// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
msa = inferMsa();
}
catch ( final IOException e ) {
- JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with "
- + _options.getMsaPrg() + "\nand the following parameters:\n\"" + _options.getMsaPrgParameters()
- + "\"\nError:" + e.getLocalizedMessage(), "Failed to Calculate MSA", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( _mf,
+ "Could not create multiple sequence alignment with "
+ + _options.getMsaPrg() + "\nand the following parameters:\n\""
+ + _options.getMsaPrgParameters() + "\"\nError:"
+ + e.getLocalizedMessage(),
+ "Failed to Calculate MSA",
+ JOptionPane.ERROR_MESSAGE );
return;
}
if ( msa == null ) {
- JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with "
- + _options.getMsaPrg() + "\nand the following parameters:\n\"" + _options.getMsaPrgParameters()
- + "\"", "Failed to Calculate MSA", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( _mf,
+ "Could not create multiple sequence alignment with "
+ + _options.getMsaPrg() + "\nand the following parameters:\n\""
+ + _options.getMsaPrgParameters() + "\"",
+ "Failed to Calculate MSA",
+ JOptionPane.ERROR_MESSAGE );
return;
}
System.out.println( msa.toString() );
System.out.println( MsaTools.calcBasicGapinessStatistics( msa ).toString() );
final MsaTools msa_tools = MsaTools.createInstance();
if ( _options.isExecuteMsaProcessing() ) {
- msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(), _options
- .getMsaProcessingMinAllowedLength(), msa );
+ msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
+ _options.getMsaProcessingMinAllowedLength(),
+ msa );
if ( msa == null ) {
JOptionPane.showMessageDialog( _mf,
"Less than two sequences longer than "
private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
try {
- final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options
- .getIntermediateFilesBase()
+ final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
+ MSA_FILE_SUFFIX ) );
_msa.write( msa_writer );
msa_writer.close();
- final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options
- .getIntermediateFilesBase()
+ final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
+ PWD_FILE_SUFFIX ) );
m.write( pwd_writer );
pwd_writer.close();