From bdf2d2a11d720d6457f52866af7ff909afe98db4 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 22 Aug 2014 22:39:20 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 10 ---- .../org/forester/archaeopteryx/Configuration.java | 23 ++++---- .../org/forester/archaeopteryx/ControlPanel.java | 61 +++++++++++++++----- .../src/org/forester/archaeopteryx/MainFrame.java | 8 --- .../forester/archaeopteryx/MainFrameApplet.java | 3 - .../archaeopteryx/MainFrameApplication.java | 3 - .../src/org/forester/archaeopteryx/Options.java | 11 ---- .../src/org/forester/archaeopteryx/TreePanel.java | 15 ++--- .../data/RenderableDomainArchitecture.java | 15 ++--- .../archaeopteryx/tools/PhylogeneticInferrer.java | 1 - .../forester/phylogeny/data/PhylogenyDataUtil.java | 2 - 11 files changed, 66 insertions(+), 86 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index fb37c4f..7f22501 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -117,7 +117,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JCheckBoxMenuItem _inverse_search_result_cbmi; private JCheckBoxMenuItem _show_overview_cbmi; private JMenuItem _choose_minimal_confidence_mi; - private JCheckBoxMenuItem _show_branch_length_values_cbmi; private JMenuItem _collapse_species_specific_subtrees; private JMenuItem _overview_placment_mi; private ButtonGroup _radio_group_1; @@ -263,9 +262,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _show_branch_length_values_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _show_confidence_stddev_cbmi ) { updateOptions( getOptions() ); } @@ -763,8 +759,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); @@ -829,7 +823,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); @@ -1344,9 +1337,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) && _show_confidence_stddev_cbmi.isSelected() ); - if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { - options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); - } options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 5df336a..e642d8e 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -101,7 +101,8 @@ public final class Configuration { { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, - { "Properties", "display", "no" }, { "Gene Name", "display", "yes" } }; + { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -129,6 +130,8 @@ public final class Configuration { final static int show_taxonomy_images = 24; final static int show_properties = 25; final static int show_gene_names = 26; + final static int show_mol_seqs = 27; + final static int write_branch_length_values = 28; static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; @@ -205,7 +208,6 @@ public final class Configuration { private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; - private boolean _show_branch_length_values = false; private boolean _show_default_node_shapes_external = false; private boolean _show_default_node_shapes_internal = false; private boolean _show_domain_labels = true; @@ -538,10 +540,6 @@ public final class Configuration { _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } - public void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; - } - public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { _show_default_node_shapes_external = show_default_node_shapes_external; } @@ -765,10 +763,6 @@ public final class Configuration { return _nh_parsing_replace_underscores; } - boolean isShowBranchLengthValues() { - return _show_branch_length_values; - } - boolean isShowOverview() { return _show_overview; } @@ -1199,9 +1193,6 @@ public final class Configuration { else if ( key.equals( "show_overview" ) ) { setShowOverview( parseBoolean( ( String ) st.nextElement() ) ); } - else if ( key.equals( "show_branch_length_values" ) ) { - setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) ); - } else if ( key.equals( "background_gradient" ) ) { setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1544,6 +1535,9 @@ public final class Configuration { else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; } + else if ( key.equals( "write_branch_length_values" ) ) { + key_index = Configuration.write_branch_length_values; + } else if ( key.equals( "write_events" ) ) { key_index = Configuration.write_events; } @@ -1562,6 +1556,9 @@ public final class Configuration { else if ( key.equals( "show_domain_architectures" ) ) { key_index = Configuration.show_domain_architectures; } + else if ( key.equals( "show_msa" ) ) { + key_index = Configuration.show_mol_seqs; + } else if ( key.equals( "show_annotations" ) ) { key_index = Configuration.show_annotation; } diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index bafb79d..789edcc 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -142,6 +142,8 @@ final class ControlPanel extends JPanel implements ActionListener { // Indices for the click-to options in the combo box private int _show_data_item; private JCheckBox _show_domain_architectures; + private JCheckBox _show_mol_seqs; + private JCheckBox _write_branch_length_values; private JCheckBox _show_events; private JCheckBox _show_gene_names; private JCheckBox _show_node_names; @@ -632,11 +634,21 @@ final class ControlPanel extends JPanel implements ActionListener { addJCheckBox( _width_branches, ch_panel ); add( ch_panel ); break; + case Configuration.write_branch_length_values: + _write_branch_length_values = new