// 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;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
-import java.awt.Polygon;
import java.awt.Rectangle;
import java.awt.RenderingHints;
+import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.geom.CubicCurve2D;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Line2D;
+import java.awt.geom.Path2D;
import java.awt.geom.QuadCurve2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import org.forester.archaeopteryx.tools.Blast;
import org.forester.archaeopteryx.tools.ImageLoader;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.writers.SequenceWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
+import org.forester.util.TaxonomyUtil;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
- private static final float PI = ( float ) ( Math.PI );
- private static final double TWO_PI = 2 * Math.PI;
- private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
- private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
- private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
- private static final short OV_BORDER = 10;
- final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
- final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
- final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
- final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
- final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
- private final static long serialVersionUID = -978349745916505029L;
- private final static int EURO_D = 10;
- private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
- private final static int MIN_ROOT_LENGTH = 3;
- private final static int MAX_SUBTREES = 100;
- private final static int MAX_NODE_FRAMES = 10;
- private final static int MOVE = 20;
- private final static NumberFormat FORMATTER_CONFIDENCE;
- private final static NumberFormat FORMATTER_BRANCH_LENGTH;
- private final static int WIGGLE = 2;
- private final static int LIMIT_FOR_HQ_RENDERING = 1000;
- private final static int CONFIDENCE_LEFT_MARGIN = 4;
- private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_DEFAULT );
- private File _treefile = null;
- private Configuration _configuration = null;
- private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
- private int _node_frame_index = 0;
- private Phylogeny _phylogeny = null;
- private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
- private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
- private int _subtree_index = 0;
- private MainPanel _main_panel = null;
- private Set<Integer> _found_nodes = null;
- private PhylogenyNode _highlight_node = null;
- private JPopupMenu _node_popup_menu = null;
- private JMenuItem _node_popup_menu_items[] = null;
- private int _longest_ext_node_info = 0;
- private float _x_correction_factor = 0.0f;
- private float _ov_x_correction_factor = 0.0f;
- private float _x_distance = 0.0f;
- private float _y_distance = 0.0f;
- private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
- private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
- private float _last_drag_point_x = 0;
- private float _last_drag_point_y = 0;
- private ControlPanel _control_panel = null;
- private int _external_node_index = 0;
- private final Polygon _polygon = new Polygon();
- private final StringBuilder _sb = new StringBuilder();
- private JColorChooser _color_chooser = null;
- private double _scale_distance = 0.0;
- private String _scale_label = null;
- private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
- private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
- private final Line2D _line = new Line2D.Float();
- private final Ellipse2D _ellipse = new Ellipse2D.Float();
- private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private Options _options = null;
- private float _ov_max_width = 0;
- private float _ov_max_height = 0;
- private int _ov_x_position = 0;
- private int _ov_y_position = 0;
- private int _ov_y_start = 0;
- private float _ov_y_distance = 0;
- private float _ov_x_distance = 0;
- private boolean _ov_on = false;
- private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
- private float _urt_factor = 1;
- private float _urt_factor_ov = 1;
- private final boolean _phy_has_branch_lengths;
- private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
- private boolean _in_ov_rect = false;
- private boolean _in_ov = false;
- private final Rectangle _ov_virtual_rectangle = new Rectangle();
- final private static double _180_OVER_PI = 180.0 / Math.PI;
- private static final float ROUNDED_D = 8;
- private int _circ_max_depth;
- private PhylogenyNode _root;
- final private Arc2D _arc = new Arc2D.Double();
- final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
- final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
- final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
- HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
- private AffineTransform _at;
- private double _max_distance_to_root = -1;
- private int _dynamic_hiding_factor = 0;
- private boolean _edited = false;
- private Popup _node_desc_popup;
- private JTextArea _rollover_popup;
- private final StringBuffer _popup_buffer = new StringBuffer();
- final private static Font POPUP_FONT = new Font( Configuration
- .getDefaultFontFamilyName(),
- Font.PLAIN,
- 12 );
- private Sequence _query_sequence = null;
- private final FontRenderContext _frc = new FontRenderContext( null,
- false,
- false );
+ final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
+ final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
+ final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
+ final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
+ final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
+ final private static double _180_OVER_PI = 180.0 / Math.PI;
+ private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
+ private final static int CONFIDENCE_LEFT_MARGIN = 4;
+ private final static int EURO_D = 10;
+ private final static NumberFormat FORMATTER_BRANCH_LENGTH;
+ private final static NumberFormat FORMATTER_CONFIDENCE;
+ private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
+ private final static int LIMIT_FOR_HQ_RENDERING = 2000;
+ private final static int MAX_NODE_FRAMES = 10;
+ private final static int MAX_SUBTREES = 100;
+ private final static int MIN_ROOT_LENGTH = 3;
+ private final static int MOVE = 20;
