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removed unneeded import
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
PhylogenyNode.java
diff --git
a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index
d37cc3b
..
25b33d7
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/
forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@
-248,10
+248,7
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
}
}
}
}
- final public List<PhylogenyNode> getAllDescendants() {
- return _descendants;
- }
-
+
/**
* Returns a List containing references to all external children of this
* PhylogenyNode.
/**
* Returns a List containing references to all external children of this
* PhylogenyNode.
@@
-468,12
+465,12
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
//TODO work on me ~~
public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
//TODO work on me ~~
- if ( isInternal() && !isCollapse() ) {
- throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
- }
if ( isRoot() ) {
return null;
}
if ( isRoot() ) {
return null;
}
+ if ( isInternal() && !isCollapse() ) {
+ throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
+ }
if ( getParent().isCollapse() ) {
throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
}
if ( getParent().isCollapse() ) {
throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
}
@@
-515,6
+512,10
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
}
return _node_data;
}
}
return _node_data;
}
+
+ public final boolean isHasNodeData() {
+ return ( !( _node_data == null || _node_data.isEmpty() ) );
+ }
final public int getNumberOfDescendants() {
if ( _descendants == null ) {
final public int getNumberOfDescendants() {
if ( _descendants == null ) {
@@
-613,9
+614,10
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
/**
* Returns whether this PhylogenyNode should be drawn as collapsed.
/**
* Returns whether this PhylogenyNode should be drawn as collapsed.
+ * Root can not be collapsed.
*/
final public boolean isCollapse() {
*/
final public boolean isCollapse() {
- return _collapse;
+ return _collapse && _parent != null;
}
/**
}
/**
@@
-636,10
+638,7
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
* @return true if this PhylogenyNode is external, false otherwise
*/
final public boolean isExternal() {
* @return true if this PhylogenyNode is external, false otherwise
*/
final public boolean isExternal() {
- if ( _descendants == null ) {
- return true;
- }
- return ( getNumberOfDescendants() < 1 );
+ return ( _descendants == null ) || ( _descendants.size() == 0 );
}
final public boolean isFirstChildNode() {
}
final public boolean isFirstChildNode() {
@@
-784,14
+783,14
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
}
/**
}
/**
- * Inserts PhylogenyNode n at the specified position i into the list of
+ * Inserts PhylogenyNode node at the specified position i into the list of
* child nodes. This does not allow null slots in the list of child nodes:
* child nodes. This does not allow null slots in the list of child nodes:
- * If i is larger than the number of child nodes, n is just added to the
- * list, not place at index i.
+ * If i is larger than the number of child nodes, node is just added to the
+ * list, not placed at index i.
*
* @param i
* the index of position where to add the child
*
* @param i
* the index of position where to add the child
- * @param n
+ * @param node
* the PhylogenyNode to add
*/
final public void setChildNode( final int i, final PhylogenyNode node ) {
* the PhylogenyNode to add
*/
final public void setChildNode( final int i, final PhylogenyNode node ) {
@@
-1022,10
+1021,6
@@
public final class PhylogenyNode implements Comparable<PhylogenyNode> {
sb.append( getNodeData().getSequence().getAccession().toString() );
sb.append( " " );
}
sb.append( getNodeData().getSequence().getAccession().toString() );
sb.append( " " );
}
- if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getMolecularSequence() ) ) {
- sb.append( getNodeData().getSequence().getMolecularSequence() );
- sb.append( " " );
- }
}
if ( sb.length() <= 1 ) {
sb.append( "[" );
}
if ( sb.length() <= 1 ) {
sb.append( "[" );