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

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

diff --git a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
new file mode 100644 (file)
index 0000000..d49c1d5
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
@@ -0,0 +1,101 @@
+/*
+ * 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 AnnotationPojo
+{
+  @Attributes(
+    required = false,
+    description = "Display character for the given annotation")
+  private String displayCharacter;
+
+  @Attributes(
+    required = false,
+    description = "Description for the annotation")
+  private String description;
+
+  @Attributes(
+    required = true,
+    enums = { "E", "H", "\u0000", ")", "(" },
+    description = "Determines what is rendered for the secondary </br>structure <ul><li>’E’ - indicates Beta Sheet/Strand <li>’H’ - indicates alpha helix </li><li> ‘\\u0000’ - indicates blank</li></ul></br>For RNA Helix (only shown when working with</br> nucleotide sequences): <ul><li> ‘(’ - indicates bases pair with columns upstream</br> (to right) </li><li> ’(’ - indicate region pairs with bases to the left</li></ul>")
+  private char secondaryStructure;
+
+  @Attributes(required = false, description = "Value of the annotation")
+  private float value;
+
+  @Attributes(
+    required = false,
+    description = "Colour of the annotation position in hex string.")
+  private String colour;
+
+  public String getDisplayCharacter()
+  {
+    return displayCharacter;
+  }
+
+  public void setDisplayCharacter(String displayCharacter)
+  {
+    this.displayCharacter = displayCharacter;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String description)
+  {
+    this.description = description;
+  }
+
+  public char getSecondaryStructure()
+  {
+    return secondaryStructure;
+  }
+
+  public void setSecondaryStructure(char secondaryStructure)
+  {
+    this.secondaryStructure = secondaryStructure;
+  }
+
+  public float getValue()
+  {
+    return value;
+  }
+
+  public void setValue(float value)
+  {
+    this.value = value;
+  }
+
+  public String getColour()
+  {
+    return colour;
+  }
+
+  public void setColour(String colour)
+  {
+    this.colour = colour;
+  }
+
+}