}
}
if ( type == '?' ) {
- if ( SequenceAccessionTools.isProtein( query ) ) {
+ if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
type = 'p';
}
else {
}
final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
- final Accession a = SequenceAccessionTools.parse( node );
+ final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
if ( a != null ) {
return a.getValue();
}
final Configuration conf,
final TreePanel tp ) {
String uri_str = null;
- final String upkb = SequenceAccessionTools.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 = SequenceAccessionTools.extractGenbankAccessor( node );
+ final String v = SequenceAccessionTools.obtainGenbankAccessorFromDataFields( node );
if ( !ForesterUtil.isEmpty( v ) ) {
try {
- if ( SequenceAccessionTools.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 = SequenceAccessionTools.extractRefSeqAccessor( node );
+ final String v = SequenceAccessionTools.obtainRefSeqAccessorFromDataFields( node );
if ( !ForesterUtil.isEmpty( v ) ) {
try {
- if ( SequenceAccessionTools.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 = SequenceAccessionTools.extractGInumber( node );
+ final String v = SequenceAccessionTools.obtainGiNumberFromDataFields( node );
if ( !ForesterUtil.isEmpty( v ) ) {
try {
uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
}
if ( ForesterUtil.isEmpty( query ) && ( node.getNodeData().getSequence().getAccession() != null )
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
- final Accession id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getAccession()
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence().getAccession()
.getValue() );
if ( id != null ) {
query = id.getValue();
}
}
if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
- final Accession id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getName() );
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence().getName() );
if ( id != null ) {
query = id.getValue();
}
}
if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
- final Accession id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getSymbol() );
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence().getSymbol() );
if ( id != null ) {
query = id.getValue();
}
}
if ( ForesterUtil.isEmpty( query )
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
- final Accession id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getGeneName() );
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence().getGeneName() );
if ( id != null ) {
query = id.getValue();
}
}
}
if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
- final Accession id = SequenceAccessionTools.parse( node.getName() );
+ final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getName() );
if ( id != null ) {
query = id.getValue();
}
_descendants = null;
}
+ public boolean isEmpty() {
+ }
+
/**
* Adds PhylogenyNode n to the list of child nodes and sets the _parent of n
* to this.
private static String obtainSeqLink( final String p ) {
String link;
- final String up_id = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( p );
+ final String up_id = SequenceAccessionTools.parseUniProtAccessorFromString( p );
if ( !ForesterUtil.isEmpty( up_id ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.UNIPROT_KB + up_id + "\" target=\"_up_window\">" + up_id
+ "</a>";
}
else {
- final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessor( p );
+ final String gb_id = SequenceAccessionTools.parseGenbankProteinAccessorFromString( p );
if ( !ForesterUtil.isEmpty( gb_id ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_PROTEIN + gb_id + "\" target=\"_up_window\">"
+ gb_id + "</a>";
}
else {
- final String gi = SequenceAccessionTools.parseGInumber( p );
+ final String gi = SequenceAccessionTools.parseGInumberFromString( p );
if ( !ForesterUtil.isEmpty( gi ) ) {
link = "<a class=\"pl\" href=\"" + ForesterUtil.NCBI_GI + gi + "\" target=\"_up_window\">gi|" + gi
+ "</a>";
//Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
//Protein: 3 letters + 5 numerals
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html
- if ( !SequenceAccessionTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "AAY423861" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "AY4238612" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "AAY4238612" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "Y423861" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "|S123456" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "ABC123456" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
return false;
}
- if ( !SequenceAccessionTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
return false;
}
- if ( SequenceAccessionTools.parseGenbankAccessor( "ABCD12345" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
return false;
}
return true;
try {
PhylogenyNode n = new PhylogenyNode();
