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

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 6f21a2a..9fd712f 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -7,8 +7,6 @@ import com.github.reinert.jjschema.Attributes;
 
 public class AlignmentAnnotationPojo
 {
-  @Attributes(required = true, description = "Serial version id for the alignAnnotation object model")
-  private String svid = "1.0";
 
   @Attributes(required = false, description = "Label for the Alignment Annotation")
   private String label;
@@ -49,9 +47,6 @@ public class AlignmentAnnotationPojo
     this.annotations = annotations;
   }
 
-  public String getSvid()
-  {
-    return svid;
-  }
+
 
 }

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")

diff --git a/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java b/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java
deleted file mode 100644 (file)
index 3385682..0000000
--- a/src/jalview/json/binding/biojson/v1/AppSettingsPojo.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package jalview.json.binding.biojson.v1;
-
-
-public class AppSettingsPojo
-{
-  // private String globalColorScheme = "none";
-
-  
-
-  public AppSettingsPojo()
-  {
-
-  }
-
-  //
-  //
-  // public void setGlobalColorScheme(String globalColorScheme)
-  // {
-  // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-  // .values())
-  // {
-  // if (cs.getJalviewName().equals(globalColorScheme))
-  // {
-  // // this.globalColorScheme = cs.getBioJsName();
-  // this.settings.put("globalColorScheme", cs.getBioJsName());
-  // break;
-  // }
-  // }
-  // }
-  //
-  // public enum JalviewBioJsColorSchemeMapper
-  // {
-  // USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
-  // null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
-  // "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
-  // new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
-  // "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
-  // "Purine/Pyrimidine", "purine",
-  // new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
-  // "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
-  // "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
-  // "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
-  // "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
-  // "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-  //
-  // // The color types below are not yet supported by BioJs MSA viewer
-  // T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
-  // "RNA Interaction type", "RNA Interaction type",
-  // new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
-  // "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
-  // "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
-  // "% Identity", "pid", new PIDColourScheme());
-  //
-  // private String jalviewName;
-  //
-  // private String bioJsName;
-  //
-  // private ColourSchemeI jvColourScheme;
-  //
-  // private JalviewBioJsColorSchemeMapper(String jalviewName,
-  // String bioJsName, ColourSchemeI jvColourScheme)
-  // {
-  // this.jalviewName = jalviewName;
-  // this.bioJsName = bioJsName;
-  // this.setJvColourScheme(jvColourScheme);
-  // }
-  //
-  // public String getJalviewName()
-  // {
-  // return jalviewName;
-  // }
-  //
-  // public String getBioJsName()
-  // {
-  // return bioJsName;
-  // }
-  //
-  // public ColourSchemeI getJvColourScheme()
-  // {
-  // return jvColourScheme;
-  // }
-  //
-  // public void setJvColourScheme(ColourSchemeI jvColourScheme)
-  // {
-  // this.jvColourScheme = jvColourScheme;
-  // }
-  //
-  // }
-
-
-}

diff --git a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
index 4c413c5..64fee65 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
@@ -7,9 +7,6 @@ import com.github.reinert.jjschema.Attributes;
 
 public class SequenceFeaturesPojo
 {
-  @Attributes(required = true, description = "Serial version id for the <b>SeqFeature</b> object")
-  private String svid = "1.0";
-
   @Attributes(required = true, description = "Start residue position for the sequence feature")
   private int xStart;
 
@@ -153,17 +150,4 @@ public class SequenceFeaturesPojo
     this.sequenceRef = sequenceRef;
   }
 
-  public String getSvid()
-  {
-    return svid;
-  }
-
-//public Map<String, Object> getOtherDetails() {
-//     return otherDetails;
-//}
-//
-//public void setOtherDetails(Map<String, Object> otherDetails) {
-//     this.otherDetails = otherDetails;
-//}
-
 }

diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
index 4bc6e3b..7c2a8fd 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
@@ -6,10 +6,9 @@ import com.github.reinert.jjschema.Attributes;
 
 public class SequenceGrpPojo
 {
-  @Attributes(required = true, description = "Serial version identifier for the <b>seqGroup</b> object model")
-  private String svid = "1.0";
-  
-  @Attributes(required = false, description = "The Colour Scheme applied to the Sequence Group")
+  @Attributes(
+    required = false,
+    description = "The <a href=\"colour_schemes.html\">Colour Scheme</a> applied to the Sequence Group")
   private String colourScheme;
 
   @Attributes(required = true, description = "The name assigned to the seqGroup")
@@ -144,9 +143,5 @@ public class SequenceGrpPojo
     this.sequenceRefs = sequenceRefs;
   }
 
-  public String getSvid()
-  {
-    return svid;
-  }
 
 }

diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java
index 5677b13..9d39d42 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequencePojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequencePojo.java
@@ -6,9 +6,6 @@ import com.github.reinert.jjschema.Attributes;
 
 public class SequencePojo
 {
-  @Attributes(required = true, description = "Serial version identifier for the <b>seqs</b> object model")
-  private String svid = "1.0";
-
   @Attributes(
     required = true,
     minLength = 3,
@@ -106,10 +103,6 @@ public class SequencePojo
     this.order = order;
   }
 
-  public String getSvid()
-  {
-    return svid;
-  }
 
   public String getType()
   {