X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=b6f94fd53de717b6c5340c70ae93cb2f3261759e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=051550798cd519fd9fa2a13e35b6946544bc553f;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 0515507..b6f94fd 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,24 +1,30 @@
 /*
- * 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 2.8.2b1)
+ * 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;
 
 /**
  * implements a random access wrapper around a particular datasource, for
@@ -38,18 +44,22 @@ public class FileParse
   // same data source
 
   protected char suffixSeparator = '#';
+
   /**
-   * character used to write newlines 
+   * character used to write newlines
    */
   protected String newline = System.getProperty("line.separator");
+
   public void setNewlineString(String nl)
   {
-    newline = 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
@@ -86,8 +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;
@@ -137,18 +146,73 @@ 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
   {
     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.toLowerCase().endsWith(".gz"))
+    {
+      try
+      {
+        InputStream inputStream = url.openStream();
+        dataIn = tryAsGzipSource(inputStream);
+        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(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+      }
+      throw q;
+    }
     // record URL as name of datasource.
     dataName = fileStr;
     return false;
@@ -200,14 +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}));
         }
       }
     }
@@ -282,8 +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);
@@ -303,7 +364,7 @@ public class FileParse
     }
     else
     {
-      throw new IOException("Unitialised Source Stream");
+      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -311,7 +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()
@@ -343,8 +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"));
     }
   }
 
@@ -385,23 +445,27 @@ 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;
   }
-  
 
   /**
    * get the underlying bufferedReader for this data source.
+   * 
    * @return null if no reader available
    * @throws IOException
    */
   public Reader getReader()
   {
-    if (dataIn != null) // Probably don't need to test for readiness && dataIn.ready())
+    if (dataIn != null) // Probably don't need to test for readiness &&
+                        // dataIn.ready())
     {
       return dataIn;
     }