More on biosilico crypto

biosilico-crypto/src/main/java/gabywald/crypto/more/BinaryConversion.java

@@ -0,0 +1,83 @@
+package gabywald.crypto.more;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * 
+ * @author Gabriel Chandesris (2023)
+ */
+public class BinaryConversion {
+
+	public static String sequence2binary(String input) {
+		// input.chars().map( c -> ((c == 65)?"00":((c == 67)?"01":((c == 71)?"10":((c == 84)?"11":""))))).forEach(System.out::println); // .collect(Collectors.joining());
+		StringBuilder result = new StringBuilder();
+		for (char c : input.toCharArray()) {
+			result.append(((c == 65)?"00":((c == 67)?"01":((c == 71)?"10":((c == 84)?"11":"")))));
+		}
+		return result.toString();
+	}
+
+	public static String binary2sequence(String input) {
+		StringBuilder output = new StringBuilder();
+		for (int i = 0 ; i <= input.length() - 2 ; i += 2) {
+			String b = input.substring(i, i + 2);
+			int k = ((b.equals("00"))?65:((b.equals("01"))?67:((b.equals("10"))?71:((b.equals("11"))?84:85))));
+			output.append((char) k);
+		}
+		return output.toString();
+	}
+
+	public static String convertStringToBinary(String input) {
+		StringBuilder result = new StringBuilder();
+		char[] chars = input.toCharArray();
+		for (char aChar : chars) {
+			// char -> int, auto-cast ; zero pads
+			result.append( String.format("%8s", Integer.toBinaryString(aChar)).replaceAll(" ", "0") );
+		}
+
+		return result.toString();
+	}
+
+	public static String convertByteArraysToBinary(byte[] input) {
+		StringBuilder result = new StringBuilder();
+		for (byte b : input) {
+			int val = b;
+			for (int i = 0; i < 8; i++) {
+				result.append((val & 128) == 0 ? 0 : 1);	  // 128 = 1000 0000
+				val <<= 1;
+			}
+		}
+		return result.toString();
+	}
+
+	public static String convertBinaryToString(String input) {
+		// return Arrays.stream(input.split(" ")).map(binary -> Integer.parseInt(binary, 2)).map(Character::toString).collect(Collectors.joining());
+		// return Arrays.stream(input.split(" ")).map(b -> Integer.parseInt(b, 2)).map(b -> Character.toString(b)).collect(Collectors.joining());
+		// return Arrays.stream(input.split(" ")).map(b -> Integer.parseInt(b, 2)).map(b -> Integer.toString(b)).collect(Collectors.joining());
+		return Arrays.stream(input.split(" ")).map(b -> Integer.parseInt(b, 2)).map(b -> ((char)b.intValue()) + "").collect(Collectors.joining());
+	}
+
+	public static String convertBinaryToAscii(String binary) {
+		// Convert binary string into ASCII.
+		StringBuilder output = new StringBuilder();
+		for (int i = 0 ; i <= binary.length() - 8 ; i += 8) {
+			int k = Integer.parseInt(binary.substring(i, i + 8), 2);
+			output.append((char) k);
+		}
+		return output.toString();
+	}
+
+	public static String prettyBinary(String binary, int blockSize, String separator) {
+		List<String> result = new ArrayList<>();
+		int index = 0;
+		while (index < binary.length()) {
+			result.add(binary.substring(index, Math.min(index + blockSize, binary.length())));
+			index += blockSize;
+		}
+
+		return result.stream().collect(Collectors.joining(separator));
+	}
+}

