Integration of David Corsars Phylip File support

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 47583f0..e8e9f2e 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -6,14 +6,16 @@
  * 
  * 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.
+ * 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 
  * 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/>.
+ * 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;
@@ -48,7 +50,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-    newline = nl;
+      newline = nl;
   }
 
   public String getNewlineString()
@@ -158,43 +160,53 @@ public class FileParse
         }
         ;
       }
-      
+
       dataIn = new BufferedReader(new FileReader(fileStr));
       dataName = fileStr;
     }
     return error;
   }
-  private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+
+  private BufferedReader tryAsGzipSource(InputStream inputStream)
+          throws Exception
   {
-    BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+    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
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
     //
-    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
-    Exception e=null;
-    if (fileStr.toLowerCase().endsWith(".gz")) {
-      try {
-          InputStream inputStream = url.openStream();
-          dataIn = tryAsGzipSource(inputStream);
-          dataName = fileStr;
-          return false;
-      } catch (Exception ex) {
-        e=ex;
+    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+    // Kenny Sabir
+    Exception e = null;
+    if (fileStr.toLowerCase().endsWith(".gz"))
+    {
+      try
+      {
+        InputStream inputStream = url.openStream();
+        dataIn = tryAsGzipSource(inputStream);
+        dataName = fileStr;
+        return false;
+      } catch (Exception ex)
+      {
+        e = ex;
       }
     }
 
-    try {
+    try
+    {
       dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q) {
-      if (e!=null)
+    } catch (IOException q)
+    {
+      if (e != null)
       {
         throw new IOException("Failed to resolve GZIP stream", e);
       }