X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=f9440fab4d2c134539e1f6f117fd90037331e826;hb=b8a88837ea01a9c6cfdde8bfa160d646eae5dbfe;hp=e97267947fb5d1bf9fe35a6b0852963f9e7e47d2;hpb=2e9cc143fa52dbdbb3e7d56b3612ab708968615a;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index e972679..f9440fa 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,13 +1,13 @@
 /*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -19,6 +19,7 @@ package jalview.io;
 
 import java.io.*;
 import java.net.*;
+import java.util.zip.GZIPInputStream;
 
 /**
  * implements a random access wrapper around a particular datasource, for
@@ -40,6 +41,21 @@ public class FileParse
   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
    */
@@ -137,7 +153,33 @@ public class FileParse
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
-    dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    //
+    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
+    Exception e=null;
+    if (fileStr.endsWith(".gz")) {
+      try {
+          InputStream inputStream = url.openStream();
+          dataIn = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+          dataIn.mark(2048);
+          dataIn.read();
+          dataIn.reset();
+          
+          dataName = fileStr;
+          return false;
+      } catch (Exception ex) {
+        e=ex;
+      }
+    }
+
+    try {
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    } catch (IOException q) {
+      if (e!=null)
+      {
+        throw new IOException("Failed to resolve GZIP stream", e);
+      }
+      throw q;
+    }
     // record URL as name of datasource.
     dataName = fileStr;
     return false;
@@ -374,32 +416,30 @@ public class FileParse
   {
     return dataName;
   }
+
   /**
    * set the (human readable) name or URI for this datasource
+   * 
    * @param dataname
    */
-  protected void setDataName(String dataname) {
+  protected void setDataName(String dataname)
+  {
     dataName = dataname;
   }
-  
 
-  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;
-  }
 }