JAL-2110 bug fixing and tidying for get cross-refs

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

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 5dfd434..18aaecf 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.AbstractList;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -36,7 +37,7 @@ public class AlignedCodonFrame
   /*
    * Data bean to hold mappings from one sequence to another
    */
-  private class SequenceToSequenceMapping
+  public class SequenceToSequenceMapping
   {
     private SequenceI fromSeq;
 
@@ -57,6 +58,54 @@ public class AlignedCodonFrame
       return String.format("From %s %s", fromSeq.getName(),
               mapping.toString());
     }
+
+    /**
+     * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
+     * 
+     * @see SequenceToSequenceMapping#hashCode()
+     */
+    @Override
+    public int hashCode()
+    {
+      return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
+              + mapping.hashCode();
+    }
+
+    /**
+     * Answers true if the objects hold the same mapping between the same two
+     * sequences
+     * 
+     * @see Mapping#equals
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (!(obj instanceof SequenceToSequenceMapping))
+      {
+        return false;
+      }
+      SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
+      if (this.mapping == null)
+      {
+        return that.mapping == null;
+      }
+      // TODO: can simplify by asserting fromSeq is a dataset sequence
+      return (this.fromSeq == that.fromSeq || (this.fromSeq != null
+              && that.fromSeq != null
+              && this.fromSeq.getDatasetSequence() != null && this.fromSeq
+              .getDatasetSequence() == that.fromSeq
+              .getDatasetSequence())) && this.mapping.equals(that.mapping);
+    }
+
+    public SequenceI getFromSeq()
+    {
+      return fromSeq;
+    }
+
+    public Mapping getMapping()
+    {
+      return mapping;
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -90,6 +139,8 @@ public class AlignedCodonFrame
 
     /*
      * if we already hold a mapping between these sequences, just add to it 
+     * note that 'adding' a duplicate map does nothing; this protects against
+     * creating duplicate mappings in AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
@@ -303,7 +354,8 @@ public class AlignedCodonFrame
 
   /**
    * Convenience method to return the first aligned sequence in the given
-   * alignment whose dataset has a mapping with the given dataset sequence.
+   * alignment whose dataset has a mapping with the given (aligned or dataset)
+   * sequence.
    * 
    * @param seq
    * 
@@ -317,11 +369,12 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq)
+      if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.mapping.to == sourceAligned.getDatasetSequence())
+          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
+                  || ssm.mapping.to == sourceAligned)
           {
             return sourceAligned;
           }
@@ -334,7 +387,8 @@ public class AlignedCodonFrame
      */
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.mapping.to == seq)
+      if (ssm.mapping.to == seq
+              || ssm.mapping.to == seq.getDatasetSequence())
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
@@ -443,13 +497,13 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns any mappings found which are to (or from) the given sequence, and
-   * to distinct sequences.
+   * Returns any mappings found which are from the given sequence, and to
+   * distinct sequences.
    * 
    * @param seq
    * @return
    */
-  public List<Mapping> getMappingsForSequence(SequenceI seq)
+  public List<Mapping> getMappingsFromSequence(SequenceI seq)
   {
     List<Mapping> result = new ArrayList<Mapping>();
     List<SequenceI> related = new ArrayList<SequenceI>();
@@ -459,7 +513,7 @@ public class AlignedCodonFrame
     for (SequenceToSequenceMapping ssm : mappings)
     {
       final Mapping mapping = ssm.mapping;
-      if (ssm.fromSeq == seqDs || mapping.to == seqDs)
+      if (ssm.fromSeq == seqDs)
       {
         if (!related.contains(mapping.to))
         {
@@ -637,4 +691,76 @@ public class AlignedCodonFrame
   {
     return mappings.isEmpty();
   }
+
+  /**
+   * Method for debug / inspection purposes only, may change in future
+   */
+  @Override
+  public String toString()
+  {
+    return mappings == null ? "null" : mappings.toString();
+  }
+
+  /**
+   * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or null
+   * if none found
+   * 
+   * @param fromSeq
+   *          aligned or dataset sequence
+   * @param toSeq
+   *          aligned or dataset sequence
+   * @return
+   */
+  public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
+  {
+    SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
+            : fromSeq.getDatasetSequence();
+    SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
+            .getDatasetSequence();
+
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      SequenceI from = mapping.fromSeq;
+      SequenceI to = mapping.mapping.to;
+      if ((from == dssFrom && to == dssTo)
+              || (from == dssTo && to == dssFrom))
+      {
+        return mapping.mapping;
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Returns a hashcode derived from the list of sequence mappings
+   * 
+   * @see SequenceToSequenceMapping#hashCode()
+   * @see AbstractList#hashCode()
+   */
+  @Override
+  public int hashCode()
+  {
+    return this.mappings.hashCode();
+  }
+
+  /**
+   * Two AlignedCodonFrame objects are equal if they hold the same ordered list
+   * of mappings
+   * 
+   * @see SequenceToSequenceMapping#
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof AlignedCodonFrame))
+    {
+      return false;
+    }
+    return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
+  }
+
+  public List<SequenceToSequenceMapping> getMappings()
+  {
+    return mappings;
+  }
 }