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Merge branch 'main' of https://github.com/VerisimilitudeX/DNAnalyzer
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@VerisimilitudeX
VerisimilitudeX committed Jun 22, 2024
2 parents 0beb9fe + a26211e commit 92fa8f3
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10 changes: 5 additions & 5 deletions src/main/java/DNAnalyzer/core/DNAAnalysis.java
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package DNAnalyzer.core;

import java.io.PrintStream;
import java.util.List;
import static java.util.Optional.ofNullable;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import DNAnalyzer.data.codon.CodonFrame;
import DNAnalyzer.utils.core.BasePairCounter;
import DNAnalyzer.utils.core.DNATools;
import DNAnalyzer.utils.core.ReadingFrames;
import DNAnalyzer.utils.protein.ProteinAnalysis;
import DNAnalyzer.utils.protein.ProteinFinder;
import java.io.PrintStream;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
* Provides functionality to analyze the DNA
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// used as helper method for output codons, handles protein decisions
public void proteinSequence(PrintStream out) {
final String dnaValue = this.dna.getDna();

if (protein != null) {
final Pattern p = Pattern.compile(protein);
final Matcher m = p.matcher(dnaValue);
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338 changes: 167 additions & 171 deletions src/main/java/DNAnalyzer/core/Properties.java
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*/
package DNAnalyzer.core;

import java.io.PrintStream;
import java.util.Arrays;
import java.util.List;
import java.util.stream.IntStream;
import static DNAnalyzer.core.DNAAnalysis.countBasePairs;

import DNAnalyzer.core.DNAAnalysis.BasePairIndex;
import static DNAnalyzer.core.DNAAnalysis.countBasePairs;
import DNAnalyzer.data.aminoAcid.AminoAcid;
import DNAnalyzer.data.aminoAcid.AminoAcidFactory;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.List;
import java.util.stream.IntStream;

/**
* Prints the list of proteins and their respective properties found in the DNA.
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*/
public class Properties {

/**
* Gets the version of the application.
*
* @return The version of the application
* @category Properties
*/
public static String getVersion() {
return "3.0.0-beta.0";
/**
* Gets the version of the application.
*
* @return The version of the application
* @category Properties
*/
public static String getVersion() {
return "3.0.0-beta.0";
}

/**
* Prints the list of proteins found in the DNA.
*
* @param proteinList The list of proteins to be printed
* @param aminoAcid The amino acid to be searched for {@code @category} Output
*/
public static void printProteinList(
final List<String> proteinList, final String aminoAcid, PrintStream out) {

// Changes the 1 letter or 3 letter abbreviation of the amino acids into the
// full name
final AminoAcid acid = AminoAcidFactory.getAminoAcid(aminoAcid);

out.println("Proteins coded for " + acid.getFullName() + ": ");
out.println("----------------------------------------------------");
short count = 1;
for (final String gene : proteinList) {
out.println(count + ". " + gene);
count++;
}

/**
* Prints the list of proteins found in the DNA.
*
* @param proteinList The list of proteins to be printed
* @param aminoAcid The amino acid to be searched for {@code @category}
* Output
*/
public static void printProteinList(
final List<String> proteinList, final String aminoAcid, PrintStream out) {

// Changes the 1 letter or 3 letter abbreviation of the amino acids into the
// full name
final AminoAcid acid = AminoAcidFactory.getAminoAcid(aminoAcid);

out.println("Proteins coded for " + acid.getFullName() + ": ");
out.println("----------------------------------------------------");
short count = 1;
for (final String gene : proteinList) {
out.println(count + ". " + gene);
count++;
}
}

/**
* Gets the GC content of a gene.
*
* @param dna The DNA sequence to be analyzed
* @return The GC content of the DNA sequence
* @category Properties
* @see
* "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);
gcContent = gcLen / dna.length();

return gcContent;
}

/**
* Calculate the total number of characters that are 'g' or 'c' of a given
* DNA String
*
* @param dna The DNA sequence that was analyzed
* @category Property
*/
public static int calculateLengthOfCG(String dna) {
int gcLength = 0;
char[] dnaCharArray = dna.toCharArray();

for (char letter : dnaCharArray) {
if (letterIsCorG(letter)) {
gcLength++;
}
}

return gcLength;
}

/**
* Gets the GC content of a gene.
*
* @param dna The DNA sequence to be analyzed
* @return The GC content of the DNA sequence
* @category Properties
* @see
* "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;
}

/**
* Checks if a letter is either 'c' or 'g'
*
* @param aLetter The letter to check
* @category Property
*/
public static boolean letterIsCorG(char aLetter) {
return (aLetter == 'c') || (aLetter == 'g');
dna = dna.toLowerCase();
float gcLen = (float) calculateLengthOfCG(dna);
gcContent = gcLen / dna.length();

return gcContent;
}

/**
* Calculate the total number of characters that are 'g' or 'c' of a given DNA String
*
* @param dna The DNA sequence that was analyzed
* @category Property
*/
public static int calculateLengthOfCG(String dna) {
int gcLength = 0;
char[] dnaCharArray = dna.toCharArray();

