import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeDataField;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
TreePanelUtil
.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
}
- if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
- && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
- .getMolecularSequence(), sb );
- }
+// if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
+// && node.getNodeData().isHasSequence()
+// && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+// TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
+// .getMolecularSequence(), sb );
+// }
final String s = sb.toString().trim();
if ( !ForesterUtil.isEmpty( s ) ) {
data.add( s );
.getSynonyms().isEmpty() );
}
- static int nodeDataIntoStringBuffer( final List<String> data, final Options optz, final StringBuilder sb ) {
+ static final int nodeDataIntoStringBuffer( final List<String> data, final Options optz, final StringBuilder sb ) {
final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
int size = 0;
- if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
- && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA )
- && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.GO_TERM_IDS ) ) {
+ if ( ( optz.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA )
+ && ( optz.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) ) {
for( final String d : data ) {
if ( !ForesterUtil.isEmpty( d ) ) {
if ( map.containsKey( d ) ) {
}
}
}
- if ( ( optz.getExtDescNodeDataToReturn() == NODE_DATA.DOMAINS_ALL )
- || ( optz.getExtDescNodeDataToReturn() == NODE_DATA.DOMAINS_COLLAPSED_PER_PROTEIN )
- || ( optz.getExtDescNodeDataToReturn() == NODE_DATA.SEQ_ANNOTATIONS ) ) {
+ if ( ( optz.getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_ALL )
+ || ( optz.getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )
+ || ( optz.getExtDescNodeDataToReturn() == NodeDataField.SEQ_ANNOTATIONS ) ) {
final ArrayList<StringInt> sis = new ArrayList<StringInt>();
for( final Entry<String, Integer> e : map.entrySet() ) {
sis.add( new StringInt( e.getKey(), e.getValue() ) );