew(void) { BiostrucAlignPtr ptr = MemNew((size_t) sizeof(BiostrucAlign)); return ptr; } /************************************************** * * BiostrucAlignFree() * **************************************************/ NLM_EXTERN BiostrucAlignPtr LIBCALL BiostrucAlignFree(BiostrucAlignPtr ptr) { if(ptr == NULL) { return NULL; } BiostrucFree(ptr -> master); AsnGenericUserSeqOfFree(ptr -> slaves, (AsnOptFreeFunc) BiostrucFree); BiostrucAnnotSetFree(ptr -> alignments); AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree); AsnGenericUserSeqOfFree(ptr -> seqalign, (AsnOptFreeFunc) SeqAnnotFree); Cn3dStyleDictionaryFree(ptr -> style_dictionary); /* paul */ Cn3dUserAnnotationsFree(ptr -> user_annotations); return MemFree(ptr); } /************************************************** * * BiostrucAlignAsnRead() * **************************************************/ NLM_EXTERN BiostrucAlignPtr LIBCALL BiostrucAlignAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BiostrucAlignPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BiostrucAlign ::= (self contained) */ atp = AsnReadId(aip, amp, BIOSTRUC_ALIGN); } else { atp = AsnLinkType(orig, BIOSTRUC_ALIGN); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BiostrucAlignNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == BIOSTRUC_ALIGN_master) { ptr -> master = BiostrucAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_slaves) { ptr -> slaves = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) BiostrucAsnRead, (AsnOptFreeFunc) BiostrucFree); if (isError && ptr -> slaves == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_alignments) { ptr -> alignments = BiostrucAnnotSetAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_sequences) { ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree); if (isError && ptr -> sequences == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_seqalign) { /* ptr -> seqalign = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree); if (isError && ptr -> seqalign == NULL) { goto erret; } */ /* yanli comment this out, add the following, Sept. 16, 1999 */ ptr -> seqalign = SeqAnnotSetAsnRead(aip, BIOSTRUC_ALIGN_seqalign, BIOSTRUC_ALIGN_seqalign_E); atp = AsnReadId(aip,amp, atp); } /* paul */ if (atp == BIOSTRUC_ALIGN_style_dictionary) { ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_user_annotations) { ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BiostrucAlignFree(ptr); goto ret; } /************************************************** * * BiostrucAlignAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BiostrucAlignAsnWrite(BiostrucAlignPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BIOSTRUC_ALIGN); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } if (ptr -> master != NULL) { if ( ! BiostrucAsnWrite(ptr -> master, aip, BIOSTRUC_ALIGN_master)) { goto erret; } } AsnGenericUserSeqOfAsnWrite(ptr -> slaves, (AsnWriteFunc) BiostrucAsnWrite, aip, BIOSTRUC_ALIGN_slaves, BIOSTRUC_ALIGN_slaves_E); if (ptr -> alignments != NULL) { if ( ! BiostrucAnnotSetAsnWrite(ptr -> alignments, aip, BIOSTRUC_ALIGN_alignments)) { goto erret; } } AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BIOSTRUC_ALIGN_sequences, BIOSTRUC_ALIGN_sequences_E); /* AsnGenericUserSeqOfAsnWrite(ptr -> seqalign, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BIOSTRUC_ALIGN_seqalign, BIOSTRUC_ALIGN_seqalign_E); */ /* yanli comment it out, and add the following, Sept. 16, 1999 */ SeqAnnotSetAsnWrite(ptr -> seqalign, aip, BIOSTRUC_ALIGN_seqalign, BIOSTRUC_ALIGN_seqalign_E); /* paul */ if (ptr -> style_dictionary != NULL) { if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, BIOSTRUC_ALIGN_style_dictionary)) { goto erret; } } if (ptr -> user_annotations != NULL) { if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, BIOSTRUC_ALIGN_user_annotations)) { goto