Comment out start and end refs

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index dca2d0c..8d2d796 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,9 +48,17 @@
             formats.addElement("PileUp");\r
             formats.addElement("PIR");\r
             formats.addElement("PFAM");\r
+            formats.addElement("PDB");\r
         }\r
 \r
+\r
+        public static String FILE = "File";\r
+        public static String URL = "URL";\r
+        public static String PASTE = "Paste";\r
+        public static String CLASSLOADER = "ClassLoader";\r
+\r
         AlignFile afile = null;\r
+        String inFile;\r
 \r
         /**\r
          * DOCUMENT ME!\r
@@ -64,41 +72,52 @@
         public SequenceI[] readFile(String inFile, String type, String format)\r
             throws java.io.IOException\r
         {\r
+            this.inFile = inFile;\r
             try\r
             {\r
-                if (format.equals("FASTA"))\r
-                {\r
-                    afile = new FastaFile(inFile, type);\r
-                }\r
-                else if (format.equals("MSF"))\r
-                {\r
-                    afile = new MSFfile(inFile, type);\r
-                }\r
-                else if (format.equals("PileUp"))\r
-                {\r
-                    afile = new PileUpfile(inFile, type);\r
-                }\r
-                else if (format.equals("CLUSTAL"))\r
-                {\r
-                    afile = new ClustalFile(inFile, type);\r
-                }\r
-                else if (format.equals("BLC"))\r
-                {\r
-                    afile = new BLCFile(inFile, type);\r
-                }\r
-                else if (format.equals("PIR"))\r
-                {\r
-                    afile = new PIRFile(inFile, type);\r
-                }\r
-                else if (format.equals("PFAM"))\r
-                {\r
-                    afile = new PfamFile(inFile, type);\r
-                }\r
+              if (format.equals("FASTA"))\r
+              {\r
+                afile = new FastaFile(inFile, type);\r
+              }\r
+              else if (format.equals("MSF"))\r
+              {\r
+                afile = new MSFfile(inFile, type);\r
+              }\r
+              else if (format.equals("PileUp"))\r
+              {\r
+                afile = new PileUpfile(inFile, type);\r
+              }\r
+              else if (format.equals("CLUSTAL"))\r
+              {\r
+                afile = new ClustalFile(inFile, type);\r
+              }\r
+              else if (format.equals("BLC"))\r
+              {\r
+                afile = new BLCFile(inFile, type);\r
+              }\r
+              else if (format.equals("PIR"))\r
+              {\r
+                afile = new PIRFile(inFile, type);\r
+              }\r
+              else if (format.equals("PFAM"))\r
+              {\r
+                afile = new PfamFile(inFile, type);\r
+              }\r
+              else if (format.equals("JnetFile"))\r
+              {\r
+                afile = new JPredFile(inFile, type);\r
+                ( (JPredFile) afile).removeNonSequences();\r
+              }\r
+              else if (format.equals("PDB"))\r
+              {\r
+                afile = new MCview.PDBfile(inFile, type);\r
+              }\r
 \r
-                return afile.getSeqsAsArray();\r
+              return afile.getSeqsAsArray();\r
             }\r
             catch (Exception e)\r
             {\r
+              e.printStackTrace();\r
               System.err.println("Failed to read alignment using the '" + format +\r
                                  "' reader.\n"+e);\r
 \r