X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;fp=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=44a6a0258fc378e6ae26f313ad4da00f5d7a8663;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=6122d6d0ba61332b8d4b9faabac1ec8f71236892;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 6122d6d..44a6a02 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -62,19 +62,18 @@ public class SiftsClientTest
   }
 
   public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home")
-          + File.separatorChar
+          .getProperty("user.home") + File.separatorChar
           + ".sifts_downloads" + File.separatorChar;
 
   private String testPDBId = "1a70";
 
   private SiftsClient siftsClient = null;
 
-  SequenceI testSeq = new Sequence(
-          "P00221",
+  SequenceI testSeq = new Sequence("P00221",
           "MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
                   + "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
-                  + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);
+                  + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.",
+          1, 147);
 
   int u = SiftsClient.UNASSIGNED;
 
@@ -190,14 +189,14 @@ public class SiftsClientTest
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
     new SiftsSettings();
-    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
-            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+            .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
     SiftsSettings.setMapWithSifts(true);
     SiftsSettings.setCacheThresholdInDays("2");
     SiftsSettings.setFailSafePIDThreshold("70");
     PDBfile pdbFile;
-    pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
-            + testPDBId + ".pdb", DataSourceType.FILE);
+    pdbFile = new PDBfile(false, false, false,
+            "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
     siftsClient = new SiftsClient(pdbFile);
   }
 
@@ -278,8 +277,8 @@ public class SiftsClientTest
 
     try
     {
-      HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
-              "A", testSeq, null);
+      HashMap<Integer, int[]> actualMapping = siftsClient
+              .getGreedyMapping("A", testSeq, null);
       Assert.assertEquals(testSeq.getStart(), 1);
       Assert.assertEquals(testSeq.getEnd(), 147);
       // Can't do Assert.assertEquals(actualMapping, expectedMapping);
@@ -317,7 +316,8 @@ public class SiftsClientTest
   }
 
   @Test(
-    groups = { "Network" },
+    groups =
+    { "Network" },
     expectedExceptions = IllegalArgumentException.class)
   private void getAtomIndexNullTest()
   {
@@ -330,18 +330,14 @@ public class SiftsClientTest
 
   }
 
-  @Test(
-groups = { "Network" },
-    expectedExceptions = SiftsException.class)
+  @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
   private void populateAtomPositionsNullTest1()
           throws IllegalArgumentException, SiftsException
   {
     siftsClient.populateAtomPositions(null, null);
   }
 
-  @Test(
-groups = { "Network" },
-    expectedExceptions = SiftsException.class)
+  @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
   private void populateAtomPositionsNullTest2()
           throws IllegalArgumentException, SiftsException
   {
@@ -360,18 +356,14 @@ groups = { "Network" },
     Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
   }
 
-  @Test(
-groups = { "Network" },
-    expectedExceptions = SiftsException.class)
+  @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
   public void getValidSourceDBRefExceptionTest() throws SiftsException
   {
     SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
     siftsClient.getValidSourceDBRef(invalidTestSeq);
   }
 
-  @Test(
-groups = { "Network" },
-    expectedExceptions = SiftsException.class)
+  @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
   public void getValidSourceDBRefExceptionXTest() throws SiftsException
   {
     SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
@@ -395,11 +387,10 @@ groups = { "Network" },
   public void getSiftsStructureMappingTest() throws SiftsException
   {
     Assert.assertTrue(SiftsSettings.isMapWithSifts());
-    StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
-            testSeq, testPDBId, "A");
+    StructureMapping strucMapping = siftsClient
+            .getSiftsStructureMapping(testSeq, testPDBId, "A");
     String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
-            + "Method: SIFTS\n\n"
-            + "P00221 :  51 - 147 Maps to \n"
+            + "Method: SIFTS\n\n" + "P00221 :  51 - 147 Maps to \n"
             + "1A70|A :  1 - 97\n\n"
             + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
             + "       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
@@ -423,8 +414,8 @@ groups = { "Network" },
     while (it.hasNext())
     {
       Map.Entry<Integer, int[]> pair = it.next();
-      Assert.assertTrue(strucMapping.getMapping()
-              .containsKey(pair.getKey()));
+      Assert.assertTrue(
+              strucMapping.getMapping().containsKey(pair.getKey()));
       Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
               pair.getValue());
     }
@@ -471,13 +462,13 @@ groups = { "Network" },
   }
 
   @Test(groups = { "Network" })
-  public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
-          SiftsException
+  public void getEntityByMostOptimalMatchedIdTest1()
+          throws IOException, SiftsException
   {
     SiftsClient siftsClientX = null;
     PDBfile pdbFile;
-    pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
-            + ".pdb", DataSourceType.FILE);
+    pdbFile = new PDBfile(false, false, false,
+            "test/jalview/io/2nq2" + ".pdb", DataSourceType.FILE);
     siftsClientX = new SiftsClient(pdbFile);
     Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
     Assert.assertEquals(entityA.getEntityId(), "A");
@@ -491,8 +482,8 @@ groups = { "Network" },
   }
 
   @Test(groups = { "Network" })
-  public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
-          SiftsException
+  public void getEntityByMostOptimalMatchedIdTest2()
+          throws IOException, SiftsException
   {
     // This test is for a SIFTS file in which entity A should map to chain P for
     // the given PDB Id. All the other chains shouldn't be mapped as there are
@@ -518,18 +509,14 @@ groups = { "Network" },
   @Test(groups = { "Network" })
   public void getLeadingIntegerFromString()
   {
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("1234abcd", -1), 1234);
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("1234", -1),
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1),
+            1234);
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1),
             1234);
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("abcd1234", -1), -1);
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("None", -1), -1);
-    Assert.assertEquals(
-            SiftsClient.getLeadingIntegerValue("Null", -1), -1);
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1),
+            -1);
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1);
+    Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1);
   }
 }