/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
_parse();
} catch (ExceptionPermissionDenied pdx)
{
- errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.rnaml_couldnt_access_datasource",
+ new String[] { pdx.getMessage() });
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
- errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_couldnt_process_data",
+ new String[] { lf.getMessage() });
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_invalid_file",
+ new String[] { iff.getMessage() });
throw new IOException(iff);
} catch (Exception x)
{
error = true;
- errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
- throw new IOException(errormessage , x);
+ errormessage = MessageManager.formatMessage(
+ "exception.ranml_problem_parsing_data",
+ new String[] { x.getMessage() });
+ throw new IOException(errormessage, x);
}
}
annot[k]).charAt(0), 0f);
}
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
- current.getID(), ann);
+ AlignmentAnnotation align = new AlignmentAnnotation(
+ "Secondary Structure",
+ current.getID().trim().length() > 0 ? "Secondary Structure for "
+ + current.getID()
+ : "", ann);
seqs[i].addAlignmentAnnotation(align);
seqs[i].setRNA(result.get(i));