From 2727ef35831c6a0d071de16ce43f058be6ab166c Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 7 Sep 2015 15:25:25 +0100
Subject: [PATCH] JAL-1831 updated BioJSON schema

---
 src/jalview/io/HtmlSvgOutput.java                    |    2 +-
 .../json/binding/biojson/v1/AlignmentPojo.java       |   18 ++++++++++--------
 .../json/binding/biojson/v1/SequenceGrpPojo.java     |    3 +--
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index c8d6975..a93cd7f 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -657,7 +657,7 @@ public class HtmlSvgOutput
     }
 
     htmlSvg.append("</script>\n");
-    htmlSvg.append("</hmtl>");
+    htmlSvg.append("</html>");
     return htmlSvg.toString();
   }
 }
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index f68ea86..9021a73 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -23,23 +23,21 @@ public class AlignmentPojo
   @Attributes(
     required = false,
     minItems = 0,
-    maxItems = 2147483647,
     exclusiveMaximum = true,
-    description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
+    description = "Alignment annotations stores symbols and graphs usually rendered </br>"
+            + "below the alignment and often reflect properties of the alignment </br>as a whole.")
   private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
 
   @Attributes(
     required = false,
     minItems = 0,
-    maxItems = 2147483647,
-    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.")
+    description = "A sequence group is a rectangular region of an alignment <br>bounded by startRes and endRes positions in the alignment <br>coordinate system for a set of sequences")
   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
 
   @Attributes(
     required = false,
     minItems = 0,
-    maxItems = 2147483647,
-    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).")
+    description = "Sequence features are properties of the individual sequences, <br>they do not change with the alignment, but are shown mapped<br> on to specific residues within the alignment")
   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
 
   @Attributes(
@@ -48,10 +46,14 @@ public class AlignmentPojo
         "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")
+    description = "The <a href=\"#colourScheme\">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")
+  @Attributes(
+	required = true, 
+	maxItems = 0, description = "AppSettings stores key=value pairs of custom application specific <br>"
+			                  + "settings (i.e visualisation settings, etc) for different applications<br>"
+			                  + "that consume or generate BioJSON")
   Map<String, Object> appSettings = new HashMap<String, Object>();
 
   public AlignmentPojo()
diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
index 7c2a8fd..e5c4395 100644
--- a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
@@ -8,7 +8,7 @@ public class SequenceGrpPojo
 {
   @Attributes(
     required = false,
-    description = "The <a href=\"colour_schemes.html\">Colour Scheme</a> applied to the Sequence Group")
+    description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group")
   private String colourScheme;
 
   @Attributes(required = true, description = "The name assigned to the seqGroup")
@@ -38,7 +38,6 @@ public class SequenceGrpPojo
   @Attributes(
     required = true,
     minItems = 1,
-    maxItems = 2147483647,
     uniqueItems = true,
     description = "An array of the unique id's for the sequences belonging to the group")
   private ArrayList<String> sequenceRefs = new ArrayList<String>();
-- 
1.7.10.2