From af5e25d369f3240ce41018957383044c12126d98 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 19 Sep 2014 03:00:00 +0000 Subject: [PATCH] in progress --- .../org/forester/analysis/TaxonomyDataManager.java | 5 +- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 7 +- .../src/org/forester/archaeopteryx/Constants.java | 4 +- .../src/org/forester/archaeopteryx/MainFrame.java | 4 +- .../forester/archaeopteryx/MainFrameApplet.java | 4 +- .../archaeopteryx/MainFrameApplication.java | 4 +- .../src/org/forester/archaeopteryx/TreePanel.java | 55 +++++---- .../src/org/forester/io/parsers/nhx/NHXParser.java | 4 +- .../org/forester/io/parsers/util/ParserUtils.java | 2 +- .../src/org/forester/phylogeny/PhylogenyNode.java | 3 - forester/java/src/org/forester/test/Test.java | 125 ++++++++------------ .../src/org/forester/util/ForesterConstants.java | 2 +- .../java/src/org/forester/util/ForesterUtil.java | 124 ++++++++++--------- .../java/src/org/forester/util/TaxonomyUtil.java | 4 +- .../org/forester/ws/seqdb/SequenceDbWsTools.java | 22 ++-- 15 files changed, 187 insertions(+), 182 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index fbc8d0c..d78720c 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -199,7 +199,10 @@ public final class TaxonomyDataManager extends RunnableProcess { } private final static List getTaxonomiesFromTaxonomyCode( final String query ) throws IOException { - if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) { + //FIXME fix "SPHAR" issue + if ( ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) + || query.equals( "SPHAR" ) /* TODO remove me, is same as Sphingomonas aromaticivorans */ + ) { final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query ); return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN ); } diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 251a43c..7ea1610 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -758,11 +758,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); } - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu @@ -932,7 +932,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void displayBasicInformation() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null ) + && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index deff15d..16f5a7d 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -42,8 +42,8 @@ public final class Constants { public final static boolean __SYNTH_LF = false; // TODO remove me public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.9897 beta"; - final static String PRG_DATE = "140828"; + final static String VERSION = "0.9898 beta"; + final static String PRG_DATE = "140918"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index fb23501..2cc0189 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -344,7 +344,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { switchColors(); } else if ( o == _display_basic_information_item ) { - displayBasicInformation( getCurrentTreePanel().getTreeFile() ); + if ( getCurrentTreePanel() != null ) { + displayBasicInformation( getCurrentTreePanel().getTreeFile() ); + } } else if ( o == _view_as_NH_item ) { viewAsNH(); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index b804681..8314448 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -215,11 +215,11 @@ public final class MainFrameApplet extends MainFrame { .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); } - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 947ed2a..318be47 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -896,11 +896,11 @@ public final class MainFrameApplication extends MainFrame { .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { - _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) ); _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); + _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); } - _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 314ee51..ce136b5 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -173,6 +173,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private static final BasicStroke STROKE_2 = new BasicStroke( 2f ); private static final double TWO_PI = 2 * Math.PI; private final static int WIGGLE = 2; + private static final String SHOW_ONLY_THIS_CONF_TYPE = "posterior probability"; //TODO remove me HashMap _nodeid_dist_to_leaf = new HashMap(); final private Arc2D _arc = new Arc2D.Double(); private AffineTransform _at; @@ -2854,13 +2855,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final List additional_nodes = new ArrayList(); if ( getFoundNodes0() != null ) { for( final Long id : getFoundNodes0() ) { - additional_nodes.add( _phylogeny.getNode( id ) ); + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); + } } } if ( getFoundNodes1() != null ) { for( final Long id : getFoundNodes1() ) { if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) { - additional_nodes.add( _phylogeny.getNode( id ) ); + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); + } } } } @@ -4042,26 +4049,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee Collections.sort( confidences ); final StringBuilder sb = new StringBuilder(); for( final Confidence confidence : confidences ) { - final double value = confidence.getValue(); - if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( value < getOptions().getMinConfidenceValue() ) { - return; - } - if ( not_first ) { - sb.append( "/" ); - } - else { - not_first = true; - } - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - if ( getOptions().isShowConfidenceStddev() ) { - if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - sb.append( "(" ); - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(), - getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - sb.append( ")" ); + if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) + || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType() + .