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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
ws
/
uniprot
/
UniProtTaxonomy.java
diff --git
a/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
b/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
index
14fa14a
..
4f62f77
100644
(file)
--- a/
forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
+++ b/
forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
@@
-43,9
+43,10
@@
public final class UniProtTaxonomy {
private final String _rank;
private final String _id;
public final static String CELLULAR_ORGANISMS = "cellular organisms";
private final String _rank;
private final String _id;
public final static String CELLULAR_ORGANISMS = "cellular organisms";
+ public final static String VIRUSES = "Viruses";
public final static UniProtTaxonomy DROSOPHILA_GENUS = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
public final static UniProtTaxonomy DROSOPHILA_GENUS = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
- "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae" },
+ "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" },
"",
"fruit flies",
"Drosophila",
"",
"fruit flies",
"Drosophila",
@@
-54,7
+55,7
@@
public final class UniProtTaxonomy {
"7215" );
public final static UniProtTaxonomy XENOPUS_GENUS = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Amphibia",
"7215" );
public final static UniProtTaxonomy XENOPUS_GENUS = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Amphibia",
- "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae" },
+ "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae", "Xenopus" },
"",
"",
"Xenopus",
"",
"",
"Xenopus",
@@
-63,7
+64,7
@@
public final class UniProtTaxonomy {
"8353" );
public final static UniProtTaxonomy CAPITELLA_TELATA_SPECIES = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Annelida", "Polychaeta", "Scolecida", "Capitellida",
"8353" );
public final static UniProtTaxonomy CAPITELLA_TELATA_SPECIES = new UniProtTaxonomy( new String[] {
CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Annelida", "Polychaeta", "Scolecida", "Capitellida",
- "Capitellidae", "Capitella" },
+ "Capitellidae", "Capitella", "Capitella teleta" },
"",
"",
"Capitella teleta",
"",
"",
"Capitella teleta",
@@
-71,6
+72,8
@@
public final class UniProtTaxonomy {
"species",
"283909" );
"species",
"283909" );
+ // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] {
+ // CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" );
public UniProtTaxonomy( final String line ) {
final String[] items = line.split( "\t" );
if ( items.length < 5 ) {
public UniProtTaxonomy( final String line ) {
final String[] items = line.split( "\t" );
if ( items.length < 5 ) {
@@
-88,7
+91,7
@@
public final class UniProtTaxonomy {
_rank = "";
}
String[] lin = null;
_rank = "";
}
String[] lin = null;
- if ( items.length > 7 ) {
+ if ( items.length > 8 ) {
lin = items[ 8 ].split( "; " );
}
_lineage = new ArrayList<String>();
lin = items[ 8 ].split( "; " );
}
_lineage = new ArrayList<String>();
@@
-133,6
+136,9
@@
public final class UniProtTaxonomy {
_synonym = synonym;
_rank = rank;
_id = id;
_synonym = synonym;
_rank = rank;
_id = id;
+ if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+ _lineage.add( _scientific_name );
+ }
}
public UniProtTaxonomy( final String[] lineage,
}
public UniProtTaxonomy( final String[] lineage,
@@
-143,8
+149,10
@@
public final class UniProtTaxonomy {
final String rank,
final String id ) {
_lineage = new ArrayList<String>();
final String rank,
final String id ) {
_lineage = new ArrayList<String>();
- for( final String l : lineage ) {
- _lineage.add( l );
+ if ( lineage != null ) {
+ for( final String l : lineage ) {
+ _lineage.add( l );
+ }
}
_code = code;
_scientific_name = scientific_name;
}
_code = code;
_scientific_name = scientific_name;
@@
-152,6
+160,9
@@
public final class UniProtTaxonomy {
_synonym = synonym;
_rank = rank;
_id = id;
_synonym = synonym;
_rank = rank;
_id = id;
+ if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+ _lineage.add( _scientific_name );
+ }
}
/**
}
/**
@@
-185,15
+196,6
@@
public final class UniProtTaxonomy {
return _lineage;
}
return _lineage;
}
- public String[] getLineageAsArray() {
- final String[] str = new String[ _lineage.size() ];
- int i = 0;
- for( final String l : _lineage ) {
- str[ i++ ] = l;
- }
- return str;
- }
-
public String getRank() {
return _rank;
}
public String getRank() {
return _rank;
}