n.setName( "tr|B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr.B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr=B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr-B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr/B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr\\B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr_B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( " tr|B3RJ64 " );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "-tr|B3RJ64-" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "-tr=B3RJ64-" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "_tr=B3RJ64_" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( " tr_tr|B3RJ64_sp|123 " );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "sp|B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "sp|B3RJ64C" );
- if ( SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "sp|B3RJ6X" );
- if ( SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp|B3RJ6" );
- if ( SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "K1PYK7_CRAGI" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
n.setName( "K1PYK7_PEA" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
return false;
}
n.setName( "K1PYK7_RAT" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
return false;
}
n.setName( "K1PYK7_PIG" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
return false;
}
n.setName( "~K1PYK7_PIG~" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
return false;
}
n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
n.setName( "K1PYKX_CRAGI" );
- if ( SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "XXXXX_CRAGI" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
return false;
}
n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
return false;
}
n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
- if ( SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
return false;
}
n = new PhylogenyNode();
org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
seq.setSymbol( "K1PYK7_CRAGI" );
n.getNodeData().addSequence( seq );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
seq.setSymbol( "tr|B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setName( "K1PYK7_CRAGI" );
n.getNodeData().addSequence( seq );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
seq.setName( "tr|B3RJ64" );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
n.getNodeData().addSequence( seq );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
n.getNodeData().addSequence( seq );
- if ( !SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
//
n = new PhylogenyNode();
n.setName( "ACP19736" );
- if ( !SequenceAccessionTools.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
return false;
}
n = new PhylogenyNode();
n.setName( "_ACP19736_" );
- if ( !SequenceAccessionTools.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
return false;
}
}
private static boolean testSequenceIdParsing() {
try {
- Accession id = SequenceAccessionTools.parse( "gb_ADF31344_segmented_worms_" );
+ Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "segmented worms|gb_ADF31344" );
+ id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "segmented worms gb_ADF31344 and more" );
+ id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "gb_AAA96518_1" );
+ id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "gb_EHB07727_1_rodents_" );
+ id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "dbj_BAF37827_1_turtles_" );
+ id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "emb_CAA73223_1_primates_" );
+ id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "mites|ref_XP_002434188_1" );
+ id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
+ id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
if ( id != null ) {
return false;
}
//
- id = SequenceAccessionTools.parse( "P4A123" );
+ id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
if ( id != null ) {
// return false;
// }
//
- id = SequenceAccessionTools.parse( "XP_12345" );
+ id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
System.out.println( "provider=" + id.getSource() );
\r
public final class SequenceAccessionTools {\r
\r
- public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern\r
- .compile( "\\b([A-Z][0-9][A-Z0-9]{3}[0-9])\\b" );\r
- public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern\r
- .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );\r
- public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern\r
- .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
// gb_ADF31344_1_segmented_worms_\r
// gb_AAA96518_1\r
// gb_EHB07727_1_rodents_\r
//Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals\r
//Protein: 3 letters + 5 numerals\r
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html\r
- private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_1 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_2 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- private final static Pattern GENBANK_PROTEIN_AC_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
- private final static Pattern GI_PATTERN = Pattern\r
- .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
+ public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GENBANK_PROT_PATTERN = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ public final static Pattern GI_PATTERN = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
