import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.data.BranchData;
+import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
- /** Value of -99.0 is used as default value. */
- public final static double DISTANCE_DEFAULT = -1024.0;
- private static int _node_count = 0;
+ private static int _node_count = 0;
private byte _indicator;
private int _id;
private int _sum_ext_nodes;
public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
//TODO work on me ~~
- if ( isInternal() ) {
- throw new UnsupportedOperationException( "attempt to get next external node of an internal node" );
+ if ( isInternal() && !isCollapse() ) {
+ throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
}
- else if ( isLastExternalNode() ) {
+ if ( isRoot() ) {
+ return null;
+ }
+ if ( getParent().isCollapse() ) {
+ throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
+ }
+ // This checks if last node.
+ PhylogenyNode n = this;
+ boolean last = true;
+ while ( !n.isRoot() ) {
+ if ( !n.isLastChildNode() ) {
+ last = false;
+ break;
+ }
+ n = n.getParent();
+ }
+ if ( last ) {
return null;
}
int index = getChildNodeIndex();
PhylogenyNode previous_node = this;
PhylogenyNode current_node = getParent();
while ( !current_node.isRoot()
- && ( ( current_node.getNumberOfDescendants() == 1 ) || previous_node.isLastChildNode() ) ) {
+ && ( current_node.isCollapse() || ( current_node.getNumberOfDescendants() == 1 ) || previous_node
+ .isLastChildNode() ) ) {
index = current_node.getChildNodeIndex();
previous_node = current_node;
current_node = current_node.getParent();
}
- current_node = current_node.getChildNode( index + 1 );
- while ( current_node.isInternal() ) {
+ if ( index < current_node.getNumberOfDescendants() - 1 ) {
+ current_node = current_node.getChildNode( index + 1 );
+ }
+ while ( current_node.isInternal() && !current_node.isCollapse() ) {
current_node = current_node.getFirstChildNode();
}
return current_node;
}
-
+
public final NodeData getNodeData() {
if ( _node_data == null ) {
_node_data = new NodeData();
_x = 0;
_y = 0;
//_node_name = "";
- _distance_parent = PhylogenyNode.DISTANCE_DEFAULT;
+ _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
_collapse = false;
_link = null;
_branch_data = null;
// ---------------------------------------------------------
// Writing of Nodes to Strings
// ---------------------------------------------------------
- final public String toNewHampshire( final boolean simple_nh, final boolean write_distance_to_parent ) {
+ final public String toNewHampshire( final boolean simple_nh,
+ final boolean write_distance_to_parent,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
final StringBuilder sb = new StringBuilder();
String data = "";
- if ( !ForesterUtil.isEmpty( getName() ) ) {
+ if ( ( svs == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) && !isExternal() ) {
+ if ( getBranchData().isHasConfidences()
+ && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+ data = Confidence.FORMATTER.format( ForesterUtil
+ .round( getBranchData().getConfidence( 0 ).getValue(),
+ PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) );
+ }
+ }
+ else if ( !ForesterUtil.isEmpty( getName() ) ) {
data = getName();
}
else if ( getNodeData().isHasTaxonomy() ) {
sb.append( data );
}
}
- if ( ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) && write_distance_to_parent ) {
+ if ( write_distance_to_parent && ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
sb.append( ":" );
sb.append( getDistanceToParent() );
}
+ if ( ( svs == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) && !isExternal()
+ && getBranchData().isHasConfidences()
+ && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) {
+ sb.append( "[" );
+ sb.append( Confidence.FORMATTER.format( ForesterUtil
+ .round( getBranchData().getConfidence( 0 ).getValue(),
+ PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) );
+ sb.append( "]" );
+ }
return sb.toString();
}
sb.append( name );
}
}
- if ( getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+ if ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
sb.append( ":" );
sb.append( getDistanceToParent() );
}
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
- return new PhylogenyNode( nhx, ForesterUtil.TAXONOMY_EXTRACTION.NO, false );
+ return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction )
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
throws NHXFormatException {
return new PhylogenyNode( nhx, taxonomy_extraction, false );
}
public static PhylogenyNode createInstanceFromNhxString( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores )
throws NHXFormatException {
return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
}
private PhylogenyNode( final String nhx,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+ final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean replace_underscores ) throws NHXFormatException {
init();
NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );