Merge pull request #340 from Ravina-Deogadkar/tests

Add Additional testcases

src/main/java/DNAnalyzer/core/Properties.java

@@ -61,9 +61,13 @@ public static void printProteinList(final List<String> proteinList, final String
 	 *      "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gc-content"
 	 */
 	public static float getGCContent(String dna) {
+		float gcContent=0;
+		if(dna.length()==0)
+			return gcContent;
+
 		dna = dna.toLowerCase();
 		float gcLen = (float) calculateLengthOfCG(dna);
-		float gcContent = gcLen / dna.length();
+		gcContent = gcLen / dna.length();
 
 		return gcContent;
 	}
@@ -143,8 +147,8 @@ public static boolean isRandomDNA(final String dna) {
 	/**
 	 * Checks if the differnce between two numbers is less or equal to 2
 	 *
-	 * @param aNumber       one number to calculate the difference
-	 * @param anotherNumber the other number to calculate the difference
+	 * @param maxPercent       one number to calculate the difference
+	 * @param minPercent the other number to calculate the difference
 	 * @return Whether the difference is less or equal to 2
 	 * @category Properties
 	 */

src/test/java/DNAnalyzer/ProteinFinderTest.java

@@ -26,15 +26,14 @@
 import DNAnalyzer.utils.protein.ProteinFinder;
 
 class ProteinFinderTest {
-	Path testFile = Path.of("C:\\Users\\garyg\\Documents\\projects\\DNAnalyzer\\assets\\dna\\random\\dnalong.fa");
 	Path projectPath = Path.of("");
 	Path dnaLongTestInput = projectPath.resolve("assets/dna/random/dnalong.fa");
 
 	@Test
 	void testGetProtein() {
 		try {
 			List<String> inputLines = Files.readAllLines(dnaLongTestInput);
-			List<String> expected = new ArrayList<String>();
+			List<String> expected = new ArrayList<>();
 			expected.add("AATTCCCTACAACGGATGCGCCGCTGATAGACTCGGGTTCTGGCGTCCGAGTGAAGATGATAA");
 			expected.add(
 					"AACCAATCTCATGATCACCAGTTCTGACGTTACAGTATTTTCGGTTGAGCAGGCCCCATGGGGCCCCCGCATGCCGAATTACGATATGATGCCCACTATCCTGTGTCTTCCAACCTTATGACTGACTTGTATGCGCTGCGAGGTCCCTCGATAGATTTGCTCCCACCCGTCCCGGAAACCATATCGACGACTTGTAGGTCTCTAA");

src/test/java/DNAnalyzer/core/PropertiesTest.java

@@ -0,0 +1,99 @@
+package DNAnalyzer.core;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class PropertiesTest {
+
+    Path projectPath = Path.of("");
+    Path dnaLongTestInput = projectPath.resolve("assets/dna/random/dnalong.fa");
+
+    String dnaString="";
+    @BeforeEach
+    void setUp() {
+        try {
+            List<String> inputLines = Files.readAllLines(dnaLongTestInput);
+            dnaString = inputLines.get(0);
+        } catch (IOException ex) {
+            Logger.getLogger(PropertiesTest.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+
+    @Test
+    void shouldGetGCContent() {
+            double expected = 0.5000109;
+            float actual = Properties.getGCContent(dnaString);
+            assertEquals(expected, actual,0.01);
+
+    }
+
+    @Test
+    void shouldGetGCContentAsZero() {
+           // List<String> inputLines = Files.readAllLines(dnaLongTestInput);
+            String testEmptyString = "";
+            double expected = 0;
+            float actual = Properties.getGCContent(testEmptyString);
+            assertEquals(expected, actual);
+    }
+
+    @Test
+    void sholudCalculateLengthOfCG() {
+            int expected = 50001033;
+            int actual = Properties.calculateLengthOfCG(dnaString);
+            assertEquals(expected, actual);
+    }
+
+    @Test
+    void sholudCalculateLengthOfCGAsZero() {
+            String testEmptyString = "";
+            int expected = 0;
+            int actual = Properties.calculateLengthOfCG(testEmptyString);
+            assertEquals(expected, actual);
+    }
+    @Test
+    void shouldLetterIsCorGReturnTrue() {
+        boolean actual = Properties.letterIsCorG('c');
+        assertTrue(actual);
+    }
+
+    @Test
+    void shouldLetterIsCorGReturnFalse() {
+        boolean actual = Properties.letterIsCorG('b');
+        assertFalse(actual);
+    }
+
+    @Test
+    void shouldIsRandomDNAReturnTrue() {
+            boolean actual = Properties.isRandomDNA(dnaString);
+            assertTrue(actual);
+    }
+
+//    @Test
+//    void shouldIsRandomDNAReturnFalse() {
+//            String testEmptyString = "";
+//            boolean actual = Properties.isRandomDNA(testEmptyString);
+//            assertFalse(actual);
+//    }
+
+    @Test
+    void shouldIsDifferenceLessOrEqualTo2ReturnTrue() {
+        boolean actual = Properties.isDifferenceLessOrEqualTo2(10,9);
+        assertTrue(actual);
+    }
+
+    @Test
+    void shouldIsDifferenceLessOrEqualTo2ReturnFalse() {
+        boolean actual = Properties.isDifferenceLessOrEqualTo2(10,1);
+        assertFalse(actual);
+    }
+
+}

