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.BinaryCharacters;
import org.forester.phylogeny.data.BranchWidth;
class NodePanel extends JPanel implements TreeSelectionListener {
- static final String DIST_ALTITUDE = "Altitude";
- static final String DIST_ALT_UNIT = "Altitude unit";
- static final String DIST_LONGITUDE = "Longitude";
- static final String DIST_LATITUDE = "Latitude";
- static final String DIST_GEODETIC_DATUM = "Geodetic datum";
- static final String DIST_DESCRIPTION = "Description";
- static final String DATE_UNIT = "Unit";
- static final String DATE_MAX = "Max";
- static final String DATE_MIN = "Min";
- static final String DATE_VALUE = "Value";
- static final String DATE_DESCRIPTION = "Description";
- static final String TAXONOMY_IDENTIFIER = "Identifier";
- static final String SEQ_ACCESSION = "Accession";
- static final String CONFIDENCE = "Confidence";
- static final String PROP = "Properties";
- static final String BINARY_CHARACTERS = "Binary characters";
- static final String REFERENCE = "Reference";
- static final String LIT_REFERENCE = "Reference";
- static final String LIT_REFERENCE_DESC = "Description";
- static final String LIT_REFERENCE_DOI = "DOI";
- static final String DISTRIBUTION = "Distribution";
- static final String DATE = "Date";
- static final String EVENTS = "Events";
- static final String SEQUENCE = "Sequence";
- static final String TAXONOMY = "Taxonomy";
- static final String BASIC = "Basic";
- static final String TAXONOMY_SCIENTIFIC_NAME = "Scientific name";
- static final String SEQ_MOL_SEQ = "Mol seq";
- static final String SEQ_TYPE = "Type";
- static final String SEQ_LOCATION = "Location";
- static final String SEQ_SYMBOL = "Symbol";
- static final String SEQ_URI = "URI";
- static final String NODE_BRANCH_LENGTH = "Branch length";
- static final String NODE_BRANCH_WIDTH = "Branch width";
- static final String NODE_BRANCH_COLOR = "Branch color";
- static final String NODE_NAME = "Name";
- static final String TAXONOMY_URI = "URI";
- static final String TAXONOMY_RANK = "Rank";
- static final String TAXONOMY_SYNONYM = "Synonym";
- static final String TAXONOMY_COMMON_NAME = "Common name";
- static final String TAXONOMY_AUTHORITY = "Authority";
- static final String TAXONOMY_CODE = "Code";
- static final String SEQ_NAME = "Name";
- static final String EVENTS_GENE_LOSSES = "Gene losses";
- static final String EVENTS_SPECIATIONS = "Speciations";
- static final String EVENTS_DUPLICATIONS = "Duplications";
- private static final long serialVersionUID = 5120159904388100771L;
- static final String CONFIDENCE_TYPE = "type";
- private final JTree _tree;
- private final JEditorPane _pane;
+ static final String BASIC = "Basic";
+ static final String BINARY_CHARACTERS = "Binary characters";
+ static final String CONFIDENCE = "Confidence";
+ static final String CONFIDENCE_TYPE = "type";
+ static final String DATE = "Date";
+ static final String DATE_DESCRIPTION = "Description";
+ static final String DATE_MAX = "Max";
+ static final String DATE_MIN = "Min";
+ static final String DATE_UNIT = "Unit";
+ static final String DATE_VALUE = "Value";
+ static final String DIST_ALT_UNIT = "Altitude unit";
+ static final String DIST_ALTITUDE = "Altitude";
+ static final String DIST_DESCRIPTION = "Description";
+ static final String DIST_GEODETIC_DATUM = "Geodetic datum";
+ static final String DIST_LATITUDE = "Latitude";
+ static final String DIST_LONGITUDE = "Longitude";
+ static final String DISTRIBUTION = "Distribution";
+ static final String EVENTS = "Events";
+ static final String EVENTS_DUPLICATIONS = "Duplications";
+ static final String EVENTS_GENE_LOSSES = "Gene losses";
+ static final String EVENTS_SPECIATIONS = "Speciations";
+ static final String LIT_REFERENCE = "Reference";
+ static final String LIT_REFERENCE_DESC = "Description";
+ static final String LIT_REFERENCE_DOI = "DOI";
+ static final String NODE_BRANCH_COLOR = "Branch color";
+ static final String NODE_BRANCH_LENGTH = "Branch length";
+ static final String NODE_BRANCH_WIDTH = "Branch width";
+ static final String NODE_NAME = "Name";
+ static final String PROP = "Properties";
+ static final String REFERENCE = "Reference";
+ static final String SEQ_ACCESSION = "Accession";
+ static final String SEQ_LOCATION = "Location";
+ static final String SEQ_MOL_SEQ = "Mol seq";
+ static final String SEQ_NAME = "Name";
+ static final String SEQ_SYMBOL = "Symbol";
+ static final String SEQ_TYPE = "Type";
+ static final String SEQ_URI = "URI";
+ static final String SEQUENCE = "Sequence";
+ static final String TAXONOMY = "Taxonomy";
+ static final String TAXONOMY_AUTHORITY = "Authority";
+ static final String TAXONOMY_CODE = "Code";
+ static final String TAXONOMY_COMMON_NAME = "Common name";
+ static final String TAXONOMY_IDENTIFIER = "Identifier";
+ static final String TAXONOMY_RANK = "Rank";
+ static final String TAXONOMY_SCIENTIFIC_NAME = "Scientific name";
+ static final String TAXONOMY_SYNONYM = "Synonym";
+ static final String TAXONOMY_URI = "URI";
+ private static final String SEQ_GENE_NAME = "Gene name";
+ private static final long serialVersionUID = 5120159904388100771L;
+ private final JEditorPane _pane;
+ private final JTree _tree;
public NodePanel( final PhylogenyNode phylogeny_node ) {
String node_name = "";
add( split_pane );
}
+ @Override
+ public void valueChanged( final TreeSelectionEvent e ) {
+ // Do nothing.
