A few more interfaces instead of implementations

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · May 22, 2010 · 648a2f4 · 648a2f4
1 parent 6317be2
commit 648a2f4
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Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptorTest.java
@@ -24,6 +24,7 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.BioPolymer;
+import org.openscience.cdk.interfaces.IBioPolymer;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.qsar.IMolecularDescriptor;
 import org.openscience.cdk.qsar.result.IDescriptorResult;
@@ -46,7 +47,7 @@ public void setUp() throws Exception {
     }
 
 	@Test public void testAACount() throws Exception {
-        BioPolymer protein = ProteinBuilderTool.createProtein("ARNDCFQEGHIPLKMSTYVW");
+        IBioPolymer protein = ProteinBuilderTool.createProtein("ARNDCFQEGHIPLKMSTYVW");
         IDescriptorResult result = descriptor.calculate(protein).getValue();
         Assert.assertTrue(result instanceof IntegerArrayResult);
         IntegerArrayResult iaResult = (IntegerArrayResult)result;
@@ -58,7 +59,7 @@ public void setUp() throws Exception {
 
 	@Test
     public void testFCount() throws Exception {
-        BioPolymer protein = ProteinBuilderTool.createProtein("FF");
+        IBioPolymer protein = ProteinBuilderTool.createProtein("FF");
         IDescriptorResult result = descriptor.calculate(protein).getValue();
         Assert.assertTrue(result instanceof IntegerArrayResult);
         IntegerArrayResult iaResult = (IntegerArrayResult)result;
@@ -67,7 +68,7 @@ public void testFCount() throws Exception {
 	}
 
 	@Test public void testTCount() throws Exception {
-        BioPolymer protein = ProteinBuilderTool.createProtein("TT");
+        IBioPolymer protein = ProteinBuilderTool.createProtein("TT");
         IDescriptorResult result = descriptor.calculate(protein).getValue();
         Assert.assertTrue(result instanceof IntegerArrayResult);
         IntegerArrayResult iaResult = (IntegerArrayResult)result;

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptorTest.java
@@ -30,6 +30,7 @@
 import org.openscience.cdk.BioPolymer;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IBioPolymer;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.IMolecularDescriptor;
 import org.openscience.cdk.qsar.result.DoubleArrayResult;
@@ -50,7 +51,7 @@ public class TaeAminoAcidDescriptorTest extends CDKTestCase {
     }
 
     @Test public void testTaeAminoAcidDescriptor() throws ClassNotFoundException, CDKException, Exception {
-        BioPolymer pepseq = ProteinBuilderTool.createProtein("ACDEFGH");
+        IBioPolymer pepseq = ProteinBuilderTool.createProtein("ACDEFGH");
         DescriptorValue result = descriptor.calculate(pepseq);
 
         DoubleArrayResult dar = (DoubleArrayResult) result.getValue();

diff --git a/src/test/org/openscience/cdk/templates/AminoAcidsTest.java b/src/test/org/openscience/cdk/templates/AminoAcidsTest.java
@@ -26,6 +26,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.AminoAcid;
+import org.openscience.cdk.interfaces.IAminoAcid;
 import org.openscience.cdk.templates.AminoAcids;
 import org.openscience.cdk.CDKTestCase;
 
@@ -45,7 +46,7 @@ public void testCreateBondMatrix() {
 
     @Test
     public void testCreateAAs() {
-        AminoAcid[] aas = AminoAcids.createAAs();
+        IAminoAcid[] aas = AminoAcids.createAAs();
         Assert.assertNotNull(aas);
         Assert.assertEquals(20, aas.length);
         for (int i=0; i<20; i++) {
@@ -60,7 +61,7 @@ public void testCreateAAs() {
 
     @Test
     public void testGetHashMapBySingleCharCode() {
-        Map<String,AminoAcid> map = AminoAcids.getHashMapBySingleCharCode();
+        Map<String,IAminoAcid> map = AminoAcids.getHashMapBySingleCharCode();
         Assert.assertNotNull(map);
         Assert.assertEquals(20, map.size());
 

diff --git a/src/test/org/openscience/cdk/tools/ProteinBuilderToolTest.java b/src/test/org/openscience/cdk/tools/ProteinBuilderToolTest.java
@@ -27,6 +27,7 @@
 import org.junit.Test;
 import org.openscience.cdk.BioPolymer;
 import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.interfaces.IBioPolymer;
 import org.openscience.cdk.tools.ProteinBuilderTool;
 
 /**
@@ -36,7 +37,7 @@ public class ProteinBuilderToolTest extends CDKTestCase {
 
     @Test
     public void testCreateProtein() throws Exception {
-        BioPolymer protein = ProteinBuilderTool.createProtein("GAGA");
+        IBioPolymer protein = ProteinBuilderTool.createProtein("GAGA");
         Assert.assertNotNull(protein);
         Assert.assertEquals(4, protein.getMonomerCount());
         Assert.assertEquals(1, protein.getStrandCount());