ABITracer Constructor with URL

MaxGreil · MaxGreil · commit e924815e1d5f · 2018-05-05T21:43:05.000+02:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
@@ -32,6 +32,8 @@
 import java.awt.Color;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
+import java.net.URL;
+import java.io.InputStream;
 
 import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
@@ -96,6 +98,28 @@ public ABITrace(File ABIFile) throws IOException {
         initData(bytes);
     }
 
+    /**
+     * The URL constructor opens an ABI file from any URL.
+     * @param ABIFile is a <code>java.net.URL</code> for an ABI trace file.
+     * @throws IOException if there is a problem reading from the URL.
+     * @throws IllegalArgumentException if the URL does not contain a valid ABI file.
+     */
+    public ABITrace( URL ABIFile ) throws IOException
+    {
+        byte[] bytes = null;
+        ByteArrayOutputStream baos = new ByteArrayOutputStream();
+        InputStream is = ABIFile.openStream();
+        BufferedInputStream bis = new BufferedInputStream(is);
+        int b;
+        while ((b = bis.read()) >= 0)
+        {
+            baos.write(b);
+        }
+        bis.close(); is.close(); baos.close();
+        bytes = baos.toByteArray();
+        initData(bytes);
+    }
+
     /**
      * The <code>byte[]</code> constructor parses an ABI file represented as a byte array.
      *
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/ABITracerTest.java
@@ -22,6 +22,7 @@
 package org.biojava.nbio.core.sequence.io;
 
 import java.io.File;
+import java.net.URL;
 import org.junit.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -50,12 +51,23 @@ public void tearDown() {
     }
 
     /**
-     * Test of process method, of class ABITracer.
+     * Test of local method, of class ABITracer.
      */
     @Test
-    public void testProcess() throws Exception {
-        logger.info("process");
+    public void testURL() throws Exception {
+        URL url = new URL("https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1");
+        Assert.assertNotNull(url);
+        ABITrace tracer = new ABITrace(url);
+        Assert.assertNotNull(tracer);
+    }
+
+    /**
+     * Test of local method, of class ABITracer.
+     */
+    @Test
+    public void testLocal() throws Exception {
         File file = new File("/3730.ab1");
+        Assert.assertNotNull(file);
         ABITrace tracer = new ABITrace(file);
         Assert.assertNotNull(tracer);
     }