erret; } } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BiostrucAlignSeqNew() * **************************************************/ NLM_EXTERN BiostrucAlignSeqPtr LIBCALL BiostrucAlignSeqNew(void) { BiostrucAlignSeqPtr ptr = MemNew((size_t) sizeof(BiostrucAlignSeq)); return ptr; } /************************************************** * * BiostrucAlignSeqFree() * **************************************************/ NLM_EXTERN BiostrucAlignSeqPtr LIBCALL BiostrucAlignSeqFree(BiostrucAlignSeqPtr ptr) { if(ptr == NULL) { return NULL; } AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree); AsnGenericUserSeqOfFree(ptr -> seqalign, (AsnOptFreeFunc) SeqAnnotFree); Cn3dStyleDictionaryFree(ptr -> style_dictionary); /* paul */ Cn3dUserAnnotationsFree(ptr -> user_annotations); return MemFree(ptr); } /************************************************** * * BiostrucAlignSeqAsnRead() * **************************************************/ NLM_EXTERN BiostrucAlignSeqPtr LIBCALL BiostrucAlignSeqAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BiostrucAlignSeqPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BiostrucAlignSeq ::= (self contained) */ atp = AsnReadId(aip, amp, BIOSTRUC_ALIGN_SEQ); } else { atp = AsnLinkType(orig, BIOSTRUC_ALIGN_SEQ); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BiostrucAlignSeqNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == BIOSTRUC_ALIGN_SEQ_sequences) { ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree); if (isError && ptr -> sequences == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_SEQ_seqalign) { /* ptr -> seqalign = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree); if (isError && ptr -> seqalign == NULL) { goto erret; } */ /* yanli comment this out, and add the following, Sept. 16, 1999 */ ptr -> seqalign = SeqAnnotSetAsnRead(aip, BIOSTRUC_ALIGN_SEQ_seqalign, BIOSTRUC_ALIGN_SEQ_seqalign_E); atp = AsnReadId(aip,amp, atp); } /* paul */ if (atp == ALIGN_SEQ_style_dictionary) { ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_user_annotations) { ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BiostrucAlignSeqFree(ptr); goto ret; } /************************************************** * * BiostrucAlignSeqAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BiostrucAlignSeqAsnWrite(BiostrucAlignSeqPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BIOSTRUC_ALIGN_SEQ); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BIOSTRUC_ALIGN_SEQ_sequences, BIOSTRUC_ALIGN_SEQ_sequences_E); /* AsnGenericUserSeqOfAsnWrite(ptr -> seqalign, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BIOSTRUC_ALIGN_SEQ_seqalign, BIOSTRUC_ALIGN_SEQ_seqalign_E); */ /* yanli comment it out, and add the following, Sept. 16, 1999 */ SeqAnnotSetAsnWrite(ptr -> seqalign, aip, BIOSTRUC_ALIGN_SEQ_seqalign, BIOSTRUC_ALIGN_SEQ_seqalign_E); /* paul */ if (ptr -> style_dictionary != NULL) { if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, ALIGN_SEQ_style_dictionary)) { goto erret; } } if (ptr -> user_annotations != NULL) { if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, BIOSTRUC_ALIGN_user_annotations)) { goto erret; } } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BiostrucSeqNew() * **************************************************/ NLM_EXTERN BiostrucSeqPtr LIBCALL BiostrucSeqNew(void) { BiostrucSeqPtr ptr = MemNew((size_t) sizeof(BiostrucSeq)); return ptr; } /************************************************** * * BiostrucSeqFree() * **************************************************/ NLM_EXTERN BiostrucSeqPtr LIBCALL BiostrucSeqFree(BiostrucSeqPtr ptr) { if(ptr == NULL) { return NULL; } BiostrucFree(ptr -> structure); AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree); Cn3dStyleDictionaryFree(ptr -> style_dictionary); /* paul */ Cn3dUserAnnotationsFree(ptr -> user_annotations); return MemFree(ptr); } /************************************************** * * BiostrucSeqAsnRead() * **************************************************/ NLM_EXTERN BiostrucSeqPtr LIBCALL BiostrucSeqAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BiostrucSeqPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BiostrucSeq ::= (self contained) */ atp = AsnReadId(aip, amp, BIOSTRUC_SEQ); } else { atp = AsnLinkType(orig, BIOSTRUC_SEQ); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BiostrucSeqNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == BIOSTRUC_SEQ_structure) { ptr -> structure = BiostrucAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_SEQ_sequences) { ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree); if (isError && ptr -> sequences == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } /* paul */ if (atp == BIOSTRUC_SEQ_style_dictionary) { ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_user_annotations) { ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BiostrucSeqFree(ptr); goto ret; } /************************************************** * * BiostrucSeqAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BiostrucSeqAsnWrite(BiostrucSeqPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BIOSTRUC_SEQ); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } if (ptr -> structure != NULL) { if ( ! BiostrucAsnWrite(ptr -> structure, aip, BIOSTRUC_SEQ_structure)) { goto erret; } } AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BIOSTRUC_SEQ_sequences, BIOSTRUC_SEQ_sequences_E); /* paul */ if (ptr -> style_dictionary != NULL) { if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, BIOSTRUC_SEQ_style_dictionary)) { goto erret; } } if (ptr -> user_annotations != NULL) { if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, BIOSTRUC_ALIGN_user_annotations)) { goto erret; } } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BiostrucSeqsNew() * **************************************************/ NLM_EXTERN BiostrucSeqsPtr LIBCALL BiostrucSeqsNew(void) { BiostrucSeqsPtr ptr = MemNew((size_t) sizeof(BiostrucSeqs)); return ptr; } /************************************************** * * BiostrucSeqsFree() * **************************************************/ NLM_EXTERN BiostrucSeqsPtr LIBCALL BiostrucSeqsFree(BiostrucSeqsPtr ptr) { if(ptr == NULL) { return NULL; } BiostrucFree(ptr -> structure); AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree); AsnGenericUserSeqOfFree(ptr -> seqalign, (AsnOptFreeFunc) SeqAnnotFree); Cn3dStyleDictionaryFree(ptr -> style_dictionary); /* paul */ Cn3dUserAnnotationsFree(ptr -> user_annotations); return MemFree(ptr); } /************************************************** * * BiostrucSeqsAsnRead() * **************************************************/ NLM_EXTERN BiostrucSeqsPtr LIBCALL BiostrucSeqsAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BiostrucSeqsPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BiostrucSeqs ::= (self contained) */ atp = AsnReadId(aip, amp, BIOSTRUC_SEQS); } else { atp = AsnLinkType(orig, BIOSTRUC_SEQS); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BiostrucSeqsNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == BIOSTRUC_SEQS_structure) { ptr -> structure = BiostrucAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_SEQS_sequences) { ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree); if (isError && ptr -> sequences == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_SEQS_seqalign) { /* ptr -> seqalign = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree); if (isError && ptr -> seqalign == NULL) { goto erret; } */ /* yanli comment it out, add following, Sept. 16, 1999 */ ptr -> seqalign = SeqAnnotSetAsnRead(aip, BIOSTRUC_SEQS_seqalign, BIOSTRUC_SEQS_seqalign_E); atp = AsnReadId(aip,amp, atp); } /* paul */ if (atp == BIOSTRUC_SEQS_style_dictionary) { ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BIOSTRUC_ALIGN_user_annotations) { ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BiostrucSeqsFree(ptr); goto ret; } /************************************************** * * BiostrucSeqsAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BiostrucSeqsAsnWrite(BiostrucSeqsPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BIOSTRUC_SEQS); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } if (ptr -> structure != NULL) { if ( ! BiostrucAsnWrite(ptr -> structure, aip, BIOSTRUC_SEQS_structure)) { goto erret; } } AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BIOSTRUC_SEQS_sequences, BIOSTRUC_SEQS_sequences_E); /* AsnGenericUserSeqOfAsnWrite(ptr -> seqalign, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BIOSTRUC_SEQS_seqalign, BIOSTRUC_SEQS_seqalign_E); */ /* yanli comment this out, and the following, Sept. 16, 1998 */ SeqAnnotSetAsnWrite(ptr -> seqalign, aip, BIOSTRUC_SEQS_seqalign, BIOSTRUC_SEQS_seqalign_E); /* paul */ if (ptr -> style_dictionary != NULL) { if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, BIOSTRUC_SEQS_style_dictionary)) { goto erret; } } if (ptr -> user_annotations != NULL) { if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, BIOSTRUC_ALIGN_user_annotations)) { goto erret; } } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BiostrucSeqsAlignsCddNew() * **************************************************/ NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddNew(void) { BiostrucSeqsAlignsCddPtr ptr = MemNew((size_t) sizeof(BiostrucSeqsAlignsCdd)); return ptr; } /************************************************** * * BiostrucSeqsAlignsCddFree() * **************************************************/ NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddFree(BiostrucSeqsAlignsCddPtr ptr) { if(ptr == NULL) { return NULL; } SeqAlignData_seq_align_dataFree(ptr -> SeqAlignData_seq_align_data); AsnGenericUserSeqOfFree(ptr -> structures, (AsnOptFreeFunc) BiostrucFree); return MemFree(ptr); } /************************************************** * * SeqAlignData_seq_align_dataFree() * **************************************************/ static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree(ValNodePtr anp) { Pointer pnt; if (anp == NULL) { return NULL; } pnt = anp->data.ptrvalue; switch (anp->choice) { default: break; case SeqAlignData_seq_align_data_bundle: BundleSeqsAlignsFree(anp -> data.ptrvalue); break; case SeqAlignData_seq_align_data_cdd: CddFree(anp -> data.ptrvalue); break; } return MemFree(anp); } /************************************************** * * BiostrucSeqsAlignsCddAsnRead() * **************************************************/ NLM_EXTERN BiostrucSeqsAlignsCddPtr LIBCALL BiostrucSeqsAlignsCddAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BiostrucSeqsAlignsCddPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BiostrucSeqsAlignsCdd ::= (self contained) */ atp = AsnReadId(aip, amp, BIOSTRUC_SEQS_ALIGNS_CDD); } else { atp = AsnLinkType(orig, BIOSTRUC_SEQS_ALIGNS_CDD); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BiostrucSeqsAlignsCddNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == SEQS_ALIGNS_CDD_seq_align_data) { ptr -> SeqAlignData_seq_align_data = SeqAlignData_seq_align_dataAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == SEQS_ALIGNS_CDD_structures) { ptr -> structures = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) BiostrucAsnRead, (AsnOptFreeFunc) BiostrucFree); if (isError && ptr -> structures == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BiostrucSeqsAlignsCddFree(ptr); goto ret; } /************************************************** * * SeqAlignData_seq_align_dataAsnRead() * **************************************************/ static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; ValNodePtr anp; Uint1 choice; Boolean isError = FALSE; Boolean