X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;fp=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=b74baf19ddf436bb479d4be93d6fe8bf8f4bdbac;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=f183e5cbbac0c32a230076d57435bbe309fb54c2;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index f183e5c..b74baf1 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -58,7 +58,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq,upSeq,upSeq_nocanonical;
+  Sequence seq, upSeq, upSeq_nocanonical;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -80,45 +80,46 @@ public class StructureChooserTest
     pdbIds.add(dbRef);
 
     seq.setPDBId(pdbIds);
-    
+
     // Uniprot sequence for 3D-Beacons mocks
-    upSeq = new Sequence("P38398", 
+    upSeq = new Sequence("P38398",
             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
-            + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
-            + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
-            + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
-            + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
-            + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
-            + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
-            + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
-            + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
-            + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
-            + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
-            + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
-            + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
-            + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
-            + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
-            + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
-            + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
-            + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
-            + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
-            + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
-            + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
-            + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
-            + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
-            + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
-            + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
-            + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
-            + "", 1,
-1863);
+                    + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+                    + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+                    + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+                    + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+                    + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+                    + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+                    + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+                    + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+                    + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+                    + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+                    + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+                    + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+                    + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+                    + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+                    + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+                    + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+                    + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+                    + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+                    + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+                    + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+                    + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+                    + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+                    + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+                    + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+                    + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+                    + "",
+            1, 1863);
     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
     upSeq_nocanonical = new Sequence(upSeq);
     upSeq.createDatasetSequence();
-    upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
-    
+    upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
     upSeq_nocanonical.createDatasetSequence();
     // not a canonical reference
-    upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+    upSeq_nocanonical.addDBRef(
+            new DBRefEntry("UNIPROT", "0", "P38398", null, false));
 
   }
 
@@ -126,8 +127,8 @@ public class StructureChooserTest
   public void tearDown() throws Exception
   {
     seq = null;
-    upSeq=null;
-    upSeq_nocanonical=null;
+    upSeq = null;
+    upSeq_nocanonical = null;
   }
 
   @Test(groups = { "Functional" })
@@ -139,21 +140,22 @@ public class StructureChooserTest
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     ThreadwaitFor(200, sc);
-    
+
     // if structures are not discovered then don't
     // populate filter options
     sc.populateFilterComboBox(false, false);
     int optionsSize = sc.getCmbFilterOption().getItemCount();
     System.out.println("Items (no data, no cache): ");
     StringBuilder items = new StringBuilder();
-    for (int p=0;p<optionsSize;p++)
+    for (int p = 0; p < optionsSize; p++)
     {
-      items.append
-      ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
+      items.append("- ")
+              .append(sc.getCmbFilterOption().getItemAt(p).getName())
+              .append("\n");
 
     }
     // report items when this fails - seems to be a race condition
-    Assert.assertEquals(items.toString(),optionsSize,2); 
+    Assert.assertEquals(items.toString(), optionsSize, 2);
 
     sc.populateFilterComboBox(true, false);
     optionsSize = sc.getCmbFilterOption().getItemCount();
@@ -165,7 +167,8 @@ public class StructureChooserTest
     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
             .getSelectedItem();
     assertEquals("Cached Structures", filterOpt.getName());
-    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    FTSRestClient
+            .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 
   }
@@ -177,23 +180,25 @@ public class StructureChooserTest
     PDBFTSRestClientTest.setMock();
 
     SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
-    StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+    StructureChooser sc = new StructureChooser(selectedSeqs,
+            upSeq_nocanonical, null);
     // mock so should be quick. Exceptions from mocked PDBFTS are expected too
     ThreadwaitFor(500, sc);
-    
+
     assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
   }
 
   @Test(groups = { "Network" })
   public void fetchStructuresInfoTest()
   {
-    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    FTSRestClient
+            .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
-    // not mocked, wait for 2s 
+    // not mocked, wait for 2s
     ThreadwaitFor(2000, sc);
-    
+
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -209,7 +214,7 @@ public class StructureChooserTest
     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     ThreadwaitFor(500, sc);
-    
+
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -219,35 +224,39 @@ public class StructureChooserTest
 
   private void ThreadwaitFor(int i, StructureChooser sc)
   {
-    long timeout = i+System.currentTimeMillis();
+    long timeout = i + System.currentTimeMillis();
     while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
     {
-      try {
+      try
+      {
         Thread.sleep(50);
       } catch (InterruptedException x)
       {
-        
+
       }
     }
-    
-  }
 
+  }
 
   @Test(groups = { "Functional" })
   public void sanitizeSeqNameTest()
   {
     String name = "ab_cdEF|fwxyz012349";
-    assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+    assertEquals(name,
+            PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove a [nn] substring
     name = "abcde12[345]fg";
-    assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+    assertEquals("abcde12fg",
+            PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove characters other than a-zA-Z0-9 | or _
     name = "ab[cd],.\t£$*!- \\\"@:e";
-    assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+    assertEquals("abcde",
+            PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     name = "abcde12[345a]fg";
-    assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+    assertEquals("abcde12345afg",
+            PDBStructureChooserQuerySource.sanitizeSeqName(name));
   }
 }