From 086a234ddca43622fd3e2db27a52d57db38462a7 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 9 Jun 2004 12:06:37 +0000
Subject: [PATCH] J2 version
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1642 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
corba/apollo.idl | 206 ++++++++++++++++
corba/ensembl.idl | 53 ++++
corba/nsdb.idl | 560 +++++++++++++++++++++++++++++++++++++++++++
corba/nsdb_write.idl | 260 ++++++++++++++++++++
corba/seqdb.idl | 131 ++++++++++
corba/types.idl | 334 ++++++++++++++++++++++++++
6 files changed, 1544 insertions(+)
create mode 100644 corba/apollo.idl
create mode 100644 corba/ensembl.idl
create mode 100644 corba/nsdb.idl
create mode 100644 corba/nsdb_write.idl
create mode 100644 corba/seqdb.idl
create mode 100644 corba/types.idl
diff --git a/corba/apollo.idl b/corba/apollo.idl
new file mode 100644
index 000000000..49b097261
--- /dev/null
+++ b/corba/apollo.idl
@@ -0,0 +1,206 @@
+// Apollo transport layer
+// all syntax subject to change
+// typedef sequence <Xxx> XxxList assumed
+// maybe some of the paramsets should be
+// more strongly typed
+//
+// Ewan Birney and Chris Mungall. Apollo list apollo@ebi.ac.uk
+//
+
+module Apollo {
+
+ exception NotSupported { string reason; }; // more exceptions to come
+ exception ProcessError { string reason; };
+ exception OutOfRange { string reason; };
+ exception NeedsUpdate { string reason;};
+
+ struct Param {
+ string name;
+ string value;
+ };
+ typedef sequence <Param> ParamList;
+
+ // use a enum for unit (%, ratio, etc)?
+ struct Score {
+ string type;
+ string value;
+ // EB - lets also have this as a number. Clients have to figure out by the
+ // type.
+ double double_value;
+ };
+ typedef sequence <Score> ScoreList;
+
+ // we should abstract out identifier aspects into
+ // a seperate struct - that way we can attach this to
+ // any kind of object
+ struct Identifier {
+ string name; //main display label
+ string description; //detailed desc
+ sequence <string> synonyms;
+ // DbXrefList dbxrefs;
+ };
+ typedef sequence <Identifier> IdentifierList;
+
+
+ enum StrandType { plus, minus};
+ // a range can be attached to any seq-featurey object
+ struct Range {
+ long range_min;
+ long range_max;
+ StrandType strand;
+ };
+
+
+ struct ResultSpan {
+ string result_id;
+ ScoreList scores;
+ Range range1;
+ Range range2;
+ };
+ typedef sequence<ResultSpan> ResultSpanList;
+
+
+ // any kind of analysis result or alignment
+ // (genscan-gene, genscan-exon, sim4exonset, sim4exon, blasthit,
+ // blast-hsp, etc)
+ struct ResultSet {
+ string result_id;
+ ScoreList scores;
+ string type;
+ ResultSpanList ResultSpans; // eg hsps for a blast hit
+ Range range1; // eg query start/end
+ Range range2; // eg subject start/end
+ };
+ typedef sequence <ResultSet> ResultSetList;
+
+
+
+ // Evidence is one of the Result lists
+ typedef string Evidence;
+
+ typedef sequence <Evidence> EvidenceList;
+
+ // collection of analysis results
+ struct Analysis {
+ // eg Blast, Pfam
+ string program;
+ ParamList parameters;
+ ResultList results;
+ };
+ typedef sequence <Analysis> AnalysisList;
+
+ // Annotation Comments etc
+
+
+ struct Person {
+ string readable_name;
+ string person_id;
+ }
+
+ typedef long TimeStamp;
+
+
+ struct Comment {
+ string comment_id;
+ string text;
+ Person person;
+ TimeStamp time;
+ };
+ typedef sequence<Comment> CommentList;
+
+
+
+ // Design decision: most of these inherit from a notional seqfeature
+ // superclass - do we (1) merge them into a single struct, with
+ // the seqfeature struct having 'type' and contained-seqfeatures
+ // or (2) have distinct structs and delegate out the commonalities.
+ // i chose the latter, with all the strcuts having a Range attribute
+
+
+ // to fetch the sequence for a gene, it has to be spliced
+ // from the exons
+ struct Exon {
+ Identifier ident;
+ Range range;
+ EvidenceList evidence_list;
+ };
+
+ typedef sequence <Exon> ExonList;
+
+ struct Transcript {
+ Identifier ident;
+ ExonList exons;
+ Range cds_Range; // start/end of translation
+ // note we don't need range including UTR, its implicit from exons
+ EvidenceList evidence_list;
+ CommentList comments;
+ };
+ typedef sequence <Transcript> TranscriptList;
+
+ enum GeneType { PROTEIN_CODING_GENE, TRNA_GENE, TRANSPOSON_GENE };
+
+ // Where does silly text annotation go?
