JAL-1705 notes about retrieving feature relationships for ensembl loci

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index b456919..978316b 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -168,6 +168,20 @@ public class EnsemblSeqProxyTest
     Assert.assertEquals(sq, DBRefUtils.processQueryToAccessionFor(esq, sq),
             "Regex for " + esq.getClass().toString() + " not correct.");
   }
+  // TODO:
+  // sequence query with ENSG and anything other than a genomic type will yield
+  // sequences with different IDs which will
+  // break the post-processing stage where DBRefs are assigned to sequences.
+  // -> multiple_sequences = true is needed additional parameter
+  // http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/x-json;type=protein;multiple_sequences=true
+  // result with four transcripts, cds, cdna, and protein products.
+  // *
+  // features for ENG -
+  // http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=cds&feature=exon&feature=transcript&content-type=text/x-gff3
+  // transcript: gives locus, all transcript products with ENSG parents
+  // gene: give all ENSG on locus
+  // exon: all exon boundaries. CDS same info.
+
   // @Test(dataProvider = "ens_seqs", suiteName = "live")
   // public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
   // throws Exception