Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
new file mode 100644 (file)
index 0000000..a9e57a9
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -0,0 +1,149 @@
+/*
+ * 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 java.util.ArrayList;
+import java.util.List;
+
+import com.github.reinert.jjschema.Attributes;
+
+public class AlignmentAnnotationPojo
+{
+
+  @Attributes(
+    required = false,
+    description = "Label for the alignment annotation")
+  private String label;
+
+  @Attributes(
+    required = false,
+    description = "Description for the alignment annotation")
+  private String description;
+
+  @Attributes(required = false)
+  private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
+
+  @Attributes(
+    required = false,
+    enums = { "0", "1", "2" },
+    description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+  private int graphType;
+
+  @Attributes(
+    required = false,
+    description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
+  private String sequenceRef;
+
+  @Attributes(
+    required = false,
+    description = "Stores display settings for an annotation")
+  private AnnotationDisplaySettingPojo annotationSettings;
+
+  @Attributes(required = false, description = "Score of the annotation")
+  private double score;
+
+  @Attributes(
+    required = false,
+    description = "The annotation generation source")
+  private String calcId;
+
+  public String getLabel()
+  {
+    return label;
+  }
+
+  public void setLabel(String label)
+  {
+    this.label = label;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String annotationId)
+  {
+    this.description = annotationId;
+  }
+
+  public List<AnnotationPojo> getAnnotations()
+  {
+    return annotations;
+  }
+
+  public void setAnnotations(List<AnnotationPojo> annotations)
+  {
+    this.annotations = annotations;
+  }
+
+  public String getSequenceRef()
+  {
+    return sequenceRef;
+  }
+
+  public void setSequenceRef(String sequenceRef)
+  {
+    this.sequenceRef = sequenceRef;
+  }
+
+  public int getGraphType()
+  {
+    return graphType;
+  }
+
+  public void setGraphType(int graphType)
+  {
+    this.graphType = graphType;
+  }
+
+  public AnnotationDisplaySettingPojo getAnnotationSettings()
+  {
+    return annotationSettings;
+  }
+
+  public void setAnnotationSettings(
+          AnnotationDisplaySettingPojo annotationSettings)
+  {
+    this.annotationSettings = annotationSettings;
+  }
+
+  public double getScore()
+  {
+    return score;
+  }
+
+  public void setScore(double score)
+  {
+    this.score = score;
+  }
+
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  public void setCalcId(String calcId)
+  {
+    this.calcId = calcId;
+  }
+
+}