Fix for parsing Jronn model*.rec on Windows.

larsonmattr · larsonmattr · commit b783627672db · 2016-01-03T17:34:43.000-06:00
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/ModelLoader.java
@@ -170,26 +170,25 @@ void loadModels() throws NumberFormatException, IOException {
 			    "model" + i + ".rec"),
 			    "ISO-8859-1"));
 	    String line = null;
-	    final Scanner scan = new Scanner(bfr);
-	    scan.useDelimiter(System.getProperty("line.separator"));
-	    final int numberOfSeqs = scan.nextInt();
+        line = bfr.readLine().trim();
+	    final int numberOfSeqs = Integer.parseInt(line);
 	    final Model model = new Model(i, numberOfSeqs);
 	    // ignore this one, its always 19 defined in RonnConstrain
-	    scan.nextInt();
+	    line = bfr.readLine();
 	    for (int j = 0; j < numberOfSeqs; j++) {
-		line = scan.next();
-		final char[] dbseq = line.trim().toCharArray();
-		assert dbseq.length < Short.MAX_VALUE;
-		model.Length[j] = (short) dbseq.length;
-		for (int dResidue = 0; dResidue < dbseq.length; dResidue++) {
-		    model.dbAA[j][dResidue] = RonnConstraint.INDEX[dbseq[dResidue] - 'A'];
-		    assert !((model.dbAA[j][dResidue] < 0) || (model.dbAA[j][dResidue] > 19));
-		}
-		model.W[j] = scan.nextFloat();
-	    }
+            line = bfr.readLine();
+            final char[] dbseq = line.trim().toCharArray();
+            assert dbseq.length < Short.MAX_VALUE;
+            model.Length[j] = (short) dbseq.length;
+            for (int dResidue = 0; dResidue < dbseq.length; dResidue++) {
+                model.dbAA[j][dResidue] = RonnConstraint.INDEX[dbseq[dResidue] - 'A'];
+                assert !((model.dbAA[j][dResidue] < 0) || (model.dbAA[j][dResidue] > 19));
+            }
+                line = bfr.readLine().trim();
+                model.W[j] = Float.parseFloat(line);
+            }
 	    ModelLoader.models.put(model.modelNum, model);
 	    bfr.close();
-	    scan.close();
 	}
     }
 
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/JronnTest.java
@@ -29,7 +29,7 @@
 
 public class JronnTest {
 
-	@Test
+	// Implemented with two platform checks.
 	public void verifyRanges() { 
   
 	Range[]	ranges = Jronn.getDisorder(new FastaSequence("name", "LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
@@ -51,4 +51,52 @@ public void verifyRanges() {
 	assertEquals(313, ranges[3].to);
 	//System.out.println(Arrays.toString(ranges));
 	}
+
+	/**
+	 * Jronn was breaking on Windows platform due to the different System.getProperty("line.separator") values
+	 * (CRLF vs LF).  This wraps the existing unit testing to show that it works on windows or unix.
+	 */
+	@Test
+	public void checkJronn() {
+		// Windows CRLF
+		ScopedProperty lineSepProp = new ScopedProperty("line.separator", "\r\n");
+		verifyRanges();
+		lineSepProp.close();
+
+		// UNIX LF
+		ScopedProperty lineSepPropUnix = new ScopedProperty("line.separator", "\n");
+		verifyRanges();
+		lineSepPropUnix.close();
+	}
+
+	/**
+	 * A scoped property helper class to check with Windows style CRLF.
+	 * Credit Thomas Klambauer, but here have removed the implement of
+	 * AutoCloseable (Java 7) for BioJava support of Java 6.
+	 */
+	public class ScopedProperty {
+
+		private final String key;
+		private final String oldValue;
+
+		/**
+		 *
+		 * @param key The System.setProperty key
+		 * @param value The System.setProperty value to switch to.
+		 */
+		public ScopedProperty(final String key, final String value) {
+			this.key = key;
+			oldValue = System.setProperty(key, value);
+		}
+
+		public void close() {
+			// Can't use setProperty(key, null) -> Throws NullPointerException.
+			if( oldValue == null ) {
+				// Previously there was no entry.
+				System.clearProperty(key);
+			} else {
+				System.setProperty(key, oldValue);
+			}
+		}
+	}
 }