+ private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
+ private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
+ private static final short OV_BORDER = 10;
+ private static final float PI = ( float ) ( Math.PI );
+ final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 12 );
+ private static final float ROUNDED_D = 8;
+ private final static long serialVersionUID = -978349745916505029L;
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final double TWO_PI = 2 * Math.PI;
+ private final static int WIGGLE = 2;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
+ HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
+ final private Arc2D _arc = new Arc2D.Double();
+ private AffineTransform _at;
+ private int _circ_max_depth;
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ private JColorChooser _color_chooser = null;
+ private Configuration _configuration = null;
+ private ControlPanel _control_panel = null;
+ private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
+ private Set<Long> _current_external_nodes = null;
+ private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
+ private int _current_external_nodes_data_buffer_change_counter = 0;
+ private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
+ private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private int _dynamic_hiding_factor = 0;
+ private boolean _edited = false;
+ private final Ellipse2D _ellipse = new Ellipse2D.Float();
+ private int _external_node_index = 0;
+ private Set<Long> _found_nodes_0 = null;
+ private Set<Long> _found_nodes_1 = null;
+ private final FontRenderContext _frc = new FontRenderContext( null,
+ false,
+ false );
+ private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private PhylogenyNode _highlight_node = null;
+ private boolean _in_ov = false;
+ private boolean _in_ov_rect = false;
+ private float _last_drag_point_x = 0;
+ private float _last_drag_point_y = 0;
+ private final Line2D _line = new Line2D.Float();
+ private int _longest_ext_node_info = 0;
+ private MainPanel _main_panel = null;
+ private double _max_distance_to_root = -1;
+ private Popup _node_desc_popup;
+ private int _node_frame_index = 0;
+ private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
+ private JPopupMenu _node_popup_menu = null;
+ private JMenuItem _node_popup_menu_items[] = null;
+ private PhylogenyNode[] _nodes_in_preorder = null;
+ private Options _options = null;
+ private float _ov_max_height = 0;
+ private float _ov_max_width = 0;
+ private boolean _ov_on = false;
+ private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
+ private final Rectangle _ov_virtual_rectangle = new Rectangle();
+ private float _ov_x_correction_factor = 0.0f;
+ private float _ov_x_distance = 0;
+ private int _ov_x_position = 0;
+ private float _ov_y_distance = 0;
+ private int _ov_y_position = 0;
+ private int _ov_y_start = 0;
+ private final boolean _phy_has_branch_lengths;
+ private Phylogeny _phylogeny = null;
+ private final Path2D.Float _polygon = new Path2D.Float();
+ private final StringBuffer _popup_buffer = new StringBuffer();
+ private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
+ private Sequence _query_sequence = null;
+ private final Rectangle2D _rectangle = new Rectangle2D.Float();
+ private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_DEFAULT );
+ private JTextArea _rollover_popup;
+ private PhylogenyNode _root;
+ private final StringBuilder _sb = new StringBuilder();
+ private double _scale_distance = 0.0;
+ private String _scale_label = null;
// expression values menu:
- private DescriptiveStatistics _statistics_for_vector_data;
- private PhylogenyNode[] _nodes_in_preorder = null;
- private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
- private int _current_external_nodes_data_buffer_change_counter = 0;
- private Set<Integer> _current_external_nodes = null;
+ private DescriptiveStatistics _statistics_for_vector_data;
+ private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
+ private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
+ private int _subtree_index = 0;
+ private File _treefile = null;
+ private float _urt_factor = 1;
+ private float _urt_factor_ov = 1;
+ final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
+ private float _x_correction_factor = 0.0f;
+ private float _x_distance = 0.0f;
+ private float _y_distance = 0.0f;
// private Image offscreenImage;
// private Graphics offscreenGraphics;
// private Dimension offscreenDimension;
requestFocusInWindow();
}
- public void checkForVectorProperties( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNodeData().getProperties() != null ) {
- final PropertiesMap pm = node.getNodeData().getProperties();
- final double[] vector = new double[ pm.getProperties().size() ];
- int counter = 0;
- for( final String ref : pm.getProperties().keySet() ) {
- if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
- final Property p = pm.getProperty( ref );
- final String value_str = p.getValue();
- final String index_str = ref
- .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
- double d = -100;
- try {
- d = Double.parseDouble( value_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
- return;
- }
- int i = -1;
- try {
- i = Integer.parseInt( index_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not parse \"" + index_str
- + "\" into index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( i < 0 ) {
- JOptionPane.showMessageDialog( this,
- "Attempt to use negative index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- vector[ i ] = d;
- ++counter;
- stats.addValue( d );
- }
- }
- final List<Double> vector_l = new ArrayList<Double>( counter );
- for( int i = 0; i < counter; ++i ) {
- vector_l.add( vector[ i ] );
- }
- node.getNodeData().setVector( vector_l );
- }
- }
- if ( stats.getN() > 0 ) {
- _statistics_for_vector_data = stats;
- }
- }
-
public synchronized Hashtable<String, BufferedImage> getImageMap() {
return getMainPanel().getImageMap();
}
getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else {
- getTreeFontSet().decreaseFontSize();
+ getTreeFontSet().decreaseFontSize( 1, false );
getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
}
}
}
- public final void setArrowCursor() {
- setCursor( ARROW_CURSOR );
- repaint();
- }
-
public final void setEdited( final boolean edited ) {
_edited = edited;
}
}
/**
+ * Set a phylogeny tree.
