JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability...

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index e8e9f2e..f9c717d 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,20 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.net.*;
+import jalview.api.AlignViewportI;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -37,6 +49,8 @@ public class FileParse
 
   public File inFile = null;
 
+  private AlignViewportI viewport;
+
   public int index = 1; // sequence counter for FileParse object created from
 
   // same data source
@@ -94,11 +108,12 @@ 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;
+    }
     index = ++from.index;
     inFile = from.inFile;
     suffixSeparator = from.suffixSeparator;
@@ -156,7 +171,7 @@ public class FileParse
         {
           warningMessage = "Failed  to resolve as a GZ stream ("
                   + x.getMessage() + ")";
-          x.printStackTrace();
+          // x.printStackTrace();
         }
         ;
       }
@@ -208,7 +223,7 @@ public class FileParse
     {
       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;
     }
@@ -263,14 +278,12 @@ 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}));
         }
       }
     }
@@ -282,7 +295,9 @@ public class FileParse
         {
           checkURLSource(fileStr);
           if (suffixSeparator == '#')
+           {
             extractSuffix(fileStr); // URL lref is stored for later reference.
+          }
         } catch (IOException e)
         {
           String suffixLess = extractSuffix(fileStr);
@@ -324,7 +339,9 @@ public class FileParse
       {
         String suffixLess = extractSuffix(fileStr);
         if (suffixLess != null)
+        {
           is = getClass().getResourceAsStream("/" + suffixLess);
+        }
       }
       if (is != null)
       {
@@ -345,8 +362,7 @@ 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);
@@ -366,15 +382,17 @@ public class FileParse
     }
     else
     {
-      throw new IOException("Unitialised Source Stream");
+      throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
     }
   }
 
   public String nextLine() throws IOException
   {
     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()
@@ -406,8 +424,7 @@ 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"));
     }
   }
 
@@ -474,4 +491,14 @@ public class FileParse
     }
     return null;
   }
+
+  public AlignViewportI getViewport()
+  {
+    return viewport;
+  }
+
+  public void setViewport(AlignViewportI viewport)
+  {
+    this.viewport = viewport;
+  }
 }