nullIsError = FALSE; AsnReadFunc func; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* SeqAlignData_seq_align_data ::= (self contained) */ atp = AsnReadId(aip, amp, SEQS_ALIGNS_CDD_seq_align_data); } else { atp = AsnLinkType(orig, SEQS_ALIGNS_CDD_seq_align_data); /* link in local tree */ } if (atp == NULL) { return NULL; } anp = ValNodeNew(NULL); if (anp == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */ goto erret; } func = NULL; atp = AsnReadId(aip, amp, atp); /* find the choice */ if (atp == NULL) { goto erret; } if (atp == CDD_seq_align_data_bundle) { choice = SeqAlignData_seq_align_data_bundle; func = (AsnReadFunc) BundleSeqsAlignsAsnRead; } else if (atp == ALIGNS_CDD_seq_align_data_cdd) { choice = SeqAlignData_seq_align_data_cdd; func = (AsnReadFunc) CddAsnRead; } anp->choice = choice; if (func != NULL) { anp->data.ptrvalue = (* func)(aip, atp); if (aip -> io_failure) goto erret; if (nullIsError && anp->data.ptrvalue == NULL) { goto erret; } } ret: AsnUnlinkType(orig); /* unlink local tree */ return anp; erret: anp = MemFree(anp); aip -> io_failure = TRUE; goto ret; } /************************************************** * * BiostrucSeqsAlignsCddAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BiostrucSeqsAlignsCddAsnWrite(BiostrucSeqsAlignsCddPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BIOSTRUC_SEQS_ALIGNS_CDD); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } if (ptr -> SeqAlignData_seq_align_data != NULL) { if ( ! SeqAlignData_seq_align_dataAsnWrite(ptr -> SeqAlignData_seq_align_data, aip, SEQS_ALIGNS_CDD_seq_align_data)) { goto erret; } } AsnGenericUserSeqOfAsnWrite(ptr -> structures, (AsnWriteFunc) BiostrucAsnWrite, aip, SEQS_ALIGNS_CDD_structures, SEQS_ALIGNS_CDD_structures_E); if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * SeqAlignData_seq_align_dataAsnWrite() * **************************************************/ static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite(SeqAlignData_seq_align_dataPtr anp, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp, writetype = NULL; Pointer pnt; AsnWriteFunc func = NULL; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) return FALSE; } if (aip == NULL) return FALSE; atp = AsnLinkType(orig, SEQS_ALIGNS_CDD_seq_align_data); /* link local tree */ if (atp == NULL) { return FALSE; } if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } av.ptrvalue = (Pointer)anp; if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) { goto erret; } pnt = anp->data.ptrvalue; switch (anp->choice) { case SeqAlignData_seq_align_data_bundle: writetype = CDD_seq_align_data_bundle; func = (AsnWriteFunc) BundleSeqsAlignsAsnWrite; break; case SeqAlignData_seq_align_data_cdd: writetype = ALIGNS_CDD_seq_align_data_cdd; func = (AsnWriteFunc) CddAsnWrite; break; } if (writetype != NULL) { retval = (* func)(pnt, aip, writetype); /* write it out */ } if (!retval) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; } /************************************************** * * BundleSeqsAlignsNew() * **************************************************/ NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsNew(void) { BundleSeqsAlignsPtr ptr = MemNew((size_t) sizeof(BundleSeqsAligns)); return ptr; } /************************************************** * * BundleSeqsAlignsFree() * **************************************************/ NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsFree(BundleSeqsAlignsPtr ptr) { if(ptr == NULL) { return NULL; } AsnGenericChoiceSeqOfFree(ptr -> sequences, (AsnOptFreeFunc) SeqEntryFree); AsnGenericUserSeqOfFree(ptr -> seqaligns, (AsnOptFreeFunc) SeqAnnotFree); BiostrucAnnotSetFree(ptr -> strucaligns); AsnGenericUserSeqOfFree(ptr -> imports, (AsnOptFreeFunc) SeqAnnotFree); Cn3dStyleDictionaryFree(ptr -> style_dictionary); Cn3dUserAnnotationsFree(ptr -> user_annotations); return