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 java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
import java.util.SortedSet;
+import java.util.TreeMap;
import javax.swing.BorderFactory;
import javax.swing.JApplet;
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;
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 );
+ private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
+ 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 = 2000;
+ 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<Long> _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 Path2D.Float _polygon = new Path2D.Float();
+ 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<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, 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 );
// 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 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<Long> _current_external_nodes = null;
// 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();
- while ( ( getLongestExtNodeInfo() > y / 2 ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize();
- 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();
}
_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();
+ // }
+ // }
+ }
+ }
+ //
}
}
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( AptxUtil.createAnnotationString( node.getNodeData()
+ .getSequence().getAnnotations() )
+ " " );
}
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 ( ForesterUtil.isEmpty( species ) ) {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
return getTreeColorSet().getTaxonomyColor();
}
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
+ 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 ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+ }
+ else {
+ c = AptxUtil.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;
+ }
+ }
+
void clearCurrentExternalNodesDataBuffer() {
setCurrentExternalNodesDataBuffer( new StringBuilder() );
}
else {
msg += "colorized one subtree";
}
+ setEdited( true );
JOptionPane.showMessageDialog( this,
msg,
"Taxonomy Colorization Completed (" + rank + ")",
return _domain_structure_e_value_thr_exp;
}
- final Set<Integer> getFoundNodes() {
+ final Set<Long> getFoundNodes() {
return _found_nodes;
}
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
setArrowCursor();
+ setEdited( true );
repaint();
}
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
+ setFoundNodes( new HashSet<Long>() );
}
getFoundNodes().add( node.getId() );
// Check if control key is down
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() {
getControlPanel().getSearchResetButton().setEnabled( true );
getControlPanel().getSearchResetButton().setVisible( true );
if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
+ setFoundNodes( new HashSet<Long>() );
}
getFoundNodes().add( node.getId() );
getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().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 ) {
+ final void setFoundNodes( final Set<Long> found_nodes ) {
_found_nodes = found_nodes;
}
}
}
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 );
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 );
}
}
}
+ 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 = AptxUtil.calculateColorFromString( ann_str, false );
getControlPanel().getAnnotationColors().put( ann_str, c );
}
if ( c == null ) {
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();
JOptionPane.ERROR_MESSAGE );
}
- final private Set<Integer> getCopiedAndPastedNodes() {
+ final private Set<Long> getCopiedAndPastedNodes() {
return getMainPanel().getCopiedAndPastedNodes();
}
- final private Set<Integer> getCurrentExternalNodes() {
+ final private Set<Long> getCurrentExternalNodes() {
return _current_external_nodes;
}
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 ) {
+ String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGenbankAccessor( node );
+ }
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractRefSeqAccessorAccessor( node );
}
- return false;
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGInumber( node );
+ }
+ return v;
}
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 {
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_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
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 ) ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
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;
- }
- else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ final String uri_str = AptxUtil.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() );
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 int box_size = getOptions().getDefaultNodeShapeSize();
final int half_box_size = box_size / 2;
- if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+ if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+ || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
drawOvalGradient( x - half_box_size,
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()
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 ) {
else if ( getControlPanel().isColorAccordingToAnnotation() ) {
g.setColor( calculateColorForAnnotation( ann ) );
}
- final String ann_str = createAnnotationString( ann );
+ final String ann_str = AptxUtil.createAnnotationString( ann );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
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;
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;
}
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() );
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 );
}
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,
}
}
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() );
}
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;
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 ( 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 = ann.toString().trim();
+ if ( ann_str.endsWith( "|" ) ) {
+ ann_str = ann_str.substring( 0, ann_str.length() - 1 );
+ }
+ 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() ) ) {
+ getOptions().getExtDescNodeDataToReturn() );
}
} // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = 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() + ")",
}
else {
setCurrentExternalNodesDataBuffer( sb );
- final String title = "External Descendants "
- + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
- + node.getNumberOfExternalNodes() + ") For Node " + node;
+ final String 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.
}
}
+ private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+ final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ if ( map.containsKey( d ) ) {
+ map.put( d, map.get( d ) + 1 );
+ }
+ else {
+ map.put( d, 1 );
+ }
+ }
+ }
+ }
+ int size = 0;
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final Entry<String, Integer> e : map.entrySet() ) {
+ final String v = e.getKey();
+ final Object c = e.getValue();
+ sb.append( v );
+ sb.append( "\t" );
+ sb.append( c );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ size = map.size();
+ }
+ else {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ sb.append( d );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = data.size();
+ }
+ return size;
+ }
+
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getName().length() > 0 )
git://source.jalview.org / jalview.git / blobdiff