+ public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "\\b([A-Z][0-9][A-Z0-9]{3}[0-9])\\b" );\r
+ public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern\r
+ .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );\r
+ public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern\r
+ .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
// RefSeq accession numbers can be distinguished from GenBank accessions \r
// by their distinct prefix format of 2 characters followed by an\r
// underscore character ('_'). For example, a RefSeq protein accession is NP_015325. \r
- private final static Pattern REFSEQ_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ private final static Pattern REFSEQ_PATTERN = Pattern\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
\r
private SequenceAccessionTools() {\r
// Hiding the constructor.\r
}\r
\r
- public static String extractGenbankAccessor( final PhylogenyNode node ) {\r
- String v = null;\r
- if ( node.getNodeData().isHasSequence() ) {\r
- final Sequence seq = node.getNodeData().getSequence();\r
- if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {\r
- v = parseGenbankAccessor( seq.getSymbol() );\r
- }\r
- if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {\r
- v = parseGenbankAccessor( seq.getGeneName() );\r
- }\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
- v = parseGenbankAccessor( seq.getName() );\r
- }\r
- if ( ForesterUtil.isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )\r
- && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
- v = parseGenbankAccessor( seq.getAccession().getValue() );\r
- }\r
+ public final static boolean isProteinDbQuery( final String query ) {\r
+ final String r1 = parseRefSeqAccessorFromString( query );\r
+ if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {\r
+ return true;\r
}\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( node.getName() ) ) {\r
- v = parseGenbankAccessor( node.getName() );\r
+ final String r2 = parseUniProtAccessorFromString( query );\r
+ if ( !ForesterUtil.isEmpty( r2 ) ) {\r
+ return true;\r
}\r
- return v;\r
+ return GENBANK_PROT_PATTERN.matcher( query ).lookingAt();\r
}\r
\r
- public static String extractGInumber( final PhylogenyNode node ) {\r
- String v = null;\r
- if ( node.getNodeData().isHasSequence() ) {\r
- final Sequence seq = node.getNodeData().getSequence();\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
- v = parseGInumber( seq.getName() );\r
+ public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) {\r
+ String a = obtainUniProtAccessorFromDataFields( n );\r
+ if ( !ForesterUtil.isEmpty( a ) ) {\r
+ return new Accession( a, Accession.UNIPROT );\r
+ }\r
+ a = obtainGenbankAccessorFromDataFields( n );\r
+ if ( !ForesterUtil.isEmpty( a ) ) {\r
+ return new Accession( a, Accession.NCBI );\r
+ }\r
+ a = obtainRefSeqAccessorFromDataFields( n );\r
+ if ( !ForesterUtil.isEmpty( a ) ) {\r
+ return new Accession( a, Accession.REFSEQ );\r
+ }\r
+ a = obtainGiNumberFromDataFields( n );\r
+ if ( !ForesterUtil.isEmpty( a ) ) {\r
+ return new Accession( a, Accession.GI );\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public final static Accession obtainFromSeqAccession( final PhylogenyNode n ) {\r
+ if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getSource() )\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getValue() ) ) {\r
+ final String source = n.getNodeData().getSequence().getAccession().getSource().toLowerCase();\r
+ final String value = n.getNodeData().getSequence().getAccession().getValue();\r
+ if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source\r
+ .equals( "sp" ) ) ) {\r
+ return new Accession( value, Accession.UNIPROT );\r
}\r
- if ( ForesterUtil.isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )\r
- && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
- v = parseGInumber( seq.getAccession().getValue() );\r
+ else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) {\r
+ return new Accession( value, Accession.EMBL );\r
+ }\r
+ else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) {\r
+ return new Accession( value, Accession.NCBI );\r
+ }\r
+ else if ( source.equals( "refseq" ) ) {\r
+ return new Accession( value, Accession.REFSEQ );\r
+ }\r
+ else if ( source.equals( "gi" ) ) {\r
+ return new Accession( value, Accession.GI );\r
}\r
}\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( node.getName() ) ) {\r
- v = parseGInumber( node.getName() );\r
- }\r
- return v;\r
+ return null;\r
}\r
\r
- public static String extractRefSeqAccessor( final PhylogenyNode node ) {\r
- String v = null;\r
- if ( node.getNodeData().isHasSequence() ) {\r
- final Sequence seq = node.getNodeData().getSequence();\r
+ public final static String obtainGenbankAccessorFromDataFields( final PhylogenyNode n ) {\r
+ String a = null;\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence seq = n.getNodeData().getSequence();\r
if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {\r
- v = parseRefSeqAccessor( seq.getSymbol() );\r
+ a = parseGenbankAccessorFromString( seq.getSymbol() );\r
}\r
if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {\r