+ *
+ * @param t
+ * an instance of a Phylogeny
+ */
+ public final void setTree( final Phylogeny t ) {
+ setNodeInPreorderToNull();
+ _phylogeny = t;
+ }
+
+ public final void setWaitCursor() {
+ setCursor( WAIT_CURSOR );
+ repaint();
+ }
+
+ @Override
+ public void update( final Graphics g ) {
+ paint( g );
+ }
+
+ final void calcMaxDepth() {
+ if ( _phylogeny != null ) {
+ _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ }
+ }
+
+ /**
* Set parameters for printing the displayed tree
*
- * @param x
- * @param y
*/
- public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
+ final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
// updateStyle(); not needed?
if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
initNodeData();
if ( recalc_longest_ext_node_info ) {
calculateLongestExtNodeInfo();
+ if ( getOptions().isAllowFontSizeChange() ) {
+ if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
+ true );
+ calculateLongestExtNodeInfo();
+ }
+ }
+ else {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
+ .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ calculateLongestExtNodeInfo();
+ }
+ }
+ }
}
int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
}
_circ_max_depth = max_depth;
setUpUrtFactor();
- }
- }
-
- /**
- * Set a phylogeny tree.
- *
- * @param t
- * an instance of a Phylogeny
- */
- public final void setTree( final Phylogeny t ) {
- setNodeInPreorderToNull();
- _phylogeny = t;
- }
-
- public final void setWaitCursor() {
- setCursor( WAIT_CURSOR );
- repaint();
- }
-
- @Override
- public void update( final Graphics g ) {
- paint( g );
- }
-
- final void calcMaxDepth() {
- if ( _phylogeny != null ) {
- _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ //
+ if ( getOptions().isAllowFontSizeChange() ) {
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ // int dynamic_hiding_factor = calcDynamicHidingFactor();
+ // if ( dynamic_hiding_factor > 1 ) {
+ // while ( dynamic_hiding_factor > 1
+ // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
+ // getTreeFontSet().decreaseFontSize( 1, true );
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
+ // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
+ // getTreeFontSet().increaseFontSize();
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ }
+ }
+ //
}
}
.getValue()
+ " " );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
}
- if ( getControlPanel().isShowGeneSymbols()
+ if ( getControlPanel().isShowSeqSymbols()
&& ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
}
+ if ( getControlPanel().isShowGeneNames()
+ && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ sum += getTreeFontSet()._fm_large
+ .stringWidth( node.getNodeData().getSequence().getGeneName() + " " );
+ }
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
- .asSimpleText()
+ sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
+ " " );
}
if ( getControlPanel().isShowDomainArchitectures()
}
final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
- String species = tax.getTaxonomyCode();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getScientificName();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getCommonName();
+ if ( getOptions().isColorByTaxonomicGroup() ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ boolean ex = false;
+ String group = null;
+ try {
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
+ }
+ catch ( final Exception e ) {
+ ex = true;
+ }
+ if ( !ex && !ForesterUtil.isEmpty( group ) ) {
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c != null ) {
+ return c;
+ }
+ }
}
- }
- if ( ForesterUtil.isEmpty( species ) ) {
return getTreeColorSet().getTaxonomyColor();
}
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
- if ( c == null ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
+ else {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ return getTreeColorSet().getTaxonomyColor();
+ }
+ Color c = null;
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
+ }
+ if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
+ }
+ if ( c == null ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+ }
+ else {
+ c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
+ getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
+ }
+ }
+ return c;
+ }
+ }
+
+ void checkForVectorProperties( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.getNodeData().getProperties() != null ) {
+ final PropertiesMap pm = node.getNodeData().getProperties();
+ final double[] vector = new double[ pm.getProperties().size() ];
+ int counter = 0;
+ for( final String ref : pm.getProperties().keySet() ) {
+ if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
+ final Property p = pm.getProperty( ref );
+ final String value_str = p.getValue();
+ final String index_str = ref
+ .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
+ double d = -100;
+ try {
+ d = Double.parseDouble( value_str );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
+ + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ int i = -1;
+ try {
+ i = Integer.parseInt( index_str );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Could not parse \"" + index_str
+ + "\" into index for vector data",
+ "Problem with Vector Data",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( i < 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Attempt to use negative index for vector data",
+ "Problem with Vector Data",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ vector[ i ] = d;
+ ++counter;
+ stats.addValue( d );
+ }
+ }
+ final List<Double> vector_l = new ArrayList<Double>( counter );
+ for( int i = 0; i < counter; ++i ) {
+ vector_l.add( vector[ i ] );
+ }
+ node.getNodeData().setVector( vector_l );
+ }
+ }
+ if ( stats.getN() > 0 ) {
+ _statistics_for_vector_data = stats;
}
- return c;
}
void clearCurrentExternalNodesDataBuffer() {
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
- AptxUtil.collapseSubtree( node, collapse );
+ TreePanelUtil.collapseSubtree( node, collapse );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
return;
}
setWaitCursor();
- AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
if ( colorizations > 0 ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
else {
msg += "colorized one subtree";
}
+ setEdited( true );
JOptionPane.showMessageDialog( this,
msg,
"Taxonomy Colorization Completed (" + rank + ")",