+ }
+
private void expandPath( final String name ) {
final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
if ( tp != null ) {
return _tree;
}
- @Override
- public void valueChanged( final TreeSelectionEvent e ) {
- // Do nothing.
- }
-
private static void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
DefaultMutableTreeNode category;
category = new DefaultMutableTreeNode( name );
top.add( category );
- addSubelement( category, REFERENCE, ann.getRef() );
- addSubelement( category, "Description", ann.getDesc() );
addSubelement( category, "Source", ann.getSource() );
addSubelement( category, "Type", ann.getType() );
addSubelement( category, "Evidence", ann.getEvidence() );
}
}
- private static void addUri( final DefaultMutableTreeNode top, final Uri uri, final String name ) {
- DefaultMutableTreeNode category;
- category = new DefaultMutableTreeNode( name );
- top.add( category );
- addSubelement( category, "Description", uri.getDescription() );
- addSubelement( category, "Type", uri.getType() );
- addSubelement( category, "URI", uri.getValue().toString() );
- }
-
private static void addAnnotations( final DefaultMutableTreeNode top,
final SortedSet<Annotation> annotations,
final DefaultMutableTreeNode category ) {
if ( ( annotations != null ) && ( annotations.size() > 0 ) ) {
category.add( new DefaultMutableTreeNode( "Annotations" ) );
final DefaultMutableTreeNode last = top.getLastLeaf();
- int i = 0;
- for( final PhylogenyData ann : annotations ) {
- addAnnotation( last, ( Annotation ) ann, "Annotation " + ( i++ ) );
- }
- }
- }
-
- private static void addUris( final DefaultMutableTreeNode top,
- final List<Uri> uris,
- final DefaultMutableTreeNode category ) {
- if ( ( uris != null ) && ( uris.size() > 0 ) ) {
- category.add( new DefaultMutableTreeNode( "URIs" ) );
- final DefaultMutableTreeNode last = top.getLastLeaf();
- int i = 0;
- for( final Uri uri : uris ) {
- if ( uri != null ) {
- addUri( last, uri, "URI " + ( i++ ) );
- }
- }
- }
- }
-
- private static void addLineage( final DefaultMutableTreeNode top,
- final List<String> lineage,
- final DefaultMutableTreeNode category ) {
- if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
- final StringBuilder sb = new StringBuilder();
- for( final String lin : lineage ) {
- if ( !ForesterUtil.isEmpty( lin ) ) {
- sb.append( lin );
- sb.append( " > " );
- }
- }
- String str = null;
- if ( sb.length() > 1 ) {
- str = sb.substring( 0, sb.length() - 3 );
- }
- if ( !ForesterUtil.isEmpty( str ) ) {
- addSubelement( category, "Lineage", str );
+ for( final Annotation ann : annotations ) {
+ addAnnotation( last, ann, ann.asText().toString() );
}
}
}
addSubelement( chars, "Present", bc.getPresentCharactersAsStringBuffer().toString() );
}
+ private static void addCrossReference( final DefaultMutableTreeNode top, final Accession x, final String name ) {
+ DefaultMutableTreeNode category;
+ category = new DefaultMutableTreeNode( name );
+ top.add( category );
+ }
+
+ private static void addCrossReferences( final DefaultMutableTreeNode top,
+ final SortedSet<Accession> xs,
+ final DefaultMutableTreeNode category ) {
+ if ( ( xs != null ) && ( xs.size() > 0 ) ) {
+ category.add( new DefaultMutableTreeNode( "Cross references" ) );
+ final DefaultMutableTreeNode last = top.getLastLeaf();
+ for( final Accession x : xs ) {
+ addCrossReference( last, x, x.asText().toString() );
+ }
+ }
+ }
+
private static void addDate( final DefaultMutableTreeNode top, final Date date, final String name ) {
DefaultMutableTreeNode category;
category = new DefaultMutableTreeNode( name );
}
}
+ private static void addLineage( final DefaultMutableTreeNode top,
+ final List<String> lineage,
+ final DefaultMutableTreeNode category ) {
+ if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
+ final StringBuilder sb = new StringBuilder();
+ for( final String lin : lineage ) {
+ if ( !ForesterUtil.isEmpty( lin ) ) {
+ sb.append( lin );
+ sb.append( " > " );
+ }
+ }
+ String str = null;
+ if ( sb.length() > 1 ) {
+ str = sb.substring( 0, sb.length() - 3 );
+ }
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ addSubelement( category, "Lineage", str );
+ }
+ }
+ }
+
private static void addProperties( final DefaultMutableTreeNode top,
final PropertiesMap properties,
final String string ) {
top.add( category );
addSubelement( category, SEQ_NAME, seq.getName() );
addSubelement( category, SEQ_SYMBOL, seq.getSymbol() );
+ addSubelement( category, SEQ_GENE_NAME, seq.getGeneName() );
if ( seq.getAccession() != null ) {
addSubelement( category, SEQ_ACCESSION, seq.getAccession().asText().toString() );
}
addSubelement( category, SEQ_LOCATION, seq.getLocation() );
addSubelement( category, SEQ_TYPE, seq.getType() );
addSubelement( category, SEQ_MOL_SEQ, seq.getMolecularSequence() );
+ if ( ( seq.getAnnotations() != null ) && !seq.getAnnotations().isEmpty() ) {
+ addAnnotations( top, seq.getAnnotations(), category );
+ }
+ if ( ( seq.getCrossReferences() != null ) && !seq.getCrossReferences().isEmpty() ) {
+ addCrossReferences( top, seq.getCrossReferences(), category );
+ }
if ( ( seq.getUris() != null ) && !seq.getUris().isEmpty() ) {
addUris( top, seq.getUris(), category );
}
- addAnnotations( top, seq.getAnnotations(), category );
}
private static void addSubelement( final DefaultMutableTreeNode node, final String name, final String value ) {
}
}
+ private static void addUri( final DefaultMutableTreeNode top, final Uri uri, final String name ) {
+ DefaultMutableTreeNode category;
+ category = new DefaultMutableTreeNode( name );
+ top.add( category );
+ addSubelement( category, "Description", uri.getDescription() );
+ addSubelement( category, "Type", uri.getType() );
+ addSubelement( category, "URI", uri.getValue().toString() );
+ }
+
+ private static void addUris( final DefaultMutableTreeNode top,
+ final List<Uri> uris,
+ final DefaultMutableTreeNode category ) {
+ if ( ( uris != null ) && ( uris.size() > 0 ) ) {
