import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
import org.forester.ws.uniprot.DatabaseTools;
import org.forester.ws.uniprot.SequenceDatabaseEntry;
import org.forester.ws.uniprot.UniProtWsTools;
import org.forester.ws.uniprot.DatabaseTools;
import org.forester.ws.uniprot.SequenceDatabaseEntry;
import org.forester.ws.uniprot.UniProtWsTools;
private final Phylogeny _phy;
private final MainFrameApplication _mf;
private final TreePanel _treepanel;
private final Phylogeny _phy;
private final MainFrameApplication _mf;
private final TreePanel _treepanel;
}
public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
}
public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
SortedSet<String> not_found = null;
try {
not_found = obtainSeqInformation( _phy );
}
catch ( final UnknownHostException e ) {
SortedSet<String> not_found = null;
try {
not_found = obtainSeqInformation( _phy );
}
catch ( final UnknownHostException e ) {
JOptionPane.showMessageDialog( _mf,
"Could not connect to \"" + getBaseUrl() + "\"",
"Network error during taxonomic information gathering",
JOptionPane.showMessageDialog( _mf,
"Could not connect to \"" + getBaseUrl() + "\"",
"Network error during taxonomic information gathering",
}
if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
seq.setName( db_entry.getSequenceName() );
}
if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
seq.setName( db_entry.getSequenceName() );