src/test/java/DNAnalyzer/utils/core/DNAToolsTest.java

@@ -0,0 +1,64 @@
+package DNAnalyzer.utils.core;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class DNAToolsTest {
+
+    DNATools dnaTools;
+    String dnaString;
+    Path projectPath = Path.of("");
+    Path dnaLongTestInput = projectPath.resolve("assets/dna/random/dnalong.fa");
+
+    @BeforeEach
+    void setUp() {
+        try {
+            List<String> inputLines = Files.readAllLines(dnaLongTestInput);
+            dnaString = inputLines.get(0);
+
+        } catch (IOException ex) {
+            Logger.getLogger(DNAToolsTest.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+
+    @Test
+    void shouldIsValidThrowException() {
+        dnaTools = new DNATools("");
+        var expected = "Invalid characters present in DNA sequence.";
+        Exception exception = assertThrows(IllegalArgumentException.class, ()->dnaTools.isValid() );
+        assertEquals(expected, exception.getMessage());
+    }
+
+    @Test
+    void shouldIsValidNotThrowException() {
+        dnaTools = new DNATools("atgc");
+        assertDoesNotThrow(()->dnaTools.isValid() );
+    }
+
+    @Test
+    void shouldReplaceDNAString() {
+        var expected = "AAAacggctcaaaacca";
+        dnaTools = new DNATools("gagacggctcaaaacca");
+        var newDnaTools = dnaTools.replace("gag", "AAA");
+        var actual = newDnaTools.getDna();
+        assertEquals(expected,actual);
+    }
+
+    @Test
+    void shouldReverseDNAString() {
+        var expected = "cagag";
+        dnaTools = new DNATools("gagac");
+        var newDnaTools = dnaTools.reverse();
+        var actual = newDnaTools.getDna();
+        assertEquals(expected,actual);
+    }
+}

src/test/java/DNAnalyzer/utils/core/ReadingFramesTest.java

@@ -0,0 +1,29 @@
+package DNAnalyzer.utils.core;
+
+import DNAnalyzer.data.codon.CodonFrame;
+import org.junit.jupiter.api.BeforeEach;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+
+
+class ReadingFramesTest {
+
+    ReadingFrames readingFrames;
+    Path projectPath = Path.of("");
+    Path dnaLongTestInput = projectPath.resolve("assets/dna/random/dnalong.fa");
+
+    @BeforeEach
+    void setUp() {
+        try {
+            List<String> inputLines = Files.readAllLines(dnaLongTestInput);
+            readingFrames= new ReadingFrames(new CodonFrame(inputLines.get(0), (short) 1, 2, 100));
+
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+}

src/test/java/DNAnalyzer/utils/protein/ProteinAnalysisTest.java

@@ -0,0 +1,31 @@
+package DNAnalyzer.utils.protein;
+
+import org.junit.jupiter.api.BeforeEach;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+
+class ProteinAnalysisTest {
+
+    Path projectPath = Path.of("");
+    Path dnaLongTestInput = projectPath.resolve("assets/dna/random/dnalong.fa");
+
+    String dnaString="";
+
+    @BeforeEach
+    void setUp() {
+        try {
+            List<String> inputLines = Files.readAllLines(dnaLongTestInput);
+            dnaString = inputLines.get(0);
+        } catch (IOException ex) {
+            Logger.getLogger(ProteinAnalysisTest.class.getName()).log(Level.SEVERE, null, ex);
+        }
+
+    }
+
+}