+ struct AnnotatedGene {
+ GeneType type;
+ Identifier ident;
+ TranscriptList transcripts;
+ CommentList comments;
+ };
+ typedef sequence <AnnotatedGene> AnnotatedGeneList;
+
+ struct GenericAnnotation {
+ Identifier ident;
+ string type;
+ ParamList qualifiers;
+ CommentList comments;
+ Range range;
+ EvidenceList evidence_list;
+ };
+
+ typedef sequence <GenericAnnotation> GenericAnnotationList;
+
+
+
+ // collection of annotations and analyses on
+ // a particular piece of sequence
+ // (could be a clone, a contig , a scaffold (order&oriented contigs), an
+ // arbitrary slice of a scaffold, a chromosome, etc)
+ interface AnnotatedRegion {
+ // bind sequence here
+ string sequence_as_string();
+ string sequence_region_as_string(in long start,in long end)
+ raises ( OutOfRange );
+
+ // gets
+ AnalysisList get_analysis_list() raises ( ProcessError ) ;
+ AnnotatedGeneList get_gene_list() raises (ProcessError);
+ GenericAnnotation get_generic_annotation() raises (ProcessError);
+
+
+ // sets
+ void save_AnnotatedGenes(in AnnotatedGeneList new,
+ in AnnotatedGeneList updated,
+ in AnnotatedGeneList dead)
+ raises (NeedsUpdate, ProcessError,OutOfRange);
+
+ void save_GenericAnnotation(in GenericAnnotationList new,
+ in GenericAnnotationList updated,
+ in GenericAnnotationList dead)
+ raises (NeedsUpdate, ProcessError, OutOfRange );
+ };
+
+ // session [or persistence handle]
+ interface Session {
+ void connect(in ParamList param_set);
+ AnnotatedRegion get_AnnotatedRegion(in string id);
+ };
+
+ // singleton;
+ interface SessionManager {
+ Session initiate_Session(in ParamList param_set);
+ Session retrieve_Session(in ParamList param_set)
+ raises (NotSupported);
+ };
+
+
+};
diff --git a/corba/ensembl.idl b/corba/ensembl.idl
new file mode 100644
index 000000000..1c5eae45d
--- /dev/null
+++ b/corba/ensembl.idl
@@ -0,0 +1,53 @@
+
+module Ensembl {
+ module artemis {
+
+ exception RequestedSequenceTooLong { };
+ exception NoEntry { string reason; };
+
+ interface BioSequence {
+ string getSubSequence(in long start,in long end) raises (RequestedSequenceTooLong);
+ long length();
+ long max_sequence_request();
+ };
+
+ struct Qualifier {
+ string name;
+ sequence<string> values;
+ };
+
+ typedef sequence <Qualifier> QualifierList;
+
+ interface Feature {
+ string getKey();
+ string getLocation();
+ QualifierList getQualifiers();
+ };
+
+ typedef sequence <Feature> FeatureList;
+
+ interface Entry {
+ string getName(); // accession number usually.
+ long getFeatureCount();
+ FeatureList getAllFeatures();
+ BioSequence getSequence();
+ };
+
+ typedef sequence<string> QualifierDefinitionList;
+ struct FeatureDefinition {
+ string key;
+ QualifierDefinitionList qualifiers;
+ };
+ typedef sequence<FeatureDefinition> FeatureDefinitionList;
+
+ typedef sequence<string> EntryNameList;
+
+ interface DB {
+ Entry getEntry(in string entryname) raises (NoEntry);
+ EntryNameList getallEntryNames();
+
+ // coordination of the ORB.
+ FeatureDefinitionList getFeatureDefinitionList();
+ };
+ };
+};
diff --git a/corba/nsdb.idl b/corba/nsdb.idl
new file mode 100644
index 000000000..4d0108904
--- /dev/null
+++ b/corba/nsdb.idl
@@ -0,0 +1,560 @@
+/* **************************************************************************
+ * $Source: //tmp/pathsoft/artemis/corba/nsdb.idl,v $
+ * $Revision: 1.1 $
+ * $Date: 2004-06-09 12:06:34 $
+ * $Author: tjc $
+ * **************************************************************************/
+// Version 2.0
+#ifndef embl_ebi_nsdb_idl
+#define embl_ebi_nsdb_idl
+
+#include "types.idl"
+#include "seqdb.idl"
+
+
+ /**
+ * IDL interfaces for the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/embl_db.html">
+ * EMBL Nucleotide Sequence Database</A>.
+ */
+ module nsdb {
+ // ====================
+ // Forward declarations
+ // ====================
+ interface NucSeq;
+ typedef sequence<NucSeq> NucSeqList;
+ interface NucFeature;
+ typedef sequence<NucFeature> NucFeatureList;
+ interface Location;
+ typedef sequence<Location> LocationList;
+ interface FeatureLocation;
+ typedef sequence<FeatureLocation> FeatureLocationList;
+ interface EntryInfo;
+ typedef sequence<EntryInfo> EntryInfoList;
+
+
+ /**
+ * If a sub-sequence is retrieved for which the location information is
+ * inexact, an InexactLocation is raised
+ */
+ exception InexactLocation { string reason;};
+
+ /**
+ * The EMBL database contains information, which is not really part of the
+ * sequence information. This information is stored in the EntryInfo.
+ */
+
+ interface EntryInfo {
+
+ /**
+ * Retrieve entry indentifier. More information on the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/usrman/id_line.html">format</A> of
+ * an entry name is available in the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/usrman/usrman.html">
+ * EMBL User Manual</A>.
+ */
+ string getEntryName();
+
+ /**
+ * The entry version defines the current version of an EMBL Sequence Database
+ * Entry. I.e. the complete set information related to a particular sequence.
+ * The Entry version is incremented whenever anything changes in the sequence or it's
+ * associated information.
+ */
+ unsigned long getEntryVersion();
+
+
+ /**
+ * Get entry status code.
+ * @see meta::nsdb
+ */
+ string getEntryStatus();
+
+
+ /**
+ * Sequence of revisions when Entry was created/changed.
+ */
+ type::RevisionList getRevisions();
+
+ /**
+ * List of secondary accession numbers. I.e. accession numbers
+ * of deprecated entries, now merged into the current entry or
+ * split over multiple entries, as decribed in the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/usrman/ac_line.html">
+ * AC line</A> documentation in the User manual.
+ */
+ type::stringList getSecondaryIds();
+
+ /**
+ * number of adenine
+ */
+ unsigned long getCountA();
+
+ /**
+ * number of cytosine
+ */
+ unsigned long getCountC();
+
+ /**
+ * number of guanine
+ */
+ unsigned long getCountG();
+
+ /**
+ * number of thymine (in DNA sequence)
+ * or
+ * number of uracil (in RNA sequence)
+ */
+ unsigned long getCountT();
+
+
+ };
+
+ // =========================
+ // Location
+ // =========================
+
+
+ /**
+ * A location is built from one or more nodes forming a tree
+ * local node IDs are only unique within a location tree
+ * the root node has id == 0
+ * the Node id defines the position of the node in the sequence<LocationNode>
+ * The value is relative to the current (parent) node
+ * e.g if the current node is at position x in the LocationNodes sequence
+ * and there is a childId with value j
+ * then the position of this child in the LocationNodes sequence will be x+j
+ */
+ interface Location {
+
+ typedef sequence<unsigned long> IdList;
+
+ /**
+ * valid types of Location Nodes in a Location
+ * are defined by LocNodeTypeCode. Currently values 1-4 are in use.
