typed search is being added

[jalview.git] / forester / java / src / org / forester / archaeopteryx / ControlPanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 8b2b585..98d5b54 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -81,6 +81,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                                                                                     Font.PLAIN,
                                                                                     9 );
     private static final String               RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
+    private static final String               SEARCH_TIP_TEXT           = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
     private static final long                 serialVersionUID          = -8463483932821545633L;
     private NodeClickAction                   _action_when_node_clicked;
     private int                               _add_new_node_item;
@@ -125,7 +126,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private int                               _paste_subtree_item;
     private int                               _reroot_cb_item;
     private JButton                           _return_to_super_tree;
-    // Search 
+    // Search
     private JLabel                            _search_found_label_0;
     private JLabel                            _search_found_label_1;
     private JButton                           _search_reset_button_0;
@@ -223,11 +224,12 @@ final class ControlPanel extends JPanel implements ActionListener {
                 }
                 displayedPhylogenyMightHaveChanged( true );
             }
-            else if ( e.getSource() == _show_domain_architectures ) {
+            else if ( e.getSource() == _show_domain_architectures  ) {
                 search0();
                 search1();
                 displayedPhylogenyMightHaveChanged( true );
             }
+            
             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
                 if ( e.getSource() == getDisplayAsPhylogramCb() ) {
                     setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
@@ -289,11 +291,15 @@ final class ControlPanel extends JPanel implements ActionListener {
                     displayedPhylogenyMightHaveChanged( true );
                 }
                 else if ( e.getSource() == _decr_domain_structure_evalue_thr ) {
-                    _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold();
+                    _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThresholdExp();
+                    search0();
+                    search1();
                     displayedPhylogenyMightHaveChanged( true );
                 }
                 else if ( e.getSource() == _incr_domain_structure_evalue_thr ) {
-                    _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold();
+                    _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThresholdExp();
+                    search0();
+                    search1();
                     displayedPhylogenyMightHaveChanged( true );
                 }
                 else if ( e.getSource() == _search_tf_0 ) {
@@ -765,7 +771,7 @@ final class ControlPanel extends JPanel implements ActionListener {
 
     /**
      * Indicates what action should be execute when a node is clicked
-     * 
+     *
      * @return the click-on action
      */
     NodeClickAction getActionWhenNodeClicked() {
@@ -1301,10 +1307,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         _sequence_colors = sequence_colors;
     }
 
-    /* GUILHEM_END */
-    /*
-     * Set up the controls from the config settings. 11/26/05
-     */
     void setupControls() {
         // The tree display options:
         setupDisplayCheckboxes();
@@ -1361,14 +1363,13 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     void setupSearchTools0() {
-        final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
         final JLabel search_label = new JLabel( "Search (A):" );
         search_label.setFont( ControlPanel.jcb_bold_font );
         if ( !getConfiguration().isUseNativeUI() ) {
             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
         }
         add( search_label );
-        search_label.setToolTipText( tip );
+        search_label.setToolTipText( SEARCH_TIP_TEXT );
         _search_found_label_0 = new JLabel();
         getSearchFoundCountsLabel0().setVisible( false );
         _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
@@ -1376,7 +1377,7 @@ final class ControlPanel extends JPanel implements ActionListener {
             _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
         }
         _search_tf_0 = new JTextField( 3 );
-        _search_tf_0.setToolTipText( tip );
+        _search_tf_0.setToolTipText( SEARCH_TIP_TEXT );
         _search_tf_0.setEditable( true );
         if ( !getConfiguration().isUseNativeUI() ) {
             _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
@@ -1422,14 +1423,13 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     void setupSearchTools1() {
-        final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
         final JLabel search_label = new JLabel( "Search (B):" );
         search_label.setFont( ControlPanel.jcb_bold_font );
         if ( !getConfiguration().isUseNativeUI() ) {
             search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
         }
         add( search_label );
-        search_label.setToolTipText( tip );
+        search_label.setToolTipText( SEARCH_TIP_TEXT );
         _search_found_label_1 = new JLabel();
         getSearchFoundCountsLabel1().setVisible( false );
         _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
@@ -1437,7 +1437,7 @@ final class ControlPanel extends JPanel implements ActionListener {
             _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
         }
         _search_tf_1 = new JTextField( 3 );
-        _search_tf_1.setToolTipText( tip );
+        _search_tf_1.setToolTipText( SEARCH_TIP_TEXT );
         _search_tf_1.setEditable( true );
         if ( !getConfiguration().isUseNativeUI() ) {
             _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
@@ -1511,16 +1511,14 @@ final class ControlPanel extends JPanel implements ActionListener {
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                                    _mainpanel.getSizeOfViewport().height,
-                                                                    true );
+                                                                    _mainpanel.getSizeOfViewport().height );
         _mainpanel.getCurrentTreePanel().resetPreferredSize();
         _mainpanel.adjustJScrollPane();
         _mainpanel.getCurrentTreePanel().repaint();
         _mainpanel.getCurrentTreePanel().validate();
         _mainpanel.validate();
         _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                                    _mainpanel.getSizeOfViewport().height,
-                                                                    true );
+                                                                    _mainpanel.getSizeOfViewport().height );
         _mainpanel.getCurrentTreePanel().resetPreferredSize();
         _mainpanel.adjustJScrollPane();
         _mainpanel.getCurrentTreePanel().repaint();
@@ -1532,8 +1530,7 @@ final class ControlPanel extends JPanel implements ActionListener {
             if ( tree_panel != null ) {
                 tree_panel.validate();
                 tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
-                                                      _mainpanel.getSizeOfViewport().height,
-                                                      true );
+                                                      _mainpanel.getSizeOfViewport().height );
                 tree_panel.resetPreferredSize();
                 tree_panel.repaint();
             }
@@ -1620,7 +1617,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     void updateDomainStructureEvaluethresholdDisplay() {
         if ( _domain_structure_evalue_thr_tf != null ) {
             _domain_structure_evalue_thr_tf.setText( "10^"
-                    + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
+                    + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
         }
     }
 
