import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
-import java.awt.Polygon;
import java.awt.Rectangle;
import java.awt.RenderingHints;
+import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.geom.CubicCurve2D;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Line2D;
+import java.awt.geom.Path2D;
import java.awt.geom.QuadCurve2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
import java.util.SortedSet;
+import java.util.TreeMap;
import javax.swing.BorderFactory;
import javax.swing.JApplet;
import org.forester.archaeopteryx.tools.Blast;
import org.forester.archaeopteryx.tools.ImageLoader;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.writers.SequenceWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
+ private static final 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 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 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 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 Path2D.Float _polygon = new Path2D.Float();
private final StringBuilder _sb = new StringBuilder();
private JColorChooser _color_chooser = null;
private double _scale_distance = 0.0;
/**
* Set parameters for printing the displayed tree
*
- * @param x
- * @param y
*/
final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
// updateStyle(); not needed?
if ( getOptions().isAllowFontSizeChange() ) {
if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
&& ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
- while ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
&& ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
true );
}
}
else {
- while ( ( getLongestExtNodeInfo() < ( x * 0.5 ) )
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
&& ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
.getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
getMainPanel().getTreeFontSet().increaseFontSize();
}
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;
}
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() ) );
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
- && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
- && ( ( 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 );
boolean first = true;
for( final Annotation a : ann ) {
if ( !first ) {
- sb.append( "|" );
+ sb.append( "+" );
}
else {
first = false;
return Blast.isContainsQueryForBlast( node );
}
- final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
- .toLowerCase() ) ) {
- return true;
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGenbankAccessor( node );
+ }
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractRefSeqAccessorAccessor( node );
}
- return false;
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGInumber( node );
+ }
+ return v;
}
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
- && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
- .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
- .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
final String title = clickto_names.get( i );
_node_popup_menu_items[ i ] = new JMenuItem( title );
if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
+ final String id = isCanOpenSeqWeb( node );
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
}
else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
return "Sequence Symbols";
case SEQUENCE_MOL_SEQ:
return "Molecular Sequences";
+ case SEQUENCE_MOL_SEQ_FASTA:
+ return "Molecular Sequences (Fasta)";
case SEQUENCE_ACC:
return "Sequence Accessors";
case TAXONOMY_SCIENTIFIC_NAME:
return "Scientific Names";
case TAXONOMY_CODE:
return "Taxonomy Codes";
+ case TAXONOMY_COMM0N_NAME:
+ return "Taxonomy Common Names";
case UNKNOWN:
return "User Selected Data";
default:
}
final private void openSeqWeb( final PhylogenyNode node ) {
- if ( !isCanOpenSeqWeb( node ) ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
- String uri_str = null;
- final Sequence seq = node.getNodeData().getSequence();
- final String source = seq.getAccession().getSource().toLowerCase();
- String url;
- if ( source.toLowerCase().equals( "ncbi" ) ) {
- url = Constants.NCBI_ALL_DATABASE_SEARCH;
- }
- else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
String uri_str = null;
final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
- && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
- final String type = tax.getIdentifier().getProvider().toLowerCase();
- final WebLink weblink = getConfiguration().getWebLink( type );
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
try {
- uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
- catch ( final UnsupportedEncodingException e ) {
+ catch ( final URISyntaxException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
+ uri_str = null;
e.printStackTrace();
}
}
- else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+ else if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+ && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+ .equalsIgnoreCase( "uniprot" ) ) ) {
try {
- uri_str = new URI( tax.getIdentifier().getValue() ).toString();
+ uri_str = "http://www.uniprot.org/taxonomy/"
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
}
- catch ( final URISyntaxException e ) {
+ catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
if ( d < box_size ) {
d = box_size;
}
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
- ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() + d ) );
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
g.setColor( c );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
g.setColor( getBackground() );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
g.setColor( c );
- g.drawPolygon( _polygon );
+ g.draw( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
- .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+ g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
+ .getYcoord() - d ), c, false ) );
g.fill( _polygon );
g.setPaint( c );
g.draw( _polygon );
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
+ _sb.setLength( 0 );
int x = 0;
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