+ * 6-10 are reserved for future use.
+ */
+ typedef long LocNodeTypeCode;
+
+ /**
+ * The sequence segment is derived from another sequence
+ */
+ const long VirtualSegment_ltc = 1;
+
+ /**
+ * The sequence segment is explicitly given as a DNA string.
+ */
+ const long PhysicalSegment_ltc = 2;
+
+ /**
+ * Sequence is unknown. Only it's (estimated) size in known.
+ */
+ const long Gap_ltc = 3;
+
+ /**
+ * defines how to link a set of LocationNodes
+ */
+ const long Operator_ltc = 4;
+
+
+
+ /**
+ * Virtual segment of a sequence.The sequence segment is derived from another sequence.
+ * <p><dl>
+ * <dt>bio_seq_id
+ * <dd>sequence from which this segment is derived
+ * <dd>contains an accession number
+ * <dt>start
+ * <dd>start position of segment (inclusive)
+ * <dt>end
+ * <dd>end position of segment (inclusive)
+ * <dd>In the case that start defines a 'between' position, end is unused
+ * <dt>complement
+ * <dd> true if segment should be complemented before any further manipulations
+ * </dl>
+ */
+ struct LocVirtualSegment {
+ string bio_seq_id;
+ type::Fuzzy start;
+ type::Fuzzy end;
+ boolean complement;
+ };
+
+ /**
+ * spacer between sequence fragments
+ */
+ typedef type::Fuzzy LocGap;
+
+ /**
+ * The sequence segment is explicitly given as a DNA string
+ * that should be inserted literally.
+ */
+ typedef string LocPhysicalSegment;
+
+ /**
+ * Location operator. This is a node in the location tree that combines
+ * nodes lower down in the tree
+ * <dl>
+ * <dt> op
+ * <dd> operator defining what to do with the nodes
+ * <dd> <dl>
+ * <dt> join
+ * <dd> The indicated elements should be joined (placed end-to-end)
+ * to form one contiguous sequence
+ * <dt> order
+ * <dd> The elements can be found in the specified order
+ * (5' to 3' direction), but nothing is implied about the
+ * reasonableness about joining them
+ * </dl>
+ * <dt> childIds
+ * <dd> identifiers of the child nodes
+ * <dd> Ids is an array of IDs relative to the current node
+ * e.g if the current node is at position x in the LocationNodes sequence
+ * and there is a childId with value j
+ * then the position of this child in the LocationNodes sequence will be x+j
+ *</dl>
+ */
+ struct LocOperator {
+ string op;
+ IdList childIds;
+ };
+
+ union LocationNode_u switch (LocNodeTypeCode) {
+ case VirtualSegment_ltc: LocVirtualSegment virtual;
+ case PhysicalSegment_ltc: LocPhysicalSegment physical;
+ case Gap_ltc: LocGap gap;
+ case Operator_ltc: LocOperator operator;
+ };
+
+ typedef sequence<LocationNode_u> LocationNodeList;
+
+ /**
+ * retrieve
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/components.html#location">
+ * string representation of location</A>
+ */
+ string getLocationString();
+
+
+ /**
+ * retrieve tree representation of location
+ */
+ LocationNodeList getNodes();
+
+
+
+ /**
+ * Create nucleotide sequence defined by location. This can imply getting
+ * fragments from multiple sequences and concatenating.
+ * If it is not possible to resolve the location into a single sequence
+ * (e.g. when it contains a 'group' operator, or gap nodes)
+ * each fragment will be returned as a seperate string. No assumption should be
+ * made on the order, if multiple fragments are returned
+ * @raises InexactLocation if an exact sequence cannot be
+ * determined due to the location being inexact
+ */
+ string getSeq()
+ raises ( InexactLocation );
+
+ };
+ /**
+ * Location of a NucFeature
+ * This interface does not allow to change the nuc_feature
+ * If a location is assigned to a nucfeature, the inverse relation
+ * should be properly updated
+ * @see NucFeature.getLocation
+ */
+ interface FeatureLocation : Location {
+
+ /**
+ * nucfeature to which the location is associated
+ */
+ NucFeature getNucFeature();
+ };
+
+
+ // ============================
+ // Features
+ // ============================
+ /**
+ * Nucleotide Sequence Feature interface. Features are <I>owned</I> by a
+ * sequence and contain information about that (and maybe other) sequence.
+ * The relation between the feature and the sequence is defined by it's
+ * location.
+ * @see Location
+ */
+
+ interface NucFeature : seqdb::Feature {
+
+ /**
+ * Qualifier TypeCode definitions.
+ * Each Qualifier type has an assigned typecode. values 1-100
+ * are reserved to allow for future extension.
+ * <p>
+ * this is a stripped down version of the <B>featuremeta</B> IDL. Types which
+ * are typedefs of the same base-type in <B>featuremeta</B> are not
+ * distinguished here.
