javadoc

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index f628699..69d6da2 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -493,7 +493,9 @@ public class Sequence implements SequenceI
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
+    }
     // JBPNote - left to user to pad the result here (TODO:Decide on this
     // policy)
     if (start >= sequence.length)
@@ -512,16 +514,7 @@ public class Sequence implements SequenceI
     return reply;
   }
 
-  /**
-   * make a new Sequence object from start to end (including gaps) over this
-   * seqeunce
-   * 
-   * @param start
-   *          int
-   * @param end
-   *          int
-   * @return SequenceI
-   */
+  @Override
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
@@ -621,14 +614,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   * 
-   * @param i
-   *          column index in alignment (from 1)
-   * 
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     int j = 0;
@@ -928,7 +914,9 @@ public class Sequence implements SequenceI
     {
       this.annotation.removeElement(annotation);
       if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
@@ -1040,7 +1028,9 @@ public class Sequence implements SequenceI
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
@@ -1082,33 +1072,6 @@ public class Sequence implements SequenceI
     return anns;
   }
 
-  /**
-   * Returns a list of any annotations on the sequence that match the given
-   * calcId (source) and label (type). Null values do not match.
-   * 
-   * @param calcId
-   * @param label
-   * @return
-   */
-  @Override
-  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
-          String label)
-  {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
-    if (annotation != null)
-    {
-      for (AlignmentAnnotation ann : annotation)
-      {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
-        {
-          result.add(ann);
-        }
-      }
-    }
-    return result;
-  }
-
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)
@@ -1264,4 +1227,28 @@ public class Sequence implements SequenceI
     return rna;
   }
 
+  /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source) and label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   */
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (this.annotation != null) {
+      for (AlignmentAnnotation ann : annotation) {
+        if (ann.calcId != null && ann.calcId.equals(calcId)
+                && ann.label != null && ann.label.equals(label))
+        {
+          result.add(ann);
+        }
+      }
+    }
+    return result;
+  }
+
 }