--- /dev/null
+package jalview.io.xdb.genbank;
+
+/**
+ * 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
+ *
+ *
+ */
+public abstract class GenBankLocation {
+ // the location is complement strand?
+ private boolean complement = false;
+
+ public GenBankLocation() {
+ }
+
+ /**
+ * The minor location in genome sequence
+ *
+ * @return position
+ */
+ public abstract int getMinor();
+
+ /**
+ * The major location in genome sequence
+ *
+ * @return position
+ */
+ public abstract int getMajor();
+
+ /**
+ * @return the complement
+ */
+ public boolean isComplement() {
+ return complement;
+ }
+
+ /**
+ * @param complement the complement to set
+ */
+ public void setComplement(boolean complement) {
+ this.complement = complement;
+ }
+}
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