inprogress

[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 2a6fdd3..f593a78 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
-// WWW: www.phylosoft.org/
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -337,6 +337,7 @@ class NodeEditPanel extends JPanel {
         }
         addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
         addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
+        addSubelementEditable( category, NodePanel.SEQ_GENE_NAME, seq.getGeneName(), PHYLOXML_TAG.SEQ_GENE_NAME );
         addSubelementEditable( category,
                                NodePanel.SEQ_ACCESSION,
                                acc.getValue(),
@@ -566,7 +567,7 @@ class NodeEditPanel extends JPanel {
     }
 
     private List<Point> obtainPoints() {
-        AptxUtil.ensurePresenceOfDistribution( getMyNode() );
+        ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
         Distribution d = getMyNode().getNodeData().getDistribution();
         if ( d.getPoints() == null ) {
             d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
@@ -734,7 +735,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_CODE:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
                 }
@@ -744,15 +745,15 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_SCIENTIFIC_NAME:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
                 break;
             case TAXONOMY_COMMON_NAME:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
                 break;
             case TAXONOMY_RANK:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 try {
                     getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
                 }
@@ -762,7 +763,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_AUTHORITY:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
                 break;
             case TAXONOMY_URI: {
@@ -780,7 +781,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                    ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
                 break;
@@ -791,7 +792,7 @@ class NodeEditPanel extends JPanel {
                 }
                 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
                     if ( !ForesterUtil.isEmpty( value ) ) {
-                        AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                        ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                         getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
                     }
                 }
@@ -800,7 +801,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_VALUE:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
                 }
@@ -810,7 +811,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case TAXONOMY_ID_PROVIDER:
-                AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+                ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
                 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
                     getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
                 }
@@ -820,19 +821,19 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_LOCATION:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setLocation( value );
                 break;
             case SEQ_MOL_SEQ:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
                 break;
             case SEQ_NAME:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 getMyNode().getNodeData().getSequence().setName( value );
                 break;
             case SEQ_SYMBOL:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setSymbol( value );
                 }
@@ -841,8 +842,12 @@ class NodeEditPanel extends JPanel {
                     break;
                 }
                 break;
+            case SEQ_GENE_NAME:
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                getMyNode().getNodeData().getSequence().setGeneName( value );
+                break;
             case SEQ_TYPE:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
                     getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
                 }
@@ -852,7 +857,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_SOURCE:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
                 }
@@ -862,7 +867,7 @@ class NodeEditPanel extends JPanel {
                 }
                 break;
             case SEQ_ACC_VALUE:
-                AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
                     getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
                 }
@@ -886,7 +891,7 @@ class NodeEditPanel extends JPanel {
                     }
                 }
                 if ( uri != null ) {
-                    AptxUtil.ensurePresenceOfSequence( getMyNode() );
+                    ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 }
                 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
                 break;
@@ -928,23 +933,23 @@ class NodeEditPanel extends JPanel {
                 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
                 break;
             case DATE_DESCRIPTION:
-                AptxUtil.ensurePresenceOfDate( getMyNode() );
+                ForesterUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setDesc( value );
                 break;
             case DATE_MAX:
-                AptxUtil.ensurePresenceOfDate( getMyNode() );
+                ForesterUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_MIN:
-                AptxUtil.ensurePresenceOfDate( getMyNode() );
+                ForesterUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
                 break;
             case DATE_UNIT:
-                AptxUtil.ensurePresenceOfDate( getMyNode() );
+                ForesterUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setUnit( value );
                 break;
             case DATE_VALUE:
-                AptxUtil.ensurePresenceOfDate( getMyNode() );
+                ForesterUtil.ensurePresenceOfDate( getMyNode() );
                 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
                 break;
             case DIST_ALT: {
@@ -963,7 +968,7 @@ class NodeEditPanel extends JPanel {
                 break;
             }
             case DIST_DESC: {
-                AptxUtil.ensurePresenceOfDistribution( getMyNode() );
+                ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
                 final Distribution d = getMyNode().getNodeData().getDistribution();
                 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
                 break;
@@ -1062,6 +1067,7 @@ class NodeEditPanel extends JPanel {
         TAXONOMY_URI,
         SEQ_SYMBOL,
         SEQ_NAME,
+        SEQ_GENE_NAME,
         SEQ_LOCATION,
         SEQ_TYPE,
         SEQ_MOL_SEQ,