JAL-3053

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f84b18d..ee9389c 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -25,6 +25,7 @@ import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -164,6 +165,64 @@ public class AlignmentAnnotation
   }
 
   /**
+   * Get the RNA Secondary Structure SequenceFeature Array if present
+   */
+  public SequenceFeature[] getRnaSecondaryStructure()
+  {
+    return this._rnasecstr;
+  }
+
+  /**
+   * Check the RNA Secondary Structure is equivalent to one in given
+   * AlignmentAnnotation param
+   */
+  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)
+  {
+    return rnaSecondaryStructureEquivalent(that, true);
+  }
+
+  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+  {
+    SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
+    SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
+    if (thisSfArray == null || thatSfArray == null)
+    {
+      return thisSfArray == null && thatSfArray == null;
+    }
+    if (thisSfArray.length != thatSfArray.length)
+    {
+      return false;
+    }
+    Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
+                                                   // like this
+    Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
+                                                   // like this
+    for (int i=0; i < thisSfArray.length; i++) {
+      SequenceFeature thisSf = thisSfArray[i];
+      SequenceFeature thatSf = thatSfArray[i];
+      if (compareType) {
+        if (thisSf.getType() == null || thatSf.getType() == null) {
+          if (thisSf.getType() == null && thatSf.getType() == null) {
+            continue;
+          } else {
+            return false;
+          }
+        }
+        if (! thisSf.getType().equals(thatSf.getType())) {
+          return false;
+        }
+      }
+      if (!(thisSf.getBegin() == thatSf.getBegin()
+              && thisSf.getEnd() == thatSf.getEnd()))
+      {
+        return false;
+      }
+    }
+    return true;
+
+  }
+
+  /**
    * map of positions in the associated annotation
    */
   private Map<Integer, Annotation> sequenceMapping;
@@ -321,10 +380,12 @@ public class AlignmentAnnotation
                 || annotations[i].secondaryStructure == 'B'
                 || annotations[i].secondaryStructure == 'C'
                 || annotations[i].secondaryStructure == 'D'
-                // || annotations[i].secondaryStructure == 'E'
+                // || annotations[i].secondaryStructure == 'E' // ambiguous on
+                // its own -- already checked above
                 || annotations[i].secondaryStructure == 'F'
                 || annotations[i].secondaryStructure == 'G'
-                // || annotations[i].secondaryStructure == 'H'
+                // || annotations[i].secondaryStructure == 'H' // ambiguous on
+                // its own -- already checked above
                 || annotations[i].secondaryStructure == 'I'
                 || annotations[i].secondaryStructure == 'J'
                 || annotations[i].secondaryStructure == 'K'
@@ -1652,4 +1713,5 @@ public class AlignmentAnnotation
     }
     return aa;
   }
+
 }