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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 a485376..5a777ca 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
@@ -185,14 +185,11 @@ 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
-        )
-        {
+        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 ) {
@@ -568,7 +565,7 @@ class NodeEditPanel extends JPanel {
     }
 
     private List<Point> obtainPoints() {
-        ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
+        Util.ensurePresenceOfDistribution( getMyNode() );
         Distribution d = getMyNode().getNodeData().getDistribution();
         if ( d.getPoints() == null ) {
             d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
@@ -679,7 +676,7 @@ class NodeEditPanel extends JPanel {
                     try {
                         final double bw = ForesterUtil.parseDouble( value );
                         if ( bw >= 0 ) {
-                            getMyNode().getBranchData().setBranchWidth( new BranchWidth(bw ) );
+                            getMyNode().getBranchData().setBranchWidth( new BranchWidth( bw ) );
                         }
                     }
                     catch ( final ParseException e ) {
@@ -690,7 +687,7 @@ class NodeEditPanel extends JPanel {
                         mtn.setUserObject( "" );
                     }
                 }
-                break;    
+                break;
             case CONFIDENCE_VALUE:
                 double confidence = Confidence.CONFIDENCE_DEFAULT_VALUE;
                 if ( !ForesterUtil.isEmpty( value ) ) {
@@ -734,7 +731,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_CODE:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
                 }
@@ -744,15 +741,15 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_SCIENTIFIC_NAME:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
                 break;
             case TAXONOMY_COMMON_NAME:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
                 break;
             case TAXONOMY_RANK:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
                 }
@@ -762,7 +759,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_AUTHORITY:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
                 break;
             case TAXONOMY_URI: {
@@ -780,7 +777,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                    Util.ensurePresenceOfTaxonomy( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
                 break;
@@ -791,7 +788,7 @@ class NodeEditPanel extends JPanel {
                 }
                 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
                     if ( !ForesterUtil.isEmpty( value ) ) {
-                        ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                        Util.ensurePresenceOfTaxonomy( getMyNode() );
                         getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
                     }
                 }
@@ -800,7 +797,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_VALUE:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
                 }
@@ -810,7 +807,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_PROVIDER:
-                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                Util.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
                 }
@@ -820,19 +817,19 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_LOCATION:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setLocation( value );
                 break;
             case SEQ_MOL_SEQ:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setMolecularSequence( value );
                 break;
             case SEQ_NAME:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setName( value );
                 break;
             case SEQ_SYMBOL:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setSymbol( value );
                 }
@@ -842,7 +839,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_TYPE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
                 }
@@ -852,7 +849,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_SOURCE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
                 }
@@ -862,7 +859,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_VALUE:
-                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                Util.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
                 }
@@ -886,7 +883,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                    Util.ensurePresenceOfSequence( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
                 break;
@@ -928,23 +925,23 @@ class NodeEditPanel extends JPanel {
                 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
                 break;
             case DATE_DESCRIPTION:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                Util.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setDesc( value );
                 break;
             case DATE_MAX:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                Util.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_MIN:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                Util.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_UNIT:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                Util.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setUnit( value );
                 break;
             case DATE_VALUE:
-                ForesterUtil.ensurePresenceOfDate( getMyNode() );
+                Util.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
                 break;
             case DIST_ALT: {
@@ -963,7 +960,7 @@ class NodeEditPanel extends JPanel {
                 break;
             }
             case DIST_DESC: {
-                ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
+                Util.ensurePresenceOfDistribution( getMyNode() );
                 final Distribution d = getMyNode().getNodeData().getDistribution();
                 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
                 break;