+ * @see featuremeta
+ */
+ typedef long QualifierTypeCode;
+
+ // values 1-100 are reserved for EBI QualifierTypeCodes
+ const long string_qtc = 1;
+ const long boolean_qtc = 2;
+ const long integer_qtc = 3;
+ const long real_qtc = 4;
+ const long TranslationException_qtc = 17;
+ const long CodonTranslation_qtc = 18;
+ const long Anticodon_qtc = 19;
+ const long SpliceConsensus_qtc = 20;
+ const long RepeatUnit_qtc = 21;
+ const long DbXref_qtc = 22;
+
+
+ union QualifierValue_u switch (QualifierTypeCode) {
+
+ // EBI typecodes
+ case boolean_qtc : boolean applicable;
+ case string_qtc : string text;
+ case integer_qtc : long integer;
+ case real_qtc : float real;
+ case TranslationException_qtc : type::TranslationException translation_exception;
+ case CodonTranslation_qtc : type::CodonTranslation codon_translation;
+ case Anticodon_qtc : type::AntiCodon anti_codon;
+ case SpliceConsensus_qtc : type::SpliceConsensus splice_consensus;
+ case RepeatUnit_qtc : type::RepeatUnit repeat_unit;
+ case DbXref_qtc : type::DbXref db_xref;
+
+ // add your own extension types below
+#ifdef ANALYSIS
+ // analysis qualifier extension
+ // see analysis.idl
+ case ANALYSIS::Analysis_qtc : ANALYSIS::Scores score;
+#endif
+ };
+
+
+ typedef sequence<QualifierValue_u> QualifierValueList;
+
+ /**
+ * Qualifier.<p>
+ * <dl>
+ * <dt> name
+ * <dd> name of the qualifier
+ * <dt> values
+ * <dd> sequence of QualifierValues. All QualifierValues associated with
+ * a single Qualifier are of the same type
+ * </dl>
+ */
+ struct Qualifier {
+ string name;
+ QualifierValueList values;
+ };
+
+ typedef sequence<Qualifier> QualifierList;
+
+ /**
+ * Retrieve sequence of qualifiers.
+ * @raises type::NoResult if no qualifiers are associated with
+ * the feature.
+ */
+ QualifierList getQualifiers()
+ raises (type::NoResult);
+
+
+
+ /**
+ * retrieve qualifier of a certain type.
+ * To find out which qualifier/feature combinations are valid, a client should
+ * query the NucFeatureMeta server.
+ * @raises type::NoResult if no qualifier of this type is associated with
+ * the feature
+ * @raises type::InvalidRelation if the requested qualifier cannot be
+ * associated to the current feature type
+ * @see metafeature::NucFeatureMeta
+ */
+ Qualifier getQualifier(in string qualifier_name)
+ raises (type::NoResult, type::InvalidRelation);
+
+
+ /**
+ * If the location of the feature references multiple sequences, get a
+ * sequence of all sequences referenced
+ * This method is equivalent to retrieving the feature location, and looping
+ * through all location nodes to find the referenced sequences, converting
+ * the accession numbers into DbXref's.
+ */
+ type::DbXrefList getNucSeqs();
+
+ /**
+ * retrieve location of feature.
+ * @raises type::NoResult if no location is associated with the feature.
+ */
+
+ FeatureLocation getLocation()
+ raises (type::NoResult);
+
+
+ };
+
+ /**
+ * Generic Nucleotide sequence interface.
+ * The accession number is retrieved using the getBioSeqId method inherited from BioSeq.
+ * @see EmblSeq
+ * @see seqdb::BioSeq
+ */
+
+ interface NucSeq : seqdb::BioSeq {
+
+
+ /**
+ * retrieve string representation of nucleotide sequence. Each character
+ * in the string is a
+ * <href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/iupac_codes.html">
+ * IUPAC nucleotide base code</A>
+ * <P>
+ * This method can be used instead of the getAnySeq()
+ * method in seqdb::BioSeq
+ * @see seqdb::BioSeq
+ */
+ string getSeq();
+
+
+ /**
+ * Checksum on sequence to allow validation.
+ *
+ */
+ unsigned long getCheckSum();
+
+ /**
+ * topology of the nucleotide sequence
+ * @see meta::nsdb
+ */
+ string getTopology();
+
+
+ /**
+ * molecule type of the nucleotide sequence
+ * @see meta::nsdb
+ */
+ string getMoleculeType();
+
+
+ /**
+ * retrieve sequence of NucFeatureList associated with
+ * the nucleotide sequence.
+ * A sequence has <I>ownership</I> of all these
+ * features. It is possible on the other hand that
+ * features, owned by another sequence, reference
+ * the current sequence. Currently there is no way to find out.
+ * @raises type::NoResult if no features are owned by the sequence
+ */
+ NucFeatureList getNucFeatures()
+ raises (type::NoResult);
+
+
+ /**
+ * A location of a NucFeature can span multiple sequences.
+ * If only the location of a feature relevant to the current
+ * sequence is required, this method will calculate that.
+ * @parm nuc_feature Feature from which location needs to be
+ * intersected with the current sequence.
+ * @raises type::InvalidRelation if the nuc_feature
+ * is not associated to the current sequence
+ */
+ Location getLocalLocation(in NucFeature nuc_feature)
+ raises (type::InvalidRelation);
+
+ /**
+ * organism(s) from which the NucSeq was obtained.
+ * If the sequence is chimeric, multiple organisms will be returned.
+ * For each organism, there should be a source feature associated
+ * with the current sequence. This source feature has a location
+ * defining which part of the sequence was derived from the specified
+ * organism.
+ * This method provides a shortcut to:
+ * invoke getNucFeaturesByKey("source"), invoke getQualifiers() on each
+ * source feature and loop through qualifiers to find DbXref.
+ * @raises type::NoResult if no source features are associated with
+ * the sequence (should never happen).
+ */
+ type::DbXrefList getOrganisms()
+ raises (type::NoResult);
+
+ /**
+ * retreive all features of a specific kind (FeatureKey)
+ * @parm key Type of features to be retrieved
+ * @raises type::NoResult if the sequence has no associated features
+ * of the requested type.
+ * @raises type::InvalidArgumentValue if the key is not a
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/feature_table.html">
+ * valid feature key</A>
+ * @see NucFeature
+ */
+ NucFeatureList getNucFeaturesByKey(in string key)
+ raises (type::NoResult, type::InvalidArgumentValue);
+
+ /**
+ * Create nucleotide sequence of the segment specified
+ * The first base in the sequence is numbered 1
+ *
+ * @parm start first base of sub-sequence (inclusive)
+ * @parm end last base of sub-sequence (inclusive)
+ * @raises type::IndexOutOfRange if start < 1
+ * or end > length
+ */
+ string getSubSeq(in unsigned long start, in unsigned long end)
+ raises (type::IndexOutOfRange);
+
+ /**
+ * Create nucleotide sequence of the location derived from the specified feature
+ * and contained in the current NucSeq.
