test defaultAAIndexProvider

otter606 · otter606 · commit b648835396e3 · 2021-08-25T21:30:12.000+01:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.java
@@ -26,5 +26,11 @@
 
 public interface AAIndexProvider {
 
-	public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName);
+	 /**
+	  * Gets a substitution matrix by its name. The matrices are defined in
+	    {@code}src/main/resources/matrices/AAINDEX.txt{@code}
+	  * @param matrixName
+	  * @return The @{code}SubstitutionMatrix{@code} or null if not exists
+	  */
+	 SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.java
@@ -42,9 +42,7 @@ public class DefaultAAIndexProvider implements AAIndexProvider {
 
 	public DefaultAAIndexProvider(){
 
-
 		InputStream inStream = getInputStreamToAAindexFile();
-
 		AAIndexFileParser parser = new AAIndexFileParser();
 
 		try {
@@ -54,14 +52,11 @@ public DefaultAAIndexProvider(){
 		}
 
 		matrices = parser.getMatrices();
-
 	}
 
 	@Override
 	public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName) {
-
 		return matrices.get(matrixName);
-
 	}
 
 	public InputStream getInputStreamToAAindexFile(){
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProviderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProviderTest.java
@@ -0,0 +1,27 @@
+package org.biojava.nbio.core.alignment.matrices;
+
+import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class DefaultAAIndexProviderTest {
+   
+    private static final String BENS940102 = "BENS940102";
+
+    DefaultAAIndexProvider provider = new DefaultAAIndexProvider();
+    @Test
+    void newAAIndexProviderReturnsNullIfNotExists(){ 
+        assertNull(provider.getMatrix("unknown"));
+    }
+
+    @Test
+    void aaIndexProviderGetByName(){ 
+        SubstitutionMatrix<AminoAcidCompound> matrix =  provider.getMatrix(BENS940102);
+        assertNotNull(matrix);
+        assertEquals(BENS940102, matrix.getName());
+    }
+}

Original file line number	Diff line number	Diff line change
`@@ -42,9 +42,7 @@ public class DefaultAAIndexProvider implements AAIndexProvider {`
`42`	`42`
`43`	`43`	`public DefaultAAIndexProvider(){`
`44`	`44`
`45`		`-`
`46`	`45`	`InputStream inStream = getInputStreamToAAindexFile();`
`47`		`-`
`48`	`46`	`AAIndexFileParser parser = new AAIndexFileParser();`
`49`	`47`
`50`	`48`	`try {`
`@@ -54,14 +52,11 @@ public DefaultAAIndexProvider(){`
`54`	`52`	`}`
`55`	`53`
`56`	`54`	`matrices = parser.getMatrices();`
`57`		`-`
`58`	`55`	`}`
`59`	`56`
`60`	`57`	`@Override`
`61`	`58`	`public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName) {`
`62`		`-`
`63`	`59`	`return matrices.get(matrixName);`
`64`		`-`
`65`	`60`	`}`
`66`	`61`
`67`	`62`	`public InputStream getInputStreamToAAindexFile(){`