JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages...

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 42a1201..081f446 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -40,6 +40,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.StringUtils;
 
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
@@ -1927,11 +1928,15 @@ public class AlignmentUtils
                     .codonTranslate(codon));
     if (trans != null && !trans.equals(residue))
     {
-      String desc = residue + "->" + trans;
+      String residue3Char = StringUtils
+              .toSentenceCase(ResidueProperties.aa2Triplet.get(residue));
+      String trans3Char = StringUtils
+              .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
+      String desc = "p." + residue3Char + peptidePos + trans3Char;
       // set score to 0f so 'graduated colour' option is offered! JAL-2060
       SequenceFeature sf = new SequenceFeature(
               SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
-              peptidePos, 0f, null);
+              peptidePos, 0f, "Jalview");
       StringBuilder attributes = new StringBuilder(32);
       String id = (String) var.variant.getValue(ID);
       if (id != null)
@@ -2109,6 +2114,26 @@ public class AlignmentUtils
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
 
+    /*
+     * add mappings between sequences to the new alignment
+     */
+    AlignedCodonFrame mappings = new AlignedCodonFrame();
+    copy.addCodonFrame(mappings);
+    for (int i = 0; i < copy.getHeight(); i++)
+    {
+      SequenceI from = seqs[i];
+      SequenceI to = copy.getSequenceAt(i);
+      if (to.getDatasetSequence() != null)
+      {
+        to = to.getDatasetSequence();
+      }
+      int start = from.getStart();
+      int end = from.getEnd();
+      MapList map = new MapList(new int[] { start, end }, new int[] {
+          start, end }, 1, 1);
+      mappings.addMap(to, from, map);
+    }
+
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {