Any character non aa or nucleotide is a space

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index af3bbec..46f223a 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -24,8 +24,6 @@ import java.net.*;
 public class FileParse\r
 {\r
   public File inFile;\r
-  public int fileSize;\r
-  public int noLines;\r
   protected String type;\r
   protected BufferedReader dataIn;\r
 \r
@@ -38,35 +36,33 @@ public class FileParse
   {\r
     this.type = type;\r
 \r
-    if (type.equals("File"))\r
+    if (type.equals(AppletFormatAdapter.FILE))\r
     {\r
       this.inFile = new File(fileStr);\r
-      this.fileSize = (int) inFile.length();\r
-\r
       dataIn = new BufferedReader(new FileReader(fileStr));\r
     }\r
-    else if (type.equals("URL"))\r
+    else if (type.equals(AppletFormatAdapter.URL))\r
     {\r
       URL url = new URL(fileStr);\r
-      this.fileSize = 0;\r
       dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
     }\r
-    else if (type.equals("Paste"))\r
+   else if (type.equals(AppletFormatAdapter.PASTE))\r
     {\r
       dataIn = new BufferedReader(new StringReader(fileStr));\r
     }\r
+    else if (type.equals(AppletFormatAdapter.CLASSLOADER))\r
+    {\r
+      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);\r
+      if (is != null)\r
+      {\r
+        dataIn = new BufferedReader(new java.io.InputStreamReader(is));\r
+      }\r
+    }\r
   }\r
 \r
   public String nextLine()\r
       throws IOException\r
   {\r
-    String next = dataIn.readLine();\r
-\r
-    if (next != null)\r
-    {\r
-      noLines++;\r
-    }\r
-\r
-    return next;\r
+    return dataIn.readLine();\r
   }\r
 }\r