Initial data commit

Task/FASTA-format/Java/fasta-format-1.java

@@ -0,0 +1,5 @@
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;

Task/FASTA-format/Java/fasta-format-2.java

@@ -0,0 +1,44 @@
+public static void main(String[] args) throws IOException {
+    List<FASTA> fastas = readFile("fastas.txt");
+    for (FASTA fasta : fastas)
+        System.out.println(fasta);
+}
+
+static List<FASTA> readFile(String path) throws IOException {
+    try (BufferedReader reader = new BufferedReader(new FileReader(path))) {
+        List<FASTA> list = new ArrayList<>();
+        StringBuilder lines = null;
+        String newline = System.lineSeparator();
+        String line;
+        while ((line = reader.readLine()) != null) {
+            if (line.startsWith(">")) {
+                if (lines != null)
+                    list.add(parseFASTA(lines.toString()));
+                lines = new StringBuilder();
+                lines.append(line).append(newline);
+            } else {
+                lines.append(line);
+            }
+        }
+        list.add(parseFASTA(lines.toString()));
+        return list;
+    }
+}
+
+static FASTA parseFASTA(String string) {
+    String description;
+    char[] sequence;
+    int indexOf = string.indexOf(System.lineSeparator());
+    description = string.substring(1, indexOf);
+    /* using 'stripLeading' will remove any additional line-separators */
+    sequence = string.substring(indexOf + 1).stripLeading().toCharArray();
+    return new FASTA(description, sequence);
+}
+
+/* using a 'char' array seems more logical */
+record FASTA(String description, char[] sequence) {
+    @Override
+    public String toString() {
+        return "%s: %s".formatted(description, new String(sequence));
+    }
+}

Task/FASTA-format/Java/fasta-format-3.java

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+import java.io.*;
+import java.util.Scanner;
+
+public class ReadFastaFile {
+
+    public static void main(String[] args) throws FileNotFoundException {
+
+        boolean first = true;
+
+        try (Scanner sc = new Scanner(new File("test.fasta"))) {
+            while (sc.hasNextLine()) {
+                String line = sc.nextLine().trim();
+                if (line.charAt(0) == '>') {
+                    if (first)
+                        first = false;
+                    else
+                        System.out.println();
+                    System.out.printf("%s: ", line.substring(1));
+                } else {
+                    System.out.print(line);
+                }
+            }
+        }
+        System.out.println();
+    }
+}