From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 11 Oct 2016 08:33:13 +0000 (+0100)
Subject: JAL-1479 small tidy of error message when Sifts mapping fails
X-Git-Tag: Release_2_10_1~28
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=290f1ace41a61281440573d87f8415e08978360a;p=jalview.git

JAL-1479 small tidy of error message when Sifts mapping fails
---

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index fb59071..e85edd2 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -390,8 +390,8 @@ public class SiftsClient implements SiftsClientI
           String pdbFile, String chain) throws SiftsException
   {
     structId = (chain == null) ? pdbId : pdbId + "|" + chain;
-    System.out.println("Getting mapping for: " + pdbId + "|" + chain
-            + " : seq- " + seq.getName());
+    System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+            + seq.getName());
 
     final StringBuilder mappingDetails = new StringBuilder(128);
     PrintStream ps = new PrintStream(System.out)
@@ -470,12 +470,14 @@ public class SiftsClient implements SiftsClientI
     int pdbStart = UNASSIGNED;
     int pdbEnd = UNASSIGNED;
 
-    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
-    Arrays.sort(keys);
-    if (keys.length < 1)
+    if (mapping.isEmpty())
     {
-      throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+      throw new SiftsException(
+              "SIFTS mapping failed - falling back on Needleman-Wunsch");
     }
+
+    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+    Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];