Merge remote-tracking branch 'origin/releases/Release_2_10_3_Branch'

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 09facbf..f7bf4d8 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;
@@ -1471,4 +1472,71 @@ 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 (a.getCalcId() == calcId || (a.getCalcId() != null
+              && calcId != null && a.getCalcId().equals(calcId)))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
 }