Merge branch 'main' into deepsource-transform-9dd95d07

.github/workflows/static.yml

@@ -35,8 +35,8 @@ jobs:
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
         with:
-          # Upload entire repository
-          path: '.'
+          # Upload all content under the web/ directory
+          path: "web/"
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v1

.gitignore

@@ -2,6 +2,7 @@
 .config/*
 bin/*
 .vs/*
+.settings/*
 
 ### Java ###
 *.class

CITATION.cff

@@ -0,0 +1,11 @@
+cff-version: "1.1.0"
+authors: 
+  -
+    family-names: Acharya
+    given-names: Piyush
+
+date-released: 2022-10-10
+doi: "10.1038/s41592-021-01101-x"
+message: "If you use this software, please cite it using these metadata."
+title: "A highly efficient, powerful, and feature-rich machine learning algorithm for analyzing DNA sequences"
+version: "2.0.0"

README.md

@@ -3,7 +3,7 @@
 </div>
 
 <p align="center">
-  <img src="https://img.shields.io/badge/copyright-pending-blue"  alt="Copyright"/>
+  <img src="https://img.shields.io/badge/copyright-2022-blue"  alt="Copyright"/>
   <img src="https://wakatime.com/badge/github/Verisimilitude11/DNAnalyzer.svg"  alt="WakaTime"/>
   <img src="https://img.shields.io/github/v/release/VERISIMILITUDE11/DNAnalyzer"  alt="Releases"/>
   <img src="https://img.shields.io/github/repo-size/Verisimilitude11/DNAnalyzer"  alt="Repository Size"/>
@@ -97,7 +97,7 @@
 </h3>
 To build and run the DNAnalyzer, you need
 
-* JDK 17 or greater
+* JDK <a href="https://www.oracle.com/java/technologies/downloads/#jdk17-windows">17</a> 
 * A JAVA\_HOME environment variable pointing to your JDK, or the Java executable in your PATH
 * <a href="https://gradle.org/install/">Gradle</a>
 
@@ -264,5 +264,5 @@ https://user-images.githubusercontent.com/27987685/194954560-5f470ecc-e733-4757-
   </code>
 </p>
 
-### Copyright Pending © 2022 DNAnalyzer. Some rights reserved. This is an open source project.
+### Copyright © 2022 Piyush Acharya & The DNAnalyzer Team. This is an open source project.
 

src/main/java/DNAnalyzer/DnaAnalyzer.java

@@ -73,6 +73,6 @@ public DnaAnalyzer printLongestProtein() {
     }
 
     private List<String> getProteins(String aminoAcid) {
-        return new ProteinFinder().getProtein(dna.getDna(), aminoAcid);
+        return ProteinFinder.getProtein(dna.getDna(), aminoAcid);
     }
 }

src/main/java/DNAnalyzer/Main.java

@@ -29,7 +29,7 @@ public class Main {
      *
      * @throws InterruptedException
      * @throws IOException
-     * @category User ExperienceF
+     * @category User Experience
      */
     public static void clearTerminal() throws InterruptedException, IOException {
         if (System.getProperty("os.name").contains("Windows")) { // if the os is Windows

src/main/java/DNAnalyzer/codon/CodonFrame.java

@@ -60,13 +60,14 @@ public int getMax() {
 
     @Override
     public boolean equals(final Object o) {
-        if (this == o)
-            return true;
-        if (!(o instanceof CodonFrame))
-            return false;
-        final CodonFrame that = (CodonFrame) o;
-        return getReadingFrame() == that.getReadingFrame() && getMin() == that.getMin() && getMax() == that.getMax()
-                && getDna().equals(that.getDna());
+        boolean result = false;
+        if (this == o) {
+            result =  true;
+        } else if (o instanceof final CodonFrame inputFrame) {
+            result = getReadingFrame() == inputFrame.getReadingFrame() && getMin() == inputFrame.getMin() && getMax() == inputFrame.getMax()
+            && getDna().equals(inputFrame.getDna());
+        }
+        return result;
     }
 
     @Override

src/main/java/DNAnalyzer/protein/ProteinFinder.java

@@ -12,77 +12,95 @@
 package DNAnalyzer.protein;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
-import DNAnalyzer.codon.*;
-import DNAnalyzer.aminoAcid.*;
+
+import DNAnalyzer.aminoAcid.AminoAcidMapping;
+import DNAnalyzer.aminoAcid.AminoAcidNames;
+import DNAnalyzer.codon.CodonDataUtils;
 
