X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=69c362ffb5916d7c512df98c3eaa9721e1fb964f;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=4b8caecc5c11bf32468a9b26dd9f74a365e2f0f0;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 4b8caec..69c362f 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,8 +22,17 @@ package jalview.io;
 
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -52,7 +61,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-    newline = nl;
+      newline = nl;
   }
 
   public String getNewlineString()
@@ -99,7 +108,9 @@ public class FileParse
       throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
+    {
       return;
+    }
     index = ++from.index;
     inFile = from.inFile;
     suffixSeparator = from.suffixSeparator;
@@ -157,7 +168,7 @@ public class FileParse
         {
           warningMessage = "Failed  to resolve as a GZ stream ("
                   + x.getMessage() + ")";
-          x.printStackTrace();
+          // x.printStackTrace();
         }
         ;
       }
@@ -281,7 +292,9 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
+           {
             extractSuffix(fileStr); // URL lref is stored for later reference.
+          }
         } catch (IOException e)
         {
           String suffixLess = extractSuffix(fileStr);
@@ -323,7 +336,9 @@ public class FileParse
       {
         String suffixLess = extractSuffix(fileStr);
         if (suffixLess != null)
+        {
           is = getClass().getResourceAsStream("/" + suffixLess);
+        }
       }
       if (is != null)
       {
@@ -371,7 +386,9 @@ public class FileParse
   public String nextLine() throws IOException
   {
     if (!error)
+    {
       return dataIn.readLine();
+    }
     throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
   }