From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 21 Apr 2017 13:08:13 +0000 (+0100)
Subject: Merge branch 'develop' into features/JAL-2393customMatrices
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~16
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fa1b96bdca9954d44de8ed08e106ace44dcf66c3;hp=bfe7fff2c9139d0ad41c8375897f1af991912138;p=jalview.git

Merge branch 'develop' into features/JAL-2393customMatrices
---

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 27bfca8..a23df4c 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -157,14 +157,14 @@ public class UniProtFTSRestClient extends FTSRestClient
     if (foundDataRow != null && foundDataRow.length > 0)
     {
       result = new ArrayList<FTSData>();
-      String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
-              .getWantedFields());
-      // System.out.println(">>>>Title row : " + titleRow);
+      boolean firstRow = true;
       for (String dataRow : foundDataRow)
       {
-        if (dataRow.equalsIgnoreCase(titleRow))
+        // The first data row is usually the header data. This should be
+        // filtered out from the rest of the data See: JAL-2485
+        if (firstRow)
         {
-          // System.out.println(">>>>>>>>>> matched!!!");
+          firstRow = false;
           continue;
         }
         // System.out.println(dataRow);
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 847377d..0e9e888 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -609,8 +609,12 @@ public class SiftsClient implements SiftsClientI
                     .getDbResNum());
           } catch (NumberFormatException nfe)
           {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
+            if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+            {
+              resNum = UNASSIGNED;
+              continue;
+            }
+            resNum = Integer.valueOf(pdbRefDb
                     .getDbResNum().split("[a-zA-Z]")[0]);
             continue;
           }