X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FJPredFile.java;h=0ee41b8c64a811653ecc74a395b3458ede94aedf;hb=10ddc20a773099eaf0dc4d9d1bbb3b88b4176ed4;hp=cadf1535555db4ded65a52c50ea3a29d3003d587;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index cadf153..0ee41b8 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -24,12 +24,11 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+
 
 /**
  * DOCUMENT ME!
@@ -264,12 +263,12 @@ public class JPredFile extends AlignFile
                 }
             }
         }
-
+        /* leave it to the parser user to actually check this.
         if (noSeqs < 1)
         {
             throw new IOException(
                 "JpredFile Parser: No sequence in the prediction!");
-        }
+        }*/
 
         maxLength = seq_entries.elementAt(0).toString().length();
 
@@ -283,9 +282,9 @@ public class JPredFile extends AlignFile
             if (!Symscores.containsKey(ids.elementAt(i)) &&
                     !isValidProteinSequence(newSeq.getSequence()))
             {
-                throw new IOException(
-                    "JPredConcise: Not a valid protein sequence - (" +
-                    ids.elementAt(i).toString() + ")");
+                throw new IOException("JPredConcise: "
+                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
+                                      +ids.elementAt(i).toString() + ")");
             }
 
             if (maxLength != seq_entries.elementAt(i).toString().length())
@@ -339,6 +338,34 @@ public class JPredFile extends AlignFile
             e.printStackTrace();
         }
     }
+    Vector annotSeqs=null;
+  /**
+   * removeNonSequences
+   */
+  public void removeNonSequences()
+  {
+    if (annotSeqs!=null)
+      return;
+    annotSeqs = new Vector();
+    Vector newseqs = new Vector();
+    int i=0;
+    int j=seqs.size();
+    for (; i<QuerySeqPosition; i++)
+        annotSeqs.add(seqs.get(i));
+      // check that no stray annotations have been added at the end.
+      {
+        SequenceI sq = (SequenceI) seqs.get(j-1);
+        if (sq.getName().toUpperCase().startsWith("JPRED")) {
+          annotSeqs.add(sq);
+          seqs.remove(--j);
+        }
+      }
+    for (; i<j; i++)
+        newseqs.add(seqs.get(i));
+
+    seqs.clear();
+    seqs = newseqs;
+  }
 }