X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=bccdd9d0e68027c046828352c3666005325abad9;hb=baf4db894c841b22eabbd31a03dd552167d43c60;hp=e0d7990ab19c5ab9405e53a78536b30bbd81a437;hpb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index e0d7990..bccdd9d 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -389,8 +389,7 @@ public final class MainFrameApplication extends MainFrame {
                     _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
                                                                                         .getWidth(),
                                                                                 _mainpanel.getCurrentTreePanel()
-                                                                                        .getHeight(),
-                                                                                getOptions().isAllowFontSizeChange() );
+                                                                                        .getHeight() );
                 }
             }
         } );
@@ -882,6 +881,8 @@ public final class MainFrameApplication extends MainFrame {
                 setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+                
+                MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
                 try {
                     getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
@@ -932,9 +933,13 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
         _options_jmenu.addSeparator();
+        _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );
+        _options_jmenu.addSeparator();
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
+        _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+        _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
         _options_jmenu.addSeparator();
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
@@ -996,6 +1001,8 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
+        customizeJMenuItem( _cycle_data_return);
+        
         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
         customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
@@ -1029,6 +1036,7 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
         customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
                 .isReplaceUnderscoresInNhParsing() );
+        customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
@@ -1290,8 +1298,7 @@ public final class MainFrameApplication extends MainFrame {
 
     void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
-                                                                    _mainpanel.getCurrentTreePanel().getHeight(),
-                                                                    true );
+                                                                    _mainpanel.getCurrentTreePanel().getHeight() );
         String file_written_to = "";
         boolean error = false;
         try {
@@ -2142,8 +2149,7 @@ public final class MainFrameApplication extends MainFrame {
         }
         if ( !getOptions().isPrintUsingActualSize() ) {
             getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,
-                                                             getOptions().getPrintSizeY() - 140,
-                                                             true );
+                                                             getOptions().getPrintSizeY() - 140 );
             getCurrentTreePanel().resetPreferredSize();
             getCurrentTreePanel().repaint();
         }
@@ -2171,9 +2177,8 @@ public final class MainFrameApplication extends MainFrame {
 
     private void printPhylogenyToPdf( final String file_name ) {
         if ( !getOptions().isPrintUsingActualSize() ) {
-            getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),
-                                                             getOptions().getPrintSizeY(),
-                                                             true );
+            getCurrentTreePanel()
+            .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );
             getCurrentTreePanel().resetPreferredSize();
             getCurrentTreePanel().repaint();
         }