Replace direct use of Sequence implementation constructors with facto…

…ry method. Rename "fasta" package to "sequence"

scripts/test_suite.args

@@ -20,7 +20,7 @@
 --add-exports org.igv/org.broad.igv.feature.dranger=junit
 --add-exports org.igv/org.broad.igv.feature.dsi=junit
 --add-exports org.igv/org.broad.igv.feature.genome=junit
---add-exports org.igv/org.broad.igv.feature.genome.fasta=junit
+--add-exports org.igv/org.broad.igv.feature.genome.sequence=junit
 --add-exports org.igv/org.broad.igv.feature.tribble=junit
 --add-exports org.igv/org.broad.igv.feature.tribble.reader=junit
 --add-exports org.igv/org.broad.igv.oauth=junit

src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java

@@ -25,6 +25,8 @@
 
 package org.broad.igv.feature.genome;
 
+import org.broad.igv.feature.genome.sequence.Sequence;
+
 /**
  * Created with IntelliJ IDEA.
  * User: jrobinso

src/main/java/org/broad/igv/feature/genome/Genome.java

@@ -38,11 +38,13 @@
 import org.broad.igv.Globals;
 import org.broad.igv.feature.Chromosome;
 import org.broad.igv.feature.Cytoband;
+import org.broad.igv.feature.genome.sequence.InMemorySequence;
+import org.broad.igv.feature.genome.sequence.Sequence;
+import org.broad.igv.feature.genome.sequence.SequenceWrapper;
 import org.broad.igv.logging.LogManager;
 import org.broad.igv.logging.Logger;
 import org.broad.igv.track.FeatureTrack;
 import org.broad.igv.track.Track;
-import org.broad.igv.ui.panel.ReferenceFrame;
 import org.broad.igv.util.ResourceLocator;
 import org.broad.igv.util.liftover.Liftover;
 

src/main/java/org/broad/igv/feature/genome/GenomeImporter.java

@@ -31,7 +31,7 @@
 
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;
-import org.broad.igv.feature.genome.fasta.FastaUtils;
+import org.broad.igv.feature.genome.sequence.FastaUtils;
 import org.broad.igv.feature.genome.load.GenomeDescriptor;
 import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.HttpUtils;

src/main/java/org/broad/igv/feature/genome/load/DotGenomeLoader.java

@@ -1,12 +1,13 @@
 package org.broad.igv.feature.genome.load;
 
 import htsjdk.tribble.Feature;
+import org.broad.igv.feature.genome.sequence.SequenceFactory;
 import org.broad.igv.logging.*;
 import org.broad.igv.feature.*;
 import org.broad.igv.feature.genome.Genome;
-import org.broad.igv.feature.genome.Sequence;
-import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
-import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
+import org.broad.igv.feature.genome.sequence.Sequence;
+import org.broad.igv.feature.genome.sequence.FastaBlockCompressedSequence;
+import org.broad.igv.feature.genome.sequence.FastaIndexedSequence;
 import org.broad.igv.feature.gff.GFFFeatureSource;
 import org.broad.igv.track.FeatureCollectionSource;
 import org.broad.igv.track.FeatureTrack;
@@ -97,11 +98,7 @@ public Genome loadGenome() throws IOException {
         if (sequencePath == null) {
             sequence = null;
         } else {
-            if (sequencePath.endsWith(".gz")) {
-                sequence = new FastaBlockCompressedSequence(sequencePath);
-            } else {
-                sequence = new FastaIndexedSequence(sequencePath);
-            }
+            sequence = SequenceFactory.getSequence(sequencePath);
             chromosOrdered = true;
         }
 

src/main/java/org/broad/igv/feature/genome/load/FastaGenomeLoader.java

@@ -1,11 +1,7 @@
 package org.broad.igv.feature.genome.load;
 
 import org.broad.igv.feature.genome.Genome;
-import org.broad.igv.feature.genome.Sequence;
-import org.broad.igv.feature.genome.SequenceWrapper;
-import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
-import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
-import org.broad.igv.feature.genome.fasta.FastaUtils;
+import org.broad.igv.feature.genome.sequence.*;
 import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.HttpUtils;
 import org.broad.igv.util.Utilities;
@@ -56,9 +52,7 @@ public Genome loadGenome() throws IOException {
             name = file.getName();
         }
 
