public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
final static String VERSION = "0.9900 beta";
- final static String PRG_DATE = "141010";
+ final static String PRG_DATE = "141013";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
"Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
_nodes_in_preorder[ i++ ] = it.next();
}
}
- //final PhylogenyNodeIterator it;
- //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
- // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
- // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
- //}
-
-
- final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) || getControlPanel().isUseVisualStyles()
- || getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
+ || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
|| ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
|| ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
- || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() );
-
-
+ || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
+ || to_graphics_file || to_pdf;
for( final PhylogenyNode element : _nodes_in_preorder ) {
- paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
- && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
+ paintNodeRectangular( g,
+ element,
+ to_pdf,
+ getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
+ dynamic_hiding_factor,
+ to_graphics_file,
+ disallow_shortcutting );
}
if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
if ( !( to_graphics_file || to_pdf ) ) {
final boolean to_pdf,
final boolean dynamically_hide,
final int dynamic_hiding_factor,
- final boolean to_graphics_file ) {
+ final boolean to_graphics_file,
+ final boolean disallow_shortcutting ) {
final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
if ( node.isCollapse() ) {
if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
}
float new_x = 0;
float new_x_min = Float.MAX_VALUE;
- final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) || getControlPanel().isUseVisualStyles()
- || getOptions().isShowDefaultNodeShapesForMarkedNodes()
- || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
- || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
- || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() );
float min_dist = 1.5f;
if ( !disallow_shortcutting ) {
if ( dynamic_hiding_factor > 4000 ) {
final float diff_y = node.getYcoord() - y2;
final float diff_x = node.getXcoord() - new_x;
if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
- || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
+ || ( diff_x < -min_dist ) ) {
paintBranchRectangular( g,
node.getXcoord(),
new_x,