JAL-2828 refactored duplicate code for searching lists of AlignmentAnnotation to...

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 6bbd566..ffc3105 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -24,6 +24,7 @@ import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -96,14 +97,13 @@ public class AlignmentAnnotation
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
    * 
-   * @param RNAannot
+   * @param rnaAnnotation
    */
-  private void _updateRnaSecStr(CharSequence RNAannot)
+  private void _updateRnaSecStr(CharSequence rnaAnnotation)
   {
     try
     {
-      bps = Rna.getModeleBP(RNAannot);
-      _rnasecstr = Rna.getBasePairs(bps);
+      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -114,8 +114,6 @@ public class AlignmentAnnotation
     {
       return;
     }
-    Rna.HelixMap(_rnasecstr);
-    // setRNAStruc(RNAannot);
 
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
@@ -244,19 +242,6 @@ public class AlignmentAnnotation
 
   private boolean isrna;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    sequenceRef = null;
-    groupRef = null;
-    super.finalize();
-  }
-
   public static int getGraphValueFromString(String string)
   {
     if (string.equalsIgnoreCase("BAR_GRAPH"))
@@ -273,12 +258,6 @@ public class AlignmentAnnotation
     }
   }
 
-  // JBPNote: what does this do ?
-  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
-  {
-    bps = Rna.getModeleBP(RNAannot);
-  }
-
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -1493,4 +1472,69 @@ public class AlignmentAnnotation
   {
     return graphMin < graphMax;
   }
+
+  public static Iterable<AlignmentAnnotation> findAnnotations(
+          Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
+          String label)
+  {
+
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+    for (AlignmentAnnotation ann : list)
+    {
+      if ((calcId == null || (ann.getCalcId() != null
+              && ann.getCalcId().equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null
+                      && ann.sequenceRef == seq))
+              && (label == null
+                      || (ann.label != null && ann.label.equals(label))))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
+  /**
+   * Answer true if any annotation matches the calcId passed in (if not null).
+   * 
+   * @param list
+   *          annotation to search
+   * @param calcId
+   * @return
+   */
+  public static boolean hasAnnotation(List<AlignmentAnnotation> list,
+          String calcId)
+  {
+
+    if (calcId != null && !"".equals(calcId))
+    {
+      for (AlignmentAnnotation a : list)
+      {
+        if (a.getCalcId() == calcId)
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  public static Iterable<AlignmentAnnotation> findAnnotation(
+          List<AlignmentAnnotation> list, String calcId)
+  {
+
+    List<AlignmentAnnotation> aa = new ArrayList<>();
+    if (calcId == null)
+    {
+      return aa;
+    }
+    for (AlignmentAnnotation a : list)
+    {
+      if (calcId.equals(a.getCalcId()))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
 }