-        FastaIndexedSequence sequence = fastaPath.endsWith(".gz") ?
-                new FastaBlockCompressedSequence(fastaPath) :
-                new FastaIndexedSequence(fastaPath);
+        Sequence sequence = SequenceFactory.getSequence(fastaPath, fastaIndexPath);
         return new Genome(id, name, sequence, true);
     }
 

src/main/java/org/broad/igv/feature/genome/load/GenbankLoader.java

@@ -3,8 +3,8 @@
 import org.broad.igv.Globals;
 import org.broad.igv.feature.FeatureDB;
 import org.broad.igv.feature.genome.Genome;
-import org.broad.igv.feature.genome.InMemorySequence;
-import org.broad.igv.feature.genome.Sequence;
+import org.broad.igv.feature.genome.sequence.InMemorySequence;
+import org.broad.igv.feature.genome.sequence.Sequence;
 import org.broad.igv.track.FeatureTrack;
 import org.broad.igv.ui.IGV;
 

src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java

@@ -7,14 +7,16 @@
 import htsjdk.tribble.CloseableTribbleIterator;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureReader;
+import org.broad.igv.feature.genome.sequence.Sequence;
+import org.broad.igv.feature.genome.sequence.SequenceFactory;
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.CytoBandFileParser;
 import org.broad.igv.feature.FeatureDB;
 import org.broad.igv.feature.NamedFeature;
 import org.broad.igv.feature.genome.Genome;
-import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
-import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
+import org.broad.igv.feature.genome.sequence.FastaBlockCompressedSequence;
+import org.broad.igv.feature.genome.sequence.FastaIndexedSequence;
 import org.broad.igv.track.TribbleFeatureSource;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.util.FileUtils;
@@ -24,8 +26,6 @@
 
 import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.util.*;
 
 public class JsonGenomeLoader extends GenomeLoader {
@@ -71,9 +71,7 @@ public Genome loadGenome() throws IOException {
                 gziIndexPath = FileUtils.getAbsolutePath(gziIndexPath, genomePath);
             }
 
-            FastaIndexedSequence sequence = fastaPath.endsWith(".gz") ?
-                    new FastaBlockCompressedSequence(fastaPath, gziIndexPath, indexPath) :
-                    new FastaIndexedSequence(fastaPath, indexPath);
+            Sequence sequence = SequenceFactory.getSequence(fastaPath, indexPath, gziIndexPath);
 
             JsonElement orderedElement = json.get("ordered");
             boolean ordered = orderedElement != null && orderedElement.getAsBoolean();

src/main/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequence.java → src/main/java/org/broad/igv/feature/genome/sequence/FastaBlockCompressedSequence.java

@@ -1,4 +1,4 @@
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
@@ -20,12 +20,12 @@ public class FastaBlockCompressedSequence extends FastaIndexedSequence {
     Mapping[] gziMappings;
     Mapping zeroMapping = new Mapping(0, 0);
 
-    public FastaBlockCompressedSequence(String path) throws IOException {
+    FastaBlockCompressedSequence(String path) throws IOException {
 
         this(path, null, null);
     }
 
-    public FastaBlockCompressedSequence(String path, String gziIndexPath, String indexPath) throws IOException {
+    FastaBlockCompressedSequence(String path, String gziIndexPath, String indexPath) throws IOException {
 
         super(path, indexPath);
 

src/main/java/org/broad/igv/feature/genome/fasta/FastaIndex.java → src/main/java/org/broad/igv/feature/genome/sequence/FastaIndex.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;

src/main/java/org/broad/igv/feature/genome/fasta/FastaIndexedSequence.java → src/main/java/org/broad/igv/feature/genome/sequence/FastaIndexedSequence.java