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) { + final double value = confidence.getValue(); + if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( value < getOptions().getMinConfidenceValue() ) { + return; + } + if ( not_first ) { + sb.append( "/" ); + } + else { + not_first = true; + } + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( getOptions().isShowConfidenceStddev() ) { + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + sb.append( "(" ); + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + sb.append( ")" ); + } } } } diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java index 449721d..4bcfb08 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java @@ -56,9 +56,9 @@ import org.forester.util.ForesterUtil; public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParser { - public final static Pattern MB_BL_PATTERN = Pattern.compile( "length_median=([^,]+)" ); + public final static Pattern MB_BL_PATTERN = Pattern.compile( "length.median=([^,]+)" ); public final static Pattern MB_PROB_PATTERN = Pattern.compile( "prob=([^,]+)" ); - public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob_stddev=([^,]+)" ); + public final static Pattern MB_PROB_SD_PATTERN = Pattern.compile( "prob.stddev=([^,]+)" ); public final static Pattern NUMBERS_ONLY_PATTERN = Pattern.compile( "^[0-9\\.]+$" ); final static public boolean REPLACE_UNDERSCORES_DEFAULT = false; private static final boolean ALLOW_ERRORS_IN_DISTANCE_TO_PARENT_DEFAULT = false; diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java index 9168c9d..6b70303 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -60,7 +60,7 @@ public final class ParserUtils { final public static String TAX_CODE_LO = "(?:[A-Z]{5})|RAT|PIG|PEA"; final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")(?:\\b|_)" ); - final public static Pattern TAXOMONY_CODE_PATTERN_A_LO = Pattern.compile( "(?:\\b|_)(" + TAX_CODE_LO + final public static Pattern TAXOMONY_CODE_PATTERN_A_LO = Pattern.compile( "_(" + TAX_CODE_LO + ")(?:\\b|_)" ); final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" ); final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_(" diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 979fafe..e7ef81b 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -971,12 +971,10 @@ public final class PhylogenyNode implements Comparable { @Override final public String toString() { final StringBuilder sb = new StringBuilder(); - if ( !ForesterUtil.isEmpty( getName() ) ) { sb.append( getName() ); sb.append( " " ); } - if ( getNodeData().isHasTaxonomy() ) { if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) { sb.append( getNodeData().getTaxonomy().getScientificName() ); @@ -1009,7 +1007,6 @@ public final class PhylogenyNode implements Comparable { sb.append( " " ); } } - if ( sb.length() <= 1 ) { sb.append( "[" ); sb.append( getId() ); diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 35b8600..0dd12a5 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -298,6 +298,15 @@ public final class Test { succeeded++; } System.out.println( "OK." ); + System.out.print( "Taxonomy data extraction: " ); + if ( Test.testExtractTaxonomyDataFromNodeName() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } System.out.print( "Taxonomy code extraction: " ); if ( Test.testExtractTaxonomyCodeFromNodeName() ) { System.out.println( "OK." ); @@ -1566,7 +1575,7 @@ public final class Test { return false; } final MolecularSequence aa2 = BasicSequence.createAaSequence( "aa3", "ARNDCQEGHILKMFPSTWYVX*-BZOJU" ); - if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZXXU" ) ) { + if ( !new String( aa2.getMolecularSequence() ).equals( "ARNDCQEGHILKMFPSTWYVX*-BZOXU" ) ) { return false; } final MolecularSequence dna1 = BasicSequence.createDnaSequence( "dna1", "ACGTUX*-?RYMKWSN" ); @@ -2171,7 +2180,6 @@ public final class Test { if ( !t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getType().equals( "characters" ) ) { return false; } - // if ( !t3_rt.getNode( "node ba" ).getNodeData().getDate().getDesc().equals( "Silurian" ) ) { return false; } @@ -3045,7 +3053,6 @@ public final class Test { if ( !isEqual( t_bx.getNode( "acd" ).getBranchData().getConfidence( 0 ).getValue(), 1 ) ) { return false; } - // final Phylogeny[] t2 = factory .create( "((((a,b),c),d),e);(((a,b),c),(d,e));(((((a,b),c),d),e),f);((((a,b),c),(d,e)),f);(((a,b),c),d,e);((a,b,c),d,e);", new NHXParser() ); @@ -3055,7 +3062,6 @@ public final class Test { for( final Phylogeny target : t2 ) { ConfidenceAssessor.evaluate( "bootstrap", ev2, target, false, 1 ); } - // final Phylogeny t4 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,G)abcdefg", new NHXParser() )[ 0 ]; final Phylogeny[] ev4 = factory.create( "(((A,B),C),(X,Y));((F,G),((A,B,C),(D,E)))", new NHXParser() ); @@ -3990,10 +3996,6 @@ public final class Test { System.out.println( entry.getSequenceName() ); return false; } - // if ( !entry.getSequenceSymbol().equals( "" ) ) { - // System.out.println( entry.getSequenceSymbol() ); - // return false; - // } if ( !entry.getGeneName().equals( "treX-like" ) ) { System.out.println( entry.getGeneName() ); return false; @@ -4013,7 +4015,6 @@ public final class Test { if ( entry.getCrossReferences().size() != 5 ) { return false; } - // final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); if ( !entry1.getAccession().equals( "ABJ16409" ) ) { return false; @@ -4037,7 +4038,6 @@ public final class Test { if ( entry1.getCrossReferences().size() != 6 ) { return false; } - // final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); if ( !entry2.getAccession().equals( "NM_184234" ) ) { return false; @@ -4089,8 +4089,6 @@ public final class Test { if ( entry3.getCrossReferences().size() != 8 ) { return false; } - // - // final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); if ( !entry4.getAccession().equals( "AAA36557" ) ) { return false; @@ -4510,6 +4508,44 @@ public final class Test { return true; } + private static boolean testExtractTaxonomyDataFromNodeName() { + try { + PhylogenyNode n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|B1AM49_HUMAN~1-2" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN|" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "tr|B1AM49|HNRPR_HUMAN~12" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "HNRPR_HUMAN" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + n = new PhylogenyNode( "HNRPR_HUMAN_X" ); + if ( !ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "HUMAN" ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testExtractTaxonomyCodeFromNodeName() { try { if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { @@ -4846,7 +4882,7 @@ public final class Test { if ( !msa_0.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "DKXASDFXSFXFKFKSXDFKSLX" ) ) { return false; } - if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPRXWXERR" ) ) { + if ( !msa_0.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "SXDFKSXLFSFPWEXPROWXERR" ) ) { return false; } if ( !msa_0.getSequenceAsString( 3 ).toString().equalsIgnoreCase( "AAAAAAAAAAAAAAAAAAAAAAA" ) ) { @@ -6326,7 +6362,6 @@ public final class Test { if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) { return false; } - // final MolecularSequence s__0 = BasicSequence.createAaSequence( "a", "A------" ); final MolecularSequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" ); final MolecularSequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" ); @@ -6454,8 +6489,6 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "h" ) ) { return false; } - // - // ext.clear(); final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ]; @@ -6484,8 +6517,6 @@ public final class Test { if ( !ext.get( 3 ).getName().equals( "gh" ) ) { return false; } - // - // ext.clear(); final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ]; @@ -6512,8 +6543,6 @@ public final class Test { if ( !ext.get( 2 ).getName().equals( "fgh" ) ) { return false; } - // - // ext.clear(); final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ]; @@ -6530,8 +6559,6 @@ public final class Test { if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) { return false; } - // - // final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ]; ext.clear(); @@ -6567,8 +6594,6 @@ public final class Test { if ( !ext.get( 7 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ]; ext.clear(); @@ -6602,8 +6627,6 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ]; ext.clear(); @@ -6637,8 +6660,6 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" ); final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ]; ext.clear(); @@ -6675,8 +6696,6 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "h" ) ) { return false; } - // - // final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ]; ext.clear(); @@ -6710,8 +6729,6 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - // - // final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ]; ext.clear(); @@ -6747,8 +6764,6 @@ public final class Test { if ( !ext.get( 6 ).getName().equals( "gh" ) ) { return false; } - // - // final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ]; ext.clear(); @@ -6780,8 +6795,6 @@ public final class Test { if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ]; ext.clear(); @@ -6816,8 +6829,6 @@ public final class Test { if ( !ext.get( 5 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" ); final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ]; ext.clear(); @@ -6848,8 +6859,6 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ]; ext.clear(); @@ -6880,8 +6889,6 @@ public final class Test { if ( !ext.get( 4 ).getName().equals( "fgh" ) ) { return false; } - // - // final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" ); final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ]; ext.clear(); @@ -7338,7 +7345,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.reset(); if ( !p.hasNext() ) { return false; @@ -7360,7 +7366,6 @@ public final class Test { if ( phy != null ) { return false; } - //// p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" ); if ( !p.hasNext() ) { return false; @@ -7382,7 +7387,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.reset(); if ( !p.hasNext() ) { return false; @@ -7404,7 +7408,6 @@ public final class Test { if ( phy != null ) { return false; } - // p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" ); if ( !p.hasNext() ) { return false; @@ -11271,8 +11274,7 @@ public final class Test { } final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" ); SequenceDbWsTools.obtainSeqInformation( n2 ); - if ( !n2.getNodeData().getSequence().getName() - .