forester_applications/src/org/forester/applications/tax_code_cleaner.java

   1 // javac -cp ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
   2 // ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/org/forester/applications/tax_code_cleaner.java
   3 // java -Xmx2048m -cp
   4 // /home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/:/home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
   5 // org.forester.applications.tax_code_cleaner
   6
   7 package org.forester.applications;
   8
   9 import java.io.File;
  10 import java.util.regex.Pattern;
  11
  12 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  13 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  14 import org.forester.io.writers.PhylogenyWriter;
  15 import org.forester.phylogeny.Phylogeny;
  16 import org.forester.phylogeny.PhylogenyNode;
  17 import org.forester.phylogeny.data.Taxonomy;
  18 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  19 import org.forester.phylogeny.factories.PhylogenyFactory;
  20 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  21 import org.forester.util.CommandLineArguments;
  22 import org.forester.util.ForesterUtil;
  23
  24 public class tax_code_cleaner {
  25
  26     private final static String BASE = "b_";
  27
  28     public static void main( final String args[] ) {
  29         File in = null;
  30         File out = null;
  31         try {
  32             CommandLineArguments cla = null;
  33             cla = new CommandLineArguments( args );
  34             in = cla.getFile( 0 );
  35             out = cla.getFile( 1 );
  36             // if ( out.exists() ) {
  37             //      System.out.println( out + " already exists" );
  38             //      System.exit( -1 );
  39             //  }
  40             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  41             final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
  42             final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
  43             final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
  44             final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
  45             int i = 0;
  46             while ( it.hasNext() ) {
  47                 final PhylogenyNode node = it.next();
  48                 processNode( node, i );
  49                 i++;
  50             }
  51             final PhylogenyWriter writer = new PhylogenyWriter();
  52             writer.toPhyloXML( out, phylogeny_0, 0 );
  53         }
  54         catch ( final Exception e ) {
  55             System.out.println( e.getLocalizedMessage() );
  56             e.printStackTrace();
  57             System.exit( -1 );
  58         }
  59     }
  60
  61     private static void processNode( final PhylogenyNode node, final int i ) throws PhyloXmlDataFormatException {
  62         if ( node.isExternal() ) {
  63             if ( node.getNodeData().isHasTaxonomy() ) {
  64                 final Taxonomy t = node.getNodeData().getTaxonomy();
  65                 if ( !ForesterUtil.isEmpty( t.getTaxonomyCode() ) ) {
  66                     final String tc = t.getTaxonomyCode();
  67                     if ( tc.equals( "ACRALC" ) ) {
  68                         t.setScientificName( "Acremonium alcalophilum" );
  69                         t.setTaxonomyCode( "AALXX" );
  70                     }
  71                     else if ( tc.equals( "AMPQU" ) ) {
  72                         t.setScientificName( "Amphimedon queenslandica" );
  73                         t.setTaxonomyCode( "AMPQE" );
  74                     }
  75                     else if ( tc.equals( "AQUAE" ) ) {
  76                         t.setScientificName( "Aquifex aeolicus (strain VF5)" );
  77                     }
  78                     else if ( tc.equals( "ASTSPC" ) ) {
  79                         t.setScientificName( "Asterochloris sp. Cgr/DA1pho" );
  80                         t.setTaxonomyCode( "ASCXX" );
  81                     }
  82                     else if ( tc.equals( "BAUCOM" ) ) {
  83                         t.setScientificName( "Baudoinia compniacensis" );
  84                         t.setTaxonomyCode( "BCOXX" );
  85                     }
  86                     else if ( tc.equals( "CAP" ) ) {
  87                         t.setScientificName( "Capitella sp.1" );