@@ -23,12 +23,10 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
 import org.broad.igv.logging.*;
-import org.broad.igv.feature.genome.Sequence;
-import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.stream.IGVSeekableStreamFactory;
 
 import java.io.ByteArrayOutputStream;
@@ -51,11 +49,12 @@ public class FastaIndexedSequence implements Sequence {
 
     private final ArrayList<String> chromoNamesList;
 
-    public FastaIndexedSequence(String path) throws IOException {
+     FastaIndexedSequence(String path) throws IOException {
         this(path, null);
     }
 
-    public FastaIndexedSequence(String path, String indexPath) throws IOException {
+
+     FastaIndexedSequence(String path, String indexPath) throws IOException {
 
         this.path = path;
 

src/main/java/org/broad/igv/feature/genome/fasta/FastaSequenceParser.java → src/main/java/org/broad/igv/feature/genome/sequence/FastaSequenceParser.java

@@ -23,14 +23,13 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
 import org.broad.igv.util.ParsingUtils;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 

src/main/java/org/broad/igv/feature/genome/fasta/FastaUtils.java → src/main/java/org/broad/igv/feature/genome/sequence/FastaUtils.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;

src/main/java/org/broad/igv/feature/genome/InMemorySequence.java → src/main/java/org/broad/igv/feature/genome/sequence/InMemorySequence.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome;
+package org.broad.igv.feature.genome.sequence;
 
 import java.util.*;
 

src/main/java/org/broad/igv/feature/genome/Sequence.java → src/main/java/org/broad/igv/feature/genome/sequence/Sequence.java

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-package org.broad.igv.feature.genome;
+package org.broad.igv.feature.genome.sequence;
 
 import org.broad.igv.ui.panel.ReferenceFrame;
 

src/main/java/org/broad/igv/feature/genome/sequence/SequenceFactory.java

@@ -0,0 +1,60 @@
+package org.broad.igv.feature.genome.sequence;
+
+import org.broad.igv.logging.LogManager;
+import org.broad.igv.logging.Logger;
+import org.broad.igv.util.FileUtils;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+
+public class SequenceFactory {
+
+    private static Logger log = LogManager.getLogger(SequenceFactory.class);
+
+    public static Sequence getSequence(String path) throws IOException {
+        return getSequence(path, null, null);
+    }
+
+
+    public static Sequence getSequence(String path, String indexPath) throws IOException {
+        return getSequence(path, indexPath, null);
+    }
+
+
+        /**
+         * Return the Sequence object for the associated paths.
+         * <p>
+         * TODO -- this logic relieds on file extensions, won't neccessarily work for signed or DRS urls
+         *
+         * @param path
+         * @param indexPath
+         * @param gziIndexPath
+         * @return
+         * @throws IOException
+         */
+    public static Sequence getSequence(String path, String indexPath, String gziIndexPath) throws IOException {
+
+        String p;
+        if (FileUtils.isRemote(path)) {
+            try {
+                p = ((new URL(path)).getPath());
+            } catch (MalformedURLException e) {
+                log.error("Error parsing url: " + path);
+                p = path;
+            }
+        } else {
+            p = path;
+        }
+
+        if (gziIndexPath != null || p.endsWith(".gz")) {
+            return new FastaBlockCompressedSequence(path, gziIndexPath, indexPath);
+        } else if (p.endsWith(".2bit")) {
+            return new TwoBitSequence(path);
+        } else {
+            return new FastaIndexedSequence(path, indexPath);
+        }
+    }
+
+}

src/main/java/org/broad/igv/feature/genome/SequenceWrapper.java → src/main/java/org/broad/igv/feature/genome/sequence/SequenceWrapper.java

@@ -27,10 +27,9 @@
  * To change this template, choose Tools | Templates
  * and open the template in the editor.
  */
-package org.broad.igv.feature.genome;
+package org.broad.igv.feature.genome.sequence;
 
 import org.broad.igv.logging.*;
-import org.broad.igv.ui.panel.ReferenceFrame;
 import org.broad.igv.util.ObjectCache;
 
 import java.util.Hashtable;

src/main/java/org/broad/igv/feature/genome/TwoBitReader.java → src/main/java/org/broad/igv/feature/genome/sequence/TwoBitReader.java

