JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0098d76..0f41850 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,19 +20,21 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.Rna;
-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;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 /**
  * DOCUMENT ME!
  * 
@@ -164,6 +166,72 @@ 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 +362,7 @@ 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;
@@ -301,27 +370,35 @@ 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 ?
+        // allow for DSSP extended code:
+        // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
+        // GHITEBS as well as C and X (for missing?)
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
                 || annotations[i].secondaryStructure == '{'
                 || annotations[i].secondaryStructure == 'A'
-                || annotations[i].secondaryStructure == 'B'
-                || annotations[i].secondaryStructure == 'C'
+                // || 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 == 'I'
+                // || annotations[i].secondaryStructure == 'G'
+                // || annotations[i].secondaryStructure == 'H' // ambiguous on
+                // its own -- already checked above
+                // || annotations[i].secondaryStructure == 'I'
                 || annotations[i].secondaryStructure == 'J'
                 || annotations[i].secondaryStructure == 'K'
                 || annotations[i].secondaryStructure == 'L'
@@ -331,12 +408,12 @@ public class AlignmentAnnotation
                 || annotations[i].secondaryStructure == 'P'
                 || annotations[i].secondaryStructure == 'Q'
                 || annotations[i].secondaryStructure == 'R'
-                || annotations[i].secondaryStructure == 'S'
-                || annotations[i].secondaryStructure == 'T'
+                // || annotations[i].secondaryStructure == 'S'
+                // || annotations[i].secondaryStructure == 'T'
                 || annotations[i].secondaryStructure == 'U'
                 || annotations[i].secondaryStructure == 'V'
                 || annotations[i].secondaryStructure == 'W'
-                || annotations[i].secondaryStructure == 'X'
+                // || annotations[i].secondaryStructure == 'X'
                 || annotations[i].secondaryStructure == 'Y'
                 || annotations[i].secondaryStructure == 'Z')
         {
@@ -367,7 +444,7 @@ 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'
@@ -472,12 +549,12 @@ public class AlignmentAnnotation
                       : annotations[index + offset].displayCharacter == null
                               || annotations[index
                                       + offset].displayCharacter
-                                              .length() == 0
-                                                      ? annotations[index
-                                                              + offset].secondaryStructure
-                                                      : annotations[index
-                                                              + offset].displayCharacter
-                                                                      .charAt(0));
+                                      .length() == 0
+                                              ? annotations[index
+                                                      + offset].secondaryStructure
+                                              : annotations[index
+                                                      + offset].displayCharacter
+                                                      .charAt(0));
     }
 
     @Override
@@ -926,7 +1003,7 @@ public class AlignmentAnnotation
           seqPos = i + startRes;
         }
 
-        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+        sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
       }
     }
 
@@ -965,7 +1042,7 @@ public class AlignmentAnnotation
     {
       for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        index = new Integer(a);
+        index = Integer.valueOf(a);
         Annotation annot = sequenceMapping.get(index);
         if (annot != null)
         {
@@ -1160,7 +1237,7 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
-      int i = description.toLowerCase().indexOf("<html>");
+      int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
       if (i > -1)
       {
         // move the html tag to before the sequence reference.
@@ -1648,4 +1725,5 @@ public class AlignmentAnnotation
     }
     return aa;
   }
+
 }