Merge branch 'features/JAL-3858_PAEsInProjects' into develop

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b6e48dc..4861dfd 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -34,6 +34,7 @@ import java.util.Map.Entry;
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
+import jalview.structure.StructureImportSettings;
 
 /**
  * DOCUMENT ME!
@@ -43,6 +44,7 @@ import jalview.analysis.WUSSParseException;
  */
 public class AlignmentAnnotation
 {
+
   private static final String ANNOTATION_ID_PREFIX = "ann";
 
   /*
@@ -96,6 +98,21 @@ public class AlignmentAnnotation
   private long invalidrnastruc = -2;
 
   /**
+   * the type of temperature factor plot (if it is one)
+   */
+  private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT;
+
+  public void setTFType(StructureImportSettings.TFType t)
+  {
+    tfType = t;
+  }
+
+  public StructureImportSettings.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
    * 
@@ -289,7 +306,7 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
-  public static final int CUSTOMRENDERER = 4;
+  public static final int CONTACT_MAP = 4;
 
   public boolean belowAlignment = true;
 
@@ -551,12 +568,12 @@ 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