+ category.add( new DefaultMutableTreeNode( "URIs" ) );
+ final DefaultMutableTreeNode last = top.getLastLeaf();
+ int i = 0;
+ for( final Uri uri : uris ) {
+ if ( uri != null ) {
+ addUri( last, uri, "URI " + ( i++ ) );
+ }
+ }
+ }
+ }
+
private static void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {
addBasics( top, phylogeny_node, BASIC );
// Taxonomy
public final class SequenceDataRetriver extends RunnableProcess {
- private final static int DEFAULT_LINES_TO_RETURN = 50;
+ private final static int DEFAULT_LINES_TO_RETURN = 4000;
private final Phylogeny _phy;
private final MainFrameApplication _mf;
private final TreePanel _treepanel;
public class GoNameSpace {
- public final static String MOLECULAR_FUNCTION_STR = "molecular_function";
- public final static String BIOLOGICAL_PROCESS_STR = "biological_process";
- public final static String CELLULAR_COMPONENT_STR = "cellular_component";
- public final static String UNASSIGNED_STR = "unassigned";
+ public final static String MOLECULAR_FUNCTION_STR = "molecular_function";
+ public final static String BIOLOGICAL_PROCESS_STR = "biological_process";
+ public final static String CELLULAR_COMPONENT_STR = "cellular_component";
+ public final static String UNASSIGNED_STR = "unassigned";
private final GoNamespaceType _type;
public GoNameSpace( final GoNamespaceType type ) {
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.PhylogenyDataUtil;
}
node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
}
- else if ( s.startsWith( NHXtags.DOMAIN_STRUCTURE ) ) {
- if ( !node_to_annotate.getNodeData().isHasSequence() ) {
- node_to_annotate.getNodeData().setSequence( new Sequence() );
- }
- node_to_annotate.getNodeData().getSequence()
- .setDomainArchitecture( new DomainArchitecture( s.substring( 3 ) ) );
- }
else if ( s.startsWith( NHXtags.SEQUENCE_ACCESSION ) ) {
if ( !node_to_annotate.getNodeData().isHasSequence() ) {
node_to_annotate.getNodeData().setSequence( new Sequence() );
*/
public final class PhyloXmlMapping {
- public static final String PHYLOGENY = "phylogeny";
- public static final String PHYLOGENY_NAME = "name";
- public static final String PHYLOGENY_DESCRIPTION = "description";
- public static final String PHYLOGENY_IS_REROOTABLE_ATTR = "rerootable";
- public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR = "branch_length_unit";
- public static final String PHYLOGENY_IS_ROOTED_ATTR = "rooted";
- public static final String PHYLOGENY_TYPE_ATTR = "type";
- public static final String CLADE = "clade";
- public static final String NODE_NAME = "name";
- public static final String NODE_COLLAPSE = "collapse";
- public static final String SEQUENCE = "sequence";
- public static final String SEQUENCE_NAME = "name";
- public static final String SEQUENCE_SYMBOL = "symbol";
public static final String ACCESSION = "accession";
+ public static final String ACCESSION_COMMENT_ATTR = "comment";
public static final String ACCESSION_SOURCE_ATTR = "source";
- public static final String SEQUENCE_LOCATION = "location";
- public static final String SEQUENCE_MOL_SEQ = "mol_seq";
- public static final String SEQUENCE_MOL_SEQ_ALIGNED_ATTR = "is_aligned";
public static final String ANNOTATION = "annotation";
public static final String ANNOTATION_DESC = "desc";
- public static final String ANNOTATION_REF_ATTR = "ref";
public static final String ANNOTATION_EVIDENCE_ATTR = "evidence";
+ public static final String ANNOTATION_REF_ATTR = "ref";
+ public static final String ANNOTATION_SOURCE_ATTR = "source";
public static final String ANNOTATION_TYPE_ATTR = "type";
- public static final String TAXONOMY = "taxonomy";
- public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name";
- public static final String TAXONOMY_COMMON_NAME = "common_name";
- public static final String TAXONOMY_CODE = "code";
- public static final String TAXONOMY_RANK = "rank";
- public static final String TAXONOMY_SYNONYM = "synonym";
- public static final String TAXONOMY_AUTHORITY = "authority";
- public static final String DISTRIBUTION = "distribution";
+ public static final String BINARY_CHARACTER = "bc";
public static final String BINARY_CHARACTERS = "binary_characters";
- public static final String BINARY_CHARACTERS_PRESENT = "present";
public static final String BINARY_CHARACTERS_GAINED = "gained";
- public static final String BINARY_CHARACTERS_LOST = "lost";
- public static final String BINARY_CHARACTERS_TYPE_ATTR = "type";
- public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR = "present_count";
public static final String BINARY_CHARACTERS_GAINED_COUNT_ATTR = "gained_count";
+ public static final String BINARY_CHARACTERS_LOST = "lost";
public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR = "lost_count";
+ public static final String BINARY_CHARACTERS_PRESENT = "present";
+ public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR = "present_count";
+ public static final String BINARY_CHARACTERS_TYPE_ATTR = "type";
public static final String BRANCH_LENGTH = "branch_length";
+ public static final String CLADE = "clade";
+ public static final String CLADE_DATE = "date";
+ public static final String CLADE_DATE_DESC = "desc";
+ public static final String CLADE_DATE_MAX = "maximum";
+ public static final String CLADE_DATE_MIN = "minimum";
+ public static final String CLADE_DATE_UNIT = "unit";
+ public static final String CLADE_DATE_VALUE = "value";
+ public static final String COLOR = "color";
+ public static final String COLOR_BLUE = "blue";
+ public static final String COLOR_GREEN = "green";
+ public static final String COLOR_RED = "red";
public static final String CONFIDENCE = "confidence";
public static final String CONFIDENCE_SD_ATTR = "stddev";
public static final String CONFIDENCE_TYPE_ATTR = "type";
- public static final String COLOR = "color";
- public static final String COLOR_RED = "red";
- public static final String COLOR_GREEN = "green";
- public static final String COLOR_BLUE = "blue";
