From f45e01876a1179983d96b9fde840614a0adf5915 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Mon, 8 Jan 2024 12:04:02 -0600 Subject: [PATCH 1/8] Changed the URLs to the mirrors from http to https. Changed the name of the URL path to reflect a change in the v2 naming. --- .../nbio/structure/scop/ScopInstallation.java | 21 +++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java index b7ee585279..019e084a5d 100644 --- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java +++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java @@ -85,8 +85,8 @@ public class ScopInstallation implements LocalScopDatabase { public static final String comFileName = "dir.com.scop.txt_"; // Download locations - public static final String SCOP_DOWNLOAD = "http://scop.berkeley.edu/downloads/parse/"; - public static final String SCOP_DOWNLOAD_ALTERNATE = "http://scop.berkeley.edu/downloads/parse/"; + public static final String SCOP_DOWNLOAD = "https://scop.berkeley.edu/downloads/parse/"; + public static final String SCOP_DOWNLOAD_ALTERNATE = "https://scop.berkeley.edu/downloads/parse/"; //public static final String NEWLINE = System.getProperty("line.separator"); public static final String FILESPLIT = System.getProperty("file.separator"); @@ -913,10 +913,19 @@ private void initScopURLs() { // first, try default scop ScopMirror primary = new ScopMirror(); // If unreachable, try alternate Berkeley location - ScopMirror alt = new ScopMirror( - SCOP_DOWNLOAD_ALTERNATE, - "dir.cla.scop.%s.txt","dir.des.scop.%s.txt", - "dir.hie.scop.%s.txt","dir.com.scop.%s.txt"); + ScopMirror alt; + if (scopVersion.startsWith("2.")) { + alt = new ScopMirror( + SCOP_DOWNLOAD_ALTERNATE, + "dir.cla.scope.%s.txt","dir.des.scope.%s.txt", + "dir.hie.scope.%s.txt","dir.com.scope.%s.txt"); + } + else { + alt = new ScopMirror( + SCOP_DOWNLOAD_ALTERNATE, + "dir.cla.scop.%s.txt","dir.des.scop.%s.txt", + "dir.hie.scop.%s.txt","dir.com.scop.%s.txt"); + } mirrors.add(primary); mirrors.add(alt); } From 96c81269b33a2e2c2ac0b09c055a81ccfb5c5303 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Sat, 13 Jan 2024 10:31:04 -0600 Subject: [PATCH 2/8] Before finding the InputStreamProvider --- .../nbio/core/sequence/io/FastaStreamer.java | 155 ++++++++++++++++++ .../biojava/nbio/core/util/MagicNumber.java | 39 +++++ .../core/sequence/io/FastaStreamerTest.java | 39 +++++ .../nbio/core/util/MagicNumberTest.java | 22 +++ .../org/biojava/nbio/core/util/example.gz | Bin 0 -> 54 bytes 5 files changed, 255 insertions(+) create mode 100644 biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaStreamer.java create mode 100644 biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java create mode 100644 biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java create mode 100644 biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/util/example.gz 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 new file mode 100644 index 0000000000..febf747a36 --- /dev/null +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaStreamer.java @@ -0,0 +1,155 @@ +package org.biojava.nbio.core.sequence.io; + +import org.biojava.nbio.core.sequence.ProteinSequence; +import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; +import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet; +import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface; +import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface; +import org.biojava.nbio.core.util.MagicNumber; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; +import java.util.Collections; +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Optional; +import java.util.Spliterator; +import java.util.Spliterators; +import java.util.function.Consumer; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; +import java.util.zip.GZIPInputStream; + +public class FastaStreamer { + + private final Path path; + private int batchSize = 1_000; + private SequenceHeaderParserInterface headerParser; + private SequenceCreatorInterface sequenceCreator; + private LinkedHashMap chunk = new LinkedHashMap<>(); + private Iterator> iterator = Collections.emptyIterator(); + private boolean closed = false; + + /** + * The constructor is private. Created via the from(...) static factory method + * + * @param path the path to the file containing the FASTA content (possibly GZipped) + */ + private FastaStreamer(final Path path) { + this.path = path; + } + + public static FastaStreamer from(final Path path) { + return new FastaStreamer(path); + } + + public static FastaStreamer from(File file) { + return from(file.toPath()); + } + + public