X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=8d2d796ae98cff03a278d8d13c64b99e2b9a73e5;hb=b0af1c02bc91ec74e941dfc8220b52f591d5df1a;hp=f8b809ea2a4b6cf77c608c628a2ef5ff1f7c2e80;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index f8b809e..8d2d796 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");
@@ -43,9 +48,17 @@
             formats.addElement("PileUp");
             formats.addElement("PIR");
             formats.addElement("PFAM");
+            formats.addElement("PDB");
         }
 
+
+        public static String FILE = "File";
+        public static String URL = "URL";
+        public static String PASTE = "Paste";
+        public static String CLASSLOADER = "ClassLoader";
+
         AlignFile afile = null;
+        String inFile;
 
         /**
          * DOCUMENT ME!
@@ -57,45 +70,60 @@
          * @return DOCUMENT ME!
          */
         public SequenceI[] readFile(String inFile, String type, String format)
+            throws java.io.IOException
         {
+            this.inFile = inFile;
             try
             {
-                if (format.equals("FASTA"))
-                {
-                    afile = new FastaFile(inFile, type);
-                }
-                else if (format.equals("MSF"))
-                {
-                    afile = new MSFfile(inFile, type);
-                }
-                else if (format.equals("PileUp"))
-                {
-                    afile = new PileUpfile(inFile, type);
-                }
-                else if (format.equals("CLUSTAL"))
-                {
-                    afile = new ClustalFile(inFile, type);
-                }
-                else if (format.equals("BLC"))
-                {
-                    afile = new BLCFile(inFile, type);
-                }
-                else if (format.equals("PIR"))
-                {
-                    afile = new PIRFile(inFile, type);
-                }
-                else if (format.equals("PFAM"))
-                {
-                    afile = new PfamFile(inFile, type);
-                }
+              if (format.equals("FASTA"))
+              {
+                afile = new FastaFile(inFile, type);
+              }
+              else if (format.equals("MSF"))
+              {
+                afile = new MSFfile(inFile, type);
+              }
+              else if (format.equals("PileUp"))
+              {
+                afile = new PileUpfile(inFile, type);
+              }
+              else if (format.equals("CLUSTAL"))
+              {
+                afile = new ClustalFile(inFile, type);
+              }
+              else if (format.equals("BLC"))
+              {
+                afile = new BLCFile(inFile, type);
+              }
+              else if (format.equals("PIR"))
+              {
+                afile = new PIRFile(inFile, type);
+              }
+              else if (format.equals("PFAM"))
+              {
+                afile = new PfamFile(inFile, type);
+              }
+              else if (format.equals("JnetFile"))
+              {
+                afile = new JPredFile(inFile, type);
+                ( (JPredFile) afile).removeNonSequences();
+              }
+              else if (format.equals("PDB"))
+              {
+                afile = new MCview.PDBfile(inFile, type);
+              }
 
-                return afile.getSeqsAsArray();
+              return afile.getSeqsAsArray();
             }
             catch (Exception e)
             {
+              e.printStackTrace();
               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 +131,19 @@
                   // 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);
+            }
         }