biosilico-crypto/src/test/java/gabywald/crypto/model/tests/BinaryBitsTests.java

@@ -0,0 +1,60 @@
+package gabywald.crypto.model.tests;
+
+import java.nio.charset.StandardCharsets;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import gabywald.crypto.more.BinaryConversion;
+
+/**
+ * 
+ * @author Gabriel Chandesris (2023)
+ */
+class BinaryBitsTests {
+
+	@Test
+	void test() {
+
+		String input = "Hello";
+		String result = BinaryConversion.convertStringToBinary(input);
+		Assertions.assertNotNull(result);
+		Assertions.assertEquals("0100100001100101011011000110110001101111", 
+								BinaryConversion.convertStringToBinary(input));
+		Assertions.assertEquals("01001000 01100101 01101100 01101100 01101111", 
+								BinaryConversion.prettyBinary(result, 8, " "));
+
+		String input02 = "a";
+		String result02 = BinaryConversion.convertByteArraysToBinary(input02.getBytes(StandardCharsets.UTF_8));
+		Assertions.assertEquals(result02, BinaryConversion.prettyBinary(result02, 8, " "));
+
+		// 0100100001100101011011000110110001101111
+		// 01001000 01100101 01101100 01101100 01101111
+		String binary01 = "0100100001100101011011000110110001101111";
+		String binary02 = "01001000 01100101 01101100 01101100 01101111";
+		Assertions.assertEquals(input, BinaryConversion.convertBinaryToString(binary02));
+		Assertions.assertEquals(input, BinaryConversion.convertBinaryToAscii(binary01));
+
+		// ACGT <=> 00 01 10 11
+//		System.out.println((int)'A'); // 65
+//		System.out.println((int)'C'); // 67
+//		System.out.println((int)'G'); // 71
+//		System.out.println((int)'T'); // 84
+//		System.out.println((int)'U'); // 85
+
+		String sequenceACTG = "ACGT";
+		String sequenceBINA = "00011011";
+		Assertions.assertEquals(sequenceBINA, BinaryConversion.sequence2binary(sequenceACTG));
+		Assertions.assertEquals(sequenceACTG, BinaryConversion.binary2sequence(sequenceBINA));
+
+		Assertions.assertEquals("", BinaryConversion.convertBinaryToString(BinaryConversion.sequence2binary("ACGT")));
+		Assertions.assertEquals("ACGT", BinaryConversion.binary2sequence(BinaryConversion.convertStringToBinary("")));
+
+		Assertions.assertEquals("00011011000110110001101100011011", BinaryConversion.sequence2binary("ACGTACGTACGTACGT"));
+		Assertions.assertEquals("ᬛ", BinaryConversion.convertBinaryToString(BinaryConversion.sequence2binary("ACGTACGTACGTACGT")));
+
+	}
+
+}

pom.xml

@@ -37,7 +37,9 @@
 		<lib.version>1.0.1</lib.version>
 		<plugin.version>3.1.8</plugin.version>
 
-		<junit.version>5.3.1</junit.version>
+		<gabywald.utilities.version>0.2.1-SNAPSHOT</gabywald.utilities.version>
+
+		<junit.version>5.6.0</junit.version>
 	</properties>
 
 	<dependencies>
@@ -48,7 +50,7 @@
 		<dependency>
 			<groupId>gabywald</groupId>
 			<artifactId>utilities</artifactId>
-			<version>0.1.0-SNAPSHOT</version>
+			<version>${gabywald.utilities.version}</version>
 		</dependency>
 
 	</dependencies>
@@ -69,6 +71,7 @@
 		</pluginManagement>
 
 		<plugins>
+			<!-- for eclipse integration -->
 			<plugin>
 				<artifactId>maven-eclipse-plugin</artifactId>
 				<configuration>
@@ -79,28 +82,28 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<version>2.8</version>
 			</plugin>
-
+			<!-- for correct compilation -->
+			<plugin>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>2.3.2</version>
+				<configuration>
+					<source>${maven.compiler.source}</source>
+					<target>${maven.compiler.target}</target>
+				</configuration>
+				<groupId>org.apache.maven.plugins</groupId>
+			</plugin>
+			<!-- for unit tests -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>2.22.0</version>
             </plugin>
+            <!-- for integration tests -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
                 <version>2.22.0</version>
             </plugin>
-
-			<plugin>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<version>2.3.2</version>
-				<configuration>
-					<source>${maven.compiler.source}</source>
-					<target>${maven.compiler.target}</target>
-				</configuration>
-				<groupId>org.apache.maven.plugins</groupId>
-			</plugin>
-
 		</plugins>
 	</build>
 </project>

src/test/resources/NeuronTests.launch

@@ -8,6 +8,7 @@
 </listAttribute>
 <stringAttribute key="org.eclipse.jdt.junit.CONTAINER" value=""/>
 <booleanAttribute key="org.eclipse.jdt.junit.KEEPRUNNING_ATTR" value="false"/>
+<stringAttribute key="org.eclipse.jdt.junit.TESTNAME" value=""/>
 <stringAttribute key="org.eclipse.jdt.junit.TEST_KIND" value="org.eclipse.jdt.junit.loader.junit5"/>
 <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
 <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="gabywald.biosilico.model.tests.NeuronTests"/>