Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch

[jalview.git] / src / jalview / io / FileParse.java

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f9440fa..b52fdfb 100755 (executable)
--- 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -142,12 +143,35 @@ public class FileParse
     }
     if (!error)
     {
+      if (fileStr.toLowerCase().endsWith(".gz"))
+      {
+        try
+        {
+          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataName = fileStr;
+          return error;
+        } catch (Exception x)
+        {
+          warningMessage = "Failed  to resolve as a GZ stream ("
+                  + x.getMessage() + ")";
+          x.printStackTrace();
+        }
+        ;
+      }
+      
       dataIn = new BufferedReader(new FileReader(fileStr));
       dataName = fileStr;
     }
     return error;
   }
-
+  private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+  {
+    BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+    inData.mark(2048);
+    inData.read();
+    inData.reset();
+    return inData;
+  }
   private boolean checkURLSource(String fileStr) throws IOException,
           MalformedURLException
   {
@@ -156,14 +180,10 @@ public class FileParse
     //
     // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
     Exception e=null;
-    if (fileStr.endsWith(".gz")) {
+    if (fileStr.toLowerCase().endsWith(".gz")) {
       try {
           InputStream inputStream = url.openStream();
-          dataIn = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
-          dataIn.mark(2048);
-          dataIn.read();
-          dataIn.reset();
-          
+          dataIn = tryAsGzipSource(inputStream);
           dataName = fileStr;
           return false;
       } catch (Exception ex) {