-join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form
- one contiguous sequence
-
-
-complement(34..126) Start at the base complementary to 126 and finish at the
- base complementary to base 34 (the feature is on the strand
- complementary to the presented strand)
-
-
-complement(join(2691..4571,4918..5163))
- Joins regions 2691 to 4571 and 4918 to 5163, then
- complements the joined segments (the feature is on the
- strand complementary to the presented strand)
-
-join(complement(4918..5163),complement(2691..4571))
- Complements regions 4918 to 5163 and 2691 to 4571, then
- joins the complemented segments (the feature is on the
- strand complementary to the presented strand)
-
-J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
- this database) with primary accession number 'J00194'
-
-join(1..100,J00194.1:100..202)
- Joins region 1..100 of the existing entry with the region
- 100..202 of remote entry J00194
-
- */
+ /*
+ * EMBL Feature support is limited. The text below is included for the benefit
+ * of any developer working on improving EMBL feature import in Jalview.
+ * Extract from EMBL feature specification see
+ * http://www.embl-ebi.ac.uk/embl/Documentation
+ * /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
+ *
+ * The location indicates the region of the presented sequence which
+ * corresponds to a feature.
+ *
+ * 3.5.2 Format and conventions The location contains at least one sequence
+ * location descriptor and may contain one or more operators with one or more
+ * sequence location descriptors. Base numbers refer to the numbering in the
+ * entry. This numbering designates the first base (5' end) of the presented
+ * sequence as base 1. Base locations beyond the range of the presented
+ * sequence may not be used in location descriptors, the only exception being
+ * location in a remote entry (see 3.5.2.1, e).
+ *
+ * Location operators and descriptors are discussed in more detail below.
+ *
+ * 3.5.2.1 Location descriptors
+ *
+ * The location descriptor can be one of the following: (a) a single base
+ * number (b) a site between two indicated adjoining bases (c) a single base
+ * chosen from within a specified range of bases (not allowed for new entries)
+ * (d) the base numbers delimiting a sequence span (e) a remote entry
+ * identifier followed by a local location descriptor (i.e., a-d)
+ *
+ * A site between two adjoining nucleotides, such as endonucleolytic cleavage
+ * site, is indicated by listing the two points separated by a carat (^). The
+ * permitted formats for this descriptor are n^n+1 (for example 55^56), or,
+ * for circular molecules, n^1, where "n" is the full length of the molecule,
+ * ie 1000^1 for circular molecule with length 1000.
+ *
+ * A single base chosen from a range of bases is indicated by the first base
+ * number and the last base number of the range separated by a single period
+ * (e.g., '12.21' indicates a single base taken from between the indicated
+ * points). From October 2006 the usage of this descriptor is restricted : it
+ * is illegal to use "a single base from a range" (c) either on its own or in
+ * combination with the "sequence span" (d) descriptor for newly created
+ * entries. The existing entries where such descriptors exist are going to be
+ * retrofitted.
+ *
+ * Sequence spans are indicated by the starting base number and the ending
+ * base number separated by two periods (e.g., '34..456'). The '<' and '>'
+ * symbols may be used with the starting and ending base numbers to indicate
+ * that an end point is beyond the specified base number. The starting and
+ * ending base positions can be represented as distinct base numbers
+ * ('34..456') or a site between two indicated adjoining bases.
+ *
+ * A location in a remote entry (not the entry to which the feature table
+ * belongs) can be specified by giving the accession-number and sequence
+ * version of the remote entry, followed by a colon ":", followed by a
+ * location descriptor which applies to that entry's sequence (i.e.
+ * J12345.1:1..15, see also examples below)
+ *
+ * 3.5.2.2 Operators
+ *
+ * The location operator is a prefix that specifies what must be done to the
+ * indicated sequence to find or construct the location corresponding to the
+ * feature. A list of operators is given below with their definitions and most
+ * common format.
+ *
+ * complement(location) Find the complement of the presented sequence in the
+ * span specified by " location" (i.e., read the complement of the presented
+ * strand in its 5'-to-3' direction)
+ *
+ * join(location,location, ... location) The indicated elements should be
+ * joined (placed end-to-end) to form one contiguous sequence
+ *
+ * order(location,location, ... location) The elements can be found in the
+ * specified order (5' to 3' direction), but nothing is implied about the
+ * reasonableness about joining them
+ *
+ * Note : location operator "complement" can be used in combination with
+ * either " join" or "order" within the same location; combinations of "join"
+ * and "order" within the same location (nested operators) are illegal.
+ *
+ *
+ *
+ * 3.5.3 Location examples
+ *
+ * The following is a list of common location descriptors with their meanings:
+ *
+ * Location Description
+ *
+ * 467 Points to a single base in the presented sequence
+ *
+ * 340..565 Points to a continuous range of bases bounded by and including the
+ * starting and ending bases
+ *
+ * <345..500 Indicates that the exact lower boundary point of a feature is
+ * unknown. The location begins at some base previous to the first base
+ * specified (which need not be contained in the presented sequence) and
+ * continues to and includes the ending base
+ *
+ * <1..888 The feature starts before the first sequenced base and continues to
+ * and includes base 888
+ *
+ * 1..>888 The feature starts at the first sequenced base and continues beyond
+ * base 888
+ *
+ * 102.110 Indicates that the exact location is unknown but that it is one of
+ * the bases between bases 102 and 110, inclusive
+ *
+ * 123^124 Points to a site between bases 123 and 124
+ *
+ * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
+ * form one contiguous sequence
+ *
+ *
+ * complement(34..126) Start at the base complementary to 126 and finish at
+ * the base complementary to base 34 (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ *
+ * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
+ * to 5163, then complements the joined segments (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ * join(complement(4918..5163),complement(2691..4571)) Complements regions
+ * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
+ * feature is on the strand complementary to the presented strand)
+ *
+ * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
+ * this database) with primary accession number 'J00194'
+ *
+ * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
+ * with the region 100..202 of remote entry J00194
+ */