X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=f8b809ea2a4b6cf77c608c628a2ef5ff1f7c2e80;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=fa2373e2df878af89ff2ece1ee7c1e82306eb2bf;hpb=b809a0696ac3ac626b4abf98bad1efad33ad2112;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index fa2373e..f8b809e 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -93,9 +93,23 @@
             }
             catch (Exception e)
             {
-                System.err.println("Failed to read alignment using the '" + format +
-                    "' reader.");
-                e.printStackTrace();
+              System.err.println("Failed to read alignment using the '" + format +
+                                 "' reader.\n"+e);
+
+              // Finally test if the user has pasted just the sequence, no id
+              if(type.equalsIgnoreCase("Paste"))
+              {
+                try{
+                  // Possible sequence is just residues with no label
+                  afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+                  return afile.getSeqsAsArray();
+                }catch(Exception ex)
+                {
+                  System.err.println("Failed to read alignment using the 'FASTA' reader.\n"+e);
+                  ex.printStackTrace();
+                }
+
+              }
             }
 
             return null;
@@ -112,7 +126,6 @@
          */
         public String formatSequences(String format,
                                       Vector seqs,
-                                      boolean dbref,
                                       boolean jvsuffix)
         {
             SequenceI[] s = new SequenceI[seqs.size()];
@@ -153,7 +166,6 @@
                     afile = new PfamFile();
                 }
 
-                afile.addDBPrefix(dbref);
                 afile.addJVSuffix(jvsuffix);
 
                 afile.setSeqs(s);