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Can now set the initial window size via configuration file for application and ArchA...
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
tools
/
PhyloInferenceDialog.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
index
399c521
..
d750a43
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
+++ b/
forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java
@@
-21,7
+21,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx.tools;
package org.forester.archaeopteryx.tools;
@@
-78,7
+78,6
@@
public class PhyloInferenceDialog extends JDialog implements ActionListener {
private JTextField _input_seqs_min_length_tf;
private JTextField _input_seqs_max_length_tf;
private JTextField _input_seqs_type_tf;
private JTextField _input_seqs_min_length_tf;
private JTextField _input_seqs_max_length_tf;
private JTextField _input_seqs_type_tf;
-
private JTextField _mafft_paramenters_tf;
private JTextField _clustalo_paramenters_tf;
private JTextField _msa_processing_max_allowed_gap_ratio_tf;
private JTextField _mafft_paramenters_tf;
private JTextField _clustalo_paramenters_tf;
private JTextField _msa_processing_max_allowed_gap_ratio_tf;
@@
-130,13
+129,10
@@
public class PhyloInferenceDialog extends JDialog implements ActionListener {
inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
inputfile_pnl_2.add( new JLabel( "Type:" ) );
inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
inputfile_pnl_2.add( _input_seqs_max_length_tf = new JTextField() );
inputfile_pnl_2.add( new JLabel( "Type:" ) );
inputfile_pnl_2.add( _input_seqs_type_tf = new JTextField() );
-
-
- inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT") );
+ inputfile_pnl_3.add( _mafft_cb = new JCheckBox( "MAFFT" ) );
inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
inputfile_pnl_3.add( new JLabel( "Parameters: " ) );
inputfile_pnl_3.add( _mafft_paramenters_tf = new JTextField() );
-
- inputfile_pnl_4.add( _clustalo_cb = new JCheckBox( "ClustalO") );
+ inputfile_pnl_4.add( _clustalo_cb = new JCheckBox( "ClustalO" ) );
inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
_input_seqs_median_length_tf.setColumns( 4 );
inputfile_pnl_4.add( new JLabel( "Parameters: " ) );
inputfile_pnl_4.add( _clustalo_paramenters_tf = new JTextField() );
_input_seqs_median_length_tf.setColumns( 4 );
@@
-151,7
+147,6
@@
public class PhyloInferenceDialog extends JDialog implements ActionListener {
_input_seqs_max_length_tf.setEditable( false );
_input_seqs_number_tf.setEditable( false );
_input_seqs_type_tf.setEditable( false );
_input_seqs_max_length_tf.setEditable( false );
_input_seqs_number_tf.setEditable( false );
_input_seqs_type_tf.setEditable( false );
-
_mafft_paramenters_tf.setColumns( 26 );
_mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
_clustalo_paramenters_tf.setColumns( 26 );
_mafft_paramenters_tf.setColumns( 26 );
_mafft_paramenters_tf.setText( "--maxiterate 1000 --localpair" );
_clustalo_paramenters_tf.setColumns( 26 );
@@
-286,7
+281,7
@@
public class PhyloInferenceDialog extends JDialog implements ActionListener {
_value = JOptionPane.CANCEL_OPTION;
if ( from_unaligned_seqs ) {
updateSeqsItems();
_value = JOptionPane.CANCEL_OPTION;
if ( from_unaligned_seqs ) {
updateSeqsItems();
- }
+ }
else {
updateMsaItems();
}
else {
updateMsaItems();
}