JAL-1620 version bump and release notes

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 69e801c..b6f94fd 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * 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.
+ * 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;
 
+import jalview.util.MessageManager;
+
 import java.io.*;
 import java.net.*;
 import java.util.zip.GZIPInputStream;
@@ -48,7 +52,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-    newline = nl;
+      newline = nl;
   }
 
   public String getNewlineString()
@@ -92,8 +96,7 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(
-              "Implementation error. Null FileParse in copy constructor");
+      throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
       return;
@@ -158,45 +161,55 @@ 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);
+        throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
       }
       throw q;
     }
@@ -251,14 +264,12 @@ public class FileParse
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException("Problem opening " + inFile
-                    + " (also tried " + suffixLess + ") : " + errormessage);
+            throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
           }
         }
         else
         {
-          throw new IOException("Problem opening " + inFile + " : "
-                  + errormessage);
+          throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
         }
       }
     }
@@ -333,8 +344,7 @@ public class FileParse
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException("Failed to read data from source:\n"
-              + errormessage);
+      throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -354,7 +364,7 @@ public class FileParse
     }
     else
     {
-      throw new IOException("Unitialised Source Stream");
+      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -362,7 +372,7 @@ public class FileParse
   {
     if (!error)
       return dataIn.readLine();
-    throw new IOException("Invalid Source Stream:" + errormessage);
+    throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
   }
 
   public boolean isValid()
@@ -394,8 +404,7 @@ public class FileParse
     }
     else
     {
-      throw new IOException(
-              "Implementation Error: Reset called for invalid source.");
+      throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
     }
   }