git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
in progress
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
NodeEditPanel.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
index
f4bbca8
..
1892411
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
+++ b/
forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
@@
-21,7
+21,7
@@
// 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/
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
package org.forester.archaeopteryx;
@@
-60,6
+60,7
@@
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.MultipleUris;
import org.forester.phylogeny.data.PhylogenyData;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.MultipleUris;
import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.Point;
import org.forester.phylogeny.data.Reference;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Point;
import org.forester.phylogeny.data.Reference;
import org.forester.phylogeny.data.Sequence;
@@
-153,7
+154,7
@@
class NodeEditPanel extends JPanel {
top.add( category );
addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
String bl = "";
top.add( category );
addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
String bl = "";
- if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
+ if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
}
addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
}
addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
@@
-651,7
+652,7
@@
class NodeEditPanel extends JPanel {
break;
case NODE_BRANCH_LENGTH:
if ( ForesterUtil.isEmpty( value ) ) {
break;
case NODE_BRANCH_LENGTH:
if ( ForesterUtil.isEmpty( value ) ) {
- getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ getMyNode().setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
}
else {
try {
}
else {
try {
@@
-713,7
+714,8
@@
class NodeEditPanel extends JPanel {
}
else {
final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
}
else {
final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
- getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type ) );
+ final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
+ getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type, sd ) );
}
break;
case CONFIDENCE_TYPE:
}
break;
case CONFIDENCE_TYPE:
@@
-727,7
+729,8
@@
class NodeEditPanel extends JPanel {
}
else {
final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
}
else {
final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
- getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value ) );
+ final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
+ getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value, sd ) );
}
break;
case TAXONOMY_CODE:
}
break;
case TAXONOMY_CODE:
@@
-822,7
+825,7
@@
class NodeEditPanel extends JPanel {
break;
case SEQ_MOL_SEQ:
ForesterUtil.ensurePresenceOfSequence( getMyNode() );
break;
case SEQ_MOL_SEQ:
ForesterUtil.ensurePresenceOfSequence( getMyNode() );
- getMyNode().getNodeData().getSequence().setMolecularSequence( value );
+ getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
break;
case SEQ_NAME:
ForesterUtil.ensurePresenceOfSequence( getMyNode() );
break;
case SEQ_NAME:
ForesterUtil.ensurePresenceOfSequence( getMyNode() );