Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Format code with autopep8 and google-java-format #238

Merged
merged 2 commits into from
Oct 22, 2022
Merged

Format code with autopep8 and google-java-format #238

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
fcf1f1b
Format code with autopep8 and google-java-format
deepsource-autofix[bot] Oct 22, 2022
cf4ae9e
Merge branch 'main' into deepsource-transform-22f93d2c
VerisimilitudeX Oct 22, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
116 changes: 64 additions & 52 deletions src/main/java/DNAnalyzer/codon/CodonDataConstants.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@
*/
package DNAnalyzer.codon;

import static java.util.Map.entry;

import DNAnalyzer.aminoAcid.*;
import java.util.*;

import static java.util.Map.entry;

/**
* Declares the codon data for the 20 amino acids
*
Expand All @@ -24,58 +24,70 @@
*/
public class CodonDataConstants {

/**
* Private CodonDataConstants class constructor to avoid initialization
*/
private CodonDataConstants() {
}
/** Private CodonDataConstants class constructor to avoid initialization */
private CodonDataConstants() {}

// Declares the start codon data for the 20 amino acids. Start and stop codons
// indicate the start and stop of an amino acid. There are 20 different amino
// acids. A protein consists of one or more chains of amino acids (called
// polypeptides) whose sequence is encoded in a gene.
protected static final List<String> Isoleucine = Arrays.asList("ATT", "ATC", "ATA");
protected static final List<String> Leucine = Arrays.asList("CTT", "CTC", "CTA", "CTG", "TTA", "TTG");
protected static final List<String> Valine = Arrays.asList("GTT", "GTC", "GTA", "GTG");
protected static final List<String> Phenylalanine = Arrays.asList("TTT", "TTC");
protected static final List<String> Methionine = Arrays.asList("ATG");
protected static final List<String> Cysteine = Arrays.asList("TGT", "TGC");
protected static final List<String> Alanine = Arrays.asList("GCT", "GCC", "GCA", "GCG");
protected static final List<String> Glycine = Arrays.asList("GGT", "GGC", "GGA", "GGG");
protected static final List<String> Proline = Arrays.asList("CCT", "CCC", "CCA", "CCG");
protected static final List<String> Threonine = Arrays.asList("ACT", "ACC", "ACA", "ACG");
protected static final List<String> Serine = Arrays.asList("TCT", "TCC", "TCA", "TCG", "AGT", "AGC");
protected static final List<String> Tyrosine = Arrays.asList("TAT", "TAC");
protected static final List<String> Tryptophan = Arrays.asList("TGG");
protected static final List<String> Glutamine = Arrays.asList("CAA", "CAG");
protected static final List<String> Asparagine = Arrays.asList("AAT", "AAC");
protected static final List<String> Histidine = Arrays.asList("CAT", "CAC");
protected static final List<String> GlutamicAcid = Arrays.asList("GAA", "GAG");
protected static final List<String> AsparticAcid = Arrays.asList("GAT", "GAC");
protected static final List<String> Lysine = Arrays.asList("AAA", "AAG");
protected static final List<String> Arginine = Arrays.asList("CGT", "CGC", "CGA", "CGG", "AGA", "AGG");
// Declares the start codon data for the 20 amino acids. Start and stop codons
// indicate the start and stop of an amino acid. There are 20 different amino
// acids. A protein consists of one or more chains of amino acids (called
// polypeptides) whose sequence is encoded in a gene.
protected static final List<String> Isoleucine = Arrays.asList("ATT", "ATC", "ATA");
protected static final List<String> Leucine =
Arrays.asList("CTT", "CTC", "CTA", "CTG", "TTA", "TTG");
protected static final List<String> Valine = Arrays.asList("GTT", "GTC", "GTA", "GTG");
protected static final List<String> Phenylalanine = Arrays.asList("TTT", "TTC");
protected static final List<String> Methionine = Arrays.asList("ATG");
protected static final List<String> Cysteine = Arrays.asList("TGT", "TGC");
protected static final List<String> Alanine = Arrays.asList("GCT", "GCC", "GCA", "GCG");
protected static final List<String> Glycine = Arrays.asList("GGT", "GGC", "GGA", "GGG");
protected static final List<String> Proline = Arrays.asList("CCT", "CCC", "CCA", "CCG");
protected static final List<String> Threonine = Arrays.asList("ACT", "ACC", "ACA", "ACG");
protected static final List<String> Serine =
Arrays.asList("TCT", "TCC", "TCA", "TCG", "AGT", "AGC");
protected static final List<String> Tyrosine = Arrays.asList("TAT", "TAC");
protected static final List<String> Tryptophan = Arrays.asList("TGG");
protected static final List<String> Glutamine = Arrays.asList("CAA", "CAG");
protected static final List<String> Asparagine = Arrays.asList("AAT", "AAC");
protected static final List<String> Histidine = Arrays.asList("CAT", "CAC");
protected static final List<String> GlutamicAcid = Arrays.asList("GAA", "GAG");
protected static final List<String> AsparticAcid = Arrays.asList("GAT", "GAC");
protected static final List<String> Lysine = Arrays.asList("AAA", "AAG");
protected static final List<String> Arginine =
Arrays.asList("CGT", "CGC", "CGA", "CGG", "AGA", "AGG");

