From 6936b57e5469c796a998d661a7a07648832ccf70 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 7 Oct 2015 17:39:59 +0100
Subject: [PATCH] JAL-1912 added documentation

---
 src/jalview/io/JSONFile.java                       |   13 +++++++-----
 .../biojson/v1/AlignmentAnnotationPojo.java        |   10 ++++++----
 .../biojson/v1/AnnotationDisplaySettingPojo.java   |   21 ++++++++++++++++++++
 .../json/binding/biojson/v1/AnnotationPojo.java    |    4 +++-
 4 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 564dd64..9e94d91 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -558,11 +558,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     .get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter") == null ? ""
                     : annot.get("displayCharacter").toString();
-            Color color = annot.get("colour") == null ? Color.white
-                    : UserColourScheme.getColourFromString(annot.get(
-                    "colour").toString());
-            annotations[count] = new Annotation(displayChar, desc, ss, val,
-                    color);
+
+            annotations[count] = new Annotation(displayChar, desc, ss, val);
+            if (annot.get("colour") != null)
+            {
+              Color color = UserColourScheme.getColourFromString(annot.get(
+                      "colour").toString());
+              annotations[count].colour = color;
+            }
           }
           ++count;
         }
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 7e729f9..a9e57a9 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -30,12 +30,12 @@ public class AlignmentAnnotationPojo
 
   @Attributes(
     required = false,
-    description = "Label for the Alignment Annotation")
+    description = "Label for the alignment annotation")
   private String label;
 
   @Attributes(
     required = false,
-    description = "Description for the Alignment Annotation")
+    description = "Description for the alignment annotation")
   private String description;
 
   @Attributes(required = false)
@@ -44,7 +44,7 @@ public class AlignmentAnnotationPojo
   @Attributes(
     required = false,
     enums = { "0", "1", "2" },
-    description = "Determines the rendered for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+    description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
   private int graphType;
 
   @Attributes(
@@ -60,7 +60,9 @@ public class AlignmentAnnotationPojo
   @Attributes(required = false, description = "Score of the annotation")
   private double score;
 
-  @Attributes(required = false, description = "Annotation generation source")
+  @Attributes(
+    required = false,
+    description = "The annotation generation source")
   private String calcId;
 
   public String getLabel()
diff --git a/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
index ac1cbe4..be50b79 100644
--- a/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
@@ -1,17 +1,38 @@
 package jalview.json.binding.biojson.v1;
 
+import com.github.reinert.jjschema.Attributes;
+
 public class AnnotationDisplaySettingPojo
 {
+
+  @Attributes(
+    required = false,
+    description = "Indicates if column label is scaled to fit within the <br>alignment column")
   private boolean scaleColLabel;
 
+  @Attributes(
+    required = false,
+    description = "Indicates if every column label is displayed.")
   private boolean showAllColLabels;
 
+  @Attributes(
+    required = false,
+    description = "Indicates if column labels is centred relative to the <br>alignment column")
   private boolean centreColLabels;
 
+  @Attributes(
+    required = false,
+    description = "Indicates if the Annotation is shown below the alignment")
   private boolean belowAlignment;
 
+  @Attributes(
+    required = false,
+    description = "Indicates if the annotation row is visible")
   private boolean visible;
 
+  @Attributes(
+    required = false,
+    description = "Indicates if annotation has a graphical symbol track")
   private boolean hasIcon;
 
   public boolean isScaleColLabel()
diff --git a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
index a4d7f17..d49c1d5 100644
--- a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
@@ -43,7 +43,9 @@ public class AnnotationPojo
   @Attributes(required = false, description = "Value of the annotation")
   private float value;
 
-  @Attributes(required = false, description = "Colour for position")
+  @Attributes(
+    required = false,
+    description = "Colour of the annotation position in hex string.")
   private String colour;
 
   public String getDisplayCharacter()
-- 
1.7.10.2