Merge branch 'features/JAL-2136_phyre2_integration' into spikes/phyre

[jalview.git] / test / jalview / io / AnnotationFileIOTest.java

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 4bc8c3b..e016f54 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -25,16 +25,17 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DynamicData;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
-import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile.ViewDef;
 import jalview.structure.StructureSelectionManager;
 
 import java.io.File;
 import java.util.Hashtable;
+import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -177,6 +178,14 @@ public class AnnotationFileIOTest
   @BeforeClass(alwaysRun = true)
   void testProcessStructModel()
   {
+    try
+    {
+
+      ssm = StructureSelectionManager.getStructureSelectionManager();
+    } catch (NullPointerException e)
+    {
+      ssm = new StructureSelectionManager();
+    }
     File alignmentFile = new File(
             "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
     String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
@@ -185,8 +194,6 @@ public class AnnotationFileIOTest
     boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
             cs, annotationFile, DataSourceType.FILE);
     Assert.assertTrue(annotationRead);
-    ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
     System.out.println("bla");
   }
   
@@ -208,9 +215,11 @@ public class AnnotationFileIOTest
 
     PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
             + pdbId);
-    String phyre2ModelDesc = AnnotationFile.generatePhyre2InfoHTMLTable(structModelHeader,
-            structModelData);
-    expectedPDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+    List<DynamicData> phyreDD = AnnotationFile
+            .generatePhyreDynamicDataList(structModelHeader,
+                    structModelData);
+    expectedPDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD);
+
     Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
   }
 
@@ -228,30 +237,6 @@ public class AnnotationFileIOTest
             expectedPhyre2FastaMappingFile);
   }
 
-  @Test(
-    groups = { "Functional" },
-    dataProvider = "phyre2InfoHTMLTableDataProvider")
-  void testGeneratePhyre2InfoHTMLTable(String caseDescription,
-          String[] header, String[] data, String expectedHtml)
-  {
-    System.out.println(">>>> Testing Case - " + caseDescription);
-    String actualHtmlGenerated = AnnotationFile
-            .generatePhyre2InfoHTMLTable(header, data);
-    System.out.println("-----> " + actualHtmlGenerated);
-    Assert.assertEquals(actualHtmlGenerated, expectedHtml);
-  }
-
-  @Test(
-    groups = { "Functional" },
-    dataProvider = "StructModelHtmlDataProvider")
-  void testIsGenerateStructInfoHtml(String caseDescription,
-          String[] header, String[] data, boolean expectedOutcome)
-  {
-    System.out.println(">>>> Testing Case - " + caseDescription);
-    boolean actual = AnnotationFile.isGenerateStructInfoHtml(header, data);
-    Assert.assertEquals(actual, expectedOutcome);
-  }
-
   @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
   void testResolveAbsolutePath(String caseDescription, String suppliedPath,
           String baseURI, String expectedURI)