// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
import 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;
- // 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<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 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<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 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<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 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();
+ if ( getOptions().isAllowFontSizeChange() ) {
+ if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
+ true );
+ calculateLongestExtNodeInfo();
+ }
+ }
+ else {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
+ .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ calculateLongestExtNodeInfo();
+ }
+ }
+ }
}
int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
}
_circ_max_depth = max_depth;
setUpUrtFactor();
- }
- }
-
- /**
- * Set a phylogeny tree.
- *
- * @param t
- * an instance of a Phylogeny
- */
- public final void setTree( final Phylogeny t ) {
- setNodeInPreorderToNull();
- _phylogeny = t;
- }
-
- public final void setWaitCursor() {
- setCursor( WAIT_CURSOR );
- repaint();
- }
-
- @Override
- public void update( final Graphics g ) {
- paint( g );
- }
-
- final void calcMaxDepth() {
- if ( _phylogeny != null ) {
- _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ //
+ if ( getOptions().isAllowFontSizeChange() ) {
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ // int dynamic_hiding_factor = calcDynamicHidingFactor();
+ // if ( dynamic_hiding_factor > 1 ) {
+ // while ( dynamic_hiding_factor > 1
+ // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
+ // getTreeFontSet().decreaseFontSize( 1, true );
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
+ // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
+ // getTreeFontSet().increaseFontSize();
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ }
+ }
+ //
}
}
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() );
+ }
+
/**
* Collapse the tree from the given node
*
else {
msg += "colorized one subtree";
}
+ setEdited( true );
JOptionPane.showMessageDialog( this,
msg,
"Taxonomy Colorization Completed (" + rank + ")",
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<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
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();
}
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 )
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;
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 );
}
// 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;
}
- final void setFoundNodes( final Set<Integer> found_nodes ) {
+ void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
+ increaseCurrentExternalNodesDataBufferChangeCounter();
+ _current_external_nodes_data_buffer = sb;
+ }
+
+ 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()
+ && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
+ && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
&& ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
_rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
+ setEdited( true );
setArrowCursor();
repaint();
}
repaint();
}
+ final private void addToCurrentExternalNodes( final long i ) {
+ if ( _current_external_nodes == null ) {
+ _current_external_nodes = new HashSet<Long>();
+ }
+ _current_external_nodes.add( i );
+ }
+
final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
final boolean is_vertical,
final Graphics g,
}
}
+ 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.
Color c = getTreeColorSet().getAnnotationColor();
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
final StringBuilder sb = new StringBuilder();
- for( Annotation a : ann ) {
+ for( final Annotation a : ann ) {
sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
}
final String ann_str = sb.toString();
setNodeInPreorderToNull();
setCutOrCopiedTree( _phylogeny.copy( node ) );
final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
for( final PhylogenyNode n : nodes ) {
node_ids.add( n.getId() );
}
repaint();
}
+ private String createAnnotationString( final SortedSet<Annotation> ann ) {
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( final Annotation a : ann ) {
+ if ( !first ) {
+ sb.append( "|" );
+ }
+ else {
+ first = false;
+ }
+ sb.append( a.asSimpleText() );
+ }
+ final String ann_str = sb.toString();
+ return ann_str;
+ }
+
final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
final String tax = PhylogenyMethods.getSpecies( node );
String label = node.getName();
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
- if ( node.isRoot() ) {
+ if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
JOptionPane.showMessageDialog( this,
"Cannot delete entire tree",
"Attempt to delete entire tree",
JOptionPane.ERROR_MESSAGE );
}
- final private Set<Integer> getCopiedAndPastedNodes() {
+ final private Set<Long> getCopiedAndPastedNodes() {
return getMainPanel().getCopiedAndPastedNodes();
}
+ final private Set<Long> getCurrentExternalNodes() {
+ return _current_external_nodes;
+ }
+
final private Phylogeny getCutOrCopiedTree() {
return getMainPanel().getCutOrCopiedTree();
}
}
}
+ 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()
}
}
+ 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() ) );
}
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() ) ) {
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:
}
}
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 ) );
}
}
}
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,
}
}
- private String createAnnotationString( final SortedSet<Annotation> ann ) {
- final StringBuilder sb = new StringBuilder();
- boolean first = true;
- for( 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,
}
return;
}
- if ( isInFoundNodes( node ) ) {
+ if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
}
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() ) {
paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
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
}
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() );
- //}
for( final PhylogenyNode element : _nodes_in_preorder ) {
paintNodeLite( g, element );
}
to_graphics_file,
radial_labels,
( high_angle + low_angle ) / 2,
- isInFoundNodes( n ) );
+ isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
return;
}
final float num_enclosed = n.getNumberOfExternalNodes();
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 ) );
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() );
}
}
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 );
}
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() ) ) {
+ 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 );
}
}
}
git://source.jalview.org / jalview.git / blobdiff