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version 0.9910 beta
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
sdi
/
SDI.java
diff --git
a/forester/java/src/org/forester/sdi/SDI.java
b/forester/java/src/org/forester/sdi/SDI.java
index
0bb74d3
..
535d99e
100644
(file)
--- a/
forester/java/src/org/forester/sdi/SDI.java
+++ b/
forester/java/src/org/forester/sdi/SDI.java
@@
-23,7
+23,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.sdi;
package org.forester.sdi;
@@
-51,18
+51,18
@@
import org.forester.util.ForesterUtil;
* "stripTree(Phylogeny,Phylogeny)" of class Phylogeny </ul> <p> The recursion
* part is accomplished by this class' method
* "geneTreePostOrderTraversal(PhylogenyNode)". <p> Requires JDK 1.2 or greater.
* "stripTree(Phylogeny,Phylogeny)" of class Phylogeny </ul> <p> The recursion
* part is accomplished by this class' method
* "geneTreePostOrderTraversal(PhylogenyNode)". <p> Requires JDK 1.2 or greater.
- *
+ *
* @see SDI#linkNodesOfG()
* @see SDI#linkNodesOfG()
- *
+ *
* @see Phylogeny#preorderReID(int)
* @see Phylogeny#preorderReID(int)
- *
+ *
* @see
* PhylogenyMethods#taxonomyBasedDeletionOfExternalNodes(Phylogeny,Phylogeny)
* @see
* PhylogenyMethods#taxonomyBasedDeletionOfExternalNodes(Phylogeny,Phylogeny)
- *
+ *
* @see #geneTreePostOrderTraversal(PhylogenyNode)
* @see #geneTreePostOrderTraversal(PhylogenyNode)
- *
+ *
* @author Christian M. Zmasek
* @author Christian M. Zmasek
- *
+ *
* @version 1.102 -- last modified: 10/02/01
*/
public class SDI {
* @version 1.102 -- last modified: 10/02/01
*/
public class SDI {
@@
-81,7
+81,7
@@
public class SDI {
* "computeMappingCost()".
* <p>
* (Last modified: 01/11/01)
* "computeMappingCost()".
* <p>
* (Last modified: 01/11/01)
- *
+ *
* @see #infer(boolean)
* @see SDI#computeMappingCostL()
* @param gene_tree
* @see #infer(boolean)
* @see SDI#computeMappingCostL()
* @param gene_tree
@@
-92,7
+92,7
@@
public class SDI {
* reference to a rooted binary species Phylogeny which might get
* stripped in the process, must have species names in the
* species name fields for all external nodes
* reference to a rooted binary species Phylogeny which might get
* stripped in the process, must have species names in the
* species name fields for all external nodes
- * @throws SDIException
+ * @throws SDIException
*/
public SDI( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException {
if ( species_tree.isEmpty() || gene_tree.isEmpty() ) {
*/
public SDI( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException {
if ( species_tree.isEmpty() || gene_tree.isEmpty() ) {
@@
-118,7
+118,7
@@
public class SDI {
* Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for
* Comparing Molecular Phylogenies. Journal of Computational Biology 4
* 177-187.
* Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for
* Comparing Molecular Phylogenies. Journal of Computational Biology 4
* 177-187.
- *
+ *
* @return the mapping cost "L"
*/
public int computeMappingCostL() {
* @return the mapping cost "L"
*/
public int computeMappingCostL() {
@@
-130,7
+130,7
@@
public class SDI {
/**
* Returns the number of duplications.
/**
* Returns the number of duplications.
- *
+ *
* @return number of duplications
*/
public int getDuplicationsSum() {
* @return number of duplications
*/
public int getDuplicationsSum() {
@@
-139,7
+139,7
@@
public class SDI {
/**
* Returns the gene tree.
/**
* Returns the gene tree.
