X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileParse.java;h=8711354bdf33f3794959401da93c6a86e8b980a9;hb=d579f105e3feca4b77ac93c52bb45f8cc39c39cd;hp=92282570b04edca16088cecd097d50fcdf528f89;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 9228257..8711354 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;
     }
@@ -294,12 +299,17 @@ 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 }));
         }
       }
     }
@@ -311,7 +321,7 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
-           {
+          {
             extractSuffix(fileStr); // URL lref is stored for later reference.
           }
         } catch (IOException e)
@@ -378,7 +388,9 @@ 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);
@@ -398,7 +410,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
+      throw new IOException(
+              MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
@@ -408,7 +421,9 @@ 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 }));
   }
 
   /**
@@ -442,18 +457,28 @@ public class FileParse
   }
 
   /**
-   * rewinds the datasource the beginning.
+   * Rewinds the datasource to the marked point if possible
+   * 
+   * @param bytesRead
    * 
    */
-  public void reset() throws IOException
+  public void reset(int bytesRead) throws IOException
   {
+    if (bytesRead >= READAHEAD_LIMIT)
+    {
+      System.err.println(String.format(
+              "File reset error: read %d bytes but reset limit is %d",
+              bytesRead, READAHEAD_LIMIT));
+    }
     if (dataIn != null && !error)
     {
       dataIn.reset();
     }
     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"));
     }
   }
 
@@ -558,7 +583,8 @@ public class FileParse
    */
   public void configureForView(AlignmentViewPanel avpanel)
   {
-    if (avpanel!=null) {
+    if (avpanel != null)
+    {
       setViewport(avpanel.getAlignViewport());
     }
     // could also set export/import settings