 /**
  * Find proteins in a DNA sequence (contains the main algorithm).
  *
  * @author Piyush Acharya (@Verisimilitude11)
+ * @author Fernando Boaglio (@boaglio)
  * @version 1.2.1
  */
 
 public class ProteinFinder {
-    /**
-     * Amino acid list
-     */
 
-    private final List<String> aminoAcidList;
     /**
-     * protein list
+     * Utility classes should not have public constructors
      */
-    private final List<String> proteinList;
-
-    /**
-     * ProteinFinder default constructor to initialize aminoAcidList and proteinList
-     */
-    public ProteinFinder() {
-        aminoAcidList = new ArrayList<>();
-        proteinList = new ArrayList<>();
+    private ProteinFinder() {
     }
 
+    private static final int QT_NUCLEOTIDES = 3;
+
     /**
      * Gets proteins from dna and amino acid
      *
-     * @param dna       dna
-     * @param aminoAcid amino acid
+     * @param dna
+     *            dna
+     * @param aminoAcid
+     *            amino acid
      * @return list of proteins
      */
-    public List<String> getProtein(final String dna, final String aminoAcid) {
-        this.aminoAcidList.addAll(CodonDataUtils.getAminoAcid(AminoAcidMapping.getAminoAcidMapping(aminoAcid)));
+    public static List<String> getProtein(final String dna, final String aminoAcid) {
 
-        int start_index;
-        int stop_index;
-        final List<String> stop = CodonDataUtils.getAminoAcid(AminoAcidNames.STOP);
+        List<String> aminoAcidList = new ArrayList<>();
+        List<String> proteinList = new ArrayList<>();
+
+        aminoAcidList.addAll(CodonDataUtils.getAminoAcid(AminoAcidMapping.getAminoAcidMapping(aminoAcid)));
+
+        int startIndex;
+        final List<String> stopCodonList = CodonDataUtils.getAminoAcid(AminoAcidNames.STOP);
 
         // Outer loop loops through the start codons for the amino acids that the user
         // entered.
         // store the start index
-        // Inner loop loops through the stop that the user entered.
-        // store the stop_index
-        // if index is not -1 then store the substring of dna with start and stop index
-        // in the protein list
-        for (final String start_codon : this.aminoAcidList) {
-            start_index = dna.indexOf(start_codon.toLowerCase());
-            for (final String stop_codon : stop) {
-                stop_index = dna.indexOf(stop_codon.toLowerCase(), start_index + 3);
-                if ((start_index != -1) && (stop_index != -1)) {
-                    this.proteinList.add(dna.substring(start_index, stop_index + 3).toUpperCase());
-                    break;
-                }
-            }
+        for (final String startCodon : aminoAcidList) {
+            startIndex = dna.indexOf(startCodon.toLowerCase());
+            addProtein(dna, proteinList, startIndex, stopCodonList);
         }
 
         // if no proteins are found, return null
-        if (this.proteinList.isEmpty()) {
+        if (proteinList.isEmpty()) {
             // Return null if no protein found in DNA sequence
             System.out.println("No proteins found");
-            return null;
+            return Collections.emptyList();
         }
 
         // Return list of proteins found in the DNA sequence
-        return this.proteinList;
+        return proteinList;
+    }
+
+    /**
+     * Add protein to protein list
+     * 
+     * @param dna
+     * @param proteinList
+     * @param startIndex
+     * @param stopCodonList
+     */
+    private static void addProtein(final String dna, List<String> proteinList, int startIndex,
+            final List<String> stopCodonList) {
+
+        // Inner loop loops through the stop that the user entered.
+        // store the stopIndex
+        // if index is not -1 then store the substring of dna with start and stop index
+        // in the protein list
+        int stopIndex;
+        for (final String stopCodon : stopCodonList) {
+
+            stopIndex = dna.indexOf(stopCodon.toLowerCase(), startIndex + QT_NUCLEOTIDES);
+
+            if ((startIndex != -1) && (stopIndex != -1)) {
+                proteinList.add(dna.substring(startIndex, stopIndex + QT_NUCLEOTIDES).toUpperCase());
+                break;
+            }
+
+        }
     }
 
 }

web/index.html

@@ -71,7 +71,7 @@ <h2 class="primary-dark">Features</h2>
 <br>
 
   <footer>
-  <p>Copyright © Piyush Acharya 2022. This is an open-source project.<br>
+  <p>Copyright © Piyush Acharya & The DNAnalyzer Team 2022. This is an open-source project.<br>
                                    </p>
 </footer>
     <script src="./index.js"></script>