@@ -1808,7 +1805,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         getSearchResetButton0().setVisible( true );
         String[] queries = null;
         List<PhylogenyNode> nodes = null;
-        if ( query_str.indexOf( ',' ) >= 0 ) {
+        if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
             queries = query_str.split( ",+" );
         }
         else {
@@ -1822,7 +1819,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                     continue;
                 }
                 query = query.trim();
-                if ( query.indexOf( '+' ) >= 0 ) {
+                if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
                                                                          tree,
                                                                          getOptions().isSearchCaseSensitive(),
@@ -1830,11 +1827,16 @@ final class ControlPanel extends JPanel implements ActionListener {
                                                                          isShowDomainArchitectures() ) );
                 }
                 else {
+                    final TreePanel tp = getMainPanel().getCurrentTreePanel();
+                   
+                    
                     nodes.addAll( PhylogenyMethods.searchData( query,
                                                                tree,
                                                                getOptions().isSearchCaseSensitive(),
                                                                !getOptions().isMatchWholeTermsOnly(),
-                                                               isShowDomainArchitectures() ) );
+                                                               getOptions().isSearchWithRegex(),
+                                                               isShowDomainArchitectures(),
+                                                               tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 )  );
                 }
             }
             if ( getOptions().isInverseSearchResult() ) {
@@ -1862,7 +1864,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         getSearchResetButton1().setVisible( true );
         String[] queries = null;
         List<PhylogenyNode> nodes = null;
-        if ( query_str.indexOf( ',' ) >= 0 ) {
+        if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
             queries = query_str.split( ",+" );
         }
         else {
@@ -1876,7 +1878,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                     continue;
                 }
                 query = query.trim();
-                if ( query.indexOf( '+' ) >= 0 ) {
+                if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
                     nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
                                                                          tree,
                                                                          getOptions().isSearchCaseSensitive(),
@@ -1884,11 +1886,14 @@ final class ControlPanel extends JPanel implements ActionListener {
                                                                          isShowDomainArchitectures() ) );
                 }
                 else {
+                    final TreePanel tp = getMainPanel().getCurrentTreePanel();
                     nodes.addAll( PhylogenyMethods.searchData( query,
                                                                tree,
                                                                getOptions().isSearchCaseSensitive(),
                                                                !getOptions().isMatchWholeTermsOnly(),
-                                                               isShowDomainArchitectures() ) );
+                                                               getOptions().isSearchWithRegex(),
+                                                               isShowDomainArchitectures(),
+                                                               tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 )  );
                 }
             }
             if ( getOptions().isInverseSearchResult() ) {
@@ -2039,51 +2044,14 @@ final class ControlPanel extends JPanel implements ActionListener {
             _get_ext_desc_data = cb_index;
             if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
                 addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
-                        .getLabelForGetExtDescendentsData() );
+                                  .getLabelForGetExtDescendentsData() );
             }
             else {
-                String s = ";";
-                switch ( getConfiguration().getExtDescNodeDataToReturn() ) {
-                    case NODE_NAME:
-                        s = "Node Names";
-                        break;
-                    case SEQUENCE_ACC:
-                        s = "Sequence Accessors";
-                        break;
-                    case SEQUENCE_MOL_SEQ:
-                        s = "Molecular Sequence";
-                        break;
-                    case SEQUENCE_MOL_SEQ_FASTA:
-                        s = "Molecular Sequence (Fasta)";
-                        break;
-                    case SEQUENCE_NAME:
-                        s = "Sequence Names";
-                        break;
-                    case GENE_NAME:
-                        s = "Gene Names";
-                        break;
-                    case SEQUENCE_SYMBOL:
-                        s = "Sequence Symbols";
-                        break;
-                    case TAXONOMY_CODE:
-                        s = "Taxonomy Codes";
-                        break;
-                    case TAXONOMY_COMM0N_NAME:
-                        s = "Taxonomy Common Names";
-                        break;
-                    case TAXONOMY_SCIENTIFIC_NAME:
-                        s = "Scientific Names";
-                        break;
-                    case UNKNOWN:
-                        s = "User Selected Data";
-                        break;
-                    default:
-                        throw new IllegalStateException( "dont know how to deal with "
-                                + getConfiguration().getExtDescNodeDataToReturn() );
-                }
-                final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
-                addClickToOption( Configuration.get_ext_desc_data, label );
+               
+                addClickToOption( Configuration.get_ext_desc_data,
+                                  getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) );
             }
+           
             if ( default_option == Configuration.get_ext_desc_data ) {
                 selected_index = cb_index;
             }