X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FGeneLocus.java;fp=src%2Fjalview%2Fdatamodel%2FGeneLocus.java;h=f81348fa303e1f1a4a4b7e811feaf69bce698afd;hb=c6ff2e8a0e898035b248933704824484df4c4018;hp=0000000000000000000000000000000000000000;hpb=8910c0162b81b32ea0760daf7509a9a5f8ec1fea;p=jalview.git diff --git a/src/jalview/datamodel/GeneLocus.java b/src/jalview/datamodel/GeneLocus.java new file mode 100644 index 0000000..f81348f --- /dev/null +++ b/src/jalview/datamodel/GeneLocus.java @@ -0,0 +1,91 @@ +package jalview.datamodel; + +import jalview.util.MapList; + +/** + * A specialisation of DBRefEntry used to hold the chromosomal coordinates for a + * (typically gene) sequence + *
source
is used to hold a species id e.g. humanversion
is used to hold assembly id e.g GRCh38accession
is used to hold the chromosome idmap
is used to hold the mapping from sequence to
+ * chromosome coordinatessource
of
+ * DBRefEntry
+ */
+ @Override
+ public String getSpeciesId()
+ {
+ return getSource();
+ }
+
+ /**
+ * Answers the genome assembly id e.g. "GRCh38", stored as field
+ * version
of DBRefEntry
+ */
+ @Override
+ public String getAssemblyId()
+ {
+ return getVersion();
+ }
+
+ /**
+ * Answers the chromosome identifier e.g. "X", stored as field
+ * accession
of DBRefEntry
+ */
+ @Override
+ public String getChromosomeId()
+ {
+ return getAccessionId();
+ }
+
+}