X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=8f826f558cd2debb82e44f5843bb429e290f0c8c;hb=c9a198a4eb76592ff9091cdba7d0299a0345ba09;hp=a5a38df7da391eef3ef84015d0ad3b351c6b03bf;hpb=566041d3e8ca1d8783b4572a695e83784c0b6bc7;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index a5a38df..8f826f5 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -170,10 +170,14 @@ public class AlignmentAnnotation
    */
   private Map<Integer, Annotation> sequenceMapping;
 
-  /** DOCUMENT ME!! */
+  /**
+   * lower range for quantitative data
+   */
   public float graphMin;
 
-  /** DOCUMENT ME!! */
+  /**
+   * Upper range for quantitative data
+   */
   public float graphMax;
 
   /**
@@ -593,6 +597,7 @@ public class AlignmentAnnotation
     if (annotations == null)
     {
       visible = false; // try to prevent renderer from displaying.
+      invalidrnastruc = -1;
       return; // this is a non-annotation row annotation - ie a sequence score.
     }
 
@@ -696,7 +701,7 @@ public class AlignmentAnnotation
     this.calcId = annotation.calcId;
     if (annotation.properties != null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
       for (Map.Entry<String, String> val : annotation.properties.entrySet())
       {
         properties.put(val.getKey(), val.getValue());
@@ -732,7 +737,7 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new HashMap<Integer, Annotation>();
+        sequenceMapping = new HashMap<>();
         Iterator<Integer> pos = annotation.sequenceMapping.keySet()
                 .iterator();
         while (pos.hasNext())
@@ -812,7 +817,7 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Map<Integer, Annotation> newmapping = new HashMap<>();
         Iterator<Integer> e = sequenceMapping.keySet().iterator();
         while (e.hasNext())
         {
@@ -862,6 +867,10 @@ public class AlignmentAnnotation
   @Override
   public String toString()
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
@@ -935,7 +944,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new HashMap<Integer, Annotation>();
+    sequenceMapping = new HashMap<>();
 
     int seqPos;
 
@@ -1141,14 +1150,14 @@ public class AlignmentAnnotation
    * @param colSel
    */
   public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
-          ColumnSelection colSel)
+          HiddenColumns hidden)
   {
     this(alignmentAnnotation);
     if (annotations == null)
     {
       return;
     }
-    colSel.makeVisibleAnnotation(this);
+    hidden.makeVisibleAnnotation(this);
   }
 
   public void setPadGaps(boolean padgaps, char gapchar)
@@ -1214,7 +1223,7 @@ public class AlignmentAnnotation
   /**
    * properties associated with the calcId
    */
-  protected Map<String, String> properties = new HashMap<String, String>();
+  protected Map<String, String> properties = new HashMap<>();
 
   /**
    * base colour for line graphs. If null, will be set automatically by
@@ -1258,7 +1267,7 @@ public class AlignmentAnnotation
             .getTo() == sq.getDatasetSequence()) : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+    Map<Integer, Annotation> mapForsq = new HashMap<>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1306,13 +1315,12 @@ public class AlignmentAnnotation
    *       already
    */
   public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
-          int from, int to,
-          int idxoffset)
+          int from, int to, int idxoffset)
   {
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
-      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+      Map<Integer, Annotation> remap = new HashMap<>();
       int index = -1;
       for (int mp[] : mapping.values())
       {
@@ -1370,7 +1378,7 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
     }
     properties.put(property, value);
   }
@@ -1411,8 +1419,89 @@ public class AlignmentAnnotation
     this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
   }
 
+  /**
+   * Returns the match for the last unmatched opening RNA helix pair symbol
+   * preceding the given column, or '(' if nothing found to match.
+   * 
+   * @param column
+   * @return
+   */
+  public String getDefaultRnaHelixSymbol(int column)
+  {
+    String result = "(";
+    if (annotations == null)
+    {
+      return result;
+    }
+
+    /*
+     * for each preceding column, if it contains an open bracket, 
+     * count whether it is still unmatched at column, if so return its pair
+     * (likely faster than the fancy alternative using stacks)
+     */
+    for (int col = column - 1; col >= 0; col--)
+    {
+      Annotation annotation = annotations[col];
+      if (annotation == null)
+      {
+        continue;
+      }
+      String displayed = annotation.displayCharacter;
+      if (displayed == null || displayed.length() != 1)
+      {
+        continue;
+      }
+      char symbol = displayed.charAt(0);
+      if (!Rna.isOpeningParenthesis(symbol))
+      {
+        continue;
+      }
+
+      /*
+       * found an opening bracket symbol
+       * count (closing-opening) symbols of this type that follow it,
+       * up to and excluding the target column; if the count is less
+       * than 1, the opening bracket is unmatched, so return its match
+       */
+      String closer = String.valueOf(Rna
+              .getMatchingClosingParenthesis(symbol));
+      String opener = String.valueOf(symbol);
+      int count = 0;
+      for (int j = col + 1; j < column; j++)
+      {
+        if (annotations[j] != null)
+        {
+          String s = annotations[j].displayCharacter;
+          if (closer.equals(s))
+          {
+            count++;
+          }
+          else if (opener.equals(s))
+          {
+            count--;
+          }
+        }
+      }
+      if (count < 1)
+      {
+        return closer;
+      }
+    }
+    return result;
+  }
+
   protected static synchronized long nextId()
   {
     return counter++;
   }
+
+  /**
+   * 
+   * @return true for rows that have a range of values in their annotation set
+   */
+  public boolean isQuantitative()
+  {
+    return graphMin < graphMax;
+  }
+
 }