+ * @raises type::InvalidRelation if the nuc_feature
+ * is not associated to the current sequence
+ * @raises InexactLocation if an exact sequence cannot be
+ * determined due to the feature's location being inexact
+ */
+ string getSubSeqByFeature(in NucFeature feature)
+ raises (type::InvalidRelation, InexactLocation);
+ /**
+ * @raises type::InvalidRelation if reference does not exist
+ * @raises type::InvalidRelation if reference is not
+ * associated to the current sequence
+ * @raises type::NoResult if there is no location associated with this reference
+ */
+ Location getReferenceLocation(in string reference_id)
+ raises (type::InvalidRelation, type::NoResult);
+ };
+
+ /**
+ * EMBL Nucleotide sequence interface. An EMBL sequence contains all information
+ * to generate a flat-file entry out of it.
+ * It defines no new behaviour but inherits from
+ * several interfaces and acts as a container of the combined functionality.
+ */
+
+ interface EmblSeq : NucSeq, seqdb::SeqInfo , EntryInfo {
+ };
+
+
+/**
+ * Entry point for Nucleotide Sequence Database.
+ * Query methods on the database are defined here.
+ * Currently this is minimal, but should be extended later on.
+ */
+interface Embl {
+
+exception Superceded { type::stringList bio_seq_ids; };
+
+ /**
+ * retrieve Nucleotide sequence, given it's accession number. If a client only supports
+ * NucSeq, and not EmblSeq, than it can widen the EmblSeq to a NucSeq (implicit).
+ * @raises type::NoResult if the accession number does not exist.
+ * @raises Superceded if the sequence referenced by the accession
+ * number does not exist any more, because it was merged, or split.
+ */
+ EmblSeq getEmblSeq(in string bio_seq_id)
+ raises (type::NoResult, Superceded);
+};
+};
+#endif // embl_ebi_nsdb_idl
diff --git a/corba/nsdb_write.idl b/corba/nsdb_write.idl
new file mode 100644
index 000000000..27a172065
--- /dev/null
+++ b/corba/nsdb_write.idl
@@ -0,0 +1,260 @@
+#ifndef EMBL_EBI_NSDB_WRITE_IDL
+#define EMBL_EBI_NSDB_WRITE_IDL
+
+#include "nsdb.idl"
+
+module nsdb {
+ exception OutOfDate { };
+
+ exception ReadOnlyException { };
+
+ exception LocationParse {
+ string reason;
+ };
+
+ exception QualifierParse {
+ string reason;
+ };
+
+ exception InvalidQualifier { };
+
+ interface EmblSeqWriter;
+ interface NucFeatureWriter;
+
+ typedef sequence<NucFeatureWriter> NucFeatureWriterList;
+
+
+ // datestamp_t is seconds since the standard "the epoch", namely
+ // January 1, 1970, 00:00:00 GMT
+ typedef long datestamp_t;
+
+ struct Datestamp {
+ datestamp_t value;
+ };
+
+ struct EntryStats {
+ string name;
+ datestamp_t last_change_time;
+ };
+
+ struct ServerInfo {
+ // Information about the loaded entries
+ sequence <EntryStats> entry_stats_list;
+ // Information about the files in the server directory
+ sequence <EntryStats> file_stats_list;
+ };
+
+ interface EmblWriter : Embl {
+
+ /**
+ * Retrieve a writable Nucleotide sequence object, given a
+ * sequence_id.
+ * @raises type::NoResult if the given sequence_id does not exist.
+ */
+ EmblSeqWriter getEmblSeqWriter (in string sequence_id)
+ raises (type::NoResult);
+
+ /**
+ * Return a ServerInfo structure for the server.
+ **/
+ ServerInfo getServerInfo ();
+ };
+
+
+ exception InvalidKey { };
+
+
+ exception CommitFailed {
+ string reason;
+ };
+
+ interface EmblSeqWriter : EmblSeq {
+
+ /**
+ * Create a new feature in this EmblSeq object.
+ * @parm key Type of the feature to be created
+ * @parm location_string The location of the new NucFeature
+ * @raises LocationParse If the location string is not a valid location.
+ * @raises type::IndexOutOfRange If any part of the location is beyond the
+ * end of the sequence
+ * @raises InvalidKey if the given key is not a possible EMBL key.
+ */
+ NucFeatureWriter createNucFeature (in string key,
+ in string location)
+ raises (LocationParse, type::IndexOutOfRange, InvalidKey,
+ ReadOnlyException);
+
+ /**
+ * Remove the given feature.
+ */
+ void remove (in NucFeature nuc_feature)
+ raises (ReadOnlyException);
+
+ /**
+ * retrieve sequence of NucFeatureList associated with
+ * the nucleotide sequence that are within the given range of bases.
+ * @raises type::NoResult if no features are owned by the sequence
+ * @raises type::IndexOutOfRange if either of start_base or end_base is
+ * less than 1 or greater than the length of the sequence.
+ */
+ NucFeatureList getNucFeaturesInRange (in long start_base, in long end_base)
+ raises (type::NoResult, type::IndexOutOfRange);
+
+
+ /**
+ * Return the number of features
+ */
+ long getNucFeatureCount ();
+
+ /**
+ * Return the ith NucFeature from this Entry. The feature are returned in
+ * a consistent order, sorted by the first base of each Feature.
+ * @raises type::IndexOutOfRange if the index is less than 0 or greater
+ * than the number of features.
+ **/
+ NucFeature getFeatureAtIndex (in long i)
+ raises (type::IndexOutOfRange);
+
+ /**
+ * Return the index of the given Feature. This does the reverse of
+ * getFeatureAtIndex (). Returns -1 if the given NucFeature is not in
+ * this EmblSeq object.
+ **/
+ long indexOf (in NucFeature feature);
+
+ /**
+ * commit any pending changes to the database immediately.
+ */
+ void commit ()
+ raises (CommitFailed);
+
+ /**
+ * Return a Datestamp that will be passed to the set methods on the
+ * EmblSeqWriter methods and NucFeatureWriter methods. The object that is
+ * returned represents the time when the entry was last changed (the last
+ * time a feature was added, removed or changed location).
