X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjson%2Fbinding%2Fbiojson%2Fv1%2FAlignmentAnnotationPojo.java;h=673b09db26f639a7b3b45384f0fa1c2937d563e7;hb=e0e94503e960ce917c5d35ce8b7c065a696d0117;hp=6f21a2a60280ab4beb16cd5bc0aa4232c758fffd;hpb=c7d9dbc9b92889077b91bcdb052032fe33fb269e;p=jalview.git
diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 6f21a2a..673b09d 100644
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -7,18 +27,45 @@ import com.github.reinert.jjschema.Attributes;
public class AlignmentAnnotationPojo
{
- @Attributes(required = true, description = "Serial version id for the alignAnnotation object model")
- private String svid = "1.0";
- @Attributes(required = false, description = "Label for the Alignment Annotation")
+ @Attributes(
+ required = false,
+ description = "Label for the alignment annotation")
private String label;
- @Attributes(required = false, description = "Description for the Alignment Annotation")
+ @Attributes(
+ required = false,
+ description = "Description for the alignment annotation")
private String description;
@Attributes(required = false)
private List annotations = new ArrayList();
+ @Attributes(
+ required = false,
+ enums =
+ { "0", "1", "2" },
+ description = "Determines the rendering for the annotation
- 0 - No graph
- 1 - Bar Graph
- 2 - Line graph
")
+ private int graphType;
+
+ @Attributes(
+ required = false,
+ description = "Reference to the sequence in the alignment
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;
@@ -49,9 +96,55 @@ public class AlignmentAnnotationPojo
this.annotations = annotations;
}
- public String getSvid()
+ 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)
{
- return svid;
+ this.calcId = calcId;
}
}