X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=01d3d8d626f1eb53767631146123f43687d57bdd;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=f19d117fbdce32223cdbfb7e8e04d36154a59ded;hpb=fe6b3fb39308b5c045849db2be75ba07824be776;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f19d117..01d3d8d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.util.MessageManager;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -117,7 +119,7 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error("Alignment(CigarArray) not yet implemented");
+    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -145,7 +147,9 @@ public class Alignment implements AlignmentI
   public SequenceI[] getSequencesArray()
   {
     if (sequences == null)
+    {
       return null;
+    }
     synchronized (sequences)
     {
       return sequences.toArray(new SequenceI[sequences.size()]);
@@ -209,7 +213,9 @@ public class Alignment implements AlignmentI
       }
     }
     if (hiddenSequences != null)
+    {
       hiddenSequences.adjustHeightSequenceAdded();
+    }
   }
 
   /**
@@ -243,7 +249,9 @@ public class Alignment implements AlignmentI
   public void finalize()
   {
     if (getDataset() != null)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -752,7 +760,9 @@ public class Alignment implements AlignmentI
         continue;
       }
       if (tIndex < temp.length)
+      {
         temp[tIndex++] = annotations[i];
+      }
     }
 
     if (swap)
@@ -948,6 +958,27 @@ public class Alignment implements AlignmentI
     else if (dataset == null && data != null)
     {
       dataset = data;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        SequenceI currentSeq = getSequenceAt(i);
+        SequenceI dsq = currentSeq.getDatasetSequence();
+        if (dsq == null)
+        {
+          dsq = currentSeq.createDatasetSequence();
+          dataset.addSequence(dsq);
+        }
+        else
+        {
+          while (dsq.getDatasetSequence() != null)
+          {
+            dsq = dsq.getDatasetSequence();
+          }
+          if (dataset.findIndex(dsq) == -1)
+          {
+            dataset.addSequence(dsq);
+          }
+        }
+      }
     }
     dataset.addAlignmentRef();
   }
@@ -1148,7 +1179,9 @@ public class Alignment implements AlignmentI
   public void setProperty(Object key, Object value)
   {
     if (alignmentProperties == null)
+    {
       alignmentProperties = new Hashtable();
+    }
 
     alignmentProperties.put(key, value);
   }
@@ -1157,9 +1190,13 @@ public class Alignment implements AlignmentI
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
+    {
       return alignmentProperties.get(key);
+    }
     else
+    {
       return null;
+    }
   }
 
   @Override
@@ -1181,7 +1218,9 @@ public class Alignment implements AlignmentI
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
+    {
       return;
+    }
     if (codonFrameList == null)
     {
       codonFrameList = new AlignedCodonFrame[]
@@ -1215,15 +1254,21 @@ public class Alignment implements AlignmentI
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
+    {
       return null;
+    }
     Vector cframes = new Vector();
     for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
+      {
         cframes.addElement(codonFrameList[f]);
+      }
     }
     if (cframes.size() == 0)
+    {
       return null;
+    }
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
@@ -1250,7 +1295,9 @@ public class Alignment implements AlignmentI
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
+    {
       return false;
+    }
     boolean removed = false;
     int i = 0, iSize = codonFrameList.length;
     while (i < iSize)
@@ -1442,6 +1489,27 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
+  /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   */
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation ann : getAlignmentAnnotation())
+    {
+      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+              && ann.sequenceRef != null && ann.sequenceRef == seq
+              && ann.label != null && ann.label.equals(label))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
   @Override
   public void moveSelectedSequencesByOne(SequenceGroup sg,
           Map<SequenceI, SequenceCollectionI> map, boolean up)
@@ -1503,6 +1571,39 @@ public class Alignment implements AlignmentI
     }
   }
 
+
+ private SequenceI seqrep=null;
+
+ /**
+  * 
+  * @return the representative sequence for this group
+  */
+ public SequenceI getSeqrep()
+ {
+   return seqrep;
+ }
+
+ /**
+  * set the representative sequence for this group. Note - this affects the
+  * interpretation of the Hidereps attribute.
+  * 
+  * @param seqrep
+  *          the seqrep to set (null means no sequence representative)
+  */
+ public void setSeqrep(SequenceI seqrep)
+ {
+   this.seqrep = seqrep;
+ }
+
+ /**
+  * 
+  * @return true if group has a sequence representative
+  */
+ public boolean hasSeqrep()
+ {
+   return seqrep != null;
+ }
+
   @Override
   public int getEndRes()
   {
@@ -1526,32 +1627,4 @@ public class Alignment implements AlignmentI
   {
     return dataset;
   }
-
-  /**
-   * Returns an iterable collection of annotations on this alignment which match
-   * the given criteria.
-   */
-  @Override
-  public Iterable<AlignmentAnnotation> findAnnotation(SequenceI datasequence,
-          String calcId, String label)
-  {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation ann : annotations)
-    {
-      // only sequence-linked annotations can qualify (have a datasequence)
-      if (ann.sequenceRef == null)
-      {
-        continue;
-      }
-      boolean matchDatasequence = (ann.sequenceRef.getDatasetSequence() == datasequence);
-      final String annCalcId = ann.getCalcId();
-      boolean matchCalcId = (annCalcId != null && annCalcId.equals(calcId));
-      boolean matchLabel = (ann.label != null && ann.label.equals(label));
-      if (matchDatasequence && matchCalcId && matchLabel)
-      {
-        result.add(ann);
-      }
-    }
-    return result;
-  }
 }