Only seek for sequences without features

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

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index ea86ae0..af3bbec 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,65 +1,72 @@
 /*\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
+ * 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
 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
+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
-  public FileParse() {}\r
-\r
-  public FileParse(String fileStr, String type) throws MalformedURLException, IOException\r
+  public FileParse()\r
   {\r
+  }\r
 \r
+  public FileParse(String fileStr, String type)\r
+      throws MalformedURLException, IOException\r
+  {\r
     this.type = type;\r
 \r
-    if (type.equals("File")) {\r
+    if (type.equals("File"))\r
+    {\r
       this.inFile = new File(fileStr);\r
-      this.fileSize = (int)inFile.length();\r
-\r
-      dataIn = new BufferedReader(new FileReader( fileStr ));\r
+      this.fileSize = (int) inFile.length();\r
 \r
-    } else if (type.equals("URL")) {\r
+      dataIn = new BufferedReader(new FileReader(fileStr));\r
+    }\r
+    else if (type.equals("URL"))\r
+    {\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
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
+    }\r
+    else if (type.equals("Paste"))\r
     {\r
       dataIn = new BufferedReader(new StringReader(fileStr));\r
     }\r
   }\r
 \r
-  public String nextLine() throws IOException {\r
+  public String nextLine()\r
+      throws IOException\r
+  {\r
     String next = dataIn.readLine();\r
-    if (next != null) {\r
+\r
+    if (next != null)\r
+    {\r
       noLines++;\r
     }\r
+\r
     return next;\r
   }\r
-\r
 }\r