MemFree(ptr); } /************************************************** * * BundleSeqsAlignsAsnRead() * **************************************************/ NLM_EXTERN BundleSeqsAlignsPtr LIBCALL BundleSeqsAlignsAsnRead(AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean isError = FALSE; AsnReadFunc func; BundleSeqsAlignsPtr ptr; if (! loaded) { if (! objmimeAsnLoad()) { return NULL; } } if (aip == NULL) { return NULL; } if (orig == NULL) { /* BundleSeqsAligns ::= (self contained) */ atp = AsnReadId(aip, amp, BUNDLE_SEQS_ALIGNS); } else { atp = AsnLinkType(orig, BUNDLE_SEQS_ALIGNS); } /* link in local tree */ if (atp == NULL) { return NULL; } ptr = BundleSeqsAlignsNew(); if (ptr == NULL) { goto erret; } if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */ goto erret; } atp = AsnReadId(aip,amp, atp); func = NULL; if (atp == BUNDLE_SEQS_ALIGNS_sequences) { ptr -> sequences = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqEntryAsnRead, (AsnOptFreeFunc) SeqEntryFree); if (isError && ptr -> sequences == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BUNDLE_SEQS_ALIGNS_seqaligns) { ptr -> seqaligns = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree); if (isError && ptr -> seqaligns == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BUNDLE_SEQS_ALIGNS_strucaligns) { ptr -> strucaligns = BiostrucAnnotSetAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == BUNDLE_SEQS_ALIGNS_imports) { ptr -> imports = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqAnnotAsnRead, (AsnOptFreeFunc) SeqAnnotFree); if (isError && ptr -> imports == NULL) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == SEQS_ALIGNS_style_dictionary) { ptr -> style_dictionary = Cn3dStyleDictionaryAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (atp == SEQS_ALIGNS_user_annotations) { ptr -> user_annotations = Cn3dUserAnnotationsAsnRead(aip, atp); if (aip -> io_failure) { goto erret; } atp = AsnReadId(aip,amp, atp); } if (AsnReadVal(aip, atp, &av) <= 0) { goto erret; } /* end struct */ ret: AsnUnlinkType(orig); /* unlink local tree */ return ptr; erret: aip -> io_failure = TRUE; ptr = BundleSeqsAlignsFree(ptr); goto ret; } /************************************************** * * BundleSeqsAlignsAsnWrite() * **************************************************/ NLM_EXTERN Boolean LIBCALL BundleSeqsAlignsAsnWrite(BundleSeqsAlignsPtr ptr, AsnIoPtr aip, AsnTypePtr orig) { DataVal av; AsnTypePtr atp; Boolean retval = FALSE; if (! loaded) { if (! objmimeAsnLoad()) { return FALSE; } } if (aip == NULL) { return FALSE; } atp = AsnLinkType(orig, BUNDLE_SEQS_ALIGNS); /* link local tree */ if (atp == NULL) { return FALSE; } if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; } if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) { goto erret; } AsnGenericChoiceSeqOfAsnWrite(ptr -> sequences, (AsnWriteFunc) SeqEntryAsnWrite, aip, BUNDLE_SEQS_ALIGNS_sequences, BUNDLE_SEQS_ALIGNS_sequences_E); AsnGenericUserSeqOfAsnWrite(ptr -> seqaligns, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BUNDLE_SEQS_ALIGNS_seqaligns, BUNDLE_SEQS_ALIGNS_seqaligns_E); if (ptr -> strucaligns != NULL) { if ( ! BiostrucAnnotSetAsnWrite(ptr -> strucaligns, aip, BUNDLE_SEQS_ALIGNS_strucaligns)) { goto erret; } } AsnGenericUserSeqOfAsnWrite(ptr -> imports, (AsnWriteFunc) SeqAnnotAsnWrite, aip, BUNDLE_SEQS_ALIGNS_imports, BUNDLE_SEQS_ALIGNS_imports_E); if (ptr -> style_dictionary != NULL) { if ( ! Cn3dStyleDictionaryAsnWrite(ptr -> style_dictionary, aip, SEQS_ALIGNS_style_dictionary)) { goto erret; } } if (ptr -> user_annotations != NULL) { if ( ! Cn3dUserAnnotationsAsnWrite(ptr -> user_annotations, aip, SEQS_ALIGNS_user_annotations)) { goto erret; } } if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) { goto erret; } retval = TRUE; erret: AsnUnlinkType(orig); /* unlink local tree */ return retval; }