2 // FORESTER -- software libraries and applications
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3 // for evolutionary biology research and applications.
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5 // Copyright (C) 2008-2009 Christian M. Zmasek
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6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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7 // Copyright (C) 2000-2001 Washington University School of Medicine
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8 // and Howard Hughes Medical Institute
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9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
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10 // All rights reserved
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12 // This library is free software; you can redistribute it and/or
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13 // modify it under the terms of the GNU Lesser General Public
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14 // License as published by the Free Software Foundation; either
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15 // version 2.1 of the License, or (at your option) any later version.
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17 // This library is distributed in the hope that it will be useful,
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18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
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19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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20 // Lesser General Public License for more details.
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22 // You should have received a copy of the GNU Lesser General Public
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23 // License along with this library; if not, write to the Free Software
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24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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26 // Contact: phylosoft @ gmail . com
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27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
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29 package org.forester.util;
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31 import java.util.regex.Matcher;
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32 import java.util.regex.Pattern;
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34 import org.forester.phylogeny.PhylogenyNode;
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35 import org.forester.phylogeny.data.Accession;
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36 import org.forester.phylogeny.data.Sequence;
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38 public final class SequenceAccessionTools {
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40 // gb_ADF31344_1_segmented_worms_
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42 // gb_EHB07727_1_rodents_
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43 // dbj_BAF37827_1_turtles_
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44 // emb_CAA73223_1_primates_
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45 // lcl_91970_unknown_
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46 // mites|ref_XP_002434188_1
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47 // ref_XP_002434188_1_mites___ticks_
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48 // ref_NP_001121530_1_frogs___toads_
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49 //The format for GenBank Accession numbers are:
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50 //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
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51 //Protein: 3 letters + 5 numerals
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52 //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
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53 public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern
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54 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
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55 public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern
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56 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
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57 public final static Pattern GENBANK_PROT_PATTERN = Pattern
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58 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
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59 public final static Pattern GI_PATTERN = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );
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60 public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "\\b([A-Z][0-9][A-Z0-9]{3}[0-9])\\b" );
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61 public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern
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62 .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
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63 public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern
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64 .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|_)" );
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65 // RefSeq accession numbers can be distinguished from GenBank accessions
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66 // by their distinct prefix format of 2 characters followed by an
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67 // underscore character ('_'). For example, a RefSeq protein accession is NP_015325.
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68 private final static Pattern REFSEQ_PATTERN = Pattern
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69 .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );
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71 private SequenceAccessionTools() {
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72 // Hiding the constructor.
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75 public final static boolean isProteinDbQuery( final String query ) {
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76 final String r1 = parseRefSeqAccessorFromString( query );
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77 if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {
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80 final String r2 = parseUniProtAccessorFromString( query );
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81 if ( !ForesterUtil.isEmpty( r2 ) ) {
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84 return GENBANK_PROT_PATTERN.matcher( query ).lookingAt();
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87 public final static Accession obtainAccessorFromDataFields( final PhylogenyNode n ) {
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88 String a = obtainUniProtAccessorFromDataFields( n );
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89 if ( !ForesterUtil.isEmpty( a ) ) {
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90 return new Accession( a, Accession.UNIPROT );
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92 a = obtainGenbankAccessorFromDataFields( n );
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93 if ( !ForesterUtil.isEmpty( a ) ) {
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94 return new Accession( a, Accession.NCBI );
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96 a = obtainRefSeqAccessorFromDataFields( n );
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97 if ( !ForesterUtil.isEmpty( a ) ) {
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98 return new Accession( a, Accession.REFSEQ );
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100 a = obtainGiNumberFromDataFields( n );
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101 if ( !ForesterUtil.isEmpty( a ) ) {
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102 return new Accession( a, Accession.GI );
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107 public final static Accession obtainFromSeqAccession( final PhylogenyNode n ) {
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108 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
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109 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getSource() )
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110 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().getValue() ) ) {
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111 final String source = n.getNodeData().getSequence().getAccession().getSource().toLowerCase();
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112 final String value = n.getNodeData().getSequence().getAccession().getValue();
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113 if ( ( source.startsWith( "uniprot" ) || source.equals( "swissprot" ) || source.equals( "trembl" ) || source
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114 .equals( "sp" ) ) ) {
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115 return new Accession( value, Accession.UNIPROT );
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117 else if ( source.equals( "embl" ) || source.equals( "ebi" ) ) {
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118 return new Accession( value, Accession.EMBL );
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120 else if ( source.equals( "ncbi" ) || source.equals( "genbank" ) ) {
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121 return new Accession( value, Accession.NCBI );
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123 else if ( source.equals( "refseq" ) ) {
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124 return new Accession( value, Accession.REFSEQ );
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126 else if ( source.equals( "gi" ) ) {
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127 return new Accession( value, Accession.GI );
