X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;fp=src%2Fjalview%2Fio%2FFileParse.java;h=71640f4bfdf45c92d8d0c7a9a86f0ca52c625459;hb=9623cea766a766683243235557ad48e6f7659e6a;hp=22213122bd40ac32ae525a526eca28b4082d05a8;hpb=6066400ed6b0fe288ebbea82389f59838a534706;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 2221312..71640f4 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -80,7 +80,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-      newline = nl;
+    newline = nl;
   }
 
   public String getNewlineString()
@@ -98,7 +98,7 @@ public class FileParse
 
   protected BufferedReader dataIn = null;
 
-  protected String errormessage = "UNITIALISED SOURCE";
+  protected String errormessage = "UNINITIALISED SOURCE";
 
   protected boolean error = true;
 
@@ -124,7 +124,9 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
     {
@@ -239,7 +241,10 @@ public class FileParse
     {
       if (e != null)
       {
-        throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+        throw new IOException(
+                MessageManager
+                        .getString("exception.failed_to_resolve_gzip_stream"),
+                e);
       }
       throw q;
     }
@@ -318,12 +323,17 @@ public class FileParse
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
+            throw new IOException(MessageManager.formatMessage(
+                    "exception.problem_opening_file_also_tried",
+                    new String[] { inFile.getName(), suffixLess,
+                        errormessage }));
           }
         }
         else
         {
-          throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.problem_opening_file",
+                  new String[] { inFile.getName(), errormessage }));
         }
       }
     }
@@ -335,7 +345,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -402,7 +412,9 @@ public class FileParse
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
-      throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
+      throw new IOException(MessageManager.formatMessage(
+              "exception.failed_to_read_data_from_source",
+              new String[] { errormessage }));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -422,7 +434,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -432,7 +445,9 @@ public class FileParse
     {
       return dataIn.readLine();
     }
-    throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
+    throw new IOException(MessageManager.formatMessage(
+            "exception.invalid_source_stream",
+            new String[] { errormessage }));
   }
 
   /**
@@ -477,7 +492,9 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
+      throw new IOException(
+              MessageManager
+                      .getString("error.implementation_error_reset_called_for_invalid_source"));
     }
   }
 
@@ -582,7 +599,8 @@ public class FileParse
    */
   public void configureForView(AlignmentViewPanel avpanel)
   {
-    if (avpanel!=null) {
+    if (avpanel != null)
+    {
       setViewport(avpanel.getAlignViewport());
     }
     // could also set export/import settings