FastaStreamer withHeaderParser(SequenceHeaderParserInterface headerParser) { + this.headerParser = headerParser; + return this; + } + + public FastaStreamer withSequenceCreator(SequenceCreatorInterface sequenceCreator) { + this.sequenceCreator = sequenceCreator; + return this; + } + + public FastaStreamer batchSize(int size) { + this.batchSize = size; + return this; + } + + /** + * 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 stream() throws IOException { + InputStream rawInput = Files.newInputStream(getPath(), StandardOpenOption.READ); + InputStream input = MagicNumber.isGZIP(getPath()) ? new GZIPInputStream(rawInput) : rawInput; + FastaReader reader = new FastaReader<>(input, getHeaderParser(), getSequenceCreator()); + Spliterator source = new Spliterators.AbstractSpliterator<>(Integer.MAX_VALUE, Spliterator.IMMUTABLE | Spliterator.NONNULL) { + @Override + public boolean tryAdvance(Consumer action) { + if (closed) { + return false; + } + ProteinSequence protein = next(reader); + if (null == protein) { + return false; + } + action.accept(protein); + return true; + } + + /** + * Fetch the next header/protein tuple from the cache. If the cache is empty, fetch another + * batch from the source file + * + * @param reader + * the input stream from which the FASTA content is read + * @return the protein sequence + */ + private ProteinSequence next(FastaReader reader) { + try { + if (!iterator.hasNext()) { + chunk = reader.process(getBatchSize()); + if (null == chunk) { + closed = true; + reader.close(); + return null; + } + iterator = chunk.entrySet().iterator(); + } + if (iterator.hasNext()) { + Map.Entry entry = iterator.next(); + return createSequence(entry.getKey(), entry.getValue()); + } + closed = true; + reader.close(); + } catch (IOException exception) { + throw new RuntimeException(String.format("I/O error reading the FASTA file from '%s'", getPath())); + } + return null; + } + }; // Spliterator + return StreamSupport.stream(source, false); + } + + /** + * Create the sequence with the information from the header. This implementation return the sequence as-is, but + * this is an opportunity for the implementer to build specifc information into the user collection space + * of the sequence + * + * @param header the original header + * @param sequence the protein sequence + * @return the sequence + */ + protected ProteinSequence createSequence(String header, ProteinSequence sequence) { + return sequence; + } + + protected Path getPath() { + return path; + } + + protected int getBatchSize() { + return batchSize; + } + + protected SequenceHeaderParserInterface getHeaderParser() { + return Optional.ofNullable(headerParser).orElse(new GenericFastaHeaderParser<>()); + } + + public SequenceCreatorInterface getSequenceCreator() { + return Optional.ofNullable(sequenceCreator).orElse(new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); + } +} diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java new file mode 100644 index 0000000000..9c6765b354 --- /dev/null +++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java @@ -0,0 +1,39 @@ +package org.biojava.nbio.core.util; + +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; + +/** + * The 'magic number' is a sequence of bytes that the beginning of a file that can be used to determine the + * file type + * + * @since 7.0.3 + * @author Gary Murphy + */ +public class MagicNumber { + + /** + * The magic number of a gzip file is 0x1F8B. (ref: https://en.wikipedia.org/wiki/Gzip#:~:text=%22gzip%22%20is%20often%20also%20used,and%20the%20operating%20system%20ID.) + * @param path the path to the file + * @return true if the file has the gzip magic number + * @throws IOException if there is an error reading the start of the file + */ + public static boolean isGZIP(Path path) throws IOException { + try ( + InputStream input = Files.newInputStream(path, StandardOpenOption.READ) + ) { + byte[] magic = new byte[2]; + int count = input.read(magic); + if (count != 2) { + return false; + } + int id = (int)magic[0] & 0x00ff; + id <<= 8; + id += (int)magic[1] & 0x00ff; + return (id == 0x1f8b); + } + } +} 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 new file mode 100644 index 0000000000..f17ba93de1 --- /dev/null +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java @@ -0,0 +1,39 @@ +package org.biojava.nbio.core.sequence.io; + +import org.biojava.nbio.core.sequence.ProteinSequence; +import org.junit.Assert; +import org.junit.Test; + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.List; +import java.util.stream.Collectors; + +/** + * Test the