Tests ABITracerTest now running

MaxGreil · MaxGreil · commit 9ecbbe0b1566 · 2018-05-06T12:25:55.000+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
@@ -91,9 +91,7 @@ public ABITrace(File ABIFile) throws IOException {
         while ((b = bis.read()) >= 0) {
             baos.write(b);
         }
-        bis.close();
-        fis.close();
-        baos.close();
+        bis.close(); fis.close(); baos.close();
         bytes = baos.toByteArray();
         initData(bytes);
     }
@@ -533,7 +531,7 @@ private boolean isABI() {
             return true;
         } else {
             for (int i = 128; i <= 130; i++) {
-                ABI[i] = (char) TraceData[i];
+                ABI[i-128] = (char) TraceData[i];
             }
             if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
                 MacJunk = 128;
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
@@ -24,12 +24,10 @@
 import java.io.File;
 import java.net.URL;
 import org.junit.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 public class ABITracerTest {
 
-    private final static Logger logger = LoggerFactory.getLogger(ABITracerTest.class);
+    private String filePath = System.getProperty("user.dir") + "/src/test/resources/3730.ab1";
 
     public ABITracerTest() {
     }
@@ -51,22 +49,24 @@ public void tearDown() {
     }
 
     /**
-     * Test of local method, of class ABITracer.
+     * Test of URL method, of class ABITracer.
      */
     @Test
     public void testURL() throws Exception {
-        URL url = new URL("https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1");
+        File file = new File(filePath);
+        Assert.assertNotNull(file);
+        URL url = file.toURI().toURL();
         Assert.assertNotNull(url);
         ABITrace tracer = new ABITrace(url);
         Assert.assertNotNull(tracer);
     }
 
     /**
-     * Test of local method, of class ABITracer.
+     * Test of Local file method, of class ABITracer.
      */
     @Test
     public void testLocal() throws Exception {
-        File file = new File("/3730.ab1");
+        File file = new File(filePath);
         Assert.assertNotNull(file);
         ABITrace tracer = new ABITrace(file);
         Assert.assertNotNull(tracer);

Original file line number	Diff line number	Diff line change
`@@ -91,9 +91,7 @@ public ABITrace(File ABIFile) throws IOException {`
`91`	`91`	`while ((b = bis.read()) >= 0) {`
`92`	`92`	`baos.write(b);`
`93`	`93`	`}`
`94`		`- bis.close();`
`95`		`- fis.close();`
`96`		`- baos.close();`
	`94`	`+ bis.close(); fis.close(); baos.close();`
`97`	`95`	`bytes = baos.toByteArray();`
`98`	`96`	`initData(bytes);`
`99`	`97`	`}`
`@@ -533,7 +531,7 @@ private boolean isABI() {`
`533`	`531`	`return true;`
`534`	`532`	`} else {`
`535`	`533`	`for (int i = 128; i <= 130; i++) {`
`536`		`- ABI[i] = (char) TraceData[i];`
	`534`	`+ ABI[i-128] = (char) TraceData[i];`
`537`	`535`	`}`
`538`	`536`	`if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {`
`539`	`537`	`MacJunk = 128;`