JAL-629 implementation of --tempfac options

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b6e48dc..636088b 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -43,6 +43,7 @@ import jalview.analysis.WUSSParseException;
  */
 public class AlignmentAnnotation
 {
+
   private static final String ANNOTATION_ID_PREFIX = "ann";
 
   /*
@@ -95,6 +96,26 @@ public class AlignmentAnnotation
    */
   private long invalidrnastruc = -2;
 
+  public static enum TFType
+  {
+    DEFAULT, PLDDT, DOSE;
+  }
+
+  /**
+   * the type of temperature factor plot (if it is one)
+   */
+  private TFType tfType = TFType.DEFAULT;
+
+  public void setTFType(TFType t)
+  {
+    tfType = t;
+  }
+
+  public TFType getTFType()
+  {
+    return tfType;
+  }
+
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
@@ -551,12 +572,12 @@ public class AlignmentAnnotation
                       : annotations[index + offset].displayCharacter == null
                               || annotations[index
                                       + offset].displayCharacter
-                                              .length() == 0
-                                                      ? annotations[index
-                                                              + offset].secondaryStructure
-                                                      : annotations[index
-                                                              + offset].displayCharacter
-                                                                      .charAt(0));
+                                      .length() == 0
+                                              ? annotations[index
+                                                      + offset].secondaryStructure
+                                              : annotations[index
+                                                      + offset].displayCharacter
+                                                      .charAt(0));
     }
 
     @Override