package org.forester.archaeopteryx.tools;
-
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
import javax.swing.JApplet;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.TreePanel;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.util.ForesterUtil;
import org.forester.ws.wabi.RestUtil;
-public class Blast {
-
- final static Pattern identifier_pattern_1 = Pattern.compile ("^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})\\s*$");
- final static Pattern identifier_pattern_2 = Pattern.compile ("^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})[|,; ].*$");
-
- public Blast() {
- }
-
-
- public static void NcbiBlastWeb( String query, JApplet applet, TreePanel p ) {
+public final class Blast {
- //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
-
-
- StringBuilder uri_str = new StringBuilder();
- uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=Proteins&QUERY=" );
+ final public static void openNcbiBlastWeb( final String query,
+ final boolean is_nucleic_acids,
+ final JApplet applet,
+ final TreePanel p ) {
+ //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
+ final StringBuilder uri_str = new StringBuilder();
+ uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=" );
+ if ( is_nucleic_acids ) {
+ uri_str.append( "Nucleotide" );
+ }
+ else {
+ uri_str.append( "Proteins" );
+ }
+ uri_str.append( "&QUERY=" );
uri_str.append( query );
try {
-
AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), applet != null, applet, "_aptx_blast" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( p, e.toString() );
e.printStackTrace();
}
-
}
- public static String obtainQueryForBlast( final PhylogenyNode node ) {
+
+ final public static String obtainQueryForBlast( final PhylogenyNode node ) {
String query = "";
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
query = node.getNodeData().getSequence().getMolecularSequence();
}
- else if ( node.getNodeData().getSequence().getAccession() != null && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
+ else if ( ( node.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
query = node.getNodeData().getSequence().getAccession().getSource() + "%7C";
}
query += node.getNodeData().getSequence().getAccession().getValue();
}
else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
- String name = node.getNodeData().getSequence().getName();
- final Matcher matcher1 = identifier_pattern_1.matcher( name );
- final Matcher matcher2 = identifier_pattern_2.matcher( name );
- String group1 = "";
- String group2 = "";
-
- if ( matcher1.matches() ) {
- group1 = matcher1.group( 1 );
- group2 = matcher1.group( 2 );
- System.out.println( "1 1=" + group1 );
-
- System.out.println( "1 2=" + group2 );
- }
- if ( matcher2.matches() ) {
- group1 = matcher2.group( 1 );
- group2 = matcher2.group( 2 );
- System.out.println( "2 1=" + group1 );
-
- System.out.println( "2 2=" + group2 );
+ final Accession acc = AptxUtil.obtainSequenceAccessionFromName( node.getNodeData().getSequence().getName() );
+ if ( acc != null ) {
+ query = acc.getSource() + "%7C" + acc.getValue();
}
- if (!ForesterUtil.isEmpty( group1 ) && !ForesterUtil.isEmpty( group2 )) {
- query = group1 + "%7C" + group2;
- }
-
}
-
-
- System.out.println( query );
-
return query;
}
+ final public static boolean isContainsQueryForBlast( final PhylogenyNode node ) {
+ return !ForesterUtil.isEmpty( obtainQueryForBlast( node ) );
+ }
- public void ddbjBlast( final String geneName ) {
+ final public void ddbjBlast( final String geneName ) {
// Retrieve accession number list which has specified gene name from searchByXMLPath of ARSA. Please click here for details of ARSA.
/*target: Sequence length is between 300bp and 1000bp.
Feature key is CDS.
Gene qualifire is same as specified gene name.*/
String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND "
- + "/ENTRY/DDBJ/length<=1000) ";
+ + "/ENTRY/DDBJ/length<=1000) ";
queryPath += "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND ";
queryPath += "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='" + geneName + "'}})";
String query = "service=ARSA&method=searchByXMLPath&queryPath=" + queryPath
- + "&returnPath=/ENTRY/DDBJ/primary-accession&offset=1&count=100";
+ + "&returnPath=/ENTRY/DDBJ/primary-accession&offset=1&count=100";
//Execute ARSA
String arsaResult = null;
try {
//Execute blastn by using searchParam of Blast with step2's sequence. Specified option is -e 0.0001 -m 8 -b 50 -v 50. It means "Extract top 50 hit which E-value is more than 0.0001.". The reference databases are specified as follows. ddbjpri(primates) ddbjrod(rodents) ddbjmam(mammals) ddbjvrt(vertebrates ) ddbjinv(invertebrates).
//Execute blastn with step3's sequence
query = "service=Blast&method=searchParam&program=blastn&database=ddbjpri ddbjrod ddbjmam ddbjvrt "
- + "ddbjinv&query=" + dnaSeq + "¶m=-m 8 -b 50 -v 50 -e 0.0001";
+ + "ddbjinv&query=" + dnaSeq + "¶m=-m 8 -b 50 -v 50 -e 0.0001";
String blastResult = null;
try {
blastResult = RestUtil.getResult( query );
for( int i = 0; i < parsedBlastResult.size(); i++ ) {
final String[] parsed = parsedBlastResult.elementAt( i );
query = "service=ARSA&method=searchByXMLPath&queryPath=/ENTRY/DDBJ/primary-accession=='" + parsed[ 0 ]
- + "'&returnPath=/ENTRY/DDBJ/organism&offset=1&count=100";
+ + "'&returnPath=/ENTRY/DDBJ/organism&offset=1&count=100";
String organism = null;
try {
organism = RestUtil.getResult( query );
git://source.jalview.org / jalview.git / blobdiff