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
return _domain_structure_e_value_thr_exp;
}
- final Set<Integer> getFoundNodes() {
- return _found_nodes;
+ final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
}
final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
setArrowCursor();
+ setEdited( true );
repaint();
}
// Check if shift key is down
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
+ getFoundNodes0().add( node.getId() );
// Check if control key is down
}
else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
root_x + ( Math.cos( angle ) * parent_radius ),
root_y + ( Math.sin( angle ) * parent_radius ),
g );
- paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
- || isInCurrentExternalNodes( c ) );
+ paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
if ( c.isExternal() ) {
- final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
+ final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
+ || isInCurrentExternalNodes( c );
if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
&& ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
return;
root_y + ( Math.sin( angle ) * parent_radius ),
g );
if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
+ g.setColor( getColorForFoundNode( c ) );
+ drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
}
}
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
- paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
}
final void paintCircularLite( final Phylogeny phy,
g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
}
- g.setStroke( new BasicStroke( 1 ) );
+ setupStroke( g );
}
else {
g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
// Position starting Y of tree
_phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
+ ( TreePanel.MOVE / 2.0f ) );
- final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
+ final int dynamic_hiding_factor = calcDynamicHidingFactor();
if ( getControlPanel().isDynamicallyHideData() ) {
if ( dynamic_hiding_factor > 1 ) {
getControlPanel().setDynamicHidingIsOn( true );
setNodeInPreorderToNull();
resetPreferredSize();
getMainPanel().adjustJScrollPane();
+ setEdited( true );
repaint();
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
getControlPanel().showWhole();
}
final void resetNodeIdToDistToLeafMap() {
- _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
+ _nodeid_dist_to_leaf = new HashMap<Long, Short>();
}
final void resetPreferredSize() {
}
final void selectNode( final PhylogenyNode node ) {
- if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
- getFoundNodes().remove( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
- if ( getFoundNodes().size() < 1 ) {
- getControlPanel().searchReset();
+ if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
+ getFoundNodes0().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ if ( getFoundNodes0().size() < 1 ) {
+ getControlPanel().searchReset0();
}
}
else {
- getControlPanel().getSearchFoundCountsLabel().setVisible( true );
- getControlPanel().getSearchResetButton().setEnabled( true );
- getControlPanel().getSearchResetButton().setVisible( true );
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
+ getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
+ getControlPanel().getSearchResetButton0().setEnabled( true );
+ getControlPanel().getSearchResetButton0().setVisible( true );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
+ getFoundNodes0().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
}
}
+ final void setArrowCursor() {
+ setCursor( ARROW_CURSOR );
+ repaint();
+ }
+
final void setControlPanel( final ControlPanel atv_control ) {
_control_panel = atv_control;
}
_current_external_nodes_data_buffer = sb;
}
- final void setFoundNodes( final Set<Integer> found_nodes ) {
- _found_nodes = found_nodes;
+ final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
+ }
+
+ final void setFoundNodes1( final Set<Long> found_nodes ) {
+ _found_nodes_1 = found_nodes;
}
final void setInOvRect( final boolean in_ov_rect ) {
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- && !getMainPanel().getOptions().isShowDefaultNodeShapes()
- && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
- }
- else {
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
- }
- try {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
- RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
- }
- catch ( final Throwable e ) {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
- }
+ _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+ // try {
+ _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
+ // }
+ // catch ( final Throwable e ) {
+ // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
+ //}
}
else {
_rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
.isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
- .isShowGeneSymbols() ) ) {
+ if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
+ .isShowSeqSymbols() ) ) {
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
else if ( getControlPanel().isShowNodeNames() ) {
_sub_phylogenies[ _subtree_index ] = _phylogeny;
_sub_phylogenies_temp_roots[ _subtree_index ] = node;
++_subtree_index;
- _phylogeny = subTree( node, _phylogeny );
+ _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
updateSubSuperTreeButton();
}
else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
return;
}
setWaitCursor();
- AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
+ setEdited( true );
setArrowCursor();
repaint();
}
repaint();
}
- final private void addToCurrentExternalNodes( final int i ) {
+ final private void addToCurrentExternalNodes( final long i ) {
if ( _current_external_nodes == null ) {
- _current_external_nodes = new HashSet<Integer>();
+ _current_external_nodes = new HashSet<Long>();
}
_current_external_nodes.add( i );
}
&& ( getCopiedAndPastedNodes() != null )
&& !to_pdf
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
}
else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
}
if ( type == '?' ) {
- if ( SequenceIdParser.isProtein( query ) ) {
+ if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
type = 'p';
}
else {
}
}
+ private final int calcDynamicHidingFactor() {
+ return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
+ }
+
/**
* Calculate the length of the distance between the given node and its
* parent.