- _sb.setLength( 0 );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ if ( _sb.length() > 0 ) {
+ _sb.setLength( 0 );
+ _sb.append( "(" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
+ }
+ }
+ else {
+ _sb.setLength( 0 );
}
if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( !node.isRoot() && !node.getParent().isCollapse() ) {
paintCollapsedNode( g, node, false, false, false );
}
return;
final boolean to_graphics_file ) {
final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
return;
}
final private void paintOvRectangle( final Graphics2D g ) {
- final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
- final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
- final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
- final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
+ final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
+ final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
+ final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
+ final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
final float width = getOvMaxWidth() / w_ratio;
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
g.setColor( getTreeColorSet().getFoundColor() );
getOvRectangle().setRect( x, y, width, height );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
if ( ( width < 6 ) && ( height < 6 ) ) {
drawRectFilled( x, y, 6, 6, g );
getOvVirtualRectangle().setRect( x, y, 6, 6 );
}
getOvVirtualRectangle().setRect( x, y, width, height );
}
+ g.setStroke( s );
}
final private void paintPhylogenyLite( final Graphics2D g ) {
.setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
for( final PhylogenyNode element : _nodes_in_preorder ) {
paintNodeLite( g, element );
}
+ g.setStroke( s );
paintOvRectangle( g );
}
else {
g.setColor( getTreeColorSet().getBranchLengthColor() );
}
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
drawLine( x1, y1, x1, y2, g );
drawLine( x2, y1, x2, y2, g );
drawLine( x1, y3, x2, y3, g );
if ( getScaleLabel() != null ) {
g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
}
+ g.setStroke( s );
}
final private int paintTaxonomy( final Graphics2D g,
_scale_label = scale_label;
}
+ private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.001 ) {
+ g.setStroke( STROKE_005 );
+ }
+ else if ( getYdistance() < 0.01 ) {
+ g.setStroke( STROKE_01 );
+ }
+ else if ( getYdistance() < 0.5 ) {
+ g.setStroke( STROKE_025 );
+ }
+ else if ( getYdistance() < 1 ) {
+ g.setStroke( STROKE_05 );
+ }
+ else if ( getYdistance() < 2 ) {
+ g.setStroke( STROKE_075 );
+ }
+ else if ( getYdistance() < 20 ) {
+ g.setStroke( STROKE_1 );
+ }
+ else {
+ g.setStroke( STROKE_2 );
+ }
+ }
+
final private void setUpUrtFactor() {
final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
: getVisibleRect().height;
data.add( n.getNodeData().getSequence().getMolecularSequence() );
}
break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ final StringBuilder sb = new StringBuilder();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ final StringBuilder ann = new StringBuilder();
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( "SYM=" );
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ ann.append( "NAME=" );
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( "ACC=" );
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( "TAXID=" );
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( "SN=" );
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( "|" );
+ }
+ }
+ String ann_str = ann.toString().trim();
+ if ( ann_str.endsWith( "|" ) ) {
+ ann_str = ann_str.substring( 0, ann_str.length() - 1 );
+ }
+ sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
+ .getMolecularSequence(), 60 ) );
+ data.add( sb.toString() );
+ }
+ break;
case SEQUENCE_ACC:
if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
data.add( n.getNodeData().getTaxonomy().getScientificName() );
}
break;
+ case TAXONOMY_COMM0N_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ break;
case TAXONOMY_CODE:
if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ getOptions().getExtDescNodeDataToReturn() );
}
} // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = makeSB( data, getOptions(), sb );
if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
|| ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
- System.out.println( d );
- }
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
+ if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+ System.out.println( sb );
}
if ( sb.length() < 1 ) {
clearCurrentExternalNodesDataBuffer();
}
}
else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
if ( sb.length() < 1 ) {
AptxUtil.showInformationMessage( this,
"No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
}
else {
setCurrentExternalNodesDataBuffer( sb );
- final String title = "External Descendants "
- + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
- + node.getNumberOfExternalNodes() + ") For Node " + node;
+ final String title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + "/"
+ + node.getNumberOfExternalNodes()
+ + " external descendats of node "
+ + node
+ + ", unique entries: " + size;
final String s = sb.toString().trim();
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
}
}
+ private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+ final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ if ( map.containsKey( d ) ) {
+ map.put( d, map.get( d ) + 1 );
+ }
+ else {
+ map.put( d, 1 );
+ }
+ }
+ }
+ }
+ int size = 0;
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final Entry<String, Integer> e : map.entrySet() ) {
+ final String v = e.getKey();
+ final Object c = e.getValue();
+ sb.append( v );
+ sb.append( "\t" );
+ sb.append( c );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ size = map.size();
+ }
+ else {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ sb.append( d );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = data.size();
+ }
+ return size;
+ }
+
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getName().length() > 0 )
git://source.jalview.org / jalview.git / blobdiff