X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=05a7212b5fba1692407ded180b6e2be9f6e29be9;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=e97267947fb5d1bf9fe35a6b0852963f9e7e47d2;hpb=2e9cc143fa52dbdbb3e7d56b3612ab708968615a;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index e972679..05a7212 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -38,7 +38,18 @@ public class FileParse
   // same data source
 
   protected char suffixSeparator = '#';
-
+  /**
+   * character used to write newlines 
+   */
+  protected String newline = System.getProperty("line.separator");
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+  public String getNewlineString()
+  {
+    return newline;
+  }
   /**
    * '#' separated string tagged on to end of filename or url that was clipped
    * off to resolve to valid filename
@@ -383,23 +394,17 @@ public class FileParse
   }
   
 
-  public Reader getReader() throws IOException
+  /**
+   * get the underlying bufferedReader for this data source.
+   * @return null if no reader available
+   * @throws IOException
+   */
+  public Reader getReader()
   {
-    if (dataIn != null && dataIn.ready())
+    if (dataIn != null) // Probably don't need to test for readiness && dataIn.ready())
     {
       return dataIn;
     }
     return null;
   }
-
-  public static String checkProtocol(String file)
-  {
-    String protocol = jalview.io.FormatAdapter.FILE;
-  
-    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
-    {
-      protocol = jalview.io.FormatAdapter.URL;
-    }
-    return protocol;
-  }
 }