JAL-1831 update all maxItems annotation to the max value for a 32-bit signed binary...

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index 2625b69..dfb60bc 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -14,16 +14,33 @@ public class AlignmentPojo
   @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
   private String svid = "1.0";
 
   @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
   private String svid = "1.0";
 

-  @Attributes(required = true, minItems = 1, maxItems = 1999999999, 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.")
+  @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.")

   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
 
   private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
 

-  @Attributes(required = false, minItems = 0, maxItems = 1999999999, exclusiveMaximum=true, description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
+  @Attributes(
+    required = false,
+    minItems = 0,
+    maxItems = 2147483647,
+    exclusiveMaximum = true,
+    description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")

   private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
 
   private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
 

-  @Attributes(required = false, minItems = 0, maxItems = 1999999999, 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.")
+  @Attributes(
+    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.")

   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
 
   private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
 

-  @Attributes(required = false, minItems = 0, maxItems = 1999999999, 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).")
+  @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).")

   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
 
   @Attributes(required = false, enums = { "None", "Custom", "Clustal",
   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
 
   @Attributes(required = false, enums = { "None", "Custom", "Clustal",

@@ -96,7 +113,7 @@ public class AlignmentPojo
 
   public void setGlobalColorScheme(String globalColorScheme)
   {
 
   public void setGlobalColorScheme(String globalColorScheme)
   {

-//       this.appSettings.put("globalColorScheme", globalColorScheme);
+    this.appSettings.put("globalColorScheme", globalColorScheme);

   }
 
   public String getColourScheme()
   }
 
   public String getColourScheme()

diff --git a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
index e493ecb..4c413c5 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
@@ -16,7 +16,11 @@ public class SequenceFeaturesPojo
   @Attributes(required = true, description = "End residue position for the sequence feature")
   private int xEnd;
 
   @Attributes(required = true, description = "End residue position for the sequence feature")
   private int xEnd;
 

-  @Attributes(required = true, minItems = 1, maxItems = 1999999999, description = "Reference to the sequence in the alignment<br> (more like a foreign key)")
+  @Attributes(
+    required = true,
+    minItems = 1,
+    maxItems = 2147483647,
+    description = "Reference to the sequence in the alignment<br> (more like a foreign key)")

   private String sequenceRef;
 
   @Attributes(required = true, description = "The name or type of the SequenceFeature")
   private String sequenceRef;
 
   @Attributes(required = true, description = "The name or type of the SequenceFeature")

diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
index 63bc426..4bc6e3b 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
@@ -36,7 +36,12 @@ public class SequenceGrpPojo
   @Attributes(required = true, description = "The index of the group’s last residue in the alignment space")
   private int endRes;
   
   @Attributes(required = true, description = "The index of the group’s last residue in the alignment space")
   private int endRes;
   

-  @Attributes(required = true, minItems = 1, maxItems = 1999999999, uniqueItems=true, description = "An array of the unique id's for the sequences belonging to the group")  
+  @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>();
 
   public String getColourScheme()
   private ArrayList<String> sequenceRefs = new ArrayList<String>();
 
   public String getColourScheme()

diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java
index 17c6506..5677b13 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequencePojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequencePojo.java
@@ -9,7 +9,11 @@ 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, description = "Serial version identifier for the <b>seqs</b> object model")
   private String svid = "1.0";
 

-  @Attributes(required = true,minLength=3,maxLength=1999999999, description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")
+  @Attributes(
+    required = true,
+    minLength = 3,
+    maxLength = 2147483647,
+    description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")

   private String seq;
 
   @Attributes(required = true, description = "Sequence name")
   private String seq;
 
   @Attributes(required = true, description = "Sequence name")