+ */
+ Datestamp getDatestamp ();
+ };
+
+
+ interface NucFeatureWriter : NucFeature {
+ /**
+ * Set the key, location and qualifiers of this NucFeature
+ * @parm key The new feature key
+ * @parm location The new feature location
+ * @raises InvalidKey if the given key is not a possible EMBL key.
+ * @raises LocationParse If the location string is not a valid location.
+ * @raises type::IndexOutOfRange If any part of the location is out
+ * of range for the sequence.
+ * @raises type::InvalidRelation if one of the qualifiers in this
+ * feature cannot be associated with the given feature key.
+ * @raises QualifierParse if the format of any the qualifiers is not
+ * appropriate for a Qualifier with the given name. For
+ * example the value part of /codon_start qualifier must be a number: 1,
+ * 2 or 3. Also thrown if a qualifier has value when it should not or
+ * vice versa.
+ * @raises InvalidQualifier if the name of the Qualifier is not a
+ * valid embl qualifier name.
+ * @raises ReadOnlyException If this Feature cannot be changed.
+ * @raises OutOfDate If the key has changed since the time given by
+ * datestamp.
+ */
+ void set (in Datestamp datestamp,
+ in string key,
+ in string location,
+ in QualifierList qualifier_list)
+ raises (InvalidKey, LocationParse, type::IndexOutOfRange,
+ type::InvalidRelation, QualifierParse,
+ InvalidQualifier, OutOfDate, ReadOnlyException);
+
+ /**
+ * Set the key of this NucFeature
+ * @parm key The new feature key
+ * @raises InvalidKey if the given key is not a possible EMBL key.
+ * @raises type::InvalidRelation if one of the qualifiers in this
+ * feature cannot be associated with the given feature key.
+ * @raises OutOfDate If the key has changed since the time given by
+ * datestamp.
+ */
+ void setKey (in Datestamp datestamp,
+ in string key)
+ raises (InvalidKey, type::InvalidRelation, OutOfDate, ReadOnlyException);
+
+ /**
+ * Set the location of this NucFeature
+ * @parm location The new feature location
+ * @raises LocationParse If the location string is not a valid location.
+ * @raises type::IndexOutOfRange If any part of the location is out
+ * of range for the sequence.
+ * @raises OutOfDate If the location has changed since the time given by
+ * datestamp.
+ */
+ void setLocation (in Datestamp datestamp,
+ in string location)
+ raises (LocationParse, type::IndexOutOfRange, OutOfDate, ReadOnlyException);
+
+ /**
+ * Set the qualifiers of this feature, replacing the current qualifiers.
+ * @raises InvalidRelationException if this Feature cannot
+ * contain one of the given qualifiers.
+ * @raises QualifierParse if the format of any the qualifiers is not
+ * appropriate for a Qualifier with the given name. For
+ * example the value part of /codon_start qualifier must be a number: 1,
+ * 2 or 3. Also thrown if a qualifier has value when it should not or
+ * vice versa.
+ * @raises InvalidQualifier if the name of the Qualifier is not a
+ * valid embl qualifier name.
+ * @raises OutOfDate if any of the qualifiers has changed since the time
+ * given by datestamp.
+ */
+ void setQualifiers (in Datestamp datestamp,
+ in QualifierList qualifier_list)
+ raises (type::InvalidRelation, QualifierParse, InvalidQualifier,
+ OutOfDate, ReadOnlyException);
+
+ /**
+ * Add the given Qualifier to this Feature. If this Feature contains a
+ * Qualifier with the same name as the new Qualifier it will be replaced.
+ * @parm qualifier The new qualifier to add.
+ * @raises InvalidRelationException if this Feature cannot
+ * contain the given Qualifier.
+ * @raises QualifierParse if the format of the qualifier is not
+ * appropriate for a Qualifier with the given name. For
+ * example the value part of /codon_start qualifier must be a number: 1,
+ * 2 or 3. Also thrown if a qualifier has value when it should not or
+ * vice versa.
+ * @raises InvalidQualifier if the name of the Qualifier is not a
+ * valid embl qualifier name.
+ * @raises OutOfDate if there is a an existing qualifier with the same
+ * name as the argument qualifier and it has changed since the time
+ * given by datestamp.
+ */
+ void setQualifier (in Datestamp datestamp,
+ in Qualifier qualifier)
+ raises (type::InvalidRelation, QualifierParse, InvalidQualifier,
+ OutOfDate, ReadOnlyException);
+
+ /**
+ * Remove the Qualifier with the given name. If there is no Qualifier
+ * with that name, then return immediately.
+ * @parm name The Qualifier name to look for.
+ * @raises OutOfDate if there is a an existing qualifier with the same
+ * name as the argument name and it has changed since the time given by
+ * the datestamp.
+ */
+ void removeQualiferByName (in Datestamp datestamp,
+ in string name)
+ raises (type::InvalidRelation, OutOfDate, ReadOnlyException);
+
+ /**
+ * Return a Datestamp that will be passed to the set methods on the
+ * EmblSeqWriter methods and NucFeatureWriter methods. The object that is
+ * returned represents the time when the feature was last changed (the
+ * last time the key, location or qualifiers changed).
+ */
+ Datestamp getDatestamp ();
+ };
+};
+
+#endif
diff --git a/corba/seqdb.idl b/corba/seqdb.idl
new file mode 100644
index 000000000..7be3f25a6
--- /dev/null
+++ b/corba/seqdb.idl
@@ -0,0 +1,131 @@
+/* **************************************************************************
+ * $Source: //tmp/pathsoft/artemis/corba/seqdb.idl,v $
+ * $Revision: 1.1 $
+ * $Date: 2004-06-09 12:06:36 $
+ * $Author: tjc $
+ * **************************************************************************/
+
+#ifndef embl_ebi_seqdb_idl
+#define embl_ebi_seqdb_idl
+
+#include "types.idl"
+/**
+ * seqdb contains the (abstract) definition
+ * of common attributes of biosequences
+ */
+ module seqdb {
+
+
+ /**
+ * generic biosequence. Provides al functionality we would like to see
+ * on any sequence.