- v = parseRefSeqAccessor( seq.getGeneName() );\r
+ a = parseGenbankAccessorFromString( seq.getGeneName() );\r
}\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
- v = parseRefSeqAccessor( seq.getName() );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
+ a = parseGenbankAccessorFromString( seq.getName() );\r
}\r
- if ( ForesterUtil.isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )\r
+ if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )\r
&& !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
- v = parseRefSeqAccessor( seq.getAccession().getValue() );\r
+ a = parseGenbankAccessorFromString( seq.getAccession().getValue() );\r
}\r
}\r
- if ( ForesterUtil.isEmpty( v ) && !ForesterUtil.isEmpty( node.getName() ) ) {\r
- v = parseRefSeqAccessor( node.getName() );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ a = parseGenbankAccessorFromString( n.getName() );\r
}\r
- return v;\r
+ return a;\r
}\r
\r
- public static String extractUniProtKbProteinSeqIdentifier( final PhylogenyNode node ) {\r
+ public final static String obtainGiNumberFromDataFields( final PhylogenyNode n ) {\r
String a = null;\r
- if ( node.getNodeData().isHasSequence() ) {\r
- final Sequence seq = node.getNodeData().getSequence();\r
- if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {\r
- a = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( seq.getSymbol() );\r
- }\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence seq = n.getNodeData().getSequence();\r
if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
- a = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( seq.getName() );\r
+ a = parseGInumberFromString( seq.getName() );\r
}\r
if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {\r
- a = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( seq.getGeneName() );\r
+ a = parseGInumberFromString( seq.getGeneName() );\r
}\r
- if ( ForesterUtil.isEmpty( a ) && ( node.getNodeData().getSequence().getAccession() != null )\r
+ if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )\r
&& !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
- a = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( seq.getAccession().getValue() );\r
+ a = parseGInumberFromString( seq.getAccession().getValue() );\r
}\r
}\r
- if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( node.getName() ) ) {\r
- a = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( node.getName() );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ a = parseGInumberFromString( n.getName() );\r
}\r
return a;\r
}\r
\r
- public static String extractUniProtKbProteinSeqIdentifier( final String str ) {\r
- Matcher m = UNIPROT_KB_PATTERN_0.matcher( str );\r
- if ( m.find() ) {\r
- return m.group( 1 );\r
- }\r
- m = UNIPROT_KB_PATTERN_1.matcher( str );\r
- if ( m.find() ) {\r
- return m.group( 1 );\r
- }\r
- m = UNIPROT_KB_PATTERN_2.matcher( str );\r
- if ( m.find() ) {\r
- return m.group();\r
- }\r
- return null;\r
- }\r
-\r
- public final static boolean isProtein( final String query ) {\r
- final String r1 = parseRefSeqAccessor( query );\r
- if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {\r
- return true;\r
- }\r
- final String r2 = extractUniProtKbProteinSeqIdentifier( query );\r
- if ( !ForesterUtil.isEmpty( r2 ) ) {\r
- return true;\r
- }\r
- return GENBANK_PROTEIN_AC_PATTERN.matcher( query ).lookingAt();\r
- }\r
-\r
- public final static Accession parse( final PhylogenyNode n ) {\r
- String v = extractUniProtKbProteinSeqIdentifier( n );\r
- if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.UNIPROT );\r
- }\r
- v = extractGenbankAccessor( n );\r
- if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.NCBI );\r
- }\r
- v = extractRefSeqAccessor( n );\r
- if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.REFSEQ );\r
+ public final static String obtainRefSeqAccessorFromDataFields( final PhylogenyNode n ) {\r
+ String a = null;\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence seq = n.getNodeData().getSequence();\r
+ if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {\r
+ a = parseRefSeqAccessorFromString( seq.getSymbol() );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {\r
+ a = parseRefSeqAccessorFromString( seq.getGeneName() );\r
+ }\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
+ a = parseRefSeqAccessorFromString( seq.getName() );\r
+ }\r
+ if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
+ a = parseRefSeqAccessorFromString( seq.getAccession().getValue() );\r
+ }\r
}\r
- v = extractGInumber( n );\r
- if ( !ForesterUtil.isEmpty( v ) ) {\r
- return new Accession( v, Accession.GI );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ a = parseRefSeqAccessorFromString( n.getName() );\r
}\r
- return null;\r
+ return a;\r
}\r
\r
- public final static Accession obtainFromSeqAccession( final PhylogenyNode node ) {\r
- if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )\r
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )\r
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {\r
- final String source = node.getNodeData().getSequence().getAccession().getSource().toLowerCase();\r