- public final static String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN = "domain";
- public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM = "from";
- public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO = "to";
- public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE = "confidence";
- public final static String SEQUENCE_X_REFS = "cross_references";
- // public final static String NODE_IDENTIFIER = "node_id";
- public final static String IDENTIFIER = "id";
- public final static String IDENTIFIER_PROVIDER_ATTR = "provider";
- public static final String URI = "uri";
- public static final String WIDTH = "width";
- public final static String EVENTS = "events";
- public final static String EVENT_TYPE = "type";
+ public static final String DISTRIBUTION = "distribution";
+ public static final String DISTRIBUTION_DESC = "desc";
public final static String EVENT_DUPLICATIONS = "duplications";
- public final static String EVENT_SPECIATIONS = "speciations";
public final static String EVENT_LOSSES = "losses";
- public final static String SEQUENCE_DOMAIN_ARCHITECURE = "domain_architecture";
- public final static String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH = "length";
- public final static String SEQUENCE_TYPE = "type";
- public static final String BINARY_CHARACTER = "bc";
- public static final String URI_DESC_ATTR = "desc";
- public static final String TYPE_ATTR = "type";
- public static final String REFERENCE = "reference";
- public static final String REFERENCE_DOI_ATTR = "doi";
- public static final String REFERENCE_DESC = "desc";
- public static final String PROPERTY = "property";
- public static final String PROPERTY_REF = "ref";
- public static final String PROPERTY_UNIT = "unit";
- public static final String PROPERTY_DATATYPE = "datatype";
- public static final String PROPERTY_APPLIES_TO = "applies_to";
+ public final static String EVENT_SPECIATIONS = "speciations";
+ public final static String EVENT_TYPE = "type";
+ public final static String EVENTS = "events";
public static final String ID_REF = "id_ref";
- public static final String ANNOTATION_SOURCE_ATTR = "source";
- public static final String DISTRIBUTION_DESC = "desc";
+ // public final static String NODE_IDENTIFIER = "node_id";
+ public final static String IDENTIFIER = "id";
+ public final static String IDENTIFIER_PROVIDER_ATTR = "provider";
+ public static final String NODE_COLLAPSE = "collapse";
+ public static final String NODE_NAME = "name";
+ public static final String PHYLOGENY = "phylogeny";
+ public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR = "branch_length_unit";
+ public static final String PHYLOGENY_DESCRIPTION = "description";
+ public static final String PHYLOGENY_IS_REROOTABLE_ATTR = "rerootable";
+ public static final String PHYLOGENY_IS_ROOTED_ATTR = "rooted";
+ public static final String PHYLOGENY_NAME = "name";
+ public static final String PHYLOGENY_TYPE_ATTR = "type";
public static final String POINT = "point";
- public static final String POINT_LONGITUDE = "long";
- public static final String POINT_LATITUDE = "lat";
public static final String POINT_ALTITUDE = "alt";
public static final String POINT_ALTITUDE_UNIT_ATTR = "alt_unit";
public static final String POINT_GEODETIC_DATUM = "geodetic_datum";
- public static final String CLADE_DATE = "date";
- public static final String CLADE_DATE_UNIT = "unit";
- public static final String CLADE_DATE_DESC = "desc";
- public static final String CLADE_DATE_MIN = "minimum";
- public static final String CLADE_DATE_MAX = "maximum";
- public static final String CLADE_DATE_VALUE = "value";
+ public static final String POINT_LATITUDE = "lat";
+ public static final String POINT_LONGITUDE = "long";
+ public final static String POLYGON = "polygon";
+ public static final String PROPERTY = "property";
+ public static final String PROPERTY_APPLIES_TO = "applies_to";
+ public static final String PROPERTY_DATATYPE = "datatype";
+ public static final String PROPERTY_REF = "ref";
+ public static final String PROPERTY_UNIT = "unit";
+ public static final String REFERENCE = "reference";
+ public static final String REFERENCE_DESC = "desc";
+ public static final String REFERENCE_DOI_ATTR = "doi";
+ public static final String SEQUENCE = "sequence";
+ public final static String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN = "domain";
+ public final static String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH = "length";
+ public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE = "confidence";
+ public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM = "from";
+ public final static String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO = "to";
+ public final static String SEQUENCE_DOMAIN_ARCHITECURE = "domain_architecture";
+ public static final String SEQUENCE_GENE_NAME = "gene_name";
+ public static final String SEQUENCE_LOCATION = "location";
+ public static final String SEQUENCE_MOL_SEQ = "mol_seq";
+ public static final String SEQUENCE_MOL_SEQ_ALIGNED_ATTR = "is_aligned";
+ public static final String SEQUENCE_NAME = "name";
public final static String SEQUENCE_RELATION = "sequence_relation";
- public final static String SEQUENCE_RELATION_TYPE = "type";
+ public final static String SEQUENCE_RELATION_DISTANCE = "distance";
public final static String SEQUENCE_RELATION_ID_REF0 = "id_ref_0";
public final static String SEQUENCE_RELATION_ID_REF1 = "id_ref_1";
- public final static String SEQUENCE_RELATION_DISTANCE = "distance";
+ public final static String SEQUENCE_RELATION_TYPE = "type";
public final static String SEQUENCE_SOURCE_ID = "id_source";
- public final static String POLYGON = "polygon";
-
+ public static final String SEQUENCE_SYMBOL = "symbol";
+ public final static String SEQUENCE_TYPE = "type";
+ public final static String SEQUENCE_X_REFS = "cross_references";
+ public static final String TAXONOMY = "taxonomy";
+ public static final String TAXONOMY_AUTHORITY = "authority";
