updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index ea86ae0..b840d73 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,65 +1,68 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.net.*;\r
-\r
-public class FileParse {\r
-\r
-  public File   inFile;\r
-  public int    fileSize;\r
-  public int    noLines;\r
-\r
-  protected String          type;\r
-  protected BufferedReader dataIn;\r
-\r
-  public FileParse() {}\r
-\r
-  public FileParse(String fileStr, String type) throws MalformedURLException, IOException\r
-  {\r
-\r
-    this.type = type;\r
-\r
-    if (type.equals("File")) {\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
-      URL url = new URL(fileStr);\r
-      this.fileSize = 0;\r
-      dataIn = new BufferedReader(new InputStreamReader( url.openStream() ));\r
-    } else if(type.equals("Paste"))\r
-    {\r
-      dataIn = new BufferedReader(new StringReader(fileStr));\r
-    }\r
-  }\r
-\r
-  public String nextLine() throws IOException {\r
-    String next = dataIn.readLine();\r
-    if (next != null) {\r
-      noLines++;\r
-    }\r
-    return next;\r
-  }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.net.*;
+
+public class FileParse
+{
+  public File inFile;
+  protected String type;
+  protected BufferedReader dataIn;
+
+  public FileParse()
+  {
+  }
+
+  public FileParse(String fileStr, String type)
+      throws MalformedURLException, IOException
+  {
+    this.type = type;
+
+    if (type.equals(AppletFormatAdapter.FILE))
+    {
+      this.inFile = new File(fileStr);
+      dataIn = new BufferedReader(new FileReader(fileStr));
+    }
+    else if (type.equals(AppletFormatAdapter.URL))
+    {
+      URL url = new URL(fileStr);
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    }
+   else if (type.equals(AppletFormatAdapter.PASTE))
+    {
+      dataIn = new BufferedReader(new StringReader(fileStr));
+    }
+    else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+    {
+      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
+      if (is != null)
+      {
+        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+    }
+  }
+
+  public String nextLine()
+      throws IOException
+  {
+    return dataIn.readLine();
+  }
+}