functionality of the {@link FastaStreamer} code + */ +public class FastaStreamerTest { + + @Test + public void stream() throws IOException { + String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile(); + Path path = Paths.get(file); + List sequences; + + sequences = FastaStreamer.from(path).stream().collect(Collectors.toList()); + Assert.assertEquals("Count", 283, sequences.size()); + + ProteinSequence sequence; + sequence = sequences.get(0); + Assert.assertEquals("A2D504_ATEGE/1-46", sequence.getOriginalHeader()); + sequence = sequences.get(sequences.size()-1); + Assert.assertEquals("Q98SJ1_CHICK/15-61", sequence.getOriginalHeader()); + + sequences = FastaStreamer.from(path) + .batchSize(2) // Ensure there isn't an edge condition loading the next buffer + .stream() + .collect(Collectors.toList()); + Assert.assertEquals("Count", 283, sequences.size()); + } +} diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java new file mode 100644 index 0000000000..eed6ae7611 --- /dev/null +++ b/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java @@ -0,0 +1,22 @@ +package org.biojava.nbio.core.util; + +import org.junit.Assert; +import org.junit.Test; + +import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; + +public class MagicNumberTest { + + @Test + public void gzip() throws IOException { + String file = this.getClass().getResource("example.gz").getFile(); + Path path = Paths.get(file); + Assert.assertTrue("GZIP file", MagicNumber.isGZIP(path)); + + file = this.getClass().getResource("build.xml").getFile(); + path = Paths.get(file); + Assert.assertFalse("Not a GZIP file", MagicNumber.isGZIP(path)); + } +} diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/util/example.gz b/biojava-core/src/test/resources/org/biojava/nbio/core/util/example.gz new file mode 100644 index 0000000000000000000000000000000000000000..0864558ee236c78ac01f1334a951d44fae728c9a GIT binary patch literal 54 zcmb2|=HQsLV^Jytb81CmZb42e1GlHH-pMoG;RXGlcmh87`keO(`=EW+*Gu;i6N7*m K+gm9H1_l5iOA`wK literal 0 HcmV?d00001 From fd3be7e9f1e3c177fbef509bfd3e795bf8969de8 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Sat, 13 Jan 2024 10:50:10 -0600 Subject: [PATCH 3/8] Removed the MagicNumber class after finding InputStreamProvider --- .../nbio/core/sequence/io/FastaStreamer.java | 9 ++-- .../biojava/nbio/core/util/MagicNumber.java | 39 ------------------ .../nbio/core/util/MagicNumberTest.java | 22 ---------- .../core/sequence/io/PF00104_small.fasta.gz | Bin 0 -> 31036 bytes 4 files changed, 3 insertions(+), 67 deletions(-) delete mode 100644 biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java delete mode 100644 biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/sequence/io/PF00104_small.fasta.gz 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 index febf747a36..f0c15c7a9e 100644 --- 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 @@ -5,14 +5,12 @@ import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet; import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface; import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface; -import org.biojava.nbio.core.util.MagicNumber; +import org.biojava.nbio.core.util.InputStreamProvider; import java.io.File; import java.io.IOException; import java.io.InputStream; -import java.nio.file.Files; import java.nio.file.Path; -import java.nio.file.StandardOpenOption; import java.util.Collections; import java.util.Iterator; import java.util.LinkedHashMap; @@ -23,7 +21,6 @@ import java.util.function.Consumer; import java.util.stream.Stream; import java.util.stream.StreamSupport; -import java.util.zip.GZIPInputStream; public class FastaStreamer { @@ -73,8 +70,8 @@ public FastaStreamer batchSize(int size) { * @throws IOException if there is an error opening the file */ public Stream stream() throws IOException { - InputStream rawInput = Files.newInputStream(getPath(), StandardOpenOption.READ); - InputStream input = MagicNumber.isGZIP(getPath()) ? new GZIPInputStream(rawInput) : rawInput; + InputStreamProvider provider = new InputStreamProvider(); + InputStream input = provider.getInputStream(getPath().toFile()); FastaReader reader = new FastaReader<>(input, getHeaderParser(), getSequenceCreator()); Spliterator source = new Spliterators.AbstractSpliterator<>(Integer.MAX_VALUE, Spliterator.IMMUTABLE | Spliterator.NONNULL) { @Override diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java deleted file mode 100644 index 9c6765b354..0000000000 --- a/biojava-core/src/main/java/org/biojava/nbio/core/util/MagicNumber.java +++ /dev/null @@ -1,39 +0,0 @@ -package