@@ -260,7+268,9 @@ public class JPredFile extends AlignFile
}
if (QuerySeqPosition == -1)
}
if (QuerySeqPosition == -1)
+ {
QuerySeqPosition = ids.size();
QuerySeqPosition = ids.size();
+ }
ids.addElement(name);
noSeqs++;
}
ids.addElement(name);
noSeqs++;
}
@@ -273,7+283,7 @@ public class JPredFile extends AlignFile
seq_entries.addElement(newseq.toString());
ids.addElement(id);
seq_entries.addElement(newseq.toString());
ids.addElement(id);
- Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
+ Symscores.put(id, new Integer(ids.size() - 1));
}
}
}
}
}
}
@@ -294,7+304,11 @@ public class JPredFile extends AlignFile
if (maxLength != seq_entries.elementAt(i).toString().length())
{
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()}));
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
}
if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
@@ -318,7+332,11 @@ public class JPredFile extends AlignFile
} catch (Exception e)
{
tal = null;
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()}));