JAL-2319 corrected reporting of SIFTS mapping

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e85edd2..27db604 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
 import jalview.xml.binding.sifts.Entry;
@@ -472,8 +473,7 @@ public class SiftsClient implements SiftsClientI
 
     if (mapping.isEmpty())
     {
-      throw new SiftsException(
-              "SIFTS mapping failed - falling back on Needleman-Wunsch");
+      throw new SiftsException("SIFTS mapping failed");
     }
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
@@ -511,13 +511,13 @@ public class SiftsClient implements SiftsClientI
     if (os != null)
     {
       MappingOutputPojo mop = new MappingOutputPojo();
-      mop.setSeqStart(pdbStart);
-      mop.setSeqEnd(pdbEnd);
+      mop.setSeqStart(seqStart);
+      mop.setSeqEnd(seqEnd);
       mop.setSeqName(seq.getName());
       mop.setSeqResidue(matchedSeq);
 
-      mop.setStrStart(seqStart);
-      mop.setStrEnd(seqEnd);
+      mop.setStrStart(pdbStart);
+      mop.setStrEnd(pdbEnd);
       mop.setStrName(structId);
       mop.setStrResidue(targetStrucSeqs.toString());
 
@@ -827,6 +827,10 @@ public class SiftsClient implements SiftsClientI
 
     if (sPojo[0].entityId != null)
     {
+      if (sPojo[0].pid < 1)
+      {
+        return null;
+      }
       for (Entity entity : entities)
       {
         if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
@@ -1001,8 +1005,10 @@ public class SiftsClient implements SiftsClientI
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            if (seqRes.charAt(i + (j * len)) == strRes
-                    .charAt(i + (j * len))
+            boolean sameChar = Comparison.isSameResidue(
+                    seqRes.charAt(i + (j * len)),
+                    strRes.charAt(i + (j * len)), false);
+            if (sameChar
                     && !jalview.util.Comparison.isGap(seqRes.charAt(i
                             + (j * len))))
             {