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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 81e869d..2a6fdd3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
@@ -52,6 +52,7 @@ import org.forester.archaeopteryx.tools.ImageLoader;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.BranchWidth;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Date;
 import org.forester.phylogeny.data.Distribution;
@@ -59,6 +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.PhylogenyDataUtil;
 import org.forester.phylogeny.data.Point;
 import org.forester.phylogeny.data.Reference;
 import org.forester.phylogeny.data.Sequence;
@@ -152,7 +154,7 @@ class NodeEditPanel extends JPanel {
         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 );
@@ -183,6 +185,12 @@ class NodeEditPanel extends JPanel {
                                "",
                                PHYLOXML_TAG.CONFIDENCE_TYPE,
                                counter );
+        String bw = "1";
+        if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
+                && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
+            bw = ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() );
+        }
+        addSubelementEditable( category, NodePanel.NODE_BRANCH_WIDTH, bw, PHYLOXML_TAG.NODE_BRANCH_WIDTH );
     }
 
     //    private void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
@@ -558,7 +566,7 @@ class NodeEditPanel extends JPanel {
     }
 
     private List<Point> obtainPoints() {
-        ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
+        AptxUtil.ensurePresenceOfDistribution( getMyNode() );
         Distribution d = getMyNode().getNodeData().getDistribution();
         if ( d.getPoints() == null ) {
             d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
@@ -644,7 +652,7 @@ class NodeEditPanel extends JPanel {
                 break;
             case NODE_BRANCH_LENGTH:
                 if ( ForesterUtil.isEmpty( value ) ) {
-                    getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+                    getMyNode().setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
                 }
                 else {
                     try {
@@ -659,6 +667,28 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 break;
+            case NODE_BRANCH_WIDTH:
+                if ( ForesterUtil.isEmpty( value ) || value.equals( "1" ) ) {
+                    if ( getMyNode().getBranchData().getBranchWidth() != null ) {
+                        getMyNode().getBranchData().setBranchWidth( new BranchWidth() );
+                    }
+                }
+                else {
+                    try {
+                        final double bw = ForesterUtil.parseDouble( value );
+                        if ( bw >= 0 ) {
+                            getMyNode().getBranchData().setBranchWidth( new BranchWidth( bw ) );
+                        }
+                    }
+                    catch ( final ParseException e ) {
+                        JOptionPane.showMessageDialog( this,
+                                                       "failed to parse branch width from: " + value,
+                                                       "Error",
+                                                       JOptionPane.ERROR_MESSAGE );
+                        mtn.setUserObject( "" );
+                    }
+                }
+                break;
             case CONFIDENCE_VALUE:
                 double confidence = Confidence.CONFIDENCE_DEFAULT_VALUE;
                 if ( !ForesterUtil.isEmpty( value ) ) {
@@ -684,7 +714,8 @@ class NodeEditPanel extends JPanel {
                 }
                 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:
@@ -698,11 +729,12 @@ class NodeEditPanel extends JPanel {
                 }
                 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:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
                 }
@@ -712,15 +744,15 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_SCIENTIFIC_NAME:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
                 break;
             case TAXONOMY_COMMON_NAME:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
                 break;
             case TAXONOMY_RANK:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
                 }
@@ -730,7 +762,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_AUTHORITY:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
                 break;
             case TAXONOMY_URI: {
@@ -748,7 +780,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                    AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
                 break;
@@ -759,7 +791,7 @@ class NodeEditPanel extends JPanel {
                 }
                 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
                     if ( !ForesterUtil.isEmpty( value ) ) {
-                        ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                        AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                         getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
                     }
                 }
@@ -768,7 +800,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_VALUE:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
                 }
@@ -778,7 +810,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_PROVIDER:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
                 }
@@ -788,19 +820,19 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_LOCATION:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setLocation( value );
                 break;
             case SEQ_MOL_SEQ:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
-                getMyNode().getNodeData().getSequence().setMolecularSequence( value );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
                 break;
             case SEQ_NAME:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setName( value );
                 break;
             case SEQ_SYMBOL:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setSymbol( value );
                 }
@@ -810,7 +842,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_TYPE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
                 }
@@ -820,7 +852,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_SOURCE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
                 }
@@ -830,7 +862,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_VALUE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
                 }
@@ -854,7 +886,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                    AptxUtil.ensurePresenceOfSequence( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
                 break;
@@ -896,23 +928,23 @@ class NodeEditPanel extends JPanel {
                 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
                 break;
             case DATE_DESCRIPTION:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                AptxUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setDesc( value );
                 break;
             case DATE_MAX:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                AptxUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_MIN:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                AptxUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_UNIT:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                AptxUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setUnit( value );
                 break;
             case DATE_VALUE:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                AptxUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
                 break;
             case DIST_ALT: {
@@ -931,7 +963,7 @@ class NodeEditPanel extends JPanel {
                 break;
             }
             case DIST_DESC: {
-                ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
+                AptxUtil.ensurePresenceOfDistribution( getMyNode() );
                 final Distribution d = getMyNode().getNodeData().getDistribution();
                 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
                 break;
@@ -1020,6 +1052,7 @@ class NodeEditPanel extends JPanel {
     private enum PHYLOXML_TAG {
         NODE_NAME,
         NODE_BRANCH_LENGTH,
+        NODE_BRANCH_WIDTH,
         TAXONOMY_CODE,
         TAXONOMY_SCIENTIFIC_NAME,
         TAXONOMY_AUTHORITY,