X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=4507019828b4fe9dc93d18d0141ed2afd4fbc457;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=42e881c56248524a536f473d70a9a61e64a47da4;hpb=1eb7d27d73beabe1a1b74fd088c1c3254a8066be;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 42e881c..4507019 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -67,7 +67,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "sto" }; // ,
+      "sto,stk" }; // ,
 
   // ".blast"
   // };
@@ -119,6 +119,21 @@ public class AppletFormatAdapter
   String inFile;
 
   /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  /**
    * check that this format is valid for reading
    * 
    * @param format
@@ -441,7 +456,7 @@ public class AppletFormatAdapter
         throw new Exception(
                 "Implementation error: Unknown file format string");
       }
-
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());
@@ -463,6 +478,18 @@ public class AppletFormatAdapter
     return null;
   }
 
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
     int i = 0;
@@ -597,11 +624,14 @@ public class AppletFormatAdapter
       if (!fp.isValid())
       {
         fp = null;
-      } else {
-      if (debug)
+      }
+      else
       {
-        System.out.println("Successful.");
-      }}
+        if (debug)
+        {
+          System.out.println("Successful.");
+        }
+      }
     } catch (Exception e)
     {
       if (debug)
@@ -690,4 +720,4 @@ public class AppletFormatAdapter
     }
     return null;
   }
-}
\ No newline at end of file
+}