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
final StringBuilder sb = new StringBuilder();
for( final Annotation a : ann ) {
- sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
+ sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
}
final String ann_str = sb.toString();
if ( !ForesterUtil.isEmpty( ann_str ) ) {
c = getControlPanel().getAnnotationColors().get( ann_str );
if ( c == null ) {
- c = AptxUtil.calculateColorFromString( ann_str );
+ c = TreePanelUtil.calculateColorFromString( ann_str, false );
getControlPanel().getAnnotationColors().put( ann_str, c );
}
if ( c == null ) {
JOptionPane.WARNING_MESSAGE );
}
- final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot colorize subtree in unrooted display type",
- "Attempt to colorize subtree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ n.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
repaint();
}
final private void colorSubtree( final PhylogenyNode node ) {
- Color intitial_color = null;
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
- && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
- intitial_color = PhylogenyMethods.getBranchColorValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot colorize subtree in unrooted display type",
+ "Attempt to colorize subtree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- intitial_color = getTreeColorSet().getBranchColor();
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
- _color_chooser.setColor( intitial_color );
- _color_chooser.setPreviewPanel( new JPanel() );
final JDialog dialog = JColorChooser
- .createDialog( this,
- "Subtree colorization",
- true,
- _color_chooser,
- new SubtreeColorizationActionListener( _color_chooser, node ),
- null );
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
dialog.setVisible( true );
}
setNodeInPreorderToNull();
setCutOrCopiedTree( _phylogeny.copy( node ) );
final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
for( final PhylogenyNode n : nodes ) {
node_ids.add( n.getId() );
}
repaint();
}
- private String createAnnotationString( final SortedSet<Annotation> ann ) {
- final StringBuilder sb = new StringBuilder();
- boolean first = true;
- for( final Annotation a : ann ) {
- if ( !first ) {
- sb.append( "|" );
- }
- else {
- first = false;
- }
- sb.append( a.asSimpleText() );
- }
- final String ann_str = sb.toString();
- return ann_str;
- }
-
final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
final String tax = PhylogenyMethods.getSpecies( node );
String label = node.getName();
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
- if ( node.isRoot() ) {
+ if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
JOptionPane.showMessageDialog( this,
"Cannot delete entire tree",
"Attempt to delete entire tree",
JOptionPane.ERROR_MESSAGE );
}
- final private Set<Integer> getCopiedAndPastedNodes() {
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1();
+ }
+ else {
+ return getTreeColorSet().getFoundColor0and1();
+ }
+ }
+
+ final private Set<Long> getCopiedAndPastedNodes() {
return getMainPanel().getCopiedAndPastedNodes();
}
- final private Set<Integer> getCurrentExternalNodes() {
+ final private Set<Long> getCurrentExternalNodes() {
return _current_external_nodes;
}
return getMainPanel().getCutOrCopiedTree();
}
+ private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes0() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
+ private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes1() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
final private float getLastDragPointX() {
return _last_drag_point_x;
}
return _ov_y_start;
}
+ final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+ for( final Accession acc : cross_refs ) {
+ if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+ pdb_ids.add( acc );
+ }
+ }
+ }
+ }
+ return pdb_ids;
+ }
+
final private double getScaleDistance() {
return _scale_distance;
}
case OPEN_TAX_WEB:
openTaxWeb( node );
break;
+ case OPEN_PDB_WEB:
+ openPdbWeb( node );
+ break;
case CUT_SUBTREE:
cutSubtree( node );
break;
return Blast.isContainsQueryForBlast( node );
}
- final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
- .toLowerCase() ) ) {
- return true;
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
+ if ( a != null ) {
+ return a.getValue();
}
- return false;
+ return null;
}
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
- && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
- .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
- .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
}
- final private boolean isInFoundNodes( final PhylogenyNode node ) {
- return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
+ private boolean isInFoundNodes( final PhylogenyNode n ) {
+ return isInFoundNodes0( n ) || isInFoundNodes1( n );
+ }
+
+ final private boolean isInFoundNodes0( final PhylogenyNode node ) {
+ return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes1( final PhylogenyNode node ) {
+ return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
}
final private boolean isInOv() {
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize();
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( plusPressed( e.getKeyCode() ) ) {
final String title = clickto_names.get( i );
_node_popup_menu_items[ i ] = new JMenuItem( title );
if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
+ final String id = isCanOpenSeqWeb( node );
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
+ final List<Accession> accs = getPdbAccs( node );
+ _node_popup_menu_items[ i ] = new JMenuItem( title );
+ if ( !ForesterUtil.isEmpty( accs ) ) {
+ if ( accs.size() == 1 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 2 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 3 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ //
}
else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
return "Node Names";
+ case GENE_NAME:
+ return "Gene Names";
case SEQUENCE_NAME:
return "Sequence Names";
case SEQUENCE_SYMBOL:
return "Sequence Symbols";
case SEQUENCE_MOL_SEQ:
return "Molecular Sequences";
+ case SEQUENCE_MOL_SEQ_FASTA:
+ return "Molecular Sequences (Fasta)";
case SEQUENCE_ACC:
return "Sequence Accessors";
case TAXONOMY_SCIENTIFIC_NAME:
return "Scientific Names";
case TAXONOMY_CODE:
return "Taxonomy Codes";
+ case TAXONOMY_COMM0N_NAME:
+ return "Taxonomy Common Names";
case UNKNOWN:
return "User Selected Data";
default:
}
}
- final private void openSeqWeb( final PhylogenyNode node ) {
- if ( !isCanOpenSeqWeb( node ) ) {
- cannotOpenBrowserWarningMessage( "sequence" );
+ final private void openPdbWeb( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = getPdbAccs( node );
+ if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+ cannotOpenBrowserWarningMessage( "PDB" );
return;
}
- String uri_str = null;
- final Sequence seq = node.getNodeData().getSequence();
