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taxonomy extraction changed
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
io
/
parsers
/
phyloxml
/
PhyloXmlMapping.java
diff --git
a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
index
7e2747d
..
9e72a30
100644
(file)
--- a/
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
+++ b/
forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.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.io.parsers.phyloxml;
package org.forester.io.parsers.phyloxml;
@@
-42,6
+42,7
@@
public final class PhyloXmlMapping {
public static final String PHYLOGENY_TYPE_ATTR = "type";
public static final String CLADE = "clade";
public static final String NODE_NAME = "name";
public static final String PHYLOGENY_TYPE_ATTR = "type";
public static final String CLADE = "clade";
public static final String NODE_NAME = "name";
+ public static final String NODE_COLLAPSE = "collapse";
public static final String SEQUENCE = "sequence";
public static final String SEQUENCE_NAME = "name";
public static final String SEQUENCE_SYMBOL = "symbol";
public static final String SEQUENCE = "sequence";
public static final String SEQUENCE_NAME = "name";
public static final String SEQUENCE_SYMBOL = "symbol";
@@
-73,6
+74,7
@@
public final class PhyloXmlMapping {
public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count";
public static final String BRANCH_LENGTH = "branch_length";
public static final String CONFIDENCE = "confidence";
public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count";
public static final String BRANCH_LENGTH = "branch_length";
public static final String CONFIDENCE = "confidence";
+ public static final String CONFIDENCE_SD_ATTR = "stddev";
public static final String CONFIDENCE_TYPE_ATTR = "type";
public static final String COLOR = "color";
public static final String COLOR_RED = "red";
public static final String CONFIDENCE_TYPE_ATTR = "type";
public static final String COLOR = "color";
public static final String COLOR_RED = "red";