+ public static final String TAXONOMY_CODE = "code";
+ public static final String TAXONOMY_COMMON_NAME = "common_name";
+ public static final String TAXONOMY_RANK = "rank";
+ public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name";
+ public static final String TAXONOMY_SYNONYM = "synonym";
+ public static final String TYPE_ATTR = "type";
+ public static final String URI = "uri";
+ public static final String URI_DESC_ATTR = "desc";
+ public static final String WIDTH = "width";
private PhyloXmlMapping() {
}
public static final String OTHER = "other";
public static final String UNKNOWN = "unknown";
- public final static Pattern SEQUENCE_SYMBOL_PATTERN = Pattern.compile( "\\S{1,30}" );
+ public final static Pattern SEQUENCE_SYMBOL_PATTERN = Pattern.compile( "\\S{1,20}" );
public final static Pattern TAXOMONY_CODE_PATTERN = Pattern
.compile( ParserUtils.TAX_CODE );
public final static Pattern LIT_REF_DOI_PATTERN = Pattern
@Override
public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException {
- if ( element.isHasAttribute( PhyloXmlMapping.ACCESSION_SOURCE_ATTR ) ) {
+ if ( element.isHasAttribute( PhyloXmlMapping.ACCESSION_SOURCE_ATTR )
+ && element.isHasAttribute( PhyloXmlMapping.ACCESSION_COMMENT_ATTR ) ) {
+ return new Accession( element.getValueAsString(),
+ element.getAttribute( PhyloXmlMapping.ACCESSION_SOURCE_ATTR ),
+ element.getAttribute( PhyloXmlMapping.ACCESSION_COMMENT_ATTR ) );
+ }
+ else if ( element.isHasAttribute( PhyloXmlMapping.ACCESSION_SOURCE_ATTR ) ) {
return new Accession( element.getValueAsString(),
element.getAttribute( PhyloXmlMapping.ACCESSION_SOURCE_ATTR ) );
}
+ else if ( element.isHasAttribute( PhyloXmlMapping.ACCESSION_COMMENT_ATTR ) ) {
+ return new Accession( element.getValueAsString(),
+ "?",
+ element.getAttribute( PhyloXmlMapping.ACCESSION_COMMENT_ATTR ) );
+ }
else {
return new Accession( element.getValueAsString(), "?" );
}
else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_NAME ) ) {
sequence.setName( child_element.getValueAsString() );
}
+ else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_GENE_NAME ) ) {
+ sequence.setGeneName( child_element.getValueAsString() );
+ }
else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_MOL_SEQ ) ) {
if ( child_element.isHasAttribute( PhyloXmlMapping.SEQUENCE_MOL_SEQ_ALIGNED_ATTR ) ) {
sequence.setMolecularSequenceAligned( Boolean.parseBoolean( child_element
}
else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_X_REFS ) ) {
for( int j = 0; j < child_element.getNumberOfChildElements(); ++j ) {
- // final XmlElement c = child_element.getChildElement( j );
- sequence.addCrossReference( ( Accession ) AccessionParser.getInstance().parse( child_element.getChildElement( j ) ) );
+ // final XmlElement c = child_element.getChildElement( j );
+ sequence.addCrossReference( ( Accession ) AccessionParser.getInstance().parse( child_element
+ .getChildElement( j ) ) );
}
//sequence.addUri( ( Uri ) UriParser.getInstance().parse( child_element ) );
}
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
match = true;
}
if ( !match && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
+ match = true;
+ }
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
match = true;
}
}
}
}
+ //
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+ if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+ if ( match( x.getComment(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getSource(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getValue(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ //
if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
I: while ( it.hasNext() ) {
match = true;
}
if ( !match && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
+ match = true;
+ }
+ if ( !match && node.getNodeData().isHasSequence()
&& match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
match = true;
}
}
}
}
+ //
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+ if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+ if ( match( x.getComment(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getSource(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getValue(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ //
if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
I: while ( it.hasNext() ) {
public final class Accession implements PhylogenyData, Comparable<Accession> {
- final private String _value;
+ final private String _comment;
final private String _source;
final private String _source_value;
+ final private String _value;
public Accession( final String value, final String source ) {
_value = value;
_source = source;
+ _comment = "";
+ if ( source != null ) {
+ _source_value = source + value;
+ }
+ else {
+ _source_value = value;
+ }
+ }
+
+ public Accession( final String value, final String source, final String comment ) {
+ _value = value;
+ _source = source;
+ _comment = comment;
if ( source != null ) {
_source_value = source + value;
}
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
if ( !ForesterUtil.isEmpty( getSource() ) ) {
- sb.append( "[" );
sb.append( getSource() );
- sb.append( "] " );
+ sb.append( ": " );
}
sb.append( getValue() );
+ if ( !ForesterUtil.isEmpty( getComment() ) ) {
+ sb.append( " (" );
+ sb.append( getComment() );
+ sb.append( ")" );
+ }
return sb;
}
@Override
+ public int compareTo( final Accession o ) {
+ if ( equals( o ) ) {
+ return 0;
+ }
+ return _source_value.compareTo( o._source_value );
+ }
+
+ @Override
public PhylogenyData copy() {
return new Accession( getValue(), getSource() );
}
}
}
+ public String getComment() {
+ return _comment;
+ }
+
public String getSource() {
return _source;
}
@Override
public int hashCode() {
-
return _source_value.hashCode();
}
@Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
if ( ForesterUtil.isEmpty( getSource() ) ) {
- PhylogenyDataUtil.appendElement( writer,
- PhyloXmlMapping.ACCESSION,
- getValue(),
- PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
