X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=8d2d796ae98cff03a278d8d13c64b99e2b9a73e5;hb=063fa7cb380bf0c3d5ec29155f4ff303c0fb6b7a;hp=dca2d0c4759d47a67efc24385bc047586f5adac7;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index dca2d0c..8d2d796 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,9 +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!
@@ -64,41 +72,52 @@
         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);