added unofficial support for concise output parsing from the JNet server to extract...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index dca2d0c..5f228fb 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -50,6 +50,12 @@
             formats.addElement("PFAM");\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
 \r
         /**\r
@@ -94,6 +100,11 @@
                 {\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
 \r
                 return afile.getSeqsAsArray();\r
             }\r