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133 public final static String obtainGenbankAccessorFromDataFields( final PhylogenyNode n ) {
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135 if ( n.getNodeData().isHasSequence() ) {
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136 final Sequence seq = n.getNodeData().getSequence();
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137 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
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138 a = parseGenbankAccessorFromString( seq.getSymbol() );
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140 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
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141 a = parseGenbankAccessorFromString( seq.getGeneName() );
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143 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
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144 a = parseGenbankAccessorFromString( seq.getName() );
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146 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
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147 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
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148 a = parseGenbankAccessorFromString( seq.getAccession().getValue() );
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151 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
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152 a = parseGenbankAccessorFromString( n.getName() );
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157 public final static String obtainGiNumberFromDataFields( final PhylogenyNode n ) {
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159 if ( n.getNodeData().isHasSequence() ) {
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160 final Sequence seq = n.getNodeData().getSequence();
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161 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
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162 a = parseGInumberFromString( seq.getName() );
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164 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
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165 a = parseGInumberFromString( seq.getGeneName() );
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167 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
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168 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
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169 a = parseGInumberFromString( seq.getAccession().getValue() );
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172 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
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173 a = parseGInumberFromString( n.getName() );
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178 public final static String obtainRefSeqAccessorFromDataFields( final PhylogenyNode n ) {
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180 if ( n.getNodeData().isHasSequence() ) {
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181 final Sequence seq = n.getNodeData().getSequence();
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182 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
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183 a = parseRefSeqAccessorFromString( seq.getSymbol() );
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185 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
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186 a = parseRefSeqAccessorFromString( seq.getGeneName() );
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188 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
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189 a = parseRefSeqAccessorFromString( seq.getName() );
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191 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
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192 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
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193 a = parseRefSeqAccessorFromString( seq.getAccession().getValue() );
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196 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
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197 a = parseRefSeqAccessorFromString( n.getName() );
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202 public final static String obtainUniProtAccessorFromDataFields( final PhylogenyNode n ) {
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204 if ( n.getNodeData().isHasSequence() ) {
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205 final Sequence seq = n.getNodeData().getSequence();
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206 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
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207 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getSymbol() );
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209 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
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210 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getName() );
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212 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
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213 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getGeneName() );
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215 if ( ForesterUtil.isEmpty( a ) && ( n.getNodeData().getSequence().getAccession() != null )
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216 && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
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217 a = SequenceAccessionTools.parseUniProtAccessorFromString( seq.getAccession().getValue() );
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220 if ( ForesterUtil.isEmpty( a ) && !ForesterUtil.isEmpty( n.getName() ) ) {
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221 a = SequenceAccessionTools.parseUniProtAccessorFromString( n.getName() );
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226 public final static Accession parseAccessorFromString( final String s ) {
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227 if ( !ForesterUtil.isEmpty( s ) ) {
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228 String v = parseUniProtAccessorFromString( s );
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229 if ( !ForesterUtil.isEmpty( v ) ) {
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230 return new Accession( v, Accession.UNIPROT );
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232 v = parseGenbankAccessorFromString( s );
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233 if ( !ForesterUtil.isEmpty( v ) ) {
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234 return new Accession( v, Accession.NCBI );
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236 v = parseRefSeqAccessorFromString( s );
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237 if ( !ForesterUtil.isEmpty( v ) ) {
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238 return new Accession( v, Accession.REFSEQ );
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240 v = parseGInumberFromString( s );
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241 if ( !ForesterUtil.isEmpty( v ) ) {
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242 return new Accession( v, Accession.GI );
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248 public final static String parseGenbankAccessorFromString( final String s ) {
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249 Matcher m = GENBANK_NUC_PATTERN_1.matcher( s );
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250 if ( m.lookingAt() ) {
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251 return m.group( 1 );
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254 m = GENBANK_NUC_PATTERN_2.matcher( s );
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255 if ( m.lookingAt() ) {
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256 return m.group( 1 );
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259 m = GENBANK_PROT_PATTERN.matcher( s );
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260 if ( m.lookingAt() ) {
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261 return m.group( 1 );
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270 public final static String parseGenbankProteinAccessorFromString( final String s ) {
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271 final Matcher m = GENBANK_PROT_PATTERN.matcher( s );
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272 if ( m.lookingAt() ) {
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273 return m.group( 1 );
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280 public final static String parseGInumberFromString( final String s ) {
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281 final Matcher m = GI_PATTERN.matcher( s );
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283 return m.group( 1 );
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288 public final static String parseRefSeqAccessorFromString( final String s ) {
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289 final Matcher m = REFSEQ_PATTERN.matcher( s );
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290 if ( m.lookingAt() ) {
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291 return m.group( 1 );
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296 public final static String parseUniProtAccessorFromString( final String s ) {
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297 Matcher m = UNIPROT_KB_PATTERN_0.matcher( s );
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299 return m.group( 1 );
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301 m = UNIPROT_KB_PATTERN_1.matcher( s );
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303 return m.group( 1 );
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305 m = UNIPROT_KB_PATTERN_2.matcher( s );
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