- "unknown",
- indentation );
+ if ( ForesterUtil.isEmpty( getComment() ) ) {
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.ACCESSION,
+ getValue(),
+ PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+ "unknown",
+ indentation );
+ }
+ else {
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.ACCESSION,
+ getValue(),
+ PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+ "unknown",
+ PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
+ getComment(),
+ indentation );
+ }
}
else {
- PhylogenyDataUtil.appendElement( writer,
- PhyloXmlMapping.ACCESSION,
- getValue(),
- PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
- getSource(),
- indentation );
+ if ( ForesterUtil.isEmpty( getComment() ) ) {
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.ACCESSION,
+ getValue(),
+ PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+ getSource(),
+ indentation );
+ }
+ else {
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.ACCESSION,
+ getValue(),
+ PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
+ getSource(),
+ PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
+ getComment(),
+ indentation );
+ }
}
}
public String toString() {
return asText().toString();
}
-
- @Override
- public int compareTo( Accession o ) {
- if ( equals( o ) ) {
- return 0;
- }
- return _source_value.compareTo( o._source_value );
- }
}
@Override
public StringBuffer asText() {
- return asSimpleText();
+ final StringBuffer sb = new StringBuffer();
+ if ( !ForesterUtil.isEmpty( getDesc() ) && !ForesterUtil.isEmpty( getRef() ) ) {
+ sb.append( getDesc() );
+ sb.append( " (" );
+ sb.append( getRef() );
+ sb.append( ")" );
+ }
+ else if ( !ForesterUtil.isEmpty( getDesc() ) ) {
+ sb.append( getDesc() );
+ }
+ else if ( !ForesterUtil.isEmpty( getRef() ) ) {
+ sb.append( getRef() );
+ }
+ return sb;
}
@Override
private String _mol_sequence;
private boolean _mol_sequence_is_aligned;
private String _name;
+ private String _gene_name;
private String _source_id;
private Accession _accession;
private String _symbol;
&& ForesterUtil.isEmpty( getSourceId() ) && ForesterUtil.isEmpty( getMolecularSequence() )
&& ( getDomainArchitecture() == null ) && ForesterUtil.isEmpty( _annotations )
&& ForesterUtil.isEmpty( _uris ) && ForesterUtil.isEmpty( _seq_relations )
- && ( getCrossReferences() == null || getCrossReferences().isEmpty() );
+ && ( ( getCrossReferences() == null ) || getCrossReferences().isEmpty() );
}
public void addAnnotation( final Annotation annotation ) {
getAnnotations().add( annotation );
}
-
- public void addCrossReference( Accession cross_reference ) {
+
+ public void addCrossReference( final Accession cross_reference ) {
if ( getCrossReferences() == null ) {
setCrossReferences( new TreeSet<Accession>() );
}
- getCrossReferences().add( cross_reference );
+ getCrossReferences().add( cross_reference );
}
-
+
public SortedSet<Accession> getCrossReferences() {
return _xrefs;
}
-
- private void setCrossReferences( TreeSet<Accession> cross_references ) {
+
+ private void setCrossReferences( final TreeSet<Accession> cross_references ) {
_xrefs = cross_references;
}
final Sequence seq = new Sequence();
seq.setAnnotations( getAnnotations() );
seq.setName( getName() );
+ seq.setGeneName( getGeneName() );
try {
seq.setSymbol( getSymbol() );
}
seq.setCrossReferences( new TreeSet<Accession>() );
for( final Accession x : getCrossReferences() ) {
if ( x != null ) {
- seq.getCrossReferences().add( x);
+ seq.getCrossReferences().add( x );
}
}
}
return _name;
}
+ public String getGeneName() {
+ return _gene_name;
+ }
+
public List<SequenceRelation> getSequenceRelations() {
if ( _seq_relations == null ) {
_seq_relations = new ArrayList<SequenceRelation>();
}
public void init() {
- setAnnotations( null );
setName( "" );
+ setGeneName( "" );
setMolecularSequence( "" );
setMolecularSequenceAligned( false );
setLocation( "" );
setUris( null );
setSequenceRelations( null );
setSourceId( null );
- setCrossReferences(null);
+ setCrossReferences( null );
+ setAnnotations( null );
}
@Override
return getAccession().isEqual( s.getAccession() );
}
return s.getMolecularSequence().equals( getMolecularSequence() ) && s.getName().equals( getName() )
- && s.getSymbol().equals( getSymbol() );
+ && s.getSymbol().equals( getSymbol() ) && s.getGeneName().equals( getGeneName() );
}
public void setAccession( final Accession accession ) {
_name = name;
}
+ public void setGeneName( final String gene_name ) {
+ _gene_name = gene_name;
+ }
+
public void setSourceId( final String source_id ) {
_source_id = source_id;
}
if ( getAccession() != null ) {
getAccession().toNHX();
}
- if ( getDomainArchitecture() != null ) {
- sb.append( getDomainArchitecture().toNHX() );
- }
return sb;
}
if ( !ForesterUtil.isEmpty( getName() ) ) {
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_NAME, getName(), indentation );
}
+ if ( !ForesterUtil.isEmpty( getGeneName() ) ) {
+ PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_GENE_NAME, getGeneName(), indentation );
+ }
if ( !ForesterUtil.isEmpty( getLocation() ) ) {
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_LOCATION, getLocation(), indentation );
}
String.valueOf( isMolecularSequenceAligned() ),
indentation );
}
- if ( getUris() != null && !getUris().isEmpty() ) {
+ if ( ( getUris() != null ) && !getUris().isEmpty() ) {
for( final Uri uri : getUris() ) {
if ( uri != null ) {
uri.toPhyloXML( writer, level, indentation );
}
}
}
- if ( getAnnotations() != null && !getAnnotations().isEmpty() ) {
+ if ( ( getAnnotations() != null ) && !getAnnotations().isEmpty() ) {
for( final PhylogenyData annotation : getAnnotations() ) {
annotation.toPhyloXML( writer, level, my_ind );
}
if ( getDomainArchitecture() != null ) {
getDomainArchitecture().toPhyloXML( writer, level, my_ind );
}
- if ( getCrossReferences() != null && !getCrossReferences().isEmpty() ) {
+ if ( ( getCrossReferences() != null ) && !getCrossReferences().isEmpty() ) {
