From 89f62b210bafac2a3341ce3fa9a360d5ea6c1c3c Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 28 Oct 2015 11:34:34 +0000
Subject: [PATCH] JAL-1887 JAL-1479 bugfix for incorrect start/end for aligned
 sequence mapping, and a bit of StructureSelectionManager
 refactoring for SIFTs

---
 .../structure/StructureSelectionManager.java       |   38 +++++++++++++++++---
 src/jalview/{io => ws/sifts}/SiftsClient.java      |    0
 test/jalview/{io => ws/sifts}/SiftsClientTest.java |    0
 3 files changed, 34 insertions(+), 4 deletions(-)
 rename src/jalview/{io => ws/sifts}/SiftsClient.java (100%)
 rename test/jalview/{io => ws/sifts}/SiftsClientTest.java (100%)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 0b3696c..38e7db3 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -33,9 +33,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
-import jalview.io.SiftsClient;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
 
 import java.io.PrintStream;
 import java.util.ArrayList;
@@ -470,9 +471,17 @@ public class StructureSelectionManager
       if (isMapViaSIFTs)
       {
         SiftsClient siftsClient = new SiftsClient(pdb.id);
-        seqToStrucMapping = siftsClient.getSiftsStructureMapping(seq,
-                pdbFile, maxChainId);
-        // TODO if SIFTs mapping fails.. then fallback to NW alignment
+        try
+        {
+          seqToStrucMapping = siftsClient.getSiftsStructureMapping(seq,
+                  pdbFile, maxChainId);
+        } catch (SiftsException e)
+        {
+          System.err
+                  .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
+          seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
+                  maxChain, pdb, maxAlignseq);
+        }
       }
       else
       {
@@ -494,6 +503,12 @@ public class StructureSelectionManager
           AlignSeq maxAlignseq)
   {
     final StringBuilder mappingDetails = new StringBuilder(128);
+    mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+            .append(NEWLINE).append("Sequence = ")
+            .append(maxChain.sequence.getSequenceAsString());
+    mappingDetails.append(NEWLINE).append("No of residues = ")
+            .append(maxChain.residues.size()).append(NEWLINE)
+            .append(NEWLINE);
     PrintStream ps = new PrintStream(System.out)
     {
       @Override
@@ -510,6 +525,21 @@ public class StructureSelectionManager
     };
 
     maxAlignseq.printAlignment(ps);
+
+    mappingDetails.append(NEWLINE).append("PDB start/end ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+    mappingDetails.append(NEWLINE).append("SEQ start/end ");
+    mappingDetails.append(
+            String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+            + (seq.getStart() - 1)));
+    mappingDetails.append(NEWLINE);
+    mappingDetails
+            .append("Mapping inferred with Needleman & Wunsch alignment");
+    mappingDetails.append(NEWLINE);
     maxChain.makeExactMapping(maxAlignseq, seq);
     jalview.datamodel.Mapping sqmpping = maxAlignseq
             .getMappingFromS1(false);
diff --git a/src/jalview/io/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
similarity index 100%
rename from src/jalview/io/SiftsClient.java
rename to src/jalview/ws/sifts/SiftsClient.java
diff --git a/test/jalview/io/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
similarity index 100%
rename from test/jalview/io/SiftsClientTest.java
rename to test/jalview/ws/sifts/SiftsClientTest.java
-- 
1.7.10.2