JAL-674 JAL-961 properties to stash additional information for an alignment annotatio...

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 012ecb3..78f64ac 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -22,17 +22,15 @@ package jalview.datamodel;
 
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
-
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import fr.orsay.lri.varna.models.rna.RNA;
-
 /**
  * DOCUMENT ME!
  * 
@@ -261,7 +259,8 @@ public class AlignmentAnnotation
       // Check for RNA secondary structure
       {
         // System.out.println(annotations[i].secondaryStructure);
-        // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
+        // TODO: 2.8.2 should this ss symbol validation check be a function in
+        // RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
@@ -604,7 +603,9 @@ public class AlignmentAnnotation
   {
     this.label = new String(annotation.label);
     if (annotation.description != null)
+    {
       this.description = new String(annotation.description);
+    }
     this.graphMin = annotation.graphMin;
     this.graphMax = annotation.graphMax;
     this.graph = annotation.graph;
@@ -659,7 +660,7 @@ public class AlignmentAnnotation
           {
             // could optimise this!
             p = (Integer) pos.nextElement();
-            Annotation a = (Annotation) annotation.sequenceMapping.get(p);
+            Annotation a = annotation.sequenceMapping.get(p);
             if (a == null)
             {
               continue;
@@ -702,13 +703,21 @@ public class AlignmentAnnotation
       return;
     }
     if (startRes < 0)
+    {
       startRes = 0;
+    }
     if (startRes >= annotations.length)
+    {
       startRes = annotations.length - 1;
+    }
     if (endRes >= annotations.length)
+    {
       endRes = annotations.length - 1;
+    }
     if (annotations == null)
+    {
       return;
+    }
     Annotation[] temp = new Annotation[endRes - startRes + 1];
     if (startRes < annotations.length)
     {
@@ -870,7 +879,9 @@ public class AlignmentAnnotation
   public void adjustForAlignment()
   {
     if (sequenceRef == null)
+    {
       return;
+    }
 
     if (annotations == null)
     {
@@ -896,7 +907,7 @@ public class AlignmentAnnotation
       {
         position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = (Annotation) sequenceMapping.get(index);
+        temp[position] = sequenceMapping.get(index);
       }
     }
 
@@ -917,8 +928,10 @@ public class AlignmentAnnotation
       if (annotations[i] == null)
       {
         if (i + 1 < iSize)
+        {
           System.arraycopy(annotations, i + 1, annotations, i, iSize - i
                   - 1);
+        }
         iSize--;
       }
       else
@@ -1056,11 +1069,15 @@ public class AlignmentAnnotation
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] == null)
+        {
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
                   ' ', 0f, null);
+        }
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
+        {
           annotations[i].displayCharacter = String.valueOf(gapchar);
+        }
       }
     }
   }
@@ -1104,6 +1121,11 @@ public class AlignmentAnnotation
   protected String calcId = "";
 
   /**
+   * properties associated with the calcId
+   */
+  protected Map<String, String> properties = new HashMap<String, String>();
+
+  /**
    * base colour for line graphs. If null, will be set automatically by
    * searching the alignment annotation
    */
@@ -1167,6 +1189,94 @@ public class AlignmentAnnotation
         // trim positions
       }
     }
+  }
 
+  /**
+   * like liftOver but more general.
+   * 
+   * Takes an array of int pairs that will be used to update the internal
+   * sequenceMapping and so shuffle the annotated positions
+   * 
+   * @param newref
+   *          - new sequence reference for the annotation row - if null,
+   *          sequenceRef is left unchanged
+   * @param mapping
+   *          array of ints containing corresponding positions
+   * @param from
+   *          - column for current coordinate system (-1 for index+1)
+   * @param to
+   *          - column for destination coordinate system (-1 for index+1)
+   * @param idxoffset
+   *          - offset added to index when referencing either coordinate system
+   * @note no checks are made as to whether from and/or to are sensible
+   * @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)
+  {
+    if (mapping != null)
+    {
+      Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+      int index = -1;
+      for (int mp[] : mapping)
+      {
+        if (index++ < 0)
+        {
+          continue;
+        }
+        Annotation ann = null;
+        if (from == -1)
+        {
+          ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
+        }
+        else
+        {
+          if (mp != null && mp.length > from)
+          {
+            ann = sequenceMapping.get(Integer.valueOf(mp[from]));
+          }
+        }
+        if (ann != null)
+        {
+          if (to == -1)
+          {
+            remap.put(Integer.valueOf(idxoffset + index), ann);
+          }
+          else
+          {
+            if (to > -1 && to < mp.length)
+            {
+              remap.put(Integer.valueOf(mp[to]), ann);
+            }
+          }
+        }
+      }
+      sequenceMapping = remap;
+      old.clear();
+      if (newref != null)
+      {
+        sequenceRef = newref;
+      }
+      adjustForAlignment();
+    }
+  }
+
+  public Object getProperty(String property)
+  {
+    if (properties == null)
+    {
+      return null;
+    }
+    return properties.get(property);
+  }
+
+  public void setProperty(String property, String value)
+  {
+    if (properties==null)
+    {
+      properties = new HashMap<String,String>();
+    }
+    properties.put(property, value);
   }
 }