X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6b100ea6e3320246a1f9614e579ba26f74b32edd;hb=af7becd656cba3835394e2dc50c2ad8d189a6d46;hp=b6a5e0f8e0082881f626fa347246c8e78e4123d5;hpb=cfed9d8a9e10be992877d6097260758ee5563630;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b6a5e0f..6b100ea 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -28,6 +28,7 @@ import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
@@ -50,7 +51,9 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
+
+  private SequenceI hmmConsensus;
 
   protected List<SequenceGroup> groups;
 
@@ -199,6 +202,7 @@ public class Alignment implements AlignmentI
         return sequences.get(i);
       }
     }
+
     return null;
   }
 
@@ -289,6 +293,32 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * Inserts a sequence at a point in the alignment.
+   * 
+   * @param i
+   *          the index of the position the sequence is to be inserted in.
+   */
+  @Override
+  public void insertSequenceAt(int i, SequenceI snew)
+  {
+    synchronized (sequences)
+    {
+      if (sequences.size() > i)
+      {
+        sequences.add(i, snew);
+        return;
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return;
+    }
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
@@ -707,7 +737,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-
+  
     for (int i = 0; i < sequences.size(); i++)
     {
       if (getSequenceAt(i).getLength() > maxLength)
@@ -715,9 +745,34 @@ public class Alignment implements AlignmentI
         maxLength = getSequenceAt(i).getLength();
       }
     }
-
+  
     return maxLength;
   }
+  /*
+  @Override
+  public int getWidth()
+  {
+    final Wrapper temp = new Wrapper();
+  
+    forEachSequence(new Consumer<SequenceI>()
+    {
+      @Override
+      public void accept(SequenceI s)
+      {
+        if (s.getLength() > temp.inner)
+        {
+          temp.inner = s.getLength();
+        }
+      }
+    }, 0, sequences.size() - 1);
+  
+    return temp.inner;
+  }
+  
+  public static class Wrapper
+  {
+    public int inner;
+  }*/
 
   /**
    * DOCUMENT ME!
@@ -1604,7 +1659,10 @@ public class Alignment implements AlignmentI
     AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
             new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
     annot.hasText = false;
-    annot.setCalcId(new String(calcId));
+    if (calcId != null)
+    {
+      annot.setCalcId(calcId);
+    }
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
     {
@@ -1619,40 +1677,21 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
-      for (AlignmentAnnotation a : alignmentAnnotation)
-      {
-        if (a.getCalcId() == calcId || (a.getCalcId() != null
-                && calcId != null && a.getCalcId().equals(calcId)))
-        {
-          aa.add(a);
-        }
-      }
+      return AlignmentAnnotation.findAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), calcId);
     }
-    return aa;
+    return Arrays.asList(new AlignmentAnnotation[] {});
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null
-              && ann.getCalcId().equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null
-                      && ann.sequenceRef == seq))
-              && (label == null
-                      || (ann.label != null && ann.label.equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   @Override
@@ -1917,6 +1956,18 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public SequenceI getHmmConsensus()
+  {
+    return hmmConsensus;
+  }
+
+  @Override
+  public void setHmmConsensus(SequenceI hmmConsensus)
+  {
+    this.hmmConsensus = hmmConsensus;
+  }
+
+  @Override
   public void setupJPredAlignment()
   {
     SequenceI repseq = getSequenceAt(0);
@@ -2027,5 +2078,4 @@ public class Alignment implements AlignmentI
       }
     }
   }
-
 }