inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanelUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 322199e..61db054 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -31,7 +31,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public class TreePanelUtil {
@@ -80,7 +80,7 @@ public class TreePanelUtil {
                                                    final Configuration conf,
                                                    final TreePanel tp ) {
         String uri_str = null;
-        final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+        final String upkb = SequenceAccessionTools.obtainUniProtAccessorFromDataFields( node );
         if ( !ForesterUtil.isEmpty( upkb ) ) {
             try {
                 uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
@@ -91,10 +91,10 @@ public class TreePanelUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String v = ForesterUtil.extractGenbankAccessor( node );
+            final String v = SequenceAccessionTools.obtainGenbankAccessorFromDataFields( node );
             if ( !ForesterUtil.isEmpty( v ) ) {
                 try {
-                    if ( SequenceIdParser.isProtein( v ) ) {
+                    if ( SequenceAccessionTools.isProteinDbQuery( v ) ) {
                         uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
                     }
                     else {
@@ -108,10 +108,10 @@ public class TreePanelUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+            final String v = SequenceAccessionTools.obtainRefSeqAccessorFromDataFields( node );
             if ( !ForesterUtil.isEmpty( v ) ) {
                 try {
-                    if ( SequenceIdParser.isProtein( v ) ) {
+                    if ( SequenceAccessionTools.isProteinDbQuery( v ) ) {
                         uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
                     }
                     else {
@@ -125,7 +125,7 @@ public class TreePanelUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String v = ForesterUtil.extractGInumber( node );
+            final String v = SequenceAccessionTools.obtainGiNumberFromDataFields( node );
             if ( !ForesterUtil.isEmpty( v ) ) {
                 try {
                     uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
@@ -165,15 +165,20 @@ public class TreePanelUtil {
         if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
         }
-        if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+        if ( cp.isShowSeqNames() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
         }
-        if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
+        if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
             TreePanelUtil
                     .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
         }
+        if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+            TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getGeneName(),
+                                                                       sb );
+        }
         if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
                 && ( node.getNodeData().getSequence().getAccession() != null )
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
@@ -195,7 +200,7 @@ public class TreePanelUtil {
             TreePanelUtil
                     .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
         }
-        if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
+        if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
                 && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
             TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
@@ -485,7 +490,7 @@ public class TreePanelUtil {
 
     final static boolean isSequenceEmpty( final Sequence seq ) {
         return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
-                && ForesterUtil.isEmpty( seq.getSymbol() );
+                && ForesterUtil.isEmpty( seq.getGeneName() ) && ForesterUtil.isEmpty( seq.getSymbol() );
     }
 
     final static boolean isTaxonomyEmpty( final Taxonomy tax ) {