- final String value = node.getNodeData().getSequence().getAccession().getValue();\r
- if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source\r
- .equals( "sp" ) ) ) {\r
- return new Accession( value, Accession.UNIPROT );\r
- }\r
- else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) {\r
- return new Accession( value, Accession.EMBL );\r
+ public final static String obtainUniProtAccessorFromDataFields( final PhylogenyNode n ) {\r
+ String a = null;\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence seq = n.getNodeData().getSequence();\r
+ if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {\r
+ a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getSymbol() );\r
}\r
- else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) {\r
- return new Accession( value, Accession.NCBI );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {\r
+ a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getName() );\r
}\r
- else if ( source.equals( "refseq" ) ) {\r
- return new Accession( value, Accession.REFSEQ );\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {\r
+ a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getGeneName() );\r
}\r
- else if ( source.equals( "gi" ) ) {\r
- return new Accession( value, Accession.GI );\r
+ if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )\r
+ && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {\r
+ a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getAccession().getValue() );\r
}\r
}\r
- return null;\r
+ if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ a = SequenceAccessionTools.parseUniProtAccessorFromString( n.getName() );\r
+ }\r
+ return a;\r
}\r
\r
- /**\r
- * Returns null if no match.\r
- * \r
- */\r
- public final static Accession parse( final String s ) {\r
+ public final static Accession parseAccessorFromString( final String s ) {\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
- String v = extractUniProtKbProteinSeqIdentifier( s );\r
+ String v = parseUniProtAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
return new Accession( v, Accession.UNIPROT );\r
}\r
- v = parseGenbankAccessor( s );\r
+ v = parseGenbankAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
return new Accession( v, Accession.NCBI );\r
}\r
- v = parseRefSeqAccessor( s );\r
+ v = parseRefSeqAccessorFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
return new Accession( v, Accession.REFSEQ );\r
}\r
- v = parseGInumber( s );\r
+ v = parseGInumberFromString( s );\r
if ( !ForesterUtil.isEmpty( v ) ) {\r
return new Accession( v, Accession.GI );\r
}\r
return null;\r
}\r
\r
- /**\r
- * Returns null if no match.\r
- * \r
- */\r
- public static String parseGenbankAccessor( final String query ) {\r
- Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );\r
+ public final static String parseGenbankAccessorFromString( final String s ) {\r
+ Matcher m = GENBANK_NUC_PATTERN_1.matcher( s );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
}\r
else {\r
- m = GENBANK_NUCLEOTIDE_AC_PATTERN_2.matcher( query );\r
+ m = GENBANK_NUC_PATTERN_2.matcher( s );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
}\r
else {\r
- m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );\r
+ m = GENBANK_PROT_PATTERN.matcher( s );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
}\r
}\r
}\r
\r
- public static String parseGenbankProteinAccessor( final String query ) {\r
- final Matcher m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );\r
+ public final static String parseGenbankProteinAccessorFromString( final String s ) {\r
+ final Matcher m = GENBANK_PROT_PATTERN.matcher( s );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
}\r
}\r
}\r
\r
- public static String parseGInumber( final String query ) {\r
- final Matcher m = GI_PATTERN.matcher( query );\r
+ public final static String parseGInumberFromString( final String s ) {\r
+ final Matcher m = GI_PATTERN.matcher( s );\r
if ( m.find() ) {\r
return m.group( 1 );\r
}\r
return null;\r
}\r
\r
- /**\r
- * Returns null if no match.\r
- * \r
- */\r
- public final static String parseRefSeqAccessor( final String query ) {\r
- final Matcher m = REFSEQ_PATTERN.matcher( query );\r
+ public final static String parseRefSeqAccessorFromString( final String s ) {\r
+ final Matcher m = REFSEQ_PATTERN.matcher( s );\r
if ( m.lookingAt() ) {\r
return m.group( 1 );\r
}\r
return null;\r
}\r
+\r
+ public final static String parseUniProtAccessorFromString( final String s ) {\r
+ Matcher m = UNIPROT_KB_PATTERN_0.matcher( s );\r
+ if ( m.find() ) {\r
+ return m.group( 1 );\r
+ }\r
+ m = UNIPROT_KB_PATTERN_1.matcher( s );\r
+ if ( m.find() ) {\r
+ return m.group( 1 );\r
+ }\r
+ m = UNIPROT_KB_PATTERN_2.matcher( s );\r
+ if ( m.find() ) {\r
+ return m.group();\r
+ }\r
+ return null;\r
+ }\r
}\r
package org.forester.ws.seqdb;
import java.io.BufferedReader;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
public final static String EMBL_DBS_REFSEQ_P = "refseqp";
public final static String EMBL_DBS_REFSEQ_N = "refseqn";
private final static String URL_ENC = "UTF-8";
- private final static boolean DEBUG = false;
+ private final static boolean DEBUG = true;
