import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+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;
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.util.StringInt;
import org.forester.ws.seqdb.UniProtTaxonomy;
public class TreePanelUtil {
- static int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
- final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
- if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
- && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- if ( map.containsKey( d ) ) {
- map.put( d, map.get( d ) + 1 );
- }
- else {
- map.put( d, 1 );
- }
- }
- }
- }
- int size = 0;
- if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
- && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
- for( final Entry<String, Integer> e : map.entrySet() ) {
- final String v = e.getKey();
- final Object c = e.getValue();
- sb.append( v );
- sb.append( "\t" );
- sb.append( c );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- size = map.size();
- }
- else {
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
- size = data.size();
- }
- return size;
- }
-
public final static String createUriForSeqWeb( final PhylogenyNode node,
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 );
}
}
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 {
}
}
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 {
}
}
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 );
return uri_str;
}
+ public static List<String> createUrisForPdbWeb( final PhylogenyNode node,
+ final List<Accession> pdb_accs,
+ final Configuration configuration,
+ final TreePanel treePanel ) {
+ final List<String> uris = new ArrayList<String>();
+ if ( !ForesterUtil.isEmpty( pdb_accs ) ) {
+ for( final Accession pdb_acc : pdb_accs ) {
+ if ( !ForesterUtil.isEmpty( pdb_acc.getValue() ) ) {
+ uris.add( ForesterUtil.PDB + pdb_acc.getValue() );
+ }
+ }
+ }
+ return uris;
+ }
+
/**
* Returns the set of distinct taxonomies of
* all external nodes of node.
* If at least one the external nodes has no taxonomy,
* null is returned.
- *
+ *
*/
public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
final List<PhylogenyNode> descs = node.getAllExternalDescendants();
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 );
+ .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() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession()
- .toString(), sb );
+ .toString(), sb );
}
if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getTaxonomyCode(), sb );
+ .getTaxonomyCode(), sb );
}
if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getScientificName(), sb );
+ .getScientificName(), sb );
}
if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
TreePanelUtil
- .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
- }
- if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
- && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
- .getMolecularSequence(), sb );
- }
+ .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 );
+ // }
final String s = sb.toString().trim();
if ( !ForesterUtil.isEmpty( s ) ) {
data.add( s );
JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
}
- final static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
- final String my_str = str.toUpperCase();
- char first = my_str.charAt( 0 );
- char second = ' ';
- char third = ' ';
- if ( my_str.length() > 1 ) {
- if ( is_taxonomy ) {
- second = my_str.charAt( 1 );
- }
- else {
- second = my_str.charAt( my_str.length() - 1 );
- }
- if ( is_taxonomy ) {
- if ( my_str.length() > 2 ) {
- if ( my_str.indexOf( " " ) > 0 ) {
- third = my_str.charAt( my_str.indexOf( " " ) + 1 );
- }
- else {
- third = my_str.charAt( 2 );
- }
- }
- }
- else if ( my_str.length() > 2 ) {
- third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
- }
- }
- first = TreePanelUtil.normalizeCharForRGB( first );
- second = TreePanelUtil.normalizeCharForRGB( second );
- third = TreePanelUtil.normalizeCharForRGB( third );
- if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
- first = 0;
- }
- else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
- second = 255;
- }
- return new Color( first, second, third );
- }
-
final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
boolean inferred = false;
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
TreePanelUtil.collapseSubtree( n, true );
if ( !n.getNodeData().isHasTaxonomy() ) {
n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData()
- .getTaxonomy().copy() );
+ .getTaxonomy().copy() );
}
inferred = true;
}
final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
for( final PhylogenyNode desc : descs ) {
desc.getBranchData()
- .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+ .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
}
}
}
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
&& n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
- .getTaxonomy() ) );
+ .getTaxonomy() ) );
TreePanelUtil.colorizeSubtree( n, c );
++colorizations;
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
if ( true_lineage_to_color_map.containsKey( lin ) ) {
TreePanelUtil
- .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+ .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
++colorizations;
success = true;
break;
if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
sb.deleteCharAt( sb.length() - 1 );
}
- if ( i < ans.size() - 1 ) {
+ if ( i < ( ans.size() - 1 ) ) {
sb.append( ", " );
}
}
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 ) {
.getSynonyms().isEmpty() );
}
- final static char normalizeCharForRGB( char c ) {
- c -= 65;
- c *= 10.2;
- c = c > 255 ? 255 : c;
- c = c < 0 ? 0 : c;
- return c;
+ 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() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA )
+ && ( optz.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) ) {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ if ( map.containsKey( d ) ) {
+ map.put( d, map.get( d ) + 1 );
+ }
+ else {
+ map.put( d, 1 );
+ }
+ }
+ }
+ 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() ) );
+ }
+ Collections.sort( sis, new StringInt.DescendingIntComparator() );
+ for( final StringInt si : sis ) {
+ sb.append( si.getString() );
+ sb.append( "\t" );
+ sb.append( si.getInt() );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ else {
+ for( final Entry<String, Integer> e : map.entrySet() ) {
+ final String v = e.getKey();
+ final Object c = e.getValue();
+ sb.append( v );
+ sb.append( "\t" );
+ sb.append( c );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = map.size();
+ }
+ else {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ sb.append( d );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = data.size();
+ }
+ return size;
+ }
+
+ final static String pdbAccToString( final List<Accession> accs, final int i ) {
+ if ( ForesterUtil.isEmpty( accs.get( i ).getComment() ) ) {
+ return accs.get( i ).getValue();
+ }
+ return accs.get( i ).getValue() + " (" + accs.get( i ).getComment().toLowerCase() + ")";
}
final static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
git://source.jalview.org / jalview.git / blobdiff