X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=5f228fb79e3bd7711952f60393a39f3e224196e4;hb=f441357783f32298b738d32d5c87000ac0e33768;hp=f8b809ea2a4b6cf77c608c628a2ef5ff1f7c2e80;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index f8b809e..5f228fb 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -34,6 +34,11 @@
         /** DOCUMENT ME!! */
         public static final Vector formats = new Vector();
 
+        public static String INVALID_CHARACTERS = "Contains invalid characters";
+
+        public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
+                                                 "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
+
         static
         {
             formats.addElement("BLC");
@@ -45,6 +50,12 @@
             formats.addElement("PFAM");
         }
 
+
+        public static String FILE = "File";
+        public static String URL = "URL";
+        public static String PASTE = "Paste";
+        public static String CLASSLOADER = "ClassLoader";
+
         AlignFile afile = null;
 
         /**
@@ -57,6 +68,7 @@
          * @return DOCUMENT ME!
          */
         public SequenceI[] readFile(String inFile, String type, String format)
+            throws java.io.IOException
         {
             try
             {
@@ -88,6 +100,11 @@
                 {
                     afile = new PfamFile(inFile, type);
                 }
+                else if (format.equals("JnetFile"))
+                {
+                  afile = new JPredFile(inFile, type);
+                  ((JPredFile)afile).removeNonSequences();
+                }
 
                 return afile.getSeqsAsArray();
             }
@@ -96,6 +113,9 @@
               System.err.println("Failed to read alignment using the '" + format +
                                  "' reader.\n"+e);
 
+              if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))
+                throw new java.io.IOException(e.getMessage());
+
               // Finally test if the user has pasted just the sequence, no id
               if(type.equalsIgnoreCase("Paste"))
               {
@@ -103,16 +123,19 @@
                   // Possible sequence is just residues with no label
                   afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
                   return afile.getSeqsAsArray();
-                }catch(Exception ex)
+                }
+                catch(Exception ex)
                 {
-                  System.err.println("Failed to read alignment using the 'FASTA' reader.\n"+e);
+                  if(ex.toString().startsWith(INVALID_CHARACTERS))
+                    throw new java.io.IOException(e.getMessage());
+
                   ex.printStackTrace();
                 }
-
               }
-            }
 
-            return null;
+              // If we get to this stage, the format was not supported
+              throw new java.io.IOException(SUPPORTED_FORMATS);
+            }
         }