X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=ee9389c04dc6697b89a8f2857e3948d4c3eb6ac1;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=6c33c1b866861f0c8b4fe82c59e4894e442b8cfc;hpb=62086b8b7a0b9436c445a94bfab5eff253adb6d5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 6c33c1b..ee9389c 100755
--- 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;
@@ -294,6 +353,7 @@ public class AlignmentAnnotation
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
+      // DEBUG System.out.println(i + ": " + annotations[i]);
       if (annotations[i] == null)
       {
         continue;
@@ -301,12 +361,15 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
+        // DEBUG System.out.println( "/H|E/ '" +
+        // annotations[i].secondaryStructure + "'");
         hasIcons |= true;
       }
       else
       // Check for RNA secondary structure
       {
-        // System.out.println(annotations[i].secondaryStructure);
+        // DEBUG System.out.println( "/else/ '" +
+        // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
@@ -317,10 +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'
@@ -367,7 +432,7 @@ public class AlignmentAnnotation
         // &&
         // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
-                && firstChar != '(' && firstChar != '[' && firstChar != '>'
+                && firstChar != '(' && firstChar != '[' && firstChar != '<'
                 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
                 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
                 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
@@ -1582,4 +1647,71 @@ public class AlignmentAnnotation
     }
   }
 
+  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;
+  }
+
 }