adding protein-translation

exercises/practice/protein-translation/.docs/instructions.md

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+# Instructions
+
+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", "UAA", "AUG"` =>
+
+Protein: `"Methionine", "Phenylalanine", "Serine"`
+
+Note the stop codon `"UAA"` 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))

exercises/practice/protein-translation/.docs/introduction.md

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+# Introduction
+
+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", "UAA", "AUG"` =>
+
+Protein: `"Methionine", "Phenylalanine", "Serine"`
+
+Note the stop codon `"UAA"` 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))

exercises/practice/protein-translation/.meta/config.json

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+{
+  "authors": [
+    "kapitaali"
+  ],
+  "files": {
+    "solution": [
+      "src/protein-translation.cob"
+    ],
+    "test": [
+      "tst/protein-translation/protein-translation.cut"
+    ],
+    "example": [
+      ".meta/proof.ci.cob"
+    ],
+    "invalidator": [
+      "test.sh",
+      "test.ps1"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

exercises/practice/protein-translation/.meta/proof.ci.cob

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+       IDENTIFICATION DIVISION.
+       PROGRAM-ID. PROTEIN-TRANSLATION.
+       AUTHOR. kapitaali.
+       ENVIRONMENT DIVISION.
+       DATA DIVISION.
+       WORKING-STORAGE SECTION.
+       01 WS-INPUT                  PIC X(60).
+       01 WS-PROTEIN                PIC X(120) VALUE SPACES.
+       01 TEMP                      PIC X(120) VALUE SPACES.
+       01 WS-ERROR                  PIC X(60).
+       01 PROT                      PIC X(3) VALUE SPACES.
+       01 CHECKED                   PIC X(14) VALUE SPACES.
+       01 INDX                      PIC 99 VALUE 1.
+       01 LEN                       PIC 99.
+       01 A                         PIC 99.
+
+       PROCEDURE DIVISION.
+
+       TRANSLATE-CODON.
+           MOVE SPACES TO WS-PROTEIN. 
+           MOVE WS-INPUT TO PROT.
+           PERFORM CHECK-CODON.
+           EVALUATE CHECKED
+              WHEN "ERROR" MOVE "Invalid codon" TO WS-ERROR
+              WHEN "STOP" MOVE " " TO WS-PROTEIN
+              WHEN OTHER MOVE CHECKED TO WS-PROTEIN
+           END-EVALUATE.
+
+
+       CHECK-CODON.
+           MOVE SPACES TO CHECKED.
+           EVALUATE PROT 
+              WHEN " " MOVE " " TO CHECKED
+              WHEN "AUG" MOVE "Methionine" TO CHECKED
+              WHEN "UUU" MOVE "Phenylalanine" TO CHECKED
+              WHEN "UUC" MOVE "Phenylalanine" TO CHECKED
+              WHEN "UUA" MOVE "Leucine" TO CHECKED
+              WHEN "UUG" MOVE "Leucine" TO CHECKED
+              WHEN "UCU" MOVE "Serine" TO CHECKED
+              WHEN "UCC" MOVE "Serine" TO CHECKED
+              WHEN "UCA" MOVE "Serine" TO CHECKED
+              WHEN "UCG" MOVE "Serine" TO CHECKED
+              WHEN "UAU" MOVE "Tyrosine" TO CHECKED
+              WHEN "UAC" MOVE "Tyrosine" TO CHECKED
+              WHEN "UGU" MOVE "Cysteine" TO CHECKED
+              WHEN "UGC" MOVE "Cysteine" TO CHECKED
+              WHEN "UGG" MOVE "Tryptophan" TO CHECKED
+              WHEN "UAA" MOVE "STOP" TO CHECKED
+              WHEN "UAG" MOVE "STOP" TO CHECKED
+              WHEN "UGA" MOVE "STOP" TO CHECKED
+              WHEN OTHER MOVE "ERROR" TO CHECKED
+           END-EVALUATE.
+
+
+       STR-LENGTH.
+           MOVE 0 TO LEN.
+           PERFORM VARYING A FROM FUNCTION LENGTH(CHECKED)
+                   BY -1 UNTIL CHECKED(A:1) <> " "
+               ADD 1 TO LEN
+           END-PERFORM.
+           COMPUTE LEN = FUNCTION LENGTH(CHECKED) - LEN.
+
+
+       TRANSLATE-RNA.           
+           PERFORM UNTIL WS-INPUT = " "
+              MOVE WS-INPUT(1:3) TO PROT
+              PERFORM CHECK-CODON
+              PERFORM STR-LENGTH
+              EVALUATE CHECKED 
+                 WHEN "ERROR" 
+                    MOVE "Invalid codon" TO WS-ERROR
+                    MOVE SPACES TO TEMP
+                    MOVE SPACES TO WS-PROTEIN 
+                    EXIT PARAGRAPH
+                 WHEN " "
+                    MOVE TEMP TO WS-PROTEIN  
+                    MOVE SPACES TO TEMP
+                    EXIT PARAGRAPH
+                 WHEN "STOP"
+                    MOVE TEMP TO WS-PROTEIN 
+                    MOVE SPACES TO TEMP
+                    EXIT PARAGRAPH
+                 WHEN OTHER 
+                    IF INDX > 1
+                       MOVE "," TO TEMP(INDX:1)
+                       ADD 1 TO INDX
+                    END-IF
+                    MOVE CHECKED TO TEMP(INDX:LEN)
+                    ADD LEN TO INDX
+              END-EVALUATE
+              MOVE WS-INPUT(4:56) TO WS-INPUT(1:56) 
+           END-PERFORM.
+           MOVE TEMP TO WS-PROTEIN.
+           MOVE SPACES TO TEMP.
+           MOVE 1 TO INDX.

