JAL-1739 reverted BioJSON schema to use one main version for the whole schema and...

[jalview.git] / src / jalview / json / binding / biojson / v1 / AlignmentPojo.java

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index f7f20bb..f68ea86 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -17,8 +17,7 @@ public class AlignmentPojo
   @Attributes(
     required = true,
     minItems = 1,
-    maxItems = 2147483647,
-    description = "A sequence group is a bracket of alignment residues spanning <br>across multiple columns and rows. These can be treated as a <br>sub-alignments.")
+           description = "An array of Sequences which makes up the Alignment")
   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
 
   @Attributes(
@@ -33,7 +32,7 @@ public class AlignmentPojo
     required = false,
     minItems = 0,
     maxItems = 2147483647,
-    description = "A sequence group is a bracket of alignment residues which <br>could span across multiple columns and/or rows. These can be <br>treated as a sub-alignments.")
+    description = "A sequence group is a region of an alignment which could <br>span across multiple columns and rows. These can be treated as<br> a sub-alignments.")
   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
 
   @Attributes(
@@ -43,9 +42,13 @@ public class AlignmentPojo
     description = "Sequence features are associated with sequences rather than <br>alignments. A sequence feature can span across multiple <br>sequences in an alignment. They indicate features generated <br>by the same analysis process or retrieved from the same database <br>(such as Uniprot features).")
   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
 
-  @Attributes(required = false, enums = { "None", "Custom", "Clustal",
-      "Zappo", "Taylor", "Nucleotide", "Pyrimidine", "Purine", "Turn",
-      "Strand", "Buried", "Hydro" })
+  @Attributes(
+    required = false,
+    enums = { "None", "User Defined", "Clustal", "Zappo", "Taylor",
+        "Nucleotide", "Pyrimidine", "Purine", "Turn", "Helix", "Strand",
+        "Buried", "Hydro", "T-Coffee Scores", "RNA Interaction type",
+        "Blosum62", "RNA Helices", "% Identity" },
+    description = "The <a href=\"colour_schemes.html\">Colour Scheme</a> applied to the alignment")
   private String colourScheme;
   
   @Attributes(required = true, maxItems = 1, description = "This is an array of key=value pairs for storing custom application <br>specific settings")