X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjson%2Fbinding%2Fbiojson%2Fv1%2FSequencePojo.java;h=56e9bcb8429eee1f51145d0596fa193b2de85fc1;hb=dc005e4ed3722c21925c026570b7219913f787e7;hp=5677b13e6135d8b48240697e563c779d31d56b10;hpb=8e2f91c6975f077f4313a516a46a5a42b6388b3a;p=jalview.git
diff --git a/src/jalview/json/binding/biojson/v1/SequencePojo.java b/src/jalview/json/binding/biojson/v1/SequencePojo.java
index 5677b13..56e9bcb 100644
--- 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 .
+ * 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 seqs object model")
- private String svid = "1.0";
-
@Attributes(
required = true,
minLength = 3,
maxLength = 2147483647,
- description = "Sequence residue characters. An aligned sequence may contain
one of the following gap characters â.â, â-â or â â")
+ description = "Sequence residue characters. An aligned sequence may contain
one of the following gap characters “.”, “-” or “ ”")
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 sequenceâs first residue in its source database,
using a one-based numbering index system")
+
+ @Attributes(
+ required = true,
+ description = "The index of the sequenceâs first residue in its source database,
using a one-based numbering index system")
private int start;
- @Attributes(required = true, description = "The index of the sequenceâs last residue in its source database,
using a one-based numbering index system")
+ @Attributes(
+ required = true,
+ description = "The index of the sequenceâs last residue in its source database,
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;