Protein Translation: Implement problem in Java language stream. (#985)

* Protein Translation: Implemented problem in Java language stream.

* Protein-translation: Update implementation with FridaTveit's suggestions.

* Fix formatting and typesafety issues.

config.json

@@ -168,6 +168,19 @@
     },
     {
       "core": false,
+      "difficulty": 3,
+      "slug": "protein-translation",
+      "topics": [
+        "arrays",
+        "conditionals",
+        "loops",
+        "strings"
+      ],
+      "unlocked_by": "rna-transcription",
+      "uuid": "1bea45f6-021e-0a80-1e53-afcd9f9a8df08c01126"
+    },
+    {
+      "core": false,
       "difficulty": 4,
       "slug": "sum-of-multiples",
       "topics": [

exercises/protein-translation/.meta/src/reference/java/ProteinTranslator.java

@@ -0,0 +1,47 @@
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+class ProteinTranslator {
+
+    private static final String[] METHIONINE = {"AUG"};
+    private static final String[] PHENYLALANINE = {"UUU", "UUC"};
+    private static final String[] LEUCINE = {"UUA", "UUG"};
+    private static final String[] SERINE = {"UCU", "UCC", "UCA", "UCG"};
+    private static final String[] TYROSINE = {"UAU", "UAC"};
+    private static final String[] CYSTEINE = {"UGU", "UGC"};
+    private static final String[] TRYPTOPHAN = {"UGG"};
+    private static final String[] STOP = {"UAA", "UAG", "UGA"};
+
+    List<String> translate(String rnaSequence) {
+
+        List<String> proteinList = new ArrayList<String>();
+
+        for (int i = 0; i < rnaSequence.length(); i += 3) {
+            String codon = rnaSequence.substring(i, i+3);
+
+            if (Arrays.asList(METHIONINE).contains(codon)) {
+                proteinList.add("Methionine");
+            } else if (Arrays.asList(PHENYLALANINE).contains(codon)) {
+                proteinList.add("Phenylalanine");
+            } else if (Arrays.asList(LEUCINE).contains(codon)) {
+                proteinList.add("Leucine");
+            } else if (Arrays.asList(SERINE).contains(codon)) {
+                proteinList.add("Serine");
+            } else if (Arrays.asList(TYROSINE).contains(codon)) {
+                proteinList.add("Tyrosine");
+            } else if (Arrays.asList(CYSTEINE).contains(codon)) {
+                proteinList.add("Cysteine");
+            } else if (Arrays.asList(TRYPTOPHAN).contains(codon)) {
+                proteinList.add("Tryptophan");
+            } else if (Arrays.asList(STOP).contains(codon)) {
+                break;
+            } else {
+                throw new IllegalArgumentException("Invalid input");
+            }
+
+        }
+
+        return proteinList;
+    }
+}

exercises/protein-translation/README.md

@@ -0,0 +1,58 @@
+#Translate RNA sequences into proteins.
+
+RNA can be broken into three nucleotide sequences called codons, and then translated to a polypeptide like so:
+
+RNA: `"AUGUUUUCU"` => translates to
+
+Codons: `"AUG", "UUU", "UCU"`
+=> which become a polypeptide with the following sequence =>
+
+Protein: `"Methionine", "Phenylalanine", "Serine"`
+
+There are 64 codons which in turn correspond to 20 amino acids; however, all of the codon sequences and resulting amino acids are not important in this exercise.  If it works for one codon, the program should work for all of them.
+However, feel free to expand the list in the test suite to include them all.
+
+There are also three terminating codons (also known as 'STOP' codons); if any of these codons are encountered (by the ribosome), all translation ends and the protein is terminated.
+
+All subsequent codons after are ignored, like this:
+
+RNA: `"AUGUUUUCUUAAAUG"` =>
+
+Codons: `"AUG", "UUU", "UCU", "UAG", "AUG"` =>
+
+Protein: `"Methionine", "Phenylalanine", "Serine"`
+
+Note the stop codon terminates the translation and the final methionine is not translated into the protein sequence.
+
+Below are the codons and resulting Amino Acids needed for the exercise.
+
+Codon                 | Protein
+:---                  | :---
+AUG                   | Methionine
+UUU, UUC              | Phenylalanine
+UUA, UUG              | Leucine
+UCU, UCC, UCA, UCG    | Serine
+UAU, UAC              | Tyrosine
+UGU, UGC              | Cysteine
+UGG                   | Tryptophan
+UAA, UAG, UGA         | STOP
+
+Learn more about [protein translation on Wikipedia](http://en.wikipedia.org/wiki/Translation_(biology))
+
+# Running the tests
+
+You can run all the tests for an exercise by entering
+
+```sh
+$ gradle test
+```
+
+in your terminal.
+
+## Source
+
+Tyler Long
+
+## Submitting Incomplete Solutions
+
+It's possible to submit an incomplete solution so you can see how others have completed the exercise.

