X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f14539b2e5b837b18e95a07ca13774271f70da37;hb=9c39e96af6b84257604da448101505361dced686;hp=1134857428850bf8e49716f31013e37c56b2c37b;hpb=49428d3a57e4f4863acbdeb3f77049ed95efd6c3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1134857..f14539b 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,6 +30,7 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -1287,6 +1288,22 @@ public class Alignment implements AlignmentI
     }
   }
 
+  /**
+   * adds a set of mappings (while ignoring any duplicates)
+   */
+  @Override
+  public void addCodonFrames(Iterable<AlignedCodonFrame> codons)
+  {
+    if (codons != null)
+    {
+      Iterator<AlignedCodonFrame> it = codons.iterator();
+      while (it.hasNext())
+      {
+        addCodonFrame(it.next());
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -1704,31 +1721,13 @@ public class Alignment implements AlignmentI
           boolean preserveUnmappedGaps)
   {
     // TODO should this method signature be the one in the interface?
-    int count = 0;
     boolean thisIsNucleotide = this.isNucleotide();
     boolean thatIsProtein = !al.isNucleotide();
     if (!thatIsProtein && !thisIsNucleotide)
     {
       return AlignmentUtils.alignProteinAsDna(this, al);
     }
-
-    char thisGapChar = this.getGapCharacter();
-    String gap = thisIsNucleotide && thatIsProtein ? String
-            .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
-            : String.valueOf(thisGapChar);
-
-    // TODO handle intron regions? Needs a 'holistic' alignment of dna,
-    // not just sequence by sequence. But how to 'gap' intron regions?
-
-    /*
-     * Get mappings from 'that' alignment's sequences to this.
-     */
-    for (SequenceI alignTo : getSequences())
-    {
-      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
-              preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
-    }
-    return count;
+    return AlignmentUtils.alignAs(this, al);
   }
 
   /**
@@ -1811,4 +1810,40 @@ public class Alignment implements AlignmentI
     }
     return null;
   }
+
+  @Override
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  {
+    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+    int startPos = alignmentStartEnd[0];
+    int endPos = alignmentStartEnd[1];
+
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
+    {
+      startPos = alignmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == -1 && higestRange[1] == -1)
+    {
+      endPos = alignmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0] - 1;
+    }
+    return new int[] { startPos, endPos };
+  }
 }