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( my_ind );
PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.SEQUENCE_X_REFS );
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( my_ind );
PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE_X_REFS );
- }
+ }
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );
PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE );
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
return false;
}
- SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
+ final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
if ( x.size() != 4 ) {
return false;
}
int c = 0;
- for( Accession acc : x ) {
+ for( final Accession acc : x ) {
if ( c == 0 ) {
if ( !acc.getSource().equals( "KEGG" ) ) {
return false;
}
if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
.getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
-
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
.equalsIgnoreCase( "433" ) ) {
return false;
}
- SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
+ final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
+ .getCrossReferences();
if ( x.size() != 4 ) {
return false;
}
int c = 0;
- for( Accession acc : x ) {
+ for( final Accession acc : x ) {
if ( c == 0 ) {
if ( !acc.getSource().equals( "KEGG" ) ) {
return false;
import java.util.List;
import org.forester.go.GoTerm;
+import org.forester.phylogeny.data.Accession;
import org.forester.util.ForesterUtil;
public final class EbiDbEntry implements SequenceDatabaseEntry {
public List<GoTerm> getGoTerms() {
return null;
}
+
+ @Override
+ public List<Accession> getCrossReferences() {
+ return null;
+ }
}
import java.util.List;
import org.forester.go.GoTerm;
+import org.forester.phylogeny.data.Accession;
public interface SequenceDatabaseEntry {
- public String getGeneName();
+ public String getAccession();
- public boolean isEmpty();
+ public String getGeneName();
- public String getAccession();
+ public List<GoTerm> getGoTerms();
public String getProvider();
public String getSequenceName();
- public String getTaxonomyScientificName();
+ public String getSequenceSymbol();
public String getTaxonomyIdentifier();
- public String getSequenceSymbol();
+ public String getTaxonomyScientificName();
- public List<GoTerm> getGoTerms();
+ public boolean isEmpty();
+
+ public List<Accession> getCrossReferences();
}
\ No newline at end of file
seq.setName( db_entry.getSequenceName() );
}
if ( !ForesterUtil.isEmpty( db_entry.getGeneName() ) ) {
- final String gn = db_entry.getGeneName().replace( ' ', '_' );
+ seq.setGeneName( db_entry.getGeneName() );
+ }
+ if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
try {
- seq.setSymbol( gn );
+ seq.setSymbol( db_entry.getSequenceSymbol() );
}
- catch ( PhyloXmlDataFormatException e ) {
+ catch ( final PhyloXmlDataFormatException e ) {
// Eat this exception.
}
}
- if ( !ForesterUtil.isEmpty( db_entry.getGeneName() ) ) {
- // seq.addAnnotation( new Annotation( "GN", db_entry.getGeneName() ) );
- }
- if ( db_entry.getGoTerms() != null && !db_entry.getGoTerms().isEmpty() ) {
+ if ( ( db_entry.getGoTerms() != null ) && !db_entry.getGoTerms().isEmpty() ) {
for( final GoTerm go : db_entry.getGoTerms() ) {
- seq.addAnnotation( new Annotation( go.getGoId().getId(), go.getName() ) );
+ final Annotation ann = new Annotation( go.getGoId().getId() );
+ ann.setDesc( go.getName() );
+ seq.addAnnotation( ann );
+ }
+ }
+ if ( ( db_entry.getCrossReferences() != null ) && !db_entry.getCrossReferences().isEmpty() ) {
+ for( final Accession x : db_entry.getCrossReferences() ) {
+ seq.addCrossReference( x );
}
}
-
final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy()
: new Taxonomy();
if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
import org.forester.go.BasicGoTerm;
import org.forester.go.GoNameSpace;
import org.forester.go.GoTerm;
+import org.forester.phylogeny.data.Accession;
import org.forester.util.ForesterUtil;
public final class UniProtEntry implements SequenceDatabaseEntry {
- public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PF]):([^;]+);" );
- private String _ac;
- private String _name;
- private String _symbol;
- private String _gene_name;
- private String _os_scientific_name;
- private String _tax_id;
- private List<GoTerm> _go_terms;
+ public final static Pattern BindingDB_PATTERN = Pattern.compile( "BindingDB;\\s+([0-9A-Z]+);" );
+ public final static Pattern CTD_PATTERN = Pattern.compile( "CTD;\\s+(\\d+);" );
+ public final static Pattern DrugBank_PATTERN = Pattern.compile( "DrugBank;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PFC]):([^;]+);" );
+ public final static Pattern KEGG_PATTERN = Pattern.compile( "KEGG;\\s+([a-z]+:[0-9]+);" );
+ public final static Pattern MIM_PATTERN = Pattern.compile( "MIM;\\s+(\\d+);" );
+ public final static Pattern NextBio_PATTERN = Pattern.compile( "NextBio;\\s+(\\d+);" );
+ public final static Pattern Orphanet_PATTERN = Pattern.compile( "Orphanet;\\s+(\\d+);\\s+([^\\.]+)" );
+ public final static Pattern PDB_PATTERN = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
+ public final static Pattern PharmGKB_PATTERN = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
+ public final static Pattern Reactome_PATTERN = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ private String _ac;
+ private ArrayList<Accession> _cross_references;
+ private String _gene_name;
+ private List<GoTerm> _go_terms;
+ private String _name;
+ private String _os_scientific_name;
+ private String _symbol;
+ private String _tax_id;
private UniProtEntry() {
}
throw new CloneNotSupportedException();
}
+ @Override
+ public String getAccession() {
+ return _ac;
+ }
+
+ @Override
+ public List<Accession> getCrossReferences() {
+ return _cross_references;
+ }
+
+ @Override
+ public String getGeneName() {
+ return _gene_name;
+ }
+
+ @Override
+ public List<GoTerm> getGoTerms() {
+ return _go_terms;
+ }
+
+ @Override