exercises/protein-translation/build.gradle

@@ -0,0 +1,18 @@
+apply plugin: "java"
+apply plugin: "eclipse"
+apply plugin: "idea"
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    testCompile "junit:junit:4.12"
+}
+
+test {
+    testLogging {
+        exceptionFormat = 'full'
+        events = ["passed", "failed", "skipped"]
+    }
+}

exercises/protein-translation/src/main/java/ProteinTranslator.java

@@ -0,0 +1,8 @@
+import java.util.List;
+
+class ProteinTranslator {
+
+    List<String> translate(String rnaSequence) {
+        throw new UnsupportedOperationException("Delete this statement and write your own implementation.");
+    }
+}

exercises/protein-translation/src/test/java/ProteinTranslatorTest.java

@@ -0,0 +1,179 @@
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+public class ProteinTranslatorTest {
+
+    private ProteinTranslator proteinTranslator;
+
+    @Before
+    public void setUp() {
+        proteinTranslator = new ProteinTranslator();
+    }
+
+    @Test
+    public void testMethionineRnaSequence() {
+        List<String> expected = Arrays.asList("Methionine");
+        assertEquals(expected, proteinTranslator.translate("AUG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testPhenylalanineRnaSequence1() {
+        List<String> expected = Arrays.asList("Phenylalanine");
+        assertEquals(expected, proteinTranslator.translate("UUU"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testPhenylalanineRnaSequence2() {
+        List<String> expected = Arrays.asList("Phenylalanine");
+        assertEquals(expected, proteinTranslator.translate("UUC"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testLeucineRnaSequence1() {
+        List<String> expected = Arrays.asList("Leucine");
+        assertEquals(expected, proteinTranslator.translate("UUA"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testLeucineRnaSequence2() {
+        List<String> expected = Arrays.asList("Leucine");
+        assertEquals(expected, proteinTranslator.translate("UUG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testSerineRnaSequence1() {
+        List<String> expected = Arrays.asList("Serine");
+        assertEquals(expected, proteinTranslator.translate("UCU"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testSerineRnaSequence2() {
+        List<String> expected = Arrays.asList("Serine");
+        assertEquals(expected, proteinTranslator.translate("UCC"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testSerineRnaSequence3() {
+        List<String> expected = Arrays.asList("Serine");
+        assertEquals(expected, proteinTranslator.translate("UCA"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testSerineRnaSequence4() {
+        List<String> expected = Arrays.asList("Serine");
+        assertEquals(expected, proteinTranslator.translate("UCG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTyrosineRnaSequence1() {
+        List<String> expected = Arrays.asList("Tyrosine");
+        assertEquals(expected, proteinTranslator.translate("UAU"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTyrosineRnaSequence2() {
+        List<String> expected = Arrays.asList("Tyrosine");
+        assertEquals(expected, proteinTranslator.translate("UAC"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testCysteineRnaSequence1() {
+        List<String> expected = Arrays.asList("Cysteine");
+        assertEquals(expected, proteinTranslator.translate("UGU"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testCysteineRnaSequence2() {
+        List<String> expected = Arrays.asList("Cysteine");
+        assertEquals(expected, proteinTranslator.translate("UGC"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTryptophanRnaSequence1() {
+        List<String> expected = Arrays.asList("Tryptophan");
+        assertEquals(expected, proteinTranslator.translate("UGG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testStopRnaSequence1() {
+        List<String> expected = Arrays.asList();
+        assertEquals(expected, proteinTranslator.translate("UAA"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testStopRnaSequence2() {
+        List<String> expected = Arrays.asList();
+        assertEquals(expected, proteinTranslator.translate("UAG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testStopRnaSequence3() {
+        List<String> expected = Arrays.asList();
+        assertEquals(expected, proteinTranslator.translate("UGA"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationOfRnaToProteinList() {
+        List<String> expected = Arrays.asList("Methionine","Phenylalanine","Tryptophan");
+        assertEquals(expected, proteinTranslator.translate("AUGUUUUGG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationStopsIfStopCodonAtBeginning() {
+        List<String> expected = Arrays.asList();
+        assertEquals(expected, proteinTranslator.translate("UAGUGG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationStopsIfStopCodonAtEnd1() {
+        List<String> expected = Arrays.asList("Tryptophan");
+        assertEquals(expected, proteinTranslator.translate("UGGUAG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationStopsIfStopCodonAtEnd2() {
+        List<String> expected = Arrays.asList("Methionine", "Phenylalanine");
+        assertEquals(expected, proteinTranslator.translate("AUGUUUUAA"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationStopsIfStopCodonInMiddle1() {
+        List<String> expected = Arrays.asList("Tryptophan");
+        assertEquals(expected, proteinTranslator.translate("UGGUAGUGG"));
+    }
+
+    @Ignore("Remove to run test")
+    @Test
+    public void testTranslationStopsIfStopCodonInMiddle2() {
+        List<String> expected = Arrays.asList("Tryptophan","Cysteine","Tyrosine");
+        assertEquals(expected, proteinTranslator.translate("UGGUGUUAUUAAUGGUUU"));
+    }
+
+}

exercises/settings.gradle

@@ -53,6 +53,7 @@ include 'phone-number'
 include 'pig-latin'
 include 'poker'
 include 'prime-factors'
+include 'protein-translation'
 include 'pythagorean-triplet'
 include 'queen-attack'
 include 'raindrops'