From: cmzmasek@gmail.com Date: Wed, 24 Dec 2014 23:57:58 +0000 (+0000) Subject: Changed list to set in search0 and 1. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a32f4076b5b309b4dcc0852d6283a2bd18785f28;p=jalview.git Changed list to set in search0 and 1. --- diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 1eb96f3..1a517c6 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9903 beta"; - final static String PRG_DATE = "141223"; + final static String PRG_DATE = "141224"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 7cac388..3bd8738 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -44,6 +44,7 @@ import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; +import java.util.Set; import javax.swing.BorderFactory; import javax.swing.DefaultListCellRenderer; @@ -571,7 +572,7 @@ final class ControlPanel extends JPanel implements ActionListener { case Configuration.color_according_to_annotation: _color_according_to_annotation = new JCheckBox( title ); _color_according_to_annotation - .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" ); + .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" ); addJCheckBox( _color_according_to_annotation, ch_panel ); add( ch_panel ); break; @@ -628,7 +629,7 @@ final class ControlPanel extends JPanel implements ActionListener { case Configuration.use_style: _use_visual_styles_cb = new JCheckBox( title ); getUseVisualStylesCb() - .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" ); + .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" ); addJCheckBox( getUseVisualStylesCb(), ch_panel ); add( ch_panel ); break; @@ -1161,13 +1162,13 @@ final class ControlPanel extends JPanel implements ActionListener { getNodeDescPopupCb().setSelected( state ); } break; - /* GUILHEM_BEG */ + /* GUILHEM_BEG */ case Configuration.show_relation_confidence: if ( _seq_relation_confidence_switch != null ) { _seq_relation_confidence_switch.setSelected( state ); } break; - /* GUILHEM_END */ + /* GUILHEM_END */ default: throw new AssertionError( "unknown checkbox: " + which ); } @@ -1577,7 +1578,7 @@ final class ControlPanel extends JPanel implements ActionListener { } else { getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel() - .getPhylogenyGraphicsType() ); + .getPhylogenyGraphicsType() ); } getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton(); getMainPanel().getControlPanel().search0(); @@ -1635,7 +1636,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); } else { final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue(); @@ -1660,7 +1661,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); treepanel.resetPreferredSize(); treepanel.updateOvSizes(); } @@ -1685,7 +1686,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); } else { final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue(); @@ -1714,7 +1715,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); treepanel.resetPreferredSize(); treepanel.updateOvSizes(); } @@ -1759,7 +1760,7 @@ final class ControlPanel extends JPanel implements ActionListener { cellHasFocus ); if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) { ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation - .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) ); + .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) ); } return component; } @@ -1803,7 +1804,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton0().setEnabled( true ); getSearchResetButton0().setVisible( true ); String[] queries = null; - List nodes = null; + Set nodes = null; if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } @@ -1812,7 +1813,7 @@ final class ControlPanel extends JPanel implements ActionListener { queries[ 0 ] = query_str.trim(); } if ( ( queries != null ) && ( queries.length > 0 ) ) { - nodes = new ArrayList(); + nodes = new HashSet(); for( String query : queries ) { if ( ForesterUtil.isEmpty( query ) ) { continue; @@ -1827,7 +1828,7 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) - : 0 ) ); + : 0 ) ); } else { nodes.addAll( PhylogenyMethods.searchData( query, @@ -1837,13 +1838,14 @@ final class ControlPanel extends JPanel implements ActionListener { getOptions().isSearchWithRegex(), isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp - .getDomainStructureEvalueThresholdExp() ) : 0 ) ); + .getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { final List all = PhylogenyMethods.obtainAllNodesAsList( tree ); all.removeAll( nodes ); - nodes = all; + nodes = new HashSet(); + nodes.addAll( all ); } } if ( ( nodes != null ) && ( nodes.size() > 0 ) ) { @@ -1864,7 +1866,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton1().setEnabled( true ); getSearchResetButton1().setVisible( true ); String[] queries = null; - List nodes = null; + Set nodes = null; if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } @@ -1873,7 +1875,7 @@ final class ControlPanel extends JPanel implements ActionListener { queries[ 0 ] = query_str.trim(); } if ( ( queries != null ) && ( queries.length > 0 ) ) { - nodes = new ArrayList(); + nodes = new HashSet(); for( String query : queries ) { if ( ForesterUtil.isEmpty( query ) ) { continue; @@ -1888,7 +1890,7 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) - : 0 ) ); + : 0 ) ); } else { nodes.addAll( PhylogenyMethods.searchData( query, @@ -1898,13 +1900,14 @@ final class ControlPanel extends JPanel implements ActionListener { getOptions().isSearchWithRegex(), isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp - .getDomainStructureEvalueThresholdExp() ) : 0 ) ); + .getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { final List all = PhylogenyMethods.obtainAllNodesAsList( tree ); all.removeAll( nodes ); - nodes = all; + nodes = new HashSet(); + nodes.addAll( all ); } } if ( ( nodes != null ) && ( nodes.size() > 0 ) ) { @@ -2049,7 +2052,7 @@ 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 { addClickToOption( Configuration.get_ext_desc_data,