// Declares the stop codon data for the 20 amino acids. Note that the stop
// codons are the same for all amino acids.
protected static final List<String> Stop = Arrays.asList("TAA", "TAG", "TGA");
// Declares the stop codon data for the 20 amino acids. Note that the stop
// codons are the same for all amino acids.
protected static final List<String> Stop = Arrays.asList("TAA", "TAG", "TGA");

// Block to put all AminoAcidNames and their respective codon data into an enum
// map for faster
// retrieval
protected static EnumMap<AminoAcidNames, List<String>> CodonDataAcidMap = new EnumMap<>(AminoAcidNames.class);
// Block to put all AminoAcidNames and their respective codon data into an enum
// map for faster
// retrieval
protected static EnumMap<AminoAcidNames, List<String>> CodonDataAcidMap =
new EnumMap<>(AminoAcidNames.class);

static {
CodonDataAcidMap.putAll(Map.ofEntries(
entry(AminoAcidNames.ISOLEUCINE, Isoleucine), entry(AminoAcidNames.LEUCINE, Leucine),
entry(AminoAcidNames.VALINE, Valine), entry(AminoAcidNames.PHENYLALANINE, Phenylalanine),
entry(AminoAcidNames.METHIONINE, Methionine), entry(AminoAcidNames.CYSTEINE, Cysteine),
entry(AminoAcidNames.ALANINE, Alanine), entry(AminoAcidNames.GLYCINE, Glycine),
entry(AminoAcidNames.PROLINE, Proline), entry(AminoAcidNames.THREONINE, Threonine),
entry(AminoAcidNames.SERINE, Serine), entry(AminoAcidNames.TYROSINE, Tyrosine),
entry(AminoAcidNames.TRYPTOPHAN, Tryptophan), entry(AminoAcidNames.GLUTAMINE, Glutamine),
entry(AminoAcidNames.ASPARAGINE, Asparagine), entry(AminoAcidNames.HISTIDINE, Histidine),
entry(AminoAcidNames.GLUTAMIC_ACID, GlutamicAcid), entry(AminoAcidNames.ASPARTIC_ACID, AsparticAcid),
entry(AminoAcidNames.LYSINE, Lysine), entry(AminoAcidNames.ARGININE, Arginine),
entry(AminoAcidNames.STOP, Stop)));
}
static {
CodonDataAcidMap.putAll(
Map.ofEntries(
entry(AminoAcidNames.ISOLEUCINE, Isoleucine),
entry(AminoAcidNames.LEUCINE, Leucine),
entry(AminoAcidNames.VALINE, Valine),
entry(AminoAcidNames.PHENYLALANINE, Phenylalanine),
entry(AminoAcidNames.METHIONINE, Methionine),
entry(AminoAcidNames.CYSTEINE, Cysteine),
entry(AminoAcidNames.ALANINE, Alanine),
entry(AminoAcidNames.GLYCINE, Glycine),
entry(AminoAcidNames.PROLINE, Proline),
entry(AminoAcidNames.THREONINE, Threonine),
entry(AminoAcidNames.SERINE, Serine),
entry(AminoAcidNames.TYROSINE, Tyrosine),
entry(AminoAcidNames.TRYPTOPHAN, Tryptophan),
entry(AminoAcidNames.GLUTAMINE, Glutamine),
entry(AminoAcidNames.ASPARAGINE, Asparagine),
entry(AminoAcidNames.HISTIDINE, Histidine),
entry(AminoAcidNames.GLUTAMIC_ACID, GlutamicAcid),
entry(AminoAcidNames.ASPARTIC_ACID, AsparticAcid),
entry(AminoAcidNames.LYSINE, Lysine),
entry(AminoAcidNames.ARGININE, Arginine),
entry(AminoAcidNames.STOP, Stop)));
}
}