X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=engine%2Fcompbio%2Fengine%2Farchive%2FArchiveManager.java;fp=engine%2Fcompbio%2Fengine%2Farchive%2FArchiveManager.java;h=9b9979e36c893d9a58f44a1e49046c44900414a4;hb=006363dc999cef4e9c49dd6a38ea0d78cbb62472;hp=dabaf3ad257547dd89a264de592100fe1686cc18;hpb=6823d2f36ff55b7ab11d674e3fe4d04dc57d6bbf;p=proteocache.git

diff --git a/engine/compbio/engine/archive/ArchiveManager.java b/engine/compbio/engine/archive/ArchiveManager.java
index dabaf3a..9b9979e 100644
--- a/engine/compbio/engine/archive/ArchiveManager.java
+++ b/engine/compbio/engine/archive/ArchiveManager.java
@@ -1,10 +1,8 @@
 package compbio.engine.archive;
 
-import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.InputStream;
+
 import java.util.Iterator;
-import java.util.Scanner;
 
 //import compbio.util.Util;
 
@@ -17,11 +15,12 @@ import java.util.Scanner;
  */
 public class ArchiveManager implements Iterator<ArchivedJob> {
 	Archive archive;
-	//private final Scanner input;
+
+	// private final Scanner input;
 	/**
 	 * Delimiter for the scanner
 	 */
-	//private final String DELIM = ">";
+	// private final String DELIM = ">";
 
 	/**
 	 * Header data can contain non-ASCII symbols and read in UTF8
@@ -36,25 +35,19 @@ public class ArchiveManager implements Iterator<ArchivedJob> {
 	 */
 	public ArchiveManager(final String mainPath) throws FileNotFoundException {
 		/*
-		input = new Scanner(new File(mainPath), "UTF8");
-		input.useDelimiter(DELIM);
-		Runtime.getRuntime().addShutdownHook(new Thread() {
-
-			@Override
-			public void run() {
-				if (input != null) {
-					input.close();
-				}
-			}
-		});
-		*/
+		 * input = new Scanner(new File(mainPath), "UTF8");
+		 * input.useDelimiter(DELIM); Runtime.getRuntime().addShutdownHook(new
+		 * Thread() {
+		 * 
+		 * @Override public void run() { if (input != null) { input.close(); } }
+		 * });
+		 */
 	}
-	
+
 	public ArchiveManager(Archive ar) {
 		archive = ar;
 	}
 
-
 	/**
 	 * {@inheritDoc}
 	 * 
@@ -63,7 +56,7 @@ public class ArchiveManager implements Iterator<ArchivedJob> {
 	 */
 	@Override
 	public boolean hasNext() {
-		//return input.hasNext();
+		// return input.hasNext();
 		return true;
 	}
 
@@ -81,12 +74,10 @@ public class ArchiveManager implements Iterator<ArchivedJob> {
 	public ArchivedJob next() {
 		String path = "bla-bla-bla";
 		/*
-		String path = input.next();
-		while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) {
-			path = fastaHeader.concat(">");
-			path = fastaHeader.concat(input.next());
-		}
-		*/
+		 * String path = input.next(); while (fastaHeader.indexOf("\n") < 0 &&
+		 * input.hasNext()) { path = fastaHeader.concat(">"); path =
+		 * fastaHeader.concat(input.next()); }
+		 */
 		return new ArchivedJob(path);
 	}
 
@@ -105,7 +96,7 @@ public class ArchiveManager implements Iterator<ArchivedJob> {
 	 * instance of the FastaReader will be possible after calling this method.
 	 */
 	public void close() {
-		//input.close();
+		// input.close();
 	}
 
 	private static ArchivedJob toFastaSequence(final String singleFastaEntry) {
@@ -115,11 +106,9 @@ public class ArchiveManager implements Iterator<ArchivedJob> {
 
 		int nlineidx = singleFastaEntry.indexOf("\n");
 		if (nlineidx < 0) {
-			throw new AssertionError(
-					"The FASTA sequence must contain the header information"
-							+ " separated by the new line from the sequence. Given sequence does not appear to "
-							+ "contain the header! Given data:\n "
-							+ singleFastaEntry);
+			throw new AssertionError("The FASTA sequence must contain the header information"
+					+ " separated by the new line from the sequence. Given sequence does not appear to "
+					+ "contain the header! Given data:\n " + singleFastaEntry);
 		}
 		String header = singleFastaEntry.substring(0, nlineidx);