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"rio" work
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
PhylogenyMethods.java
diff --git
a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index
67e9b52
..
f839fd6
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/
forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@
-159,6
+159,12
@@
public class PhylogenyMethods {
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+ if ( node1 == null ) {
+ throw new IllegalArgumentException( "first argument (node) is null" );
+ }
+ if ( node2 == null ) {
+ throw new IllegalArgumentException( "second argument (node) is null" );
+ }
if ( node1 == node2 ) {
return node1;
}
if ( node1 == node2 ) {
return node1;
}
@@
-211,6
+217,12
@@
public class PhylogenyMethods {
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
+ if ( node1 == null ) {
+ throw new IllegalArgumentException( "first argument (node) is null" );
+ }
+ if ( node2 == null ) {
+ throw new IllegalArgumentException( "second argument (node) is null" );
+ }
while ( node1 != node2 ) {
if ( node1.getId() > node2.getId() ) {
node1 = node1.getParent();
while ( node1 != node2 ) {
if ( node1.getId() > node2.getId() ) {
node1 = node1.getParent();
@@
-1692,10
+1704,6
@@
public class PhylogenyMethods {
TAXONOMY_ID;
}
TAXONOMY_ID;
}
- public static enum TAXONOMY_EXTRACTION {
- NO, YES, PFAM_STYLE_ONLY;
- }
-
public static enum DESCENDANT_SORT_PRIORITY {
TAXONOMY, SEQUENCE, NODE_NAME;
}
public static enum DESCENDANT_SORT_PRIORITY {
TAXONOMY, SEQUENCE, NODE_NAME;
}