private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return )
throws IOException {
if ( ext_nodes_only && node.isInternal() ) {
continue;
}
- // String query = null;
- // Accession id = null;
- // Accession acc = SequenceAccessionTools.obtain( node );
- //
- //
- // Db db = Db.NONE;
- // if ( node.getNodeData().isHasSequence()
- // && ( node.getNodeData().getSequence().getAccession() != null )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- // && ( node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
- // .startsWith( "uniprot" )
- // || node.getNodeData().getSequence().getAccession().getValue()
- // .equalsIgnoreCase( "swissprot" )
- // || node.getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "trembl" ) || node
- // .getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "sp" ) ) ) {
- // query = node.getNodeData().getSequence().getAccession().getValue();
- // db = Db.UNIPROT;
- // }
- // else if ( node.getNodeData().isHasSequence()
- // && ( node.getNodeData().getSequence().getAccession() != null )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- // && ( node.getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "embl" ) || node
- // .getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "ebi" ) ) ) {
- // query = node.getNodeData().getSequence().getAccession().getValue();
- // db = Db.EMBL;
- // }
- // else if ( node.getNodeData().isHasSequence()
- // && ( node.getNodeData().getSequence().getAccession() != null )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- // && ( node.getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "ncbi" ) || node
- // .getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "genbank" ) ) ) {
- // query = node.getNodeData().getSequence().getAccession().getValue();
- // // db = Db.NCBI;
- // }
- // else if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- // && node.getNodeData().getSequence().getAccession().getValue().equalsIgnoreCase( "refseq" ) ) {
- // query = node.getNodeData().getSequence().getAccession().getValue();
- // db = Db.REFSEQ;
- // }
- // else {
Accession acc = SequenceAccessionTools.obtainFromSeqAccession( node );
- // if ( ( query = SequenceAccessionTools.extractUniProtKbProteinSeqIdentifier( node ) ) != null ) {
- // db = Db.UNIPROT;
- // }
- // else if ( node.getNodeData().isHasSequence() ) {
- // if ( ( id = SequenceAccessionTools.parse( node.getName() ) ) != null ) {
- // if ( id.getSource() == Accession.NCBI ) {
- // // db = Db.NCBI;
- // }
- // else if ( id.getSource() == Accession.REFSEQ ) {
- // db = Db.REFSEQ;
- // }
- // }
- // else if ( ( id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getName() ) ) != null ) {
- // if ( id.getSource() == Accession.NCBI ) {
- // // = Db.NCBI;
- // }
- // else if ( id.getSource() == Accession.REFSEQ ) {
- // db = Db.REFSEQ;
- // }
- // }
- // else if ( ( id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getGeneName() ) ) != null ) {
- // if ( id.getSource() == Accession.NCBI ) {
- // // db = Db.NCBI;
- // }
- // else if ( id.getSource() == Accession.REFSEQ ) {
- // db = Db.REFSEQ;
- // }
- // }
- // else if ( ( id = SequenceAccessionTools.parse( node.getNodeData().getSequence().getSymbol() ) ) != null ) {
- // if ( id.getSource() == Accession.NCBI ) {
- // // db = Db.NCBI;
- // }
- // else if ( id.getSource() == Accession.REFSEQ ) {
- // db = Db.REFSEQ;
- // }
- // }
- // }
- // }
if ( ( acc == null )
|| ForesterUtil.isEmpty( acc.getSource() )
|| ForesterUtil.isEmpty( acc.getValue() )
|| ( ( acc.getSource() != Accession.UNIPROT ) && ( acc.getSource() != Accession.EMBL ) && ( acc
.getSource() != Accession.REFSEQ ) ) ) {
- acc = SequenceAccessionTools.parse( node );
+ acc = SequenceAccessionTools.obtainAccessorFromDataFields( node );
}
if ( ( acc == null )
|| ForesterUtil.isEmpty( acc.getSource() )
if ( DEBUG ) {
System.out.println( "uniprot: " + query );
}
- db_entry = obtainUniProtEntry( query, lines_to_return );
+ try {
+ db_entry = obtainUniProtEntry( query, lines_to_return );
+ }
+ catch ( FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
else if ( acc.getSource() == Accession.EMBL ) {
if ( DEBUG ) {
System.out.println( "embl: " + query );
}
- db_entry = obtainEmblEntry( new Accession( query ), lines_to_return );
+ try {
+ db_entry = obtainEmblEntry( new Accession( query ), lines_to_return );
+ }
+ catch ( FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
else if ( acc.getSource() == Accession.REFSEQ ) {
if ( DEBUG ) {
System.out.println( "refseq: " + query );
}
- db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
+ try {
+ db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
+ }
+ catch ( FileNotFoundException e ) {
+ // Eat this, and move to next.
+ }
}
if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence()
node.getNodeData().setSequence( seq );
}
else {
+ node.i
not_found.add( node.getName() );
}
try {
if ( _go_terms == null ) {
_go_terms = new ArrayList<GoTerm>();
}
- System.out.println( "GOTERM ADDED: " + g );
_go_terms.add( g );
}
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 ) );
}
}
git://source.jalview.org / jalview.git / commitdiff