X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=3f9b9d819a68c7824adbc847b608f637d3bf9ac3;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=e7f9ff1288b2332899d670f3c61d0f24a6da93ae;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index e7f9ff1..3f9b9d8 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -57,9 +57,9 @@ public class PDBSequenceFetcherTest
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // ensure 'add annotation from structure' is selected
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+    Cache.setPropertyNoSave("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+    Cache.setPropertyNoSave("ADD_SS_ANN",
             Boolean.TRUE.toString());
 
     sf = new SequenceFetcher();
@@ -76,7 +76,7 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
+    Cache.setPropertyNoSave("PDB_DOWNLOAD_FORMAT", "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
     assertTrue(response != null);
@@ -149,7 +149,7 @@ public class PDBSequenceFetcherTest
         // chains in structure have a mapping to data in the structure
         List<SequenceFeature> prev = null;
         int lastp = -1;
-        for (int col = 1; col <= sq.getLength(); col++)
+        for (int col = 1, ns = sq.getLength(); col <= ns; col++)
         {
           List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
           if (sf.size() != 1)