- *
+ *
* @return gene tree
*/
public Phylogeny getGeneTree() {
* @return gene tree
*/
public Phylogeny getGeneTree() {
@@
-148,7
+148,7
@@
public class SDI {
/**
* Returns the species tree.
/**
* Returns the species tree.
- *
+ *
* @return species tree
*/
public Phylogeny getSpeciesTree() {
* @return species tree
*/
public Phylogeny getSpeciesTree() {
@@
-175,7
+175,7
@@
public class SDI {
* the species tree must be labelled in preorder.
* <p>
* (Last modified: 01/11/01)
* the species tree must be labelled in preorder.
* <p>
* (Last modified: 01/11/01)
- *
+ *
* @param g
* starting node of a gene tree - normally the root
*/
* @param g
* starting node of a gene tree - normally the root
*/
@@
-213,7
+213,7
@@
public class SDI {
* links (sets the field "link" of PhylogenyNode) each external
* PhylogenyNode of gene_tree to the external PhylogenyNode of species_tree
* which has the same species name.
* links (sets the field "link" of PhylogenyNode) each external
* PhylogenyNode of gene_tree to the external PhylogenyNode of species_tree
* which has the same species name.
- * @throws SDIException
+ * @throws SDIException
*/
final void linkNodesOfG() throws SDIException {
final Map<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
*/
final void linkNodesOfG() throws SDIException {
final Map<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
@@
-225,7
+225,7
@@
public class SDI {
final String tax_str = SDIutil.taxonomyToString( s, tax_comp_base );
if ( speciestree_ext_nodes.containsKey( tax_str ) ) {
throw new IllegalArgumentException( "taxonomy [" + s.getNodeData().getTaxonomy()
final String tax_str = SDIutil.taxonomyToString( s, tax_comp_base );
if ( speciestree_ext_nodes.containsKey( tax_str ) ) {
throw new IllegalArgumentException( "taxonomy [" + s.getNodeData().getTaxonomy()
- + "] is not unique in species phylogeny" );
+ + "] is not unique in species phylogeny" );
}
speciestree_ext_nodes.put( tax_str, s );
}
}
speciestree_ext_nodes.put( tax_str, s );
}
@@
-236,7
+236,7
@@
public class SDI {
final PhylogenyNode s = speciestree_ext_nodes.get( tax_str );
if ( s == null ) {
throw new IllegalArgumentException( "taxonomy [" + g.getNodeData().getTaxonomy()
final PhylogenyNode s = speciestree_ext_nodes.get( tax_str );
if ( s == null ) {
throw new IllegalArgumentException( "taxonomy [" + g.getNodeData().getTaxonomy()
- + "] not present in species tree" );
+ + "] not present in species tree" );
}
g.setLink( s );
}
}
g.setLink( s );
}
@@
-250,7
+250,7
@@
public class SDI {
* To be used ONLY by method "SDIunrooted.fastInfer(Phylogeny,Phylogeny)".
* <p>
* (Last modfied: 10/02/01)
* To be used ONLY by method "SDIunrooted.fastInfer(Phylogeny,Phylogeny)".
* <p>
* (Last modfied: 10/02/01)
- *
+ *
* @param prev_root_was_dup
* true if the previous root was a duplication, false otherwise
* @param prev_root_c1
* @param prev_root_was_dup
* true if the previous root was a duplication, false otherwise
* @param prev_root_c1
@@
-403,7
+403,7
@@
public class SDI {
final HashMap<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
if ( _species_tree.getFirstExternalNode().isRoot() ) {
speciestree_ext_nodes.put( _species_tree.getFirstExternalNode().getNodeData().getTaxonomy().getIdentifier()
final HashMap<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
if ( _species_tree.getFirstExternalNode().isRoot() ) {
speciestree_ext_nodes.put( _species_tree.getFirstExternalNode().getNodeData().getTaxonomy().getIdentifier()
- .getValue(), _species_tree.getFirstExternalNode() );
+ .getValue(), _species_tree.getFirstExternalNode() );
}
else {
for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
}
else {
for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {