Merge branch 'develop' into features/JAL-1152annotationSorting

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 78f64ac..0731991 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -25,6 +25,8 @@ import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Hashtable;
@@ -45,17 +47,24 @@ public class AlignmentAnnotation
    */
   public boolean autoCalculated = false;
 
+  /**
+   * unique ID for this annotation, used to match up the same annotation row
+   * shown in multiple views and alignments
+   */
   public String annotationId;
 
+  /**
+   * the sequence this annotation is associated with (or null)
+   */
   public SequenceI sequenceRef;
 
-  /** DOCUMENT ME!! */
+  /** label shown in dropdown menus and in the annotation label area */
   public String label;
 
-  /** DOCUMENT ME!! */
+  /** longer description text shown as a tooltip */
   public String description;
 
-  /** DOCUMENT ME!! */
+  /** Array of annotations placed in the current coordinate system */
   public Annotation[] annotations;
 
   public ArrayList<SimpleBP> bps = null;
@@ -105,6 +114,9 @@ public class AlignmentAnnotation
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
 
+  /**
+   * map of positions in the associated annotation
+   */
   public java.util.Hashtable<Integer, Annotation> sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -624,6 +636,14 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
+    if (annotation.properties!=null)
+    {
+      properties = new HashMap<String,String>();
+      for (Map.Entry<String, String> val:annotation.properties.entrySet())
+      {
+        properties.put(val.getKey(), val.getValue());
+      }
+    }
     if (this.hasScore = annotation.hasScore)
     {
       this.score = annotation.score;
@@ -632,9 +652,9 @@ public class AlignmentAnnotation
     {
       threshold = new GraphLine(annotation.threshold);
     }
+    Annotation[] ann = annotation.annotations;
     if (annotation.annotations != null)
     {
-      Annotation[] ann = annotation.annotations;
       this.annotations = new Annotation[ann.length];
       for (int i = 0; i < ann.length; i++)
       {
@@ -647,24 +667,26 @@ public class AlignmentAnnotation
           }
         }
       }
-      ;
-      if (annotation.sequenceRef != null)
+    }
+    if (annotation.sequenceRef != null)
+    {
+      this.sequenceRef = annotation.sequenceRef;
+      if (annotation.sequenceMapping != null)
       {
-        this.sequenceRef = annotation.sequenceRef;
-        if (annotation.sequenceMapping != null)
+        Integer p = null;
+        sequenceMapping = new Hashtable();
+        Enumeration pos = annotation.sequenceMapping.keys();
+        while (pos.hasMoreElements())
         {
-          Integer p = null;
-          sequenceMapping = new Hashtable();
-          Enumeration pos = annotation.sequenceMapping.keys();
-          while (pos.hasMoreElements())
+          // could optimise this!
+          p = (Integer) pos.nextElement();
+          Annotation a = annotation.sequenceMapping.get(p);
+          if (a == null)
+          {
+            continue;
+          }
+          if (ann != null)
           {
-            // could optimise this!
-            p = (Integer) pos.nextElement();
-            Annotation a = annotation.sequenceMapping.get(p);
-            if (a == null)
-            {
-              continue;
-            }
             for (int i = 0; i < ann.length; i++)
             {
               if (ann[i] == a)
@@ -674,10 +696,10 @@ public class AlignmentAnnotation
             }
           }
         }
-        else
-        {
-          this.sequenceMapping = null;
-        }
+      }
+      else
+      {
+        this.sequenceMapping = null;
       }
     }
     // TODO: check if we need to do this: JAL-952
@@ -1262,7 +1284,7 @@ public class AlignmentAnnotation
     }
   }
 
-  public Object getProperty(String property)
+  public String getProperty(String property)
   {
     if (properties == null)
     {
@@ -1279,4 +1301,18 @@ public class AlignmentAnnotation
     }
     properties.put(property, value);
   }
+
+  public boolean hasProperties()
+  {
+    return properties != null && properties.size() > 0;
+  }
+
+  public Collection<String> getProperties()
+  {
+    if (properties == null)
+    {
+      return Collections.EMPTY_LIST;
+    }
+    return properties.keySet();
+  }
 }