- final String source = seq.getAccession().getSource().toLowerCase();
- String url;
- if ( source.toLowerCase().equals( "ncbi" ) ) {
- url = Constants.NCBI_ALL_DATABASE_SEARCH;
+ final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_strs ) ) {
+ for( final String uri_str : uri_strs ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
}
else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
+ cannotOpenBrowserWarningMessage( "PDB" );
}
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
+ }
+
+ final private void openSeqWeb( final PhylogenyNode node ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ return;
}
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
String uri_str = null;
final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
- && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
- final String type = tax.getIdentifier().getProvider().toLowerCase();
- final WebLink weblink = getConfiguration().getWebLink( type );
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
try {
- uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
- catch ( final UnsupportedEncodingException e ) {
+ catch ( final URISyntaxException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
+ uri_str = null;
e.printStackTrace();
}
}
- else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+ else if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+ && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+ .equalsIgnoreCase( "uniprot" ) ) ) {
try {
- uri_str = new URI( tax.getIdentifier().getValue() ).toString();
+ uri_str = "http://www.uniprot.org/taxonomy/"
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
}
- catch ( final URISyntaxException e ) {
+ catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
}
if ( node.isExternal() ) {
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
}
}
c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- c = getTreeColorSet().getFoundColor();
+ c = getColorForFoundNode( node );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
if ( d < box_size ) {
d = box_size;
}
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
- ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() + d ) );
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
g.setColor( c );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
g.setColor( getBackground() );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
g.setColor( c );
- g.drawPolygon( _polygon );
+ g.draw( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
- .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+ g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
+ .getYcoord() - d ), c, false ) );
g.fill( _polygon );
g.setPaint( c );
g.draw( _polygon );
final boolean to_pdf,
final boolean to_graphics_file ) {
final List<Confidence> confidences = node.getBranchData().getConfidences();
- // if ( confidences.size() == 1 ) {
- // final double value = node.getBranchData().getConfidence( 0 ).getValue();
- // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
- // return;
- // }
- // conf_str = FORMATTER_CONFIDENCE.format( value );
- // }
- // else if ( confidences.size() > 1 ) {
- boolean one_ok = false;
boolean not_first = false;
Collections.sort( confidences );
final StringBuilder sb = new StringBuilder();
- String conf_str = "";
for( final Confidence confidence : confidences ) {
final double value = confidence.getValue();
if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( value >= getOptions().getMinConfidenceValue() ) {
- one_ok = true;
+ if ( value < getOptions().getMinConfidenceValue() ) {
+ return;
}
if ( not_first ) {
sb.append( "/" );
}
}
}
- //}
- if ( one_ok ) {
- conf_str = sb.toString();
- }
}
- if ( conf_str.length() > 0 ) {
+ if ( sb.length() > 0 ) {
final double parent_x = node.getParent().getXcoord();
double x = node.getXcoord();
g.setFont( getTreeFontSet().getSmallFont() );
else {
g.setColor( getTreeColorSet().getConfidenceColor() );
}
+ final String conf_str = sb.toString();
TreePanel
.drawString( conf_str,
parent_x
}
}
- final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
- final int box_size = getOptions().getDefaultNodeShapeSize();
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- g.setColor( getTreeColorSet().getFoundColor() );
- g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
- }
-
final private void paintGainedAndLostCharacters( final Graphics2D g,
final PhylogenyNode node,
final String gained,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
- final boolean to_graphics_file,
- final boolean is_in_found_nodes ) {
+ final boolean to_graphics_file ) {
if ( node.isCollapse() ) {
return;
}
// if this node should be highlighted, do so
if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
drawOval( x - 8, y - 8, 16, 16, g );
drawOval( x - 9, y - 8, 17, 17, g );
drawOval( x - 9, y - 9, 18, 18, g );
}
- if ( is_in_found_nodes ) {
- paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
- }
- else {
+ if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
+ || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+ || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
+ .isDuplication()
+ || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) ) ) {
+ final double box_size = getOptions().getDefaultNodeShapeSize();
+ final double half_box_size = box_size / 2.0;
Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
}
- else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
+ else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ outline_color = getColorForFoundNode( node );
+ }
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationBoxColor();
outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
- else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
- outline_color = getTaxonomyBasedColor( node );
- }
else {
outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
outline_color = getTreeColorSet().getBranchColorForPdf();
}
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
- final int half_box_size = box_size / 2;
- if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- to_pdf ? Color.WHITE : outline_color,
- to_pdf ? outline_color : getBackground(),
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
- }
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
- g.setColor( outline_color );
- drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
- }
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
+ : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
}
- else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- to_pdf ? Color.WHITE : outline_color,
- to_pdf ? outline_color : getBackground(),
- outline_color );
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
- }
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
- g.setColor( outline_color );
- drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
+ }
+ else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
+ drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
+ : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
}
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
+ _sb.setLength( 0 );
int x = 0;
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
- _sb.setLength( 0 );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ if ( _sb.length() > 0 ) {
+ _sb.setLength( 0 );
+ _sb.append( "(" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
+ }
+ }
+ else {
+ _sb.setLength( 0 );
}
if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( node.getName() );
}
if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeData().getSequence().getSymbol() );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
else if ( getControlPanel().isColorAccordingToAnnotation() ) {
g.setColor( calculateColorForAnnotation( ann ) );
}
- final String ann_str = createAnnotationString( ann );
+ final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( !node.isRoot() && !node.getParent().isCollapse() ) {
paintCollapsedNode( g, node, false, false, false );
}
return;
}
if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
+ g.setColor( getColorForFoundNode( node ) );
+ drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
float new_x = 0;
if ( !node.isExternal() && !node.isCollapse() ) {
final boolean to_graphics_file ) {
final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
return;
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
if ( dynamically_hide
&& !is_in_found_nodes
}
}
if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowGeneNames()
+ if ( getControlPanel().isShowSeqNames()
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
+ " " );
}
- if ( getControlPanel().isShowGeneSymbols()
+ if ( getControlPanel().isShowSeqSymbols()
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
+ " " );
}
+ if ( getControlPanel().isShowGeneNames()
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
+ + " " );
+ }
if ( getControlPanel().isShowSequenceAcc()
&& ( node.getNodeData().getSequence().getAccession() != null ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
.getAccession().toString()
+ " " );
}
+ if ( getControlPanel().isShowAnnotation()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions()
+ .isShowAnnotationRefSource() )
+ + " " );
+ }
}
if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
}
final private void paintOvRectangle( final Graphics2D g ) {
- final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
- final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
- final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
- final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
+ final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
+ final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
+ final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
+ final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
final float width = getOvMaxWidth() / w_ratio;
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
getOvRectangle().setRect( x, y, width, height );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
if ( ( width < 6 ) && ( height < 6 ) ) {
drawRectFilled( x, y, 6, 6, g );
getOvVirtualRectangle().setRect( x, y, 6, 6 );
}
getOvVirtualRectangle().setRect( x, y, width, height );
}
+ g.setStroke( s );
}
final private void paintPhylogenyLite( final Graphics2D g ) {
.setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
for( final PhylogenyNode element : _nodes_in_preorder ) {
paintNodeLite( g, element );
}
+ g.setStroke( s );
paintOvRectangle( g );
}
final double w = PhylogenyMethods.getBranchWidthValue( root );
drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
}
- paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
+ paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
}
final private void paintScale( final Graphics2D g,
else {
g.setColor( getTreeColorSet().getBranchLengthColor() );
}
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
drawLine( x1, y1, x1, y2, g );
drawLine( x2, y1, x2, y2, g );
drawLine( x1, y3, x2, y3, g );
if ( getScaleLabel() != null ) {
g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
}
+ g.setStroke( s );
}
final private int paintTaxonomy( final Graphics2D g,
}
else if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
- paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc )
- || isInCurrentExternalNodes( desc ) );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
}
if ( n.isRoot() ) {
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
}
}
desc.setXSecondary( new_x );
desc.setYSecondary( new_y );
if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
+ g.setColor( getColorForFoundNode( desc ) );
+ drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
g.setColor( getTreeColorSet().getOvColor() );
}
paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
}
}
if ( getCopiedAndPastedNodes() == null ) {
- setCopiedAndPastedNodes( new HashSet<Integer>() );
+ setCopiedAndPastedNodes( new HashSet<Long>() );
}
final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
for( final PhylogenyNode n : nodes ) {
node_ids.add( n.getId() );
}
sb.append( " " );
}
final Property p = properties.getProperty( ref );
- sb.append( getPartAfterColon( p.getRef() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
sb.append( "=" );
sb.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( getPartAfterColon( p.getUnit() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
return sb;
}
- final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
+ final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
getMainPanel().setCopiedAndPastedNodes( nodeIds );
}
_scale_label = scale_label;
}
+ private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.001 ) {
+ g.setStroke( STROKE_005 );
+ }
+ else if ( getYdistance() < 0.01 ) {
+ g.setStroke( STROKE_01 );
+ }
+ else if ( getYdistance() < 0.5 ) {
+ g.setStroke( STROKE_025 );
+ }
+ else if ( getYdistance() < 1 ) {
+ g.setStroke( STROKE_05 );
+ }
+ else if ( getYdistance() < 2 ) {
+ g.setStroke( STROKE_075 );
+ }
+ else if ( getYdistance() < 20 ) {
+ g.setStroke( STROKE_1 );
+ }
+ else {
+ g.setStroke( STROKE_2 );
+ }
+ }
+
final private void setUpUrtFactor() {
final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
: getVisibleRect().height;
private void showExtDescNodeData( final PhylogenyNode node ) {
final List<String> data = new ArrayList<String>();
- for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+ final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
+ }
+ if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
+ }
+ for( final PhylogenyNode n : nodes ) {
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
if ( !ForesterUtil.isEmpty( n.getName() ) ) {
data.add( n.getNodeData().getSequence().getName() );
}
break;
+ case GENE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ data.add( n.getNodeData().getSequence().getGeneName() );
+ }