+ public String getProvider() {
+ return "uniprot";
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _name;
+ }
+
+ @Override
+ public String getSequenceSymbol() {
+ return _symbol;
+ }
+
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os_scientific_name;
+ }
+
+ @Override
+ public boolean isEmpty() {
+ return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
+ && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
+ && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() )
+ && ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences()
+ .isEmpty() ) );
+ }
+
+ private void addCrossReference( final Accession accession ) {
+ if ( _cross_references == null ) {
+ _cross_references = new ArrayList<Accession>();
+ }
+ System.out.println( "XREF ADDED: " + accession );
+ _cross_references.add( accession );
+ }
+
+ private void addGoTerm( final BasicGoTerm g ) {
+ if ( _go_terms == null ) {
+ _go_terms = new ArrayList<GoTerm>();
+ }
+ System.out.println( "GOTERM ADDED: " + g );
+ _go_terms.add( g );
+ }
+
+ private void setAc( final String ac ) {
+ if ( _ac == null ) {
+ _ac = ac;
+ }
+ }
+
+ private void setGeneName( final String gene_name ) {
+ if ( _gene_name == null ) {
+ _gene_name = gene_name;
+ }
+ }
+
+ private void setOsScientificName( final String os_scientific_name ) {
+ if ( _os_scientific_name == null ) {
+ _os_scientific_name = os_scientific_name;
+ }
+ }
+
+ private void setSequenceName( final String name ) {
+ if ( _name == null ) {
+ _name = name;
+ }
+ }
+
+ private void setSequenceSymbol( final String symbol ) {
+ _symbol = symbol;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
final UniProtEntry e = new UniProtEntry();
for( final String line : lines ) {
}
else if ( line.startsWith( "DR" ) ) {
if ( line.indexOf( "GO;" ) > 0 ) {
- Matcher m = GO_PATTERN.matcher( line );
+ final Matcher m = GO_PATTERN.matcher( line );
if ( m.find() ) {
- String id = m.group( 1 );
- String ns_str = m.group( 2 );
- String desc = m.group( 3 );
+ final String id = m.group( 1 );
+ final String ns_str = m.group( 2 );
+ final String desc = m.group( 3 );
String gns = GoNameSpace.BIOLOGICAL_PROCESS_STR;
- if ( ns_str.equals( "F" ) ) {
- gns = GoNameSpace.MOLECULAR_FUNCTION_STR;
- }
-
+ if ( ns_str.equals( "F" ) ) {
+ gns = GoNameSpace.MOLECULAR_FUNCTION_STR;
+ }
+ else if ( ns_str.equals( "C" ) ) {
+ gns = GoNameSpace.CELLULAR_COMPONENT_STR;
+ }
System.out.println( "GO:" + id + " " + desc + " " + ns_str );
-
- e.addGoTerm( new BasicGoTerm( id, desc, gns, false ) );
+ e.addGoTerm( new BasicGoTerm( id, desc, gns, false ) );
+ }
+ }
+ else if ( line.indexOf( "PDB;" ) > 0 ) {
+ final Matcher m = PDB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "PDB", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "KEGG;" ) > 0 ) {
+ final Matcher m = KEGG_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "KEGG" ) );
+ }
+ }
+ else if ( line.indexOf( "CTD;" ) > 0 ) {
+ final Matcher m = CTD_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "CTD" ) );
+ }
+ }
+ else if ( line.indexOf( "MIM;" ) > 0 ) {
+ final Matcher m = MIM_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "MIM" ) );
+ }
+ }
+ else if ( line.indexOf( "Orphanet;" ) > 0 ) {
+ final Matcher m = Orphanet_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "Orphanet", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "PharmGKB;" ) > 0 ) {
+ final Matcher m = PharmGKB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "PharmGKB" ) );
+ }
+ }
+ else if ( line.indexOf( "BindingDB;" ) > 0 ) {
+ final Matcher m = BindingDB_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "BindingDB" ) );
+ }
+ }
+ else if ( line.indexOf( "DrugBank;" ) > 0 ) {
+ final Matcher m = DrugBank_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "DrugBank", m.group( 2 ) ) );
+ }
+ }
+ else if ( line.indexOf( "NextBio;" ) > 0 ) {
+ final Matcher m = NextBio_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "NextBio" ) );
+ }
+ }
+ else if ( line.indexOf( "Reactome;" ) > 0 ) {
+ final Matcher m = Reactome_PATTERN.matcher( line );
+ if ( m.find() ) {
+ e.addCrossReference( new Accession( m.group( 1 ), "Reactome", m.group( 2 ) ) );
}
}
}
}
return e;
}
-
- private void addGoTerm( BasicGoTerm g ) {
- if ( _go_terms == null ) {
- _go_terms = new ArrayList<GoTerm>();
- }
- _go_terms.add( g );
-
- }
-
- private void setSequenceSymbol( String symbol ) {
- _symbol = symbol;
- }
-
- @Override
- public String getAccession() {
- return _ac;
- }
-
- private void setAc( final String ac ) {
- if ( _ac == null ) {
- _ac = ac;
- }
- }
-
- @Override
- public String getSequenceName() {
- return _name;
- }
-
- private void setSequenceName( final String name ) {
- if ( _name == null ) {
- _name = name;
- }
- }
-
- @Override
- public String getTaxonomyScientificName() {
- return _os_scientific_name;
- }
-
- private void setOsScientificName( final String os_scientific_name ) {
- if ( _os_scientific_name == null ) {
- _os_scientific_name = os_scientific_name;
- }
- }
-
- @Override
- public String getTaxonomyIdentifier() {
- return _tax_id;
- }
-
- private void setTaxId( final String tax_id ) {
- if ( _tax_id == null ) {
- _tax_id = tax_id;
- }
- }
-
- private void setGeneName( final String gene_name ) {
- if ( _gene_name == null ) {
- _gene_name = gene_name;
- }
- }
-
- @Override
- public List<GoTerm> getGoTerms() {
- return _go_terms;
- }
-
-
- @Override
- public String getSequenceSymbol() {
- return _symbol;
- }
-
- @Override
- public boolean isEmpty() {
- return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
- && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
- && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil
- .isEmpty( getSequenceSymbol() ) && ( getGoTerms() == null || getGoTerms().isEmpty() ) );
- }
-
- @Override
- public String getProvider() {
- return "uniprot";
- }
-
- @Override
- public String getGeneName() {
- return _gene_name;
- }
}
git://source.jalview.org / jalview.git / commitdiff