X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fschemes%2FResiduePropertiesTest.java;h=28f39d858012fbd9df809ec33b54494c53c07628;hb=HEAD;hp=b68ca6898ddc84879f7f20cd8c6c5f4c05589139;hpb=6dacd9d2805d0899a59329fdc4e43dfacdf93044;p=jalview.git

diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index b68ca68..28f39d8 100644
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -25,12 +25,23 @@ import static org.testng.AssertJUnit.assertNull;
 
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
+
 public class ResiduePropertiesTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test 'standard' codon translations (no ambiguity codes)
    */
@@ -211,7 +222,8 @@ public class ResiduePropertiesTest
      */
     residues = ResidueProperties.getResidues(true, true);
     Collections.sort(residues);
-    assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
+    assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
+            residues.toString());
   }
 
   @Test(groups = { "Functional" })
@@ -1556,4 +1568,72 @@ public class ResiduePropertiesTest
     assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
     assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetDssp3State()
+  {
+    assertNull(ResidueProperties.getDssp3state(null));
+    assertEquals("", ResidueProperties.getDssp3state(""));
+    String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
+    String bar = "                                    E  E HHH                 ";
+    assertEquals(bar, ResidueProperties.getDssp3state(foo));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPhysicoChemicalProperties()
+  {
+    checkProperty("aromatic", "FYWH-*");
+    checkProperty("aliphatic", "IVL-*");
+    checkProperty("tiny", "GAS-*");
+    checkProperty("small", "VCTGACSDNP-*");
+    checkProperty("charged", "HKRDE-*");
+    checkProperty("negative", "DE-*");
+    checkProperty("polar", "YWHRKTSNDEQ-*X");
+    checkProperty("positive", "HKR-*");
+    checkProperty("proline", "P-*");
+    checkProperty("hydrophobic", "MILVFYWHKTGAC-*X");
+  }
+
+  /**
+   * Verify that the residues in the list have the named property, and other
+   * residues do not
+   * 
+   * @param property
+   * @param residues
+   */
+  void checkProperty(String property, String residues)
+  {
+    Map<String, Integer> props = ResidueProperties.propHash.get(property);
+
+    /*
+     * assert residues have the property (value 1 in lookup)
+     */
+    for (char res : residues.toCharArray())
+    {
+      assertEquals(res + " should be " + property, 1,
+              props.get(String.valueOf(res)).intValue());
+    }
+
+    /*
+     * assert other residues do not (value 0 in lookup)
+     */
+    for (String res : ResidueProperties.aa)
+    {
+      if (!residues.contains(res))
+      {
+        Integer propValue = props.get(String.valueOf(res));
+
+        if (propValue != null)
+        {
+          /*
+           * conservation calculation assigns unexpected symbols
+           * the same value as '-'; here we just check those which
+           * explicitly do not have the property
+           */
+          assertEquals(res + " should not be " + property, 0,
+                  propValue.intValue());
+        }
+      }
+    }
+  }
 }