X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=559d12033d052e9273027c2b467d6bc62e6e5102;hb=789f3450d14e1f922072f4288833afab71993667;hp=907a20f4a49eca1171d523609fe02028c2a2d811;hpb=08bd889bc13de7415319ea7202d8afb27879c18d;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 907a20f..559d120 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -21,7 +21,7 @@ // 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; @@ -34,9 +34,9 @@ import java.awt.GradientPaint; 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; @@ -54,6 +54,7 @@ import java.awt.geom.Arc2D; 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; @@ -100,6 +101,7 @@ import org.forester.archaeopteryx.phylogeny.data.RenderableVector; 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; @@ -129,111 +131,119 @@ import org.forester.util.SequenceIdParser; 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; - // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not - // being static anymore (02/20/2009). - 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 _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 _urt_nodeid_angle_map = new HashMap(); - final private HashMap _urt_nodeid_index_map = new HashMap(); - final private Set _collapsed_external_nodeid_set = new HashSet(); - HashMap _nodeid_dist_to_leaf = new HashMap(); - 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 _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 _urt_nodeid_angle_map = new HashMap(); + final private HashMap _urt_nodeid_index_map = new HashMap(); + final private Set _collapsed_external_nodeid_set = new HashSet(); + HashMap _nodeid_dist_to_leaf = new HashMap(); + 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 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 _current_external_nodes = null; // private Image offscreenImage; // private Graphics offscreenGraphics; // private Dimension offscreenDimension; @@ -305,65 +315,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 vector_l = new ArrayList( 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 getImageMap() { return getMainPanel().getImageMap(); } @@ -402,7 +353,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getControlPanel().displayedPhylogenyMightHaveChanged( true ); } else { - getTreeFontSet().decreaseFontSize(); + getTreeFontSet().decreaseFontSize( 1, false ); getControlPanel().displayedPhylogenyMightHaveChanged( true ); } } @@ -497,11 +448,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - public final void setArrowCursor() { - setCursor( ARROW_CURSOR ); - repaint(); - } - public final void setEdited( final boolean edited ) { _edited = edited; } @@ -511,17 +457,61 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } /** + * 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 ); @@ -568,33 +558,27 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } _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(); + // } + // } + } + } + // } } @@ -712,25 +696,92 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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() ); + getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); + } + else { + c = AptxUtil.calculateColorFromString( tax.getScientificName() ); + 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 vector_l = new ArrayList( 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() ); + } + /** * Collapse the tree from the given node * @@ -806,6 +857,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { msg += "colorized one subtree"; } + setEdited( true ); JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Completed (" + rank + ")", @@ -877,11 +929,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _control_panel; } + String getCurrentExternalNodesDataBufferAsString() { + return _current_external_nodes_data_buffer.toString(); + } + + int getCurrentExternalNodesDataBufferChangeCounter() { + return _current_external_nodes_data_buffer_change_counter; + } + final int getDomainStructureEvalueThreshold() { return _domain_structure_e_value_thr_exp; } - final Set getFoundNodes() { + final Set getFoundNodes() { return _found_nodes; } @@ -1096,6 +1156,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee PhylogenyMethods.midpointRoot( _phylogeny ); resetNodeIdToDistToLeafMap(); setArrowCursor(); + setEdited( true ); repaint(); } @@ -1137,7 +1198,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { // Yes, so add to _found_nodes if ( getFoundNodes() == null ) { - setFoundNodes( new HashSet() ); + setFoundNodes( new HashSet() ); } getFoundNodes().add( node.getId() ); // Check if control key is down @@ -1238,6 +1299,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final void mouseMoved( final MouseEvent e ) { requestFocusInWindow(); + if ( _current_external_nodes != null ) { + _current_external_nodes = null; + repaint(); + } if ( getControlPanel().isNodeDescPopup() ) { if ( _node_desc_popup != null ) { _node_desc_popup.hide(); @@ -1269,8 +1334,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final PhylogenyNode node = findNode( e.getX(), e.getY() ); if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { - // cursor is over a tree node - if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) + if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) { + for( final PhylogenyNode n : node.getAllExternalDescendants() ) { + addToCurrentExternalNodes( n.getId() ); + } + setCursor( HAND_CURSOR ); + repaint(); + } + else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) @@ -1327,9 +1398,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ) ); + paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) + || isInCurrentExternalNodes( c ) ); if ( c.isExternal() ) { - final boolean is_in_found_nodes = isInFoundNodes( c ); + final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c ); if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) { return; @@ -1356,7 +1428,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee root_x + ( Math.cos( angle ) * parent_radius ), root_y + ( Math.sin( angle ) * parent_radius ), g ); - if ( isInFoundNodes( c ) ) { + if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); } @@ -1461,7 +1533,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() ) ); @@ -1483,7 +1555,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee // 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 ); @@ -1671,6 +1743,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setNodeInPreorderToNull(); resetPreferredSize(); getMainPanel().adjustJScrollPane(); + setEdited( true ); repaint(); if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { getControlPanel().showWhole(); @@ -1678,7 +1751,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final void resetNodeIdToDistToLeafMap() { - _nodeid_dist_to_leaf = new HashMap(); + _nodeid_dist_to_leaf = new HashMap(); } final void resetPreferredSize() { @@ -1725,18 +1798,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getControlPanel().getSearchResetButton().setEnabled( true ); getControlPanel().getSearchResetButton().setVisible( true ); if ( getFoundNodes() == null ) { - setFoundNodes( new HashSet() ); + setFoundNodes( new HashSet() ); } 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; } - final void setFoundNodes( final Set found_nodes ) { + void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) { + increaseCurrentExternalNodesDataBufferChangeCounter(); + _current_external_nodes_data_buffer = sb; + } + + final void setFoundNodes( final Set found_nodes ) { _found_nodes = found_nodes; } @@ -1803,21 +1886,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } 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 ); @@ -1951,6 +2026,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _control_panel.getColorBranchesCb() != null ) { _control_panel.getColorBranchesCb().setSelected( true ); } + setEdited( true ); setArrowCursor(); repaint(); } @@ -2123,6 +2199,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } + final private void addToCurrentExternalNodes( final long i ) { + if ( _current_external_nodes == null ) { + _current_external_nodes = new HashSet(); + } + _current_external_nodes.add( i ); + } + final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node, final boolean is_vertical, final Graphics g, @@ -2215,6 +2298,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + 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. @@ -2330,7 +2417,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setNodeInPreorderToNull(); setCutOrCopiedTree( _phylogeny.copy( node ) ); final List nodes = PhylogenyMethods.getAllDescendants( node ); - final Set node_ids = new HashSet( nodes.size() ); + final Set node_ids = new HashSet( nodes.size() ); for( final PhylogenyNode n : nodes ) { node_ids.add( n.getId() ); } @@ -2339,6 +2426,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } + private String createAnnotationString( final SortedSet 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(); @@ -2409,7 +2512,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - if ( node.isRoot() ) { + if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) { JOptionPane.showMessageDialog( this, "Cannot delete entire tree", "Attempt to delete entire tree", @@ -2607,10 +2710,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); } - final private Set getCopiedAndPastedNodes() { + final private Set getCopiedAndPastedNodes() { return getMainPanel().getCopiedAndPastedNodes(); } + final private Set getCurrentExternalNodes() { + return _current_external_nodes; + } + final private Phylogeny getCutOrCopiedTree() { return getMainPanel().getCutOrCopiedTree(); } @@ -2754,6 +2861,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + final private void increaseCurrentExternalNodesDataBufferChangeCounter() { + _current_external_nodes_data_buffer_change_counter++; + } + final private void increaseOvSize() { if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) ) && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() @@ -2802,30 +2913,27 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); } - return false; + if ( ForesterUtil.isEmpty( v ) ) { + v = ForesterUtil.extractRefSeqAccessorAccessor( node ); + } + 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 { @@ -2833,6 +2941,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) { + return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) ); + } + final private boolean isInFoundNodes( final PhylogenyNode node ) { return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ); } @@ -2884,7 +2996,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() ) ) { @@ -3041,7 +3153,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ) ); @@ -3116,6 +3235,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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: @@ -3131,35 +3252,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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() ); @@ -3182,32 +3285,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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 ) { @@ -3227,7 +3332,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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 ) { @@ -3237,11 +3342,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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() ); @@ -3446,7 +3550,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } if ( node.isExternal() ) { - paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); + paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) + || isInCurrentExternalNodes( node ) ); } } @@ -3550,30 +3655,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); @@ -3741,7 +3846,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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, @@ -3823,6 +3930,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() @@ -3861,11 +3969,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ) { @@ -4035,22 +4148,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - private String createAnnotationString( final SortedSet 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 void paintNodeDataUnrootedCirc( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, @@ -4191,12 +4288,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ) ) { + if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g ); } @@ -4243,9 +4340,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean dynamically_hide, final int dynamic_hiding_factor, final boolean to_graphics_file ) { - final boolean is_in_found_nodes = isInFoundNodes( node ); + 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; @@ -4325,7 +4422,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee child_node.setYcoord( y2 ); y2 += _y_distance * child_node.getNumberOfExternalNodes(); } - paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); + paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) + || isInCurrentExternalNodes( node ) ); } if ( dynamically_hide && !is_in_found_nodes @@ -4431,16 +4529,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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 ); @@ -4460,22 +4560,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } getOvVirtualRectangle().setRect( x, y, width, height ); } + g.setStroke( s ); } final private void paintPhylogenyLite( final Graphics2D g ) { - //System.out.println( getVisibleRect().x + " " + getVisibleRect().y ); _phylogeny .getRoot() .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() .getWidth() ) ) ) ); _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); - //final PhylogenyNodeIterator it; - //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - // paintNodeLite( g, it.next() ); - //} + final Stroke s = g.getStroke(); + g.setStroke( STROKE_05 ); for( final PhylogenyNode element : _nodes_in_preorder ) { paintNodeLite( g, element ); } + g.setStroke( s ); paintOvRectangle( g ); } @@ -4527,12 +4626,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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, @@ -4658,7 +4760,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee to_graphics_file, radial_labels, ( high_angle + low_angle ) / 2, - isInFoundNodes( n ) ); + isInFoundNodes( n ) || isInCurrentExternalNodes( n ) ); return; } final float num_enclosed = n.getNumberOfExternalNodes(); @@ -4706,7 +4808,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ) ); + paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) + || isInCurrentExternalNodes( desc ) ); } if ( n.isRoot() ) { paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); @@ -4752,7 +4855,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) ); desc.setXSecondary( new_x ); desc.setYSecondary( new_y ); - if ( isInFoundNodes( desc ) ) { + if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g ); g.setColor( getTreeColorSet().getOvColor() ); @@ -4817,10 +4920,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } if ( getCopiedAndPastedNodes() == null ) { - setCopiedAndPastedNodes( new HashSet() ); + setCopiedAndPastedNodes( new HashSet() ); } final List nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy ); - final Set node_ids = new HashSet( nodes.size() ); + final Set node_ids = new HashSet( nodes.size() ); for( final PhylogenyNode n : nodes ) { node_ids.add( n.getId() ); } @@ -4860,7 +4963,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return sb; } - final private void setCopiedAndPastedNodes( final Set nodeIds ) { + final private void setCopiedAndPastedNodes( final Set nodeIds ) { getMainPanel().setCopiedAndPastedNodes( nodeIds ); } @@ -4912,6 +5015,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _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; @@ -4965,6 +5092,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() ) ) { + if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + sb.append( SequenceWriter.toFasta( n.getNodeData().getSequence().getName(), n.getNodeData() + .getSequence().getMolecularSequence(), 60 ) ); + } + else { + sb.append( SequenceWriter.toFasta( n.getName(), 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() ) ) { @@ -4991,40 +5133,53 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + getOptions().getExtDescNodeDataToReturn() ); } } // for loop - if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + 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 ) ) { - System.out.println( d ); + if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + System.out.println( d ); + } + sb.append( d ); + sb.append( ForesterUtil.LINE_SEPARATOR ); } } + if ( sb.length() < 1 ) { + clearCurrentExternalNodesDataBuffer(); + } + else { + setCurrentExternalNodesDataBuffer( sb ); + } } 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( "\n" ); + 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" ); + clearCurrentExternalNodesDataBuffer(); } else { + setCurrentExternalNodesDataBuffer( sb ); final String title = "External Descendants " + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/" + node.getNumberOfExternalNodes() + ") For Node " + node; + final String s = sb.toString().trim(); if ( getMainPanel().getMainFrame() == null ) { // Must be "E" applet version. final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - final String s = sb.toString().trim(); ae.showTextFrame( s, title ); - ae.setCurrentExternalNodesDataBuffer( s ); } else { - getMainPanel().getMainFrame().showTextFrame( sb.toString(), title ); + getMainPanel().getMainFrame().showTextFrame( s, title ); } } }