exercises/practice/protein-translation/bin/fetch-cobolcheck

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+#!/usr/bin/env bash
+
+# This file is a copy of the
+# https://github.com/exercism/configlet/blob/main/scripts/fetch-configlet file.
+# Please submit bugfixes/improvements to the above file to ensure that all tracks benefit from the changes.
+
+# set -eo pipefail
+
+readonly LATEST='https://api.github.com/repos/0xE282B0/cobol-check/releases/latest'
+
+case "$(uname)" in
+  Darwin*)   os='mac'     ;;
+  Linux*)    os='linux'   ;;
+  Windows*)  os='windows' ;;
+  MINGW*)    os='windows' ;;
+  MSYS_NT-*) os='windows' ;;
+  *)         os='linux'   ;;
+esac
+
+case "${os}" in
+  windows*) ext='.exe' ;;
+  *)        ext='' ;;
+esac
+
+arch="$(uname -m)"
+
+curlopts=(
+  --silent
+  --show-error
+  --fail
+  --location
+  --retry 3
+)
+
+if [[ -n "${GITHUB_TOKEN}" ]]; then
+  curlopts+=(--header "authorization: Bearer ${GITHUB_TOKEN}")
+fi
+
+suffix="${os}-${arch}${ext}"
+
+get_download_url() {
+  curl "${curlopts[@]}" --header 'Accept: application/vnd.github.v3+json' "${LATEST}" |
+    grep "\"browser_download_url\": \".*/download/.*/cobol-check.*${suffix}\"$" |
+    cut -d'"' -f4
+}
+
+main() {
+  if [[ -d ./bin ]]; then
+    output_dir="./bin"
+  elif [[ $PWD == */bin ]]; then
+    output_dir="$PWD"
+  else
+    echo "Error: no ./bin directory found. This script should be ran from a repo root." >&2
+    return 1
+  fi
+
+  output_path="${output_dir}/cobolcheck${ext}"
+  download_url="$(get_download_url)"
+  curl "${curlopts[@]}" --output "${output_path}" "${download_url}"
+  chmod +x "${output_path}"
+}
+
+main

exercises/practice/protein-translation/bin/fetch-cobolcheck.ps1

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+# This file is a copy of the
+# https://github.com/exercism/configlet/blob/main/scripts/fetch-configlet.ps1 file.
+# Please submit bugfixes/improvements to the above file to ensure that all tracks
+# benefit from the changes.
+
+$ErrorActionPreference = "Stop"
+$ProgressPreference = "SilentlyContinue"
+
+$requestOpts = @{
+    Headers           = If ($env:GITHUB_TOKEN) { @{ Authorization = "Bearer ${env:GITHUB_TOKEN}" } } Else { @{ } }
+    MaximumRetryCount = 3
+    RetryIntervalSec  = 1
+}
+
+$arch = If ([Environment]::Is64BitOperatingSystem) { "amd64" } Else { "x86" }
+$fileName = "cobol-check-windows-$arch.exe"
+
+Function Get-DownloadUrl {
+    $latestUrl = "https://api.github.com/repos/0xE282B0/cobol-check/releases/latest"
+    Invoke-RestMethod -Uri $latestUrl -PreserveAuthorizationOnRedirect @requestOpts
+    | Select-Object -ExpandProperty assets
+    | Where-Object { $_.browser_download_url -match $FileName }
+    | Select-Object -ExpandProperty browser_download_url
+}
+
+$downloadUrl = Get-DownloadUrl
+$outputFile = Join-Path -Path $PSScriptRoot -ChildPath "cobolcheck.exe"
+Invoke-WebRequest -Uri $downloadUrl -OutFile $outputFile @requestOpts