JCheckBox( title ); + addJCheckBox( _write_branch_length_values, ch_panel ); + add( ch_panel ); + break; case Configuration.show_domain_architectures: _show_domain_architectures = new JCheckBox( title ); addJCheckBox( _show_domain_architectures, ch_panel ); add( ch_panel ); break; + case Configuration.show_mol_seqs: + _show_mol_seqs = new JCheckBox( title ); + addJCheckBox( _show_mol_seqs, ch_panel ); + add( ch_panel ); + break; case Configuration.show_seq_names: _show_seq_names = new JCheckBox( title ); addJCheckBox( _show_seq_names, ch_panel ); @@ -873,10 +885,18 @@ final class ControlPanel extends JPanel implements ActionListener { return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() ); } + boolean isWriteBranchLengthValues() { + return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() ); + } + boolean isShowDomainArchitectures() { return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() ); } + public boolean isShowMolSequences() { + return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() ); + } + boolean isShowGeneNames() { return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() ); } @@ -1087,6 +1107,16 @@ final class ControlPanel extends JPanel implements ActionListener { _show_domain_architectures.setSelected( state ); } break; + case Configuration.write_branch_length_values: + if ( _write_branch_length_values != null ) { + _write_branch_length_values.setSelected( state ); + } + break; + case Configuration.show_mol_seqs: + if ( _show_mol_seqs != null ) { + _show_mol_seqs.setSelected( state ); + } + break; case Configuration.show_seq_names: if ( _show_seq_names != null ) { _show_seq_names.setSelected( state ); @@ -2218,6 +2248,18 @@ final class ControlPanel extends JPanel implements ActionListener { addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) ); setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) ); } + if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) { + addCheckbox( Configuration.write_confidence_values, + _configuration.getDisplayTitle( Configuration.write_confidence_values ) ); + setCheckbox( Configuration.write_confidence_values, + _configuration.doCheckOption( Configuration.write_confidence_values ) ); + } + if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) { + addCheckbox( Configuration.write_branch_length_values, + _configuration.getDisplayTitle( Configuration.write_branch_length_values ) ); + setCheckbox( Configuration.write_branch_length_values, + _configuration.doCheckOption( Configuration.write_branch_length_values ) ); + } if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) { addCheckbox( Configuration.show_binary_characters, _configuration.getDisplayTitle( Configuration.show_binary_characters ) ); @@ -2236,11 +2278,9 @@ final class ControlPanel extends JPanel implements ActionListener { setCheckbox( Configuration.show_domain_architectures, _configuration.doCheckOption( Configuration.show_domain_architectures ) ); } - if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) { - addCheckbox( Configuration.write_confidence_values, - _configuration.getDisplayTitle( Configuration.write_confidence_values ) ); - setCheckbox( Configuration.write_confidence_values, - _configuration.doCheckOption( Configuration.write_confidence_values ) ); + if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) { + addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) ); + setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) ); } if ( _configuration.doDisplayOption( Configuration.write_events ) ) { addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) ); @@ -2370,17 +2410,11 @@ final class ControlPanel extends JPanel implements ActionListener { if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) { getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( true ); } - if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) { - getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( false ); - } } else { if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) { getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( false ); } - if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) { - getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( true ); - } } } } @@ -2455,9 +2489,4 @@ final class ControlPanel extends JPanel implements ActionListener { CHANGE_NODE_FONT, COLOR_NODE_FONT; } - - public boolean isShowMolSequences() { - // TODO Auto-generated method stub - return true; - } } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 1cf79b0..fb23501 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -98,7 +98,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Branch Length Values"; static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; static final String DISPLAY_SCALE_LABEL = "Scale"; static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; @@ -184,7 +183,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - JCheckBoxMenuItem _show_branch_length_values_cbmi; JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; @@ -460,9 +458,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _show_branch_length_values_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _color_by_taxonomic_group_cbmi ) { updateOptions( getOptions() ); } @@ -1337,9 +1332,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) && _show_confidence_stddev_cbmi.isSelected() ); - if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { - options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); - } if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 9713b4f..b804681 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -212,8 +212,6 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); @@ -275,7 +273,6 @@ public final class MainFrameApplet extends MainFrame { getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 30721ca..40d9581 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -893,8 +893,6 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); @@ -1001,7 +999,6 @@ public final class MainFrameApplication extends MainFrame { getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 2bf8471..727838a 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -77,7 +77,6 @@ final public class Options { private double _scale_bar_length; private boolean _search_case_sensitive; private boolean _show_annotation_ref_source; - private boolean _show_branch_length_values; private boolean _show_confidence_stddev; private boolean _show_default_node_shapes_external; private boolean _show_default_node_shapes_internal; @@ -272,10 +271,6 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; - } - boolean isShowConfidenceStddev() { return _show_confidence_stddev; } @@ -414,10 +409,6 @@ final public class Options { _search_case_sensitive = search_case_sensitive; } - final void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; - } - void setShowConfidenceStddev( final boolean show_confidence_stddev ) { _show_confidence_stddev = show_confidence_stddev; } @@ -446,7 +437,6 @@ final public class Options { _default_node_shape = NodeShape.CIRCLE; _default_node_fill = NodeFill.GRADIENT; _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - _show_branch_length_values = false; _internal_number_are_confidence_for_nh_parsing = false; _show_scale = false; _antialias_screen = true; @@ -507,7 +497,6 @@ final public class Options { if ( configuration != null ) { instance.setAntialiasScreen( configuration.isAntialiasScreen() ); instance.setShowScale( configuration.isShowScale() ); - instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() ); instance.setShowOverview( configuration.isShowOverview() ); instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() ); instance.setCladogramType( configuration.getCladogramType() ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 3f6496b..e96c197 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -4312,7 +4312,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) { return 0; } - if ( getOptions().isShowBranchLengthValues() + if ( getControlPanel().isWriteBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { @@ -4883,14 +4883,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; rs.setRenderingHeight( h > 1 ? h : 2 ); if ( getControlPanel().isDrawPhylogram() ) { - - rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), - node.getYcoord() - ( h / 2 ), - g, - this, - to_pdf ); - - + rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), + node.getYcoord() - ( h / 2 ), + g, + this, + to_pdf ); } else { rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java index d70eb12..1fe52bc 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java @@ -43,7 +43,6 @@ import org.forester.archaeopteryx.Constants; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.data.DomainArchitecture; import org.forester.phylogeny.data.PhylogenyData; -import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.ProteinDomain; import org.forester.util.ForesterUtil; @@ -56,8 +55,8 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple private final DomainArchitecture _domain_structure; private int _e_value_threshold_exp = E_VALUE_THRESHOLD_EXP_DEFAULT; private final Rectangle2D _rectangle = new Rectangle2D.Float(); - private float _rendering_factor_width = 1; - private float _rendering_height = 0; + private float _rendering_factor_width = 1; + private float _rendering_height = 0; public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) { _domain_structure = domain_structure; @@ -201,13 +200,9 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple else { g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF ); } - g.drawString( d.getName(), - xa, - y1 - + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent() - + _rendering_height ); - - + g.drawString( d.getName(), xa, y1 + + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent() + + _rendering_height ); } drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf ); } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index 57d9c3c..8b89646 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -146,7 +146,6 @@ public class PhylogeneticInferrer extends RunnableProcess { final Phylogeny phy = nj.execute( m ); PhylogenyMethods.addMolecularSeqsToTree( phy, msa ); PhylogenyMethods.extractFastaInformation( phy ); - return phy; } diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java index 5718086..76d60b7 100644 --- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java +++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java @@ -371,8 +371,6 @@ public final class PhylogenyDataUtil { org.forester.util.ForesterUtil.roundToInt( y2 ) ); } - - public static String replaceIllegalXmlCharacters( final String value ) { String v = value.replaceAll( "&", "&" ); v = v.replaceAll( "<", "<" ); -- 1.7.10.2