Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2289ac6..2dafc0c 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -54,11 +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;
 
@@ -76,14 +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>());
 
@@ -196,14 +185,7 @@ public class Alignment implements AlignmentI
     return AlignmentUtils.getSequencesByName(this);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public SequenceI getSequenceAt(int i)
   {
@@ -217,8 +199,32 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
+  public SequenceI getSequenceAtAbsoluteIndex(int i)
+  {
+    SequenceI seq = null;
+    if (getHiddenSequences().getSize() > 0)
+    {
+      seq = getHiddenSequences().getHiddenSequence(i);
+      if (seq == null)
+      {
+        // didn't find the sequence in the hidden sequences, get it from the
+        // alignment
+        int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+        seq = getSequenceAt(index);
+      }
+    }
+    else
+    {
+      seq = getSequenceAt(i);
+    }
+    return seq;
+  }
+
   /**
-   * 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
    */
@@ -329,30 +335,21 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(SequenceI s)
   {
-    deleteSequence(findIndex(s));
+    synchronized (sequences)
+    {
+      deleteSequence(findIndex(s));
+    }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(int i)
   {
-    if (i > -1 && i < getHeight())
+    synchronized (sequences)
     {
-      synchronized (sequences)
+      if (i > -1 && i < getHeight())
       {
         sequences.remove(i);
         hiddenSequences.adjustHeightSequenceDeleted(i);
@@ -360,23 +357,36 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    synchronized (sequences)
+    {
+      if (i > -1 && i < getHeight())
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
-  public SequenceGroup findGroup(SequenceI s)
+  public SequenceGroup findGroup(SequenceI seq, int position)
   {
     synchronized (groups)
     {
-      for (int i = 0; i < this.groups.size(); i++)
+      for (SequenceGroup sg : groups)
       {
-        SequenceGroup sg = groups.get(i);
-
-        if (sg.getSequences(null).contains(s))
+        if (sg.getSequences(null).contains(seq))
         {
-          return sg;
+          if (position >= sg.getStartRes() && position <= sg.getEndRes())
+          {
+            return sg;
+          }
         }
       }
     }
@@ -661,7 +671,7 @@ 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;
 
@@ -676,22 +686,19 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public int getHeight()
   {
     return sequences.size();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+  @Override
+  public int getAbsoluteHeight()
+  {
+    return sequences.size() + getHiddenSequences().getSize();
+  }
+
   @Override
   public int getWidth()
   {
@@ -777,6 +784,12 @@ public class Alignment implements AlignmentI
     return true;
   }
 
+  @Override
+  public boolean isHidden(int alignmentIndex)
+  {
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+  }
+
   /**
    * Delete all annotations, including auto-calculated if the flag is set true.
    * Returns true if at least one annotation was deleted, else false.
@@ -977,29 +990,9 @@ 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
@@ -1018,6 +1011,10 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
+      if (data == this)
+      {
+        throw new IllegalArgumentException("Circular dataset reference");
+      }
       if (!(data instanceof Alignment))
       {
         throw new Error(
@@ -1590,7 +1587,6 @@ public class Alignment implements AlignmentI
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    assert (name != null);
     if (annotations != null)
     {
       for (AlignmentAnnotation annot : getAlignmentAnnotation())
@@ -1622,14 +1618,18 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+    if (alignmentAnnotation != null)
     {
-      if (a.getCalcId() == calcId
-              || (a.getCalcId() != null && calcId != null && a.getCalcId()
-                      .equals(calcId)))
+      for (AlignmentAnnotation a : alignmentAnnotation)
       {
-        aa.add(a);
+        if (a.getCalcId() == calcId
+                || (a.getCalcId() != null && calcId != null && a
+                        .getCalcId().equals(calcId)))
+        {
+          aa.add(a);
+        }
       }
     }
     return aa;
@@ -1837,7 +1837,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**