org.biojava.nbio.core.util; - -import java.io.IOException; -import java.io.InputStream; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.StandardOpenOption; - -/** - * The 'magic number' is a sequence of bytes that the beginning of a file that can be used to determine the - * file type - * - * @since 7.0.3 - * @author Gary Murphy - */ -public class MagicNumber { - - /** - * The magic number of a gzip file is 0x1F8B. (ref: https://en.wikipedia.org/wiki/Gzip#:~:text=%22gzip%22%20is%20often%20also%20used,and%20the%20operating%20system%20ID.) - * @param path the path to the file - * @return true if the file has the gzip magic number - * @throws IOException if there is an error reading the start of the file - */ - public static boolean isGZIP(Path path) throws IOException { - try ( - InputStream input = Files.newInputStream(path, StandardOpenOption.READ) - ) { - byte[] magic = new byte[2]; - int count = input.read(magic); - if (count != 2) { - return false; - } - int id = (int)magic[0] & 0x00ff; - id <<= 8; - id += (int)magic[1] & 0x00ff; - return (id == 0x1f8b); - } - } -} diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java deleted file mode 100644 index eed6ae7611..0000000000 --- a/biojava-core/src/test/java/org/biojava/nbio/core/util/MagicNumberTest.java +++ /dev/null @@ -1,22 +0,0 @@ -package org.biojava.nbio.core.util; - -import org.junit.Assert; -import org.junit.Test; - -import java.io.IOException; -import java.nio.file.Path; -import java.nio.file.Paths; - -public class MagicNumberTest { - - @Test - public void gzip() throws IOException { - String file = this.getClass().getResource("example.gz").getFile(); - Path path = Paths.get(file); - Assert.assertTrue("GZIP file", MagicNumber.isGZIP(path)); - - file = this.getClass().getResource("build.xml").getFile(); - path = Paths.get(file); - Assert.assertFalse("Not a GZIP file", MagicNumber.isGZIP(path)); - } -} diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/sequence/io/PF00104_small.fasta.gz b/biojava-core/src/test/resources/org/biojava/nbio/core/sequence/io/PF00104_small.fasta.gz new file mode 100644 index 0000000000000000000000000000000000000000..d4a340c73d7c9684bb281e06ca52bc6228403414 GIT binary patch literal 31036 zcmV(_K-9kHe-DbVJV|Nk#;HwRg^NJl!^*C*%PjjGs+O^^h!uzK}E)8F_`JU$#=d68Of 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zxWe|slWIKT?cve*EdhUcY(|winHcglO++=tqbK_E0OL7z7Iv_V0JfKs0X`QAU@pi> z_^ZU`9UGJQUNWsuIXo68v##s+NR!3@bIdwh>zx=EC^~@y_NN*|=;q;hg^_O%#chK~ zN=K^Hq&UO+5)C3}*4Y)FwMwaO-D%6aPYVLoup&&8j6ajk}5@N~XjECApy zdP-mFQu?Z-O_P*Y2qV4v63=+qz+c8M`hxj?R%g-?_KZkVqIn+EU-Q9g(A6`@WIVBacuvDj> zpTlnXIWmd?OFZG{pnmN~`8f^%KIG$v{2VgEEBPrur^hR15S!c-QHrhQP;Ez~87k}T2d+PW9!0kO5;r9MNJCXqv HRiFX@f9c@5 literal 0 HcmV?d00001 From ef665e26ce560ac2c14af46535e250f61336d84b Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Sun, 14 Jan 2024 07:37:34 -0600 Subject: [PATCH 4/8] Added comments --- .../org/biojava/nbio/core/sequence/io/FastaStreamer.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) 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 index f0c15c7a9e..0311bddc2b 100644 --- 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 @@ -22,6 +22,13 @@ import java.util.stream.Stream; import java.util.stream.StreamSupport; +/** + * Read from a FASTA file (or gzipped FASTA file) and create a Java stream of {@link ProteinSequence} objects + * for use in a functional programming paradigm. + * + * @author Gary Murphy + * @since 7.0.3 + */ public class FastaStreamer { private final Path path; @@ -123,7 +130,7 @@ private ProteinSequence next(FastaReader rea /** * Create the sequence with the information from the header. This implementation return the sequence as-is, but - * this is an opportunity for the implementer to build specifc information into the user collection space + * this is an opportunity for the implementer to build specific information into the user collection space * of the sequence * * @param header the original header From 26b21d7c4c47f6020fa0a6950778b1046e301336 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Sun, 14 Jan 2024 09:40:58 -0600 Subject: [PATCH 5/8] Added access to the iterable --- .../nbio/core/sequence/io/FastaStreamer.java | 26 ++++++++++++++++--- .../core/sequence/io/FastaStreamerTest.java | 11 ++++++++ 2 files changed, 34 insertions(+), 3 deletions(-) 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 index 0311bddc2b..803287cb90 100644 --- 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: + * 
+	 *     for(ProteinSequence sequence : FastaStreamer.from(path).each()) {
+	 *         .
+	 *         .
