Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / test / jalview / ws / PDBSequenceFetcherTest.java

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index d1e32b9..3f9b9d8 100644 (file)
--- 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);
@@ -149,18 +149,15 @@ 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)
           {
-            errors.append(
-                    str.id + ": " +
-                            "Expected one feature at column (position): "
-                            + (col - 1)
-                            + " (" + sq.findPosition(col - 1) + ")"
-                            + ": saw "
-                            + sf.size());
+            errors.append(str.id + ": "
+                    + "Expected one feature at column (position): "
+                    + (col - 1) + " (" + sq.findPosition(col - 1) + ")"
+                    + ": saw " + sf.size());
             errors.append("\n");
             if (prev != null)
             {