JAL-2418 source formatting

[jalview.git] / src / jalview / json / binding / biojson / v1 / SequencePojo.java

diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java
index 5677b13..56e9bcb 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/SequencePojo.java
+++ b/src/jalview/json/binding/biojson/v1/SequencePojo.java
@@ -1,50 +1,78 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.json.binding.biojson.v1;
 
 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,
     maxLength = 2147483647,
-    description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")
+    description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters &#x201c;.&#x201d;, &#x201c;-&#x201d; or &#x201c;&nbsp;&#x201d;")
   private String seq;
 
   @Attributes(required = true, description = "Sequence name")
   private String name;
 
-  @Attributes(required = false, description = "Sequence type", enums = {"DNA", "RNA", "Protein"})
+  @Attributes(
+    required = false,
+    description = "Sequence type",
+    enums =
+    { "DNA", "RNA", "Protein" })
   private String type;
 
-  @Attributes(required = true, description = "Unique identifier for a given Sequence")
+  @Attributes(
+    required = true,
+    description = "Unique identifier for a given Sequence")
   private String id;
-  
-  @Attributes(required = false, description = "The order/position of a sequence in the alignment space")
+
+  @Attributes(
+    required = false,
+    description = "The order/position of a sequence in the alignment space")
   private int order;
-  
-  @Attributes(required = true, description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
+
+  @Attributes(
+    required = true,
+    description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
   private int start;
 
-  @Attributes(required = true, description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
+  @Attributes(
+    required = true,
+    description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
   private int end;
 
-
   public SequencePojo()
   {
   }
 
-  public SequencePojo(int start, int end, String id, String name, String seq)
+  public SequencePojo(int start, int end, String id, String name,
+          String seq)
   {
     this.id = id;
     this.name = name;
     this.seq = seq;
   }
+
   public String getSeq()
   {
     return seq;
@@ -106,11 +134,6 @@ public class SequencePojo
     this.order = order;
   }
 
-  public String getSvid()
-  {
-    return svid;
-  }
-
   public String getType()
   {
     return type;