+ break;
case SEQUENCE_SYMBOL:
if ( n.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
data.add( n.getNodeData().getSequence().getMolecularSequence() );
}
break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ final StringBuilder sb = new StringBuilder();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ final StringBuilder ann = new StringBuilder();
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( "SYM=" );
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ ann.append( "NAME=" );
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ ann.append( "GN=" );
+ ann.append( n.getNodeData().getSequence().getGeneName() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( "ACC=" );
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( "TAXID=" );
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( "SN=" );
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( "|" );
+ }
+ }
+ String ann_str;
+ if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+ ann_str = ann.substring( 0, ann.length() - 1 );
+ }
+ else {
+ ann_str = ann.toString();
+ }
+ sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
+ .getMolecularSequence(), 60 ) );
+ data.add( sb.toString() );
+ }
+ break;
case SEQUENCE_ACC:
if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
data.add( n.getNodeData().getTaxonomy().getScientificName() );
}
break;
+ case TAXONOMY_COMM0N_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ break;
case TAXONOMY_CODE:
if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
}
break;
case UNKNOWN:
- AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
break;
default:
throw new IllegalArgumentException( "unknown data element: "
+ getOptions().getExtDescNodeDataToReturn() );
}
} // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
|| ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
- System.out.println( d );
- }
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
+ if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+ System.out.println( sb );
}
if ( sb.length() < 1 ) {
clearCurrentExternalNodesDataBuffer();
}
}
else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
if ( sb.length() < 1 ) {
- AptxUtil.showInformationMessage( this,
- "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
- "Descendants of selected node do not contain selected data" );
+ TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
+ + ")", "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
setCurrentExternalNodesDataBuffer( sb );
- final String title = "External Descendants "
- + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
- + node.getNumberOfExternalNodes() + ") For Node " + node;
+ String title;
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + " nodes, unique entries: "
+ + size;
+ }
+ else {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + "/"
+ + node.getNumberOfExternalNodes()
+ + " external descendats of node "
+ + node
+ + ", unique entries: " + size;
+ }
final String s = sb.toString().trim();
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getName().length() > 0 )
- || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
- || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
- || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
- || node.getBranchData().isHasConfidences() ) {
+ || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
+ .getTaxonomy() ) )
+ || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
+ .getSequence() ) ) || ( node.getNodeData().isHasDate() )
+ || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
_popup_buffer.setLength( 0 );
short lines = 0;
if ( node.getName().length() > 0 ) {
lines++;
_popup_buffer.append( node.getName() );
}
- if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
+ if ( node.getNodeData().isHasTaxonomy()
+ && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
lines++;
boolean enc_data = false;
final Taxonomy tax = node.getNodeData().getTaxonomy();
}
}
}
- if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
+ if ( node.getNodeData().isHasSequence()
+ && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
lines++;
boolean enc_data = false;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "]" );
enc_data = true;
}
+ if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getGeneName() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
if ( enc_data ) {
_popup_buffer.append( " " );
for( final String ref : properties.getPropertyRefs() ) {
_popup_buffer.append( "\n" );
final Property p = properties.getProperty( ref );
- _popup_buffer.append( getPartAfterColon( p.getRef() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
_popup_buffer.append( "=" );
_popup_buffer.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
}
_rollover_popup
.setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
- if ( isInFoundNodes( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
+ if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
+ }
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
_rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
}
}
- final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
- g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
- }
-
final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
}
- final private static String getPartAfterColon( final String s ) {
- final int i = s.indexOf( ':' );
- if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
- return s;
- }
- return s.substring( i + 1, s.length() );
- }
-
- final private static boolean isSequenceEmpty( final Sequence seq ) {
- return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
- && ForesterUtil.isEmpty( seq.getSymbol() );
- }
-
- final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
- return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
- && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
- .getSynonyms().isEmpty() );
- }
-
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
- final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
- final Phylogeny new_phy = new Phylogeny();
- new_phy.setRooted( true );
- new_phy.setName( source_phy.getName() );
- new_phy.setDescription( source_phy.getDescription() );
- new_phy.setType( source_phy.getType() );
- new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
- new_phy.setConfidence( source_phy.getConfidence() );
- new_phy.setIdentifier( source_phy.getIdentifier() );
- new_phy.setRoot( new_root.copyNodeDataShallow() );
- int i = 0;
- for( final PhylogenyNode n : new_root.getDescendants() ) {
- new_phy.getRoot().setChildNode( i++, n );
- }
- return new_phy;
- }
-
final private class SubtreeColorizationActionListener implements ActionListener {
- JColorChooser _chooser;
- PhylogenyNode _node;
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
@Override
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
- colorizeSubtree( c, _node );
+ colorizeSubtree( c, _node, _additional_nodes );
}
}
}