+	 *         .
+	 *     }
+	 *
+ * + * @return an iterable suitable for an iteration loop + */ + public Iterable 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 stream() throws IOException { + public Stream 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 reader = new FastaReader<>(input, getHeaderParser(), getSequenceCreator()); Spliterator 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 index f17ba93de1..614c6f06c8 100644 --- 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); + } } From d081b125792b8d07c4eb37f3dfc8d4575aef2335 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Fri, 26 Jan 2024 07:14:06 -0600 Subject: [PATCH 6/8] Changed the version to 7.1.0-SNAPSHOT. Made changes per review. --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- .../biojava/nbio/core/sequence/io/FastaStreamer.java | 10 +++++----- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 2 +- 15 files changed, 36 insertions(+), 36 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 908f2d28c2..84fdbf3a7e 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT org.biojava biojava-structure - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 002fbb6b0b..6ce294e7e3 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index fb44bbadd3..b0e4fa55c0 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT 4.0.0 biojava-core 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 index 803287cb90..601c1226ec 100644 --- 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 @@ -10,6 +10,7 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; +import java.io.UncheckedIOException; import java.nio.file.Path; import java.util.Collections; import java.util.Iterator; @@ -27,7 +28,7 @@ * for use in a functional programming paradigm. * * @author Gary Murphy - * @since 7.0.3 + * @since 7.1.0 */ public class FastaStreamer { @@ -135,12 +136,12 @@ private ProteinSequence next(FastaReader rea } if (iterator.hasNext()) { Map.Entry entry = iterator.next(); - return createSequence(entry.getKey(), entry.getValue()); + return createSequence(entry.getValue()); } closed = true; reader.close(); } catch (IOException exception) { - throw new RuntimeException(String.format("I/O error reading the FASTA file from '%s'", getPath())); + throw new UncheckedIOException(String.format("I/O error reading the FASTA file from '%s'", getPath()), exception); } return null; } @@ -153,11 +154,10 @@ private ProteinSequence next(FastaReader rea * this is an opportunity for the implementer to build specific information into the user collection space * of the sequence * - * @param header the original header * @param sequence the protein sequence * @return the sequence */ - protected ProteinSequence createSequence(String header, ProteinSequence sequence) { + protected ProteinSequence createSequence(ProteinSequence sequence) { return sequence; } diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 2b213d7de5..f0d8e13c2f 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT 4.0.0 biojava-genome @@ -71,13 +71,13 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index d02011571c..cee137b4c1 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index ff8771babc..a7e07100c4 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 1fb8967489..e4b3c3cdf2 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 36d3ec3b2b..dd4b460858 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT org.biojava biojava-structure - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT org.biojava biojava-structure-gui - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index c86173990f..67548aca4a 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 8b3522352b..3cc7cbe005 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index bd779d4ba0..8afe66b114 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-structure biojava-structure @@ -44,13 +44,13 @@ org.biojava biojava-alignment - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 61bcb2369f..c9c0c60a55 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 86cf1004f9..258814c27d 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 1b079ca711..efcddb8feb 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.0.3-SNAPSHOT + 7.1.0-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the From 2d1f32ea7a04ca92ca6b26a2e1381d0d44e61a01 Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Fri, 26 Jan 2024 07:16:51 -0600 Subject: [PATCH 7/8] Missed a RuntimeException. Changed to UncheckedIOException --- .../java/org/biojava/nbio/core/sequence/io/FastaStreamer.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index 601c1226ec..c9184dfd13 100644 --- 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 @@ -98,7 +98,7 @@ public Stream stream() { try { input = provider.getInputStream(getPath().toFile()); } catch (IOException exception) { - throw new RuntimeException(exception); + throw new UncheckedIOException(exception); } FastaReader reader = new FastaReader<>(input, getHeaderParser(), getSequenceCreator()); Spliterator source = new Spliterators.AbstractSpliterator<>(Integer.MAX_VALUE, Spliterator.IMMUTABLE | Spliterator.NONNULL) { From 84998b92ab0ba0b57a378d47d93e1451d5827d2e Mon Sep 17 00:00:00 2001 From: Gary Murphy Date: Tue, 30 Jan 2024 07:19:52 -0600 Subject: [PATCH 8/8] Added an entry to the changelog for FastaStreamer --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47ae621112..c615c97558 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,12 @@ BioJava Changelog ----------------- +BioJava 7.1.0 - future release +============================== +### Added +* Class `FastaStreamer` to read FASTA-formatted files using Java streams + + BioJava 7.0.2 ============================== ### Added