+ */
+ interface BioSeq {
+
+ /**
+ * retrieve unique identifier
+ */
+ string getBioSeqId();
+
+
+
+ /**
+ * length (nr of elements) of the biosequence
+ */
+ unsigned long getLength();
+
+
+ /**
+ * sequence of objects describing the elements in the biosequence
+ * This is a generic description. Most subclasses
+ * will define more convenient methods for accessing the biosequence.
+ * @returns any containing an set of objects. The any should have
+ * a typecode tk_array.
+ */
+ any getAnySeq();
+
+
+
+ /**
+ * Return current version of the BioSeq. returns 0 if versioning is not
+ * implemented on the bioseq.
+ */
+ unsigned long getBioSeqVersion();
+
+ };
+
+ /**
+ * generic Feature. Only has a key to identify it's type, an ID to
+ * identify the instance and a version.
+ */
+ interface Feature {
+
+ /**
+ * feature identifier.
+ */
+ string getFeatureId();
+
+
+
+ /**
+ * Feature types are defined by a key.
+ */
+ string getKey();
+
+
+
+ /**
+ * return current version of the feature. returns 0 if
+ * no versioning is implemented.
+ */
+ unsigned long getFeatureVersion();
+
+ };
+
+ /**
+ * Information associated with a sequence
+ */
+ interface SeqInfo {
+ /**
+ * short (one line) description
+ */
+ string getDescription()
+ raises (type::NoResult);
+
+
+ /**
+ * sequence of keywords, describing the characteristics of the sequence
+ */
+ type::stringList getKeywords()
+ raises (type::NoResult);
+
+
+ /**
+ * sequence of comments, describing the characteristics of the sequence
+ */
+ type::stringList getComments()
+ raises (type::NoResult);
+
+
+ /**
+ * cross references to other databases containing related or additional
+ * information
+ */
+ type::DbXrefList getDbXrefs()
+ raises (type::NoResult);
+
+ /**
+ * cross references to the EMBL publication database
+ * information
+ */
+ type::DbXrefList getReferences()
+ raises (type::NoResult);
+
+ };
+
+ };
+
+
+
+
+#endif // embl_ebi_seqdb_idl
diff --git a/corba/types.idl b/corba/types.idl
new file mode 100644
index 000000000..717f3cb6e
--- /dev/null
+++ b/corba/types.idl
@@ -0,0 +1,334 @@
+/* **************************************************************************
+ * $Source: //tmp/pathsoft/artemis/corba/types.idl,v $
+ * $Revision: 1.1 $
+ * $Date: 2004-06-09 12:06:37 $
+ * $Author: tjc $
+ * **************************************************************************/
+#ifndef embl_ebi_types_idl
+#define embl_ebi_types_idl
+/**
+ * The type module contains types (typedefs and structs) that are shared
+ * between several modules of the EMBL::EBI suite.
+ * It should be included within the module EMBL::EBI.
+ */
+module type {
+ /**
+ * sequence of strings.
+ */
+ typedef sequence<string> stringList;
+
+ typedef sequence<long> longList;
+
+ typedef sequence<unsigned long> ulongList;
+
+ /**
+ * If a query in a database returns no results, the NoResult is raised
+ */
+ exception NoResult {};
+
+ /**
+ * If no write permission is granted (i.e. a set-method cannot be performed)
+ * the NoWritePermission is raised
+ */
+ exception NoWritePermission { string reason;};
+
+ /**
+ * If an object reference given as an input parameter is invalid, in the
+ * context of the current interface, an InvalidRelation is raised
+ */
+ exception InvalidRelation { string reason;};
+
+ /**
+ * If a number indicating a position in a sequence is
+ * outside the limits of the sequence, or more elements are associated to
+ * an object than it can handle,
+ * an IndexOutOfRange exception is raised
+ */
+ exception IndexOutOfRange { string reason; };
+
+/**
+ * controlled values (i.e. an attribute can only contain a value taken
+ * from a well defined range of values, or an in parameter to a method has a
+ * restricted set of acceptable values) are presented as typescodes, used in
+ * as union. If a method tries to set a controlled value
+ * attribute/parameter to an invalid value, an invalidValue is raised
+ */
+ exception InvalidArgumentValue { string reason; };
+
+
+ /**
+ * a sequence (e.g. string) with an expected defined format cannot be parsed
+ */
+ exception ParseError { string reason; };
+
+ /**
+ * Date is a struct to describe a date, independent of any report format
+ * <dl>
+ * <dt>day
+ * <dd>day of month as a number between 1-31 (inclusive)
+ * <dt>month
+ * <dd> month of the year as a number between 1-12 (inclusive)
+ * <dt>year
+ * <dd>year as a 4 digit number
+ * </dl>
+ */
+ struct Date {
+ unsigned short day;
+ unsigned short month;
+ unsigned short year;
+ };
+
+ typedef sequence<Date> DateList;
+
+
+ /**
+ * A person information : this is used to specify the authors
+ * <p><dl>
+ * <dt>surname
+ * <dd>the person surname
+ * <dt>firstname
+ * <dd>the person firstname
+ * <dt>midinitial
+ * <dd>the person mid initial
+ * <dl><p>
+ */
+ struct Person {
+ string surname;
+ string firstname;
+ string midinitial;
+ };
+ typedef sequence<Person> PersonList;
+
+ /**
+ * Revision
+ * <dl>
+ * <dt>date
+ * <dd>datestamp of revision
+ * <dt>type
+ * <dd>type of revision. Valid types are defined in meta
+ * </dl>
+ */
+ struct Revision {
+ Date date;
+ string type;
+ };
+
+ typedef sequence<Revision> RevisionList;
+
+ /**
+ * Database cross-reference. The list of valid database identifiers
+ * used by the collaboration is defined at the
+ * <A href="http://www.ncbi.nlm.nih.gov/collab/db_xref.html">NCBI
+ collaborative web server</A>
+ * <dl>
+ * <dt>db
+ * <dd>database identifier
+ * <dt>primary_id
+ * <dd>object identifier in the database
+ * <dt>version
+ * <dd> if the referenced database supports versioning, version
+ * refers to the version of the object, when the cross-reference
+ * was generated. If can be used to verify that a cross-reference
+ * is up to date.
