X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjson%2Fbinding%2Fbiojson%2Fv1%2FAlignmentPojo.java;h=94d1bde8d755337d3780f7499aa33519ecf91a47;hb=6a18ba9e7e4bd4deee0337dfd072b959596ca4b5;hp=9021a73bd20122f176e8be558c8ba51c54e72871;hpb=2727ef35831c6a0d071de16ce43f058be6ab166c;p=jalview.git
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
index 9021a73..94d1bde 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -1,6 +1,25 @@
+/*
+ * 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 java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -8,16 +27,20 @@ import java.util.Map;
import com.github.reinert.jjschema.Attributes;
-@Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
+@Attributes(
+ title = "BioJSON",
+ description = "A specification for the representation and exchange of bioinformatics data")
public class AlignmentPojo
{
- @Attributes(required = true, description = "Serial version identifier for BioJSON schema")
+ @Attributes(
+ required = true,
+ description = "Serial version identifier for BioJSON schema")
private String svid = "1.0";
@Attributes(
required = true,
minItems = 1,
- description = "An array of Sequences which makes up the Alignment")
+ description = "An array of Sequences which makes up the Alignment")
private List seqs = new ArrayList();
@Attributes(
@@ -42,18 +65,20 @@ public class AlignmentPojo
@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" },
+ 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 Colour Scheme applied to the alignment")
private String colourScheme;
-
+
@Attributes(
- required = true,
- maxItems = 0, description = "AppSettings stores key=value pairs of custom application specific
"
- + "settings (i.e visualisation settings, etc) for different applications
"
- + "that consume or generate BioJSON")
+ required = true,
+ maxItems = 0,
+ description = "AppSettings stores key=value pairs of custom application specific
"
+ + "settings (i.e visualisation settings, etc) for different applications
"
+ + "that consume or generate BioJSON")
Map appSettings = new HashMap();
public AlignmentPojo()