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) { + if ( !n2.getNodeData().getSequence().getName().equals( "Danio rerio B-cell CLL/lymphoma 2a (bcl2a), mRNA" ) ) { return false; } if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) { @@ -11411,7 +11413,6 @@ public final class Test { System.out.println( "provider=" + id.getSource() ); return false; } - // id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" ); if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() ) || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) { @@ -11616,14 +11617,12 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -11633,7 +11632,6 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -11641,7 +11639,6 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -11650,14 +11647,12 @@ public final class Test { if ( !s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); @@ -11666,7 +11661,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); @@ -11676,7 +11670,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -11684,49 +11677,42 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) ); if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) ); @@ -11734,7 +11720,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) ); @@ -11742,7 +11727,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -11750,7 +11734,6 @@ public final class Test { if ( s0.match( query_nodes ) ) { return false; } - // query_nodes = new HashSet(); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) ); query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) ); @@ -12535,7 +12518,6 @@ public final class Test { System.out.println( n17.toString() ); return false; } - // final PhylogenyNode n18 = PhylogenyNode .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) { @@ -12562,13 +12544,6 @@ public final class Test { System.out.println( n21.toString() ); return false; } - final PhylogenyNode n22 = PhylogenyNode - .createInstanceFromNhxString( "NEMVE_Nematostella_vectensis", - NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); - if ( !n22.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) { - System.out.println( n22.toString() ); - return false; - } final PhylogenyNode n23 = PhylogenyNode .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE ); diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index f8fc57b..a4f6bcd 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,7 +27,7 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.035"; + public final static String FORESTER_VERSION = "1.036"; public final static String FORESTER_DATE = "140811"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 58271c3..8d36a6e 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -105,9 +105,6 @@ public final class ForesterUtil { FORMATTER_3 = new DecimalFormat( "#.###", dfs ); } - private ForesterUtil() { - } - final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) { if ( sb.length() > 0 ) { sb.append( separator ); @@ -204,6 +201,39 @@ public final class ForesterUtil { } } + /** + * Helper method for calcColor methods. + * + * @param smallercolor_component_x + * color component the smaller color + * @param largercolor_component_x + * color component the larger color + * @param x + * factor + * @return an int representing a color component + */ + final private static int calculateColorComponent( final double smallercolor_component_x, + final double largercolor_component_x, + final double x ) { + return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) ); + } + + /** + * Helper method for calcColor methods. + * + * + * @param value + * the value + * @param larger + * the largest value + * @param smaller + * the smallest value + * @return a normalized value between larger and smaller + */ + final private static double calculateColorFactor( final double value, final double larger, final double smaller ) { + return ( 255.0 * ( value - smaller ) ) / ( larger - smaller ); + } + public static int calculateOverlap( final Domain domain, final List covered_positions ) { int overlap_count = 0; for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) { @@ -497,6 +527,22 @@ public final class ForesterUtil { return ForesterUtil.LINE_SEPARATOR; } + final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) { + if ( mol_seq.contains( "L" ) || mol_seq.contains( "I" ) || mol_seq.contains( "E" ) || mol_seq.contains( "H" ) + || mol_seq.contains( "D" ) || mol_seq.contains( "Q" ) ) { + return TYPE.AA; + } + else { + if ( mol_seq.contains( "T" ) ) { + return TYPE.DNA; + } + else if ( mol_seq.contains( "U" ) ) { + return TYPE.RNA; + } + } + return null; + } + final public static void increaseCountingMap( final Map counting_map, final String item_name ) { if ( !counting_map.containsKey( item_name ) ) { counting_map.put( item_name, 1 ); @@ -1052,6 +1098,20 @@ public final class ForesterUtil { System.out.println( "[" + prg_name + "] > " + message ); } + public static List readUrl( final String url_str ) throws IOException { + final URL url = new URL( url_str ); + final URLConnection urlc = url.openConnection(); + //urlc.setRequestProperty( "User-Agent", "" ); + final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) ); + String line; + final List result = new ArrayList(); + while ( ( line = in.readLine() ) != null ) { + result.add( line ); + } + in.close(); + return result; + } + /** * * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => @@ -1203,6 +1263,11 @@ public final class ForesterUtil { return false; } + final private static String[] splitString( final String str ) { + final String regex = "[\\s;,]+"; + return str.split( regex ); + } + final public static String stringArrayToString( final String[] a ) { return stringArrayToString( a, ", " ); } @@ -1348,57 +1413,6 @@ public final class ForesterUtil { return sb.toString(); } - /** - * Helper method for calcColor methods. - * - * @param smallercolor_component_x - * color component the smaller color - * @param largercolor_component_x - * color component the larger color - * @param x - * factor - * @return an int representing a color component - */ - final private static int calculateColorComponent( final double smallercolor_component_x, - final double largercolor_component_x, - final double x ) { - return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) ); - } - - final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) { - if ( mol_seq.contains( "L" ) || mol_seq.contains( "I" ) || mol_seq.contains( "E" ) || mol_seq.contains( "H" ) - || mol_seq.contains( "D" ) || mol_seq.contains( "Q" ) ) { - return TYPE.AA; - } - else { - if ( mol_seq.contains( "T" ) ) { - return TYPE.DNA; - } - else if ( mol_seq.contains( "U" ) ) { - return TYPE.RNA; - } - } - return null; - } - - /** - * Helper method for calcColor methods. - * - * - * @param value - * the value - * @param larger - * the largest value - * @param smaller - * the smallest value - * @return a normalized value between larger and smaller - */ - final private static double calculateColorFactor( final double value, final double larger, final double smaller ) { - return ( 255.0 * ( value - smaller ) ) / ( larger - smaller ); - } - - final private static String[] splitString( final String str ) { - final String regex = "[\\s;,]+"; - return str.split( regex ); + private ForesterUtil() { } } diff --git a/forester/java/src/org/forester/util/TaxonomyUtil.java b/forester/java/src/org/forester/util/TaxonomyUtil.java index ee5427a..ef38563 100644 --- a/forester/java/src/org/forester/util/TaxonomyUtil.java +++ b/forester/java/src/org/forester/util/TaxonomyUtil.java @@ -182,7 +182,8 @@ public final class TaxonomyUtil { put( "MNELE", "ctenophora" ); put( "AMPQE", "porifera" ); put( "MONBE", "choanoflagellida" ); - put( "SALS5", "choanoflagellida" ); + put( "SALS5", "choanoflagellida" ); //TODO remove me + put( "SALR5", "choanoflagellida" ); put( "AMOPA", "ichthyophonida & filasterea" ); put( "SARXX", "ichthyophonida & filasterea" ); put( "CAPO3", "ichthyophonida & filasterea" ); @@ -578,6 +579,7 @@ public final class TaxonomyUtil { FAKE_CODE_TO_ID_MAP.put( "CTEXX", 283909 ); FAKE_CODE_TO_ID_MAP.put( "HMAXX", 6085 ); FAKE_CODE_TO_ID_MAP.put( "SARXX", 72019 ); + FAKE_CODE_TO_ID_MAP.put( "SPHAR", 72019 ); //TODO is same as Sphingomonas aromaticivorans FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408 ); FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344 ); FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275 ); diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index fde5351..606d35a 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -55,17 +55,17 @@ import org.forester.util.SequenceAccessionTools; public final class SequenceDbWsTools { - public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/"; - public final static int DEFAULT_LINES_TO_RETURN = 4000; - public final static String EMBL_DBS_REFSEQ_N = "refseqn"; - public final static String EMBL_DBS_REFSEQ_P = "refseqp"; - public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id="; - public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id="; - public final static String EMBL_EMBL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id="; - private final static boolean DEBUG = true; - private final static String URL_ENC = "UTF-8"; - private final static int SLEEP = 200; - private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = true; + public final static String BASE_UNIPROT_URL = "http://www.uniprot.org/"; + public final static int DEFAULT_LINES_TO_RETURN = 4000; + public final static String EMBL_DBS_REFSEQ_N = "refseqn"; + public final static String EMBL_DBS_REFSEQ_P = "refseqp"; + public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id="; + public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id="; + public final static String EMBL_EMBL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id="; + private final static boolean DEBUG = true; + private final static String URL_ENC = "UTF-8"; + private final static int SLEEP = 200; + private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false; public static List getTaxonomiesFromCommonNameStrict( final String cn, final int max_taxonomies_return ) -- 1.7.10.2