+ * <dt>label
+ * <dd>secondary identifier, possibly used to indicate a sub/super-part of
+ * the primary object or an alternative name to the primary id.
+ * The label can contain information for the convenience
+ * of the user, but no assumptions should be made on the long-term
+ * stability of it.
+ * </dl>
+ */
+ struct DbXref {
+ string db;
+ string primary_id;
+ unsigned long version;
+ string label;
+ };
+
+ typedef sequence<DbXref> DbXrefList;
+
+ /**
+ * Amino Acid. This can be any amino acid, including modified or unusual ones.
+ * <P>
+ * <dl>
+ * <dt> code
+ * <dd> <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/aa_abbrevs.html">
+ * IUPAC-IUB</A> one-letter code if the amino acid has one assigned
+ * <dd> othwerwise the code will be a blank character
+ * <dt> name
+ * <dd> descriptive name of the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/aa_abbrevs.html">
+ * Amino Acid</A> or
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/modified_aa.html">
+ * modified or unusual Amino Acid</A>
+ * <dt> abbreviation
+ * <dd> abbreviated name of the
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/aa_abbrevs.html">
+ * Amino Acid</A> or
+ * <A href="http://www.ebi.ac.uk/ebi_docs/embl_db/ft/modified_aa.html">
+ * modified or unusual Amino Acid</A>
+ *</dl>
+ */
+ struct AminoAcid {
+ char code;
+ string name;
+ string abbreviation;
+ };
+ typedef sequence<AminoAcid> AminoAcidList;
+
+ /**
+ * Translation rule specifying the amino acid encoded by a codon.
+ * Standard rules are defined by the genetic code of an organism.
+ * If a CDS uses non-standard rules, this can be annotated with
+ * qualifier codon (value type CodonTranslation_s).
+ * <p>
+ * <dt> codon
+ * <dd> literal sequence of the codon.
+ * <dt> amino_acid
+ * <dd> amino acid used.
+ * <dd> No modified AA are allowed.
+ */
+ struct CodonTranslation {
+ string codon;
+ AminoAcid amino_acid;
+ };
+ typedef sequence<CodonTranslation> CodonTranslationList;
+
+ /**
+ * Location of the anticodon of tRNA and the amino acid for which
+ * it codes.
+ * <p>
+ * <dl>
+ * <dt> start
+ * <dd> start position of the anticodon
+ * <dt> end
+ * <dd> end position of the anticodon
+ * <dt> amino_acid
+ * <dd> amino acid used.
+ * <dd> No modified AA are allowed.
+ * </dl>
+ */
+ struct AntiCodon {
+ long start;
+ long end;
+ AminoAcid amino_acid;
+ };
+ typedef sequence<AntiCodon> AntiCodonList;
+
+
+ /**
+ * Translation exception of a single triplet within a sequence.
+ * <p>
+ * <dl>
+ * <dt> primary_acc
+ * <dd> This attribute is likely to change in the future. It is very rarely
+ * used, but it is needed for translation exceptions on CDS's
+ * spanning entries
+ * <dt> start
+ * <dd> startposition of exception in the sequence.
+ * <dt> end
+ * <dd> endposition of exception in the sequence
+ * <dt> amino_acid
+ * <dd> amino acid used in this exception.
+ * <dd> No modified AA are allowed.
+ *</dl>
+ */
+ struct TranslationException {
+ string primary_acc;
+ long start;
+ long end;
+ AminoAcid amino_acid;
+ };
+ typedef sequence<TranslationException> TranslationExceptionList;
+
+ /**
+ * flag to indicate that the splice site consensus sequence is not
+ * present at one of the feature's splice junctions
+ * If no qualifier is present, the default is that both splice sites
+ * contain the consensus
+ */
+ struct SpliceConsensus {
+ boolean five_cons;
+ boolean three_cons;
+ };
+ typedef sequence<SpliceConsensus> SpliceConsensusList;
+
+
+ /**
+ * A RepeatUnit identifies the exact unit that is being repeated. It can be
+ * either a base range, or can refer to the label of a labeled repeat_unit
+ * feature (but not both; this datatype is likely to be superceded by a
+ * union).
+ * <dt> start
+ * <dd> position of first base in the first occurrence of the repeated segment
+ * <dt> end
+ * <dd> position of the last base in first occurence of the repeated segment
+ * <dt> label
+ * <dd> Currently, usually a textual description of the repeating segment,
+ * but can refer to a labeled repeat_unit feature.
+ * This attribute may in future become a proper DbXref to a feature;
+ */
+ struct RepeatUnit {
+ long start;
+ long end;
+ string label;
+ };
+ typedef sequence<RepeatUnit> RepeatUnitList;
+
+ /**
+ * a position can be fuzzy. FuzzyType
+ * defines how to interprete the combination of value and size, to define
+ * the range of fuzziness.
+ * Currently values 1-5 are in use.
+ * 5-10 are reserved for future use.
+ */
+ typedef long FuzzyTypeCode;
+
+
+ /**
+ * value is an exact position
+ */
+ const long Exact_ftc = 1;
+
+ /**
+ *A single base chosen from a range or span of bases is indicated
+ * by the first base number (value) and the last base number of the range
+ * (value+size) inclusive.
+ */
+ const long In_ftc = 2;
+
+ /**
+ * A site between two points (nucleotides), such as an endonucleolytic
+ * cleavage site. The site is a single position between 2 consecutive bases
+ * in the range. The range is defined by value, value+size (inclusive)
+ */
+ const long Between_ftc = 3;
+
+
+ /**
+ * an end point is undefined but behind (and does not include) the
+ * base number specified in value.
+ * size is unused.
+ */
+ const long Less_ftc = 4;
+
+
+ /**
+ * an end point is undefined but before (and does not include) the
+ * base number specified in value.
+ * size is unused.
+ */
+ const long Greater_ftc = 5;
+
+ struct Fuzzy {
+ long value;
+ long size;
+ FuzzyTypeCode type;
+ };
+ typedef sequence<Fuzzy> FuzzyList;
+
+};
+
+#endif
+
+
--
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