Added access to the iterable

hilbertglm · hilbertglm · commit 26b21d7c4c47 · 2024-01-14T09:40:58.000-06:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaStreamer.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaStreamer.java
@@ -71,14 +71,34 @@ public FastaStreamer batchSize(int size) {
 		return this;
 	}
 
+	/**
+	 * Enable iteration through the proteins in the file using syntax such as:
+	 * <pre>
+	 *     for(ProteinSequence sequence : FastaStreamer.from(path).each()) {
+	 *         .
+	 *         .
+	 *         .
+	 *     }
+	 * </pre>
+	 *
+	 * @return an iterable suitable for an iteration loop
+	 */
+	public Iterable<ProteinSequence> each() {
+		return () -> stream().iterator();
+	}
+
 	/**
 	 * Create a stream of protein sequences from the contents of the path
 	 * @return the stream
-	 * @throws IOException if there is an error opening the file
 	 */
-	public Stream<ProteinSequence> stream() throws IOException {
+	public Stream<ProteinSequence> stream() {
 		InputStreamProvider provider = new InputStreamProvider();
-		InputStream input = provider.getInputStream(getPath().toFile());
+		InputStream input;
+		try {
+			input = provider.getInputStream(getPath().toFile());
+		} catch (IOException exception) {
+			throw new RuntimeException(exception);
+		}
 		FastaReader<ProteinSequence, AminoAcidCompound> reader = new FastaReader<>(input, getHeaderParser(), getSequenceCreator());
 		Spliterator<ProteinSequence> source = new Spliterators.AbstractSpliterator<>(Integer.MAX_VALUE, Spliterator.IMMUTABLE | Spliterator.NONNULL) {
 			@Override
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java
@@ -36,4 +36,15 @@ public void stream() throws IOException {
 				.collect(Collectors.toList());
 		Assert.assertEquals("Count", 283, sequences.size());
 	}
+
+	@Test
+	public void iterate() {
+		String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile();
+		Path path = Paths.get(file);
+		int count = 0;
+		for (ProteinSequence sequence : FastaStreamer.from(path).each()) {
+			count++;
+		}
+		Assert.assertEquals("Count", 283, count);
+	}
 }
