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
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 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                         _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_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_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 );
@@ -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 );
-           
             _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();
-              }
+        }
         else {
             updateMsaItems();
         }