X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=56bfd74e604ae135c1b7ef5b0e9ba07bdd9fbed2;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=95141e60c182a7c12be392cecb9dfdcc0f9d0af0;hpb=57dd16688caa6dacaeaf465bab3ee8b6126e1a51;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 95141e6..56bfd74 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,11 +24,11 @@ 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;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -79,7 +79,7 @@ public class AlignmentAnnotation
   /** Array of annotations placed in the current coordinate system */
   public Annotation[] annotations;
 
-  public ArrayList<SimpleBP> bps = null;
+  public List<SimpleBP> bps = null;
 
   /**
    * RNA secondary structure contact positions
@@ -96,14 +96,13 @@ 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
     {
-      _rnasecstr = Rna.GetBasePairs(RNAannot);
-      bps = Rna.GetModeleBP(RNAannot);
+      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -114,8 +113,6 @@ public class AlignmentAnnotation
     {
       return;
     }
-    Rna.HelixMap(_rnasecstr);
-    // setRNAStruc(RNAannot);
 
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
@@ -170,10 +167,14 @@ 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;
 
   /**
@@ -245,6 +246,7 @@ public class AlignmentAnnotation
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     sequenceRef = null;
@@ -268,12 +270,6 @@ public class AlignmentAnnotation
     }
   }
 
-  // JBPNote: what does this do ?
-  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
-  {
-    bps = Rna.GetModeleBP(RNAannot);
-  }
-
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -484,7 +480,7 @@ public class AlignmentAnnotation
       this(0, annotations.length);
     }
 
-    public AnnotCharSequence(int start, int end)
+    AnnotCharSequence(int start, int end)
     {
       offset = start;
       max = end;
@@ -592,6 +588,7 @@ 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.
     }
 
@@ -861,6 +858,10 @@ public class AlignmentAnnotation
   @Override
   public String toString()
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
@@ -1140,14 +1141,14 @@ 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)
@@ -1304,15 +1305,15 @@ public class AlignmentAnnotation
    * @note caller should add the remapped annotation to newref if they have not
    *       already
    */
-  public void remap(SequenceI newref, int[][] mapping, int from, int to,
-          int idxoffset)
+  public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
+          int from, int to, int idxoffset)
   {
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
       Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
-      for (int mp[] : mapping)
+      for (int mp[] : mapping.values())
       {
         if (index++ < 0)
         {
@@ -1409,8 +1410,88 @@ 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;
+  }
 }