JAL-2360 simplify nucleotide flag, remove setter

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 35ee8c4..290707d 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
@@ -53,11 +54,7 @@ public class Alignment implements AlignmentI
 
   protected char gapCharacter = '-';
 
-  protected int type = NUCLEOTIDE;
-
-  public static final int PROTEIN = 0;
-
-  public static final int NUCLEOTIDE = 1;
+  private boolean nucleotide = true;
 
   public boolean hasRNAStructure = false;
 
@@ -75,14 +72,7 @@ public class Alignment implements AlignmentI
     hiddenSequences = new HiddenSequences(this);
     codonFrameList = new ArrayList<AlignedCodonFrame>();
 
-    if (Comparison.isNucleotide(seqs))
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
+    nucleotide = Comparison.isNucleotide(seqs);
 
     sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
@@ -217,7 +207,9 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+   * this currently does not recalculate whether or not the alignment is
+   * nucleotide, so mixed alignments may have undefined behaviour.
    * 
    * @param snew
    */
@@ -660,7 +652,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
-  public int findIndex(SearchResults results)
+  public int findIndex(SearchResultsI results)
   {
     int i = 0;
 
@@ -976,29 +968,9 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setNucleotide(boolean b)
-  {
-    if (b)
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
-  }
-
-  @Override
   public boolean isNucleotide()
   {
-    if (type == NUCLEOTIDE)
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
+    return nucleotide;
   }
 
   @Override
@@ -1054,6 +1026,7 @@ public class Alignment implements AlignmentI
   private void resolveAndAddDatasetSeq(SequenceI currentSeq,
           Set<SequenceI> seqs, boolean createDatasetSequence)
   {
+    SequenceI alignedSeq = currentSeq;
     if (currentSeq.getDatasetSequence() != null)
     {
       currentSeq = currentSeq.getDatasetSequence();
@@ -1088,12 +1061,19 @@ public class Alignment implements AlignmentI
         {
           if (dbr.getMap() != null && dbr.getMap().getTo() != null)
           {
+            if (dbr.getMap().getTo() == alignedSeq)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
             if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              throw new Error("Implementation error: Map.getTo() for dbref"
-                      + dbr + " is not a dataset sequence.");
-              // TODO: if this happens, could also rewrite the reference to
-              // point to new dataset sequence
+              throw new Error(
+                      "Implementation error: Map.getTo() for dbref " + dbr
+                              + " from " + curDs.getName()
+                              + " is not a dataset sequence.");
             }
             // we recurse to add all forward references to dataset sequences via
             // DBRefs/etc
@@ -1115,7 +1095,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1828,7 +1808,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**