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[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
5a777ca
..
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 );
@@
-565,7
+566,7
@@
class NodeEditPanel extends JPanel {
}
private List<Point> obtainPoints() {
}
private List<Point> obtainPoints() {
- Util.ensurePresenceOfDistribution( getMyNode() );
+ ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
Distribution d = getMyNode().getNodeData().getDistribution();
if ( d.getPoints() == null ) {
d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
Distribution d = getMyNode().getNodeData().getDistribution();
if ( d.getPoints() == null ) {
d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
@@
-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:
@@
-727,11
+729,12
@@
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:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
try {
getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
}
try {
getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
}
@@
-741,15
+744,15
@@
class NodeEditPanel extends JPanel {
}
break;
case TAXONOMY_SCIENTIFIC_NAME:
}
break;
case TAXONOMY_SCIENTIFIC_NAME:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setScientificName( value );
break;
case TAXONOMY_COMMON_NAME:
getMyNode().getNodeData().getTaxonomy().setScientificName( value );
break;
case TAXONOMY_COMMON_NAME:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setCommonName( value );
break;
case TAXONOMY_RANK:
getMyNode().getNodeData().getTaxonomy().setCommonName( value );
break;
case TAXONOMY_RANK:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
try {
getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
}
try {
getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
}
@@
-759,7
+762,7
@@
class NodeEditPanel extends JPanel {
}
break;
case TAXONOMY_AUTHORITY:
}
break;
case TAXONOMY_AUTHORITY:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setAuthority( value );
break;
case TAXONOMY_URI: {
getMyNode().getNodeData().getTaxonomy().setAuthority( value );
break;
case TAXONOMY_URI: {
@@
-777,7
+780,7
@@
class NodeEditPanel extends JPanel {
}
}
if ( uri != null ) {
}
}
if ( uri != null ) {
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
}
addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
break;
}
addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
break;
@@
-788,7
+791,7
@@
class NodeEditPanel extends JPanel {
}
else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
if ( !ForesterUtil.isEmpty( value ) ) {
}
else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
if ( !ForesterUtil.isEmpty( value ) ) {
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
}
}
getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
}
}
@@
-797,7
+800,7
@@
class NodeEditPanel extends JPanel {
}
break;
case TAXONOMY_ID_VALUE:
}
break;
case TAXONOMY_ID_VALUE:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
}
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
}
@@
-807,7
+810,7
@@
class NodeEditPanel extends JPanel {
}
break;
case TAXONOMY_ID_PROVIDER:
}
break;
case TAXONOMY_ID_PROVIDER:
- Util.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
}
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
}
@@
-817,19
+820,19
@@
class NodeEditPanel extends JPanel {
}
break;
case SEQ_LOCATION:
}
break;
case SEQ_LOCATION:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
getMyNode().getNodeData().getSequence().setLocation( value );
break;
case SEQ_MOL_SEQ:
getMyNode().getNodeData().getSequence().setLocation( value );
break;
case SEQ_MOL_SEQ:
- Util.ensurePresenceOfSequence( getMyNode() );
- getMyNode().getNodeData().getSequence().setMolecularSequence( value );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+ getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
break;
case SEQ_NAME:
break;
case SEQ_NAME:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
getMyNode().getNodeData().getSequence().setName( value );
break;
case SEQ_SYMBOL:
getMyNode().getNodeData().getSequence().setName( value );
break;
case SEQ_SYMBOL:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
try {
getMyNode().getNodeData().getSequence().setSymbol( value );
}
try {
getMyNode().getNodeData().getSequence().setSymbol( value );
}
@@
-839,7
+842,7
@@
class NodeEditPanel extends JPanel {
}
break;
case SEQ_TYPE:
}
break;
case SEQ_TYPE:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
try {
getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
}
try {
getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
}
@@
-849,7
+852,7
@@
class NodeEditPanel extends JPanel {
}
break;
case SEQ_ACC_SOURCE:
}
break;
case SEQ_ACC_SOURCE:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
}
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
}
@@
-859,7
+862,7
@@
class NodeEditPanel extends JPanel {
}
break;
case SEQ_ACC_VALUE:
}
break;
case SEQ_ACC_VALUE:
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
}
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
}
@@
-883,7
+886,7
@@
class NodeEditPanel extends JPanel {
}
}
if ( uri != null ) {
}
}
if ( uri != null ) {
- Util.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
}
addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
break;
}
addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
break;
@@
-925,23
+928,23
@@
class NodeEditPanel extends JPanel {
getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
break;
case DATE_DESCRIPTION:
getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
break;
case DATE_DESCRIPTION:
- Util.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setDesc( value );
break;
case DATE_MAX:
getMyNode().getNodeData().getDate().setDesc( value );
break;
case DATE_MAX:
- Util.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
break;
case DATE_MIN:
getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
break;
case DATE_MIN:
- Util.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
break;
case DATE_UNIT:
getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
break;
case DATE_UNIT:
- Util.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setUnit( value );
break;
case DATE_VALUE:
getMyNode().getNodeData().getDate().setUnit( value );
break;
case DATE_VALUE:
- Util.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
break;
case DIST_ALT: {
getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
break;
case DIST_ALT: {
@@
-960,7
+963,7
@@
class NodeEditPanel extends JPanel {
break;
}
case DIST_DESC: {
break;
}
case DIST_DESC: {
- Util.ensurePresenceOfDistribution( getMyNode() );
+ ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
final Distribution d = getMyNode().getNodeData().getDistribution();
getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
break;
final Distribution d = getMyNode().getNodeData().getDistribution();
getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
break;