JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 7ccd9cf..88e9a9c 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -47,7 +47,7 @@ public class AlignmentView
    * one or more ScGroup objects, which are referenced by each seqCigar's group
    * membership
    */
-  private List<ScGroup> scGroups=null;
+  private List<ScGroup> scGroups = null;
 
   private boolean isNa = false;
 
@@ -133,7 +133,7 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
-    List<List<SequenceI>> seqsets=new ArrayList<List<SequenceI>>();
+    List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
     // get the alignment's group list and make a copy
     List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
     List<SequenceGroup> gg = alignment.getGroups();
@@ -241,7 +241,9 @@ public class AlignmentView
   {
     if (!seqcigararray.isSeqCigarArray())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
     }
     // contigs = seqcigararray.applyDeletions();
     contigs = seqcigararray.getDeletedRegions();
@@ -298,8 +300,7 @@ public class AlignmentView
   {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[]
-    {
+    return new Object[] {
         SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
                 contigs), colsel };
   }
@@ -474,12 +475,8 @@ public class AlignmentView
     for (int i = 0, j = sequences.length; i < j; i++)
     {
       aln[i] = sequences[i].getSeq(c);
-    }
-    // Remove hidden regions from sequence objects.
-    String seqs[] = getSequenceStrings(c);
-    for (int i = 0, j = aln.length; i < j; i++)
-    {
-      aln[i].setSequence(seqs[i]);
+      // Remove hidden regions from sequence
+      aln[i].setSequence(getASequenceString(c, i));
     }
     return aln;
   }
@@ -667,7 +664,9 @@ public class AlignmentView
   {
     if (sequences == null || width <= 0)
     {
-      throw new Error(MessageManager.getString("error.empty_view_cannot_be_updated"));
+      throw new Error(
+              MessageManager
+                      .getString("error.empty_view_cannot_be_updated"));
     }
     if (nvismsa == null)
     {
@@ -697,7 +696,17 @@ public class AlignmentView
               j++;
               if (mseq.length != sequences.length)
               {
-                throw new Error(MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(mseq.length).toString(),Integer.valueOf(sequences.length).toString() }));
+                throw new Error(
+                        MessageManager
+                                .formatMessage(
+                                        "error.mismatch_between_number_of_sequences_in_block",
+                                        new String[] {
+                                            Integer.valueOf(j).toString(),
+                                            Integer.valueOf(mseq.length)
+                                                    .toString(),
+                                            Integer.valueOf(
+                                                    sequences.length)
+                                                    .toString() }));
               }
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded
               // here.
@@ -850,25 +859,30 @@ public class AlignmentView
               else
               {
                 // place gaps.
-                throw new Error(MessageManager.getString("error.padding_not_yet_implemented"));
+                throw new Error(
+                        MessageManager
+                                .getString("error.padding_not_yet_implemented"));
               }
             }
           }
         }
       }
-      return new Object[]
-      { alignment, columnselection };
+      return new Object[] { alignment, columnselection };
     }
     else
     {
       if (nvismsa.length != 1)
       {
-        throw new Error(MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", new String[]{Integer.valueOf(nvismsa.length).toString()}));
+        throw new Error(
+                MessageManager
+                        .formatMessage(
+                                "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+                                new String[] { Integer.valueOf(
+                                        nvismsa.length).toString() }));
       }
       if (nvismsa[0] != null)
       {
-        return new Object[]
-        { nvismsa[0], new ColumnSelection() };
+        return new Object[] { nvismsa[0], new ColumnSelection() };
       }
       else
       {
@@ -929,8 +943,7 @@ public class AlignmentView
     }
     else
     {
-      return new int[]
-      { 0, width };
+      return new int[] { 0, width };
     }
   }