From fce1dd217a498f97f794c622b3651a33b8210932 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 26 May 2020 14:21:49 +0100
Subject: [PATCH] JAL-3624 log when SIFTS mapping fails

---
 .../structure/StructureSelectionManager.java       |   27 ++++++++++----------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 798b07a..8c3816e 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,8 +20,20 @@
  */
 package jalview.structure;
 
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;
@@ -45,18 +57,6 @@ import jalview.util.Platform;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.PDBfile;
@@ -430,7 +430,8 @@ public class StructureSelectionManager
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;
-      e.printStackTrace();
+      Cache.log.error("SIFTS mapping failed", e);
+      Cache.log.error("Falling back on Needleman & Wunsch alignment");
       siftsClient = null;
     }
 
-- 
1.7.10.2