@@ -1,4 +1,4 @@
-package org.broad.igv.feature.genome;
+package org.broad.igv.feature.genome.sequence;
 
 /**
  * Reader for UCSC ".2bit" sequence files. Reference: https://genome.ucsc.edu/FAQ/FAQformat.html#format7

src/main/java/org/broad/igv/feature/genome/TwoBitSequence.java → src/main/java/org/broad/igv/feature/genome/sequence/TwoBitSequence.java

@@ -1,4 +1,4 @@
-package org.broad.igv.feature.genome;
+package org.broad.igv.feature.genome.sequence;
 
 import java.io.IOException;
 import java.util.List;
@@ -7,7 +7,7 @@ public class TwoBitSequence implements Sequence{
 
     private TwoBitReader reader;
 
-    public TwoBitSequence(String path) throws IOException {
+    protected TwoBitSequence(String path) throws IOException {
         this.reader = new TwoBitReader(path);
     }
 

src/main/java/org/broad/igv/tools/IgvTools.java

@@ -54,7 +54,7 @@
 import org.broad.igv.feature.GFFParser;
 import org.broad.igv.feature.Mutation;
 import org.broad.igv.feature.genome.*;
-import org.broad.igv.feature.genome.fasta.FastaUtils;
+import org.broad.igv.feature.genome.sequence.FastaUtils;
 import org.broad.igv.feature.genome.load.GenomeDescriptor;
 import org.broad.igv.feature.tribble.CodecFactory;
 import org.broad.igv.feature.tribble.GFFCodec;

src/main/java/org/broad/igv/util/TutorialUtils.java

@@ -30,7 +30,9 @@
 import htsjdk.samtools.util.CloseableIterator;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.genome.ChromosomeNameComparator;
-import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
+import org.broad.igv.feature.genome.sequence.FastaIndexedSequence;
+import org.broad.igv.feature.genome.sequence.Sequence;
+import org.broad.igv.feature.genome.sequence.SequenceFactory;
 import org.broad.igv.sam.SAMAlignment;
 import org.broad.igv.sam.reader.AlignmentReader;
 import org.broad.igv.sam.reader.AlignmentReaderFactory;
@@ -56,7 +58,7 @@ public static void main(String[] args) throws IOException {
 
     static void extractFasta(String inputFasta, String outputFasta, String regionsFile) throws IOException {
 
-        FastaIndexedSequence inFasta = new FastaIndexedSequence(inputFasta);
+        Sequence inFasta = SequenceFactory.getSequence(inputFasta);
 
         List<Region> regions = parseRegions(new File(regionsFile));
 

src/test/java/org/broad/igv/feature/genome/GenomeTest.java

@@ -26,7 +26,8 @@
 package org.broad.igv.feature.genome;
 
 import org.broad.igv.AbstractHeadlessTest;
-import org.broad.igv.feature.genome.fasta.FastaIndex;
+import org.broad.igv.feature.genome.sequence.FastaIndex;
+import org.broad.igv.feature.genome.sequence.Sequence;
 import org.broad.igv.util.TestUtils;
 import org.junit.Assume;
 import org.junit.Rule;

src/test/java/org/broad/igv/feature/genome/TwoBitReaderTest.java

@@ -1,5 +1,6 @@
 package org.broad.igv.feature.genome;
 
+import org.broad.igv.feature.genome.sequence.TwoBitReader;
 import org.broad.igv.util.TestUtils;
 import org.junit.Test;
 

src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java → src/test/java/org/broad/igv/feature/genome/sequence/FastaBlockCompressedSequenceTest.java

@@ -1,6 +1,5 @@
-package org.broad.igv.feature.genome.fasta;
+package org.broad.igv.feature.genome.sequence;
 
-import org.broad.igv.feature.genome.Sequence;
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;