From 8a5564b7645e73b98bcc1338b4d58937b43e5133 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 21 Aug 2015 10:50:35 +0100
Subject: [PATCH] JAL-1831 updated json schema doc

---
 src/jalview/io/HtmlSvgOutput.java                      |    7 ++++---
 src/jalview/json/binding/biojson/v1/AlignmentPojo.java |    2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 16b2647..6612db3 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -98,7 +98,8 @@ public class HtmlSvgOutput
               .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
       if (isEmbbedBioJSON)
       {
-      AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+        AlignmentExportData exportData = jalview.gui.AlignFrame
+                .getAlignmentForExport(
               JSONFile.FILE_DESC, av);
       if (exportData.getSettings().isCancelled())
       {
@@ -107,8 +108,8 @@ public class HtmlSvgOutput
         jsonData = new FormatAdapter(ap, exportData.getSettings())
               .formatSequences(JSONFile.FILE_DESC, exportData
                       .getAlignment(), exportData.getOmitHidden(),
-                      exportData.getStartEndPostions(), ap
-                              .getAlignViewport().getColumnSelection());
+                        exportData.getStartEndPostions(),
+                        av.getColumnSelection());
       }
       String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
       FileOutputStream out = new FileOutputStream(file);
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index dfb60bc..f7f20bb 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -33,7 +33,7 @@ public class AlignmentPojo
     required = false,
     minItems = 0,
     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 = "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.")
   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
 
   @Attributes(
-- 
1.7.10.2