for (char letter : dnaCharArray) {
if (letterIsCorG(letter)) {
gcLength++;
}
}

/**
* Prints the nucleotide count of the DNA sequence.
*
* @param dna The DNA sequence that was analyzed {@code @category} Output
*/
public static void printNucleotideCount(final String dna, PrintStream out) {
out.println("Nucleotide count:");
long[] counts = countBasePairs(dna);
out.println(
"A"
+ ": "
+ counts[BasePairIndex.ADENINE]
+ " ("
+ (float) counts[BasePairIndex.ADENINE] / dna.length() * 100
+ "%)");
out.println(
"T"
+ ": "
+ counts[BasePairIndex.THYMINE]
+ " ("
+ (float) counts[BasePairIndex.THYMINE] / dna.length() * 100
+ "%)");
out.println(
"G"
+ ": "
+ counts[BasePairIndex.GUANINE]
+ " ("
+ (float) counts[BasePairIndex.GUANINE] / dna.length() * 100
+ "%)");
out.println(
"C"
+ ": "
+ counts[BasePairIndex.CYTOSINE]
+ " ("
+ (float) counts[BasePairIndex.CYTOSINE] / dna.length() * 100
+ "%)");
out.println(
"N"
+ ": "
+ counts[BasePairIndex.UNKNOWN]
+ " ("
+ (((float) counts[BasePairIndex.UNKNOWN] / dna.length()) * 100)
+ "%)");
out.println("Total: " + dna.length());
}

/**
* Checks if the DNA sequence is random or not.
*
* @param dna The DNA sequence that was analyzed
* @return Whether the DNA sequence is random or not {@code @category}
* Properties
*/
public static boolean isRandomDNA(final String dna) {
long[] nucleotideCount = countBasePairs(dna);
int[] percentages
= Arrays.stream(nucleotideCount).mapToInt(c -> nucleotidePercentage(c, dna)).toArray();

int a = percentages[BasePairIndex.ADENINE];
int t = percentages[BasePairIndex.THYMINE];
int g = percentages[BasePairIndex.GUANINE];
int c = percentages[BasePairIndex.CYTOSINE];

IntStream diffs
= IntStream.of(
Math.abs(a - t),
Math.abs(a - g),
Math.abs(a - c),
Math.abs(t - g),
Math.abs(t - c),
Math.abs(g - c));

return diffs.allMatch(diff -> diff <= 2);
}

/**
* Calculates the percentage of given amount of nucleotide in the dna
* sequence/
*
* @param nucleotideCount Number of nucleotides (int)
* @param dna DNA sequence
* @return the percentage of nucleotides in that DNA sequence
*/
private static int nucleotidePercentage(final long nucleotideCount, final String dna) {
return (int) (((float) nucleotideCount) / dna.length() * 100);
}
return gcLength;
}

/**
* Checks if a letter is either 'c' or 'g'
*
* @param aLetter The letter to check
* @category Property
*/
public static boolean letterIsCorG(char aLetter) {
return (aLetter == 'c') || (aLetter == 'g');
}

/**
* Prints the nucleotide count of the DNA sequence.
*
* @param dna The DNA sequence that was analyzed {@code @category} Output
*/
public static void printNucleotideCount(final String dna, PrintStream out) {
out.println("Nucleotide count:");
long[] counts = countBasePairs(dna);
out.println(
"A"
+ ": "
+ counts[BasePairIndex.ADENINE]
+ " ("
+ (float) counts[BasePairIndex.ADENINE] / dna.length() * 100
+ "%)");
out.println(
"T"
+ ": "
+ counts[BasePairIndex.THYMINE]
+ " ("
+ (float) counts[BasePairIndex.THYMINE] / dna.length() * 100
+ "%)");
out.println(
"G"
+ ": "
+ counts[BasePairIndex.GUANINE]
+ " ("
+ (float) counts[BasePairIndex.GUANINE] / dna.length() * 100
+ "%)");
out.println(
"C"
+ ": "
+ counts[BasePairIndex.CYTOSINE]
+ " ("
+ (float) counts[BasePairIndex.CYTOSINE] / dna.length() * 100
+ "%)");
out.println(
"N"
+ ": "
+ counts[BasePairIndex.UNKNOWN]
+ " ("
+ (((float) counts[BasePairIndex.UNKNOWN] / dna.length()) * 100)
+ "%)");
out.println("Total: " + dna.length());
}

/**
* Checks if the DNA sequence is random or not.
*
* @param dna The DNA sequence that was analyzed
* @return Whether the DNA sequence is random or not {@code @category} Properties
*/
public static boolean isRandomDNA(final String dna) {
long[] nucleotideCount = countBasePairs(dna);
int[] percentages =
Arrays.stream(nucleotideCount).mapToInt(c -> nucleotidePercentage(c, dna)).toArray();

int a = percentages[BasePairIndex.ADENINE];
int t = percentages[BasePairIndex.THYMINE];
int g = percentages[BasePairIndex.GUANINE];
int c = percentages[BasePairIndex.CYTOSINE];

IntStream diffs =
IntStream.of(
Math.abs(a - t),
Math.abs(a - g),
Math.abs(a - c),
Math.abs(t - g),
Math.abs(t - c),
Math.abs(g - c));

return diffs.allMatch(diff -> diff <= 2);
}

/**
* Calculates the percentage of given amount of nucleotide in the dna sequence/
*
* @param nucleotideCount Number of nucleotides (int)
* @param dna DNA sequence
* @return the percentage of nucleotides in that DNA sequence
*/
private static int nucleotidePercentage(final long nucleotideCount, final String dna) {
return (int) (((float) nucleotideCount) / dna.length() * 100);
}
}
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