  88                         t.setTaxonomyCode( "CTEXX" );
  89                     }
  90                     else if ( tc.equals( "CAPOWC" ) ) {
  91                         t.setScientificName( "Capsaspora owczarzaki (strain ATCC 30864)" );
  92                         t.setTaxonomyCode( "CAPO3" );
  93                     }
  94                     else if ( tc.equals( "CHLVUL" ) ) {
  95                         t.setScientificName( "Chlorella variabilis" );
  96                         t.setTaxonomyCode( "CHLVA" );
  97                     }
  98                     else if ( tc.equals( "CITCLE" ) ) {
  99                         t.setScientificName( "Citrus clementina" );
 100                         t.setTaxonomyCode( "CCLXX" );
 101                     }
 102                     else if ( tc.equals( "CLAGRA" ) ) {
 103                         t.setScientificName( "Cladonia grayi" );
 104                         t.setTaxonomyCode( "" );
 105                     }
 106                     else if ( tc.equals( "COEREV" ) ) {
 107                         t.setScientificName( "Coemansia reversa" );
 108                         t.setTaxonomyCode( "CREXX" );
 109                     }
 110                     else if ( tc.equals( "CONPUT" ) ) {
 111                         t.setScientificName( "Coniophora puteana" );
 112                         t.setTaxonomyCode( "CPUXX" );
 113                     }
 114                     else if ( tc.equals( "DICSQU" ) ) {
 115                         t.setScientificName( "Dichomitus squalens" );
 116                         t.setTaxonomyCode( "DICSQ" );
 117                     }
 118                     else if ( tc.equals( "FOMPIN" ) ) {
 119                         t.setScientificName( "Fomitopsis pinicola" );
 120                         t.setTaxonomyCode( "FPIXX" );
 121                     }
 122                     else if ( tc.equals( "GONPRO" ) ) {
 123                         t.setScientificName( "Gonapodya prolifera" );
 124                         t.setTaxonomyCode( "GONPR" );
 125                     }
 126                     else if ( tc.equals( "GYMLUX" ) ) {
 127                         t.setScientificName( "Gymnopus luxurians" );
 128                         t.setTaxonomyCode( "" );
 129                     }
 130                     else if ( tc.equals( "HYDPIN" ) ) {
 131                         t.setScientificName( "Hydnomerulius pinastri" );
 132                         t.setTaxonomyCode( "" );
 133                     }
 134                     else if ( tc.equals( "JAAARG" ) ) {
 135                         t.setScientificName( "Jaapia argillacea" );
 136                         t.setTaxonomyCode( "" );
 137                     }
 138                     else if ( tc.equals( "MYCPOP" ) ) {
 139                         t.setScientificName( "Mycosphaerella populorum" );
 140                         t.setTaxonomyCode( "MYCPS" );
 141                     }
 142                     else if ( tc.equals( "MYCTHE" ) ) {
 143                         t.setScientificName( "Myceliophthora thermophila" );
 144                         t.setTaxonomyCode( "THIHA" );
 145                     }
 146                     else if ( tc.equals( "OIDMAI" ) ) {
 147                         t.setScientificName( "Oidiodendron maius" );
 148                         t.setTaxonomyCode( "" );
 149                     }
 150                     else if ( tc.equals( "PANVIR" ) ) {
 151                         t.setScientificName( "Panicum virgatum" );
 152                         t.setTaxonomyCode( "PANVG" );
 153                     }
 154                     else if ( tc.equals( "PIRSPE" ) ) {
 155                         t.setScientificName( "Piromyces sp. E2" );
 156                         t.setTaxonomyCode( "PIRSE" );
 157                     }
 158                     else if ( tc.equals( "SAICOM" ) ) {
 159                         t.setScientificName( "Saitoella complicata" );
 160                         t.setTaxonomyCode( "" );
 161                     }
 162                     else if ( tc.equals( "SERLAC" ) ) {
 163                         t.setScientificName( "Serpula lacrymans" );
 164                         t.setTaxonomyCode( "SERL9" );
 165                     }
 166                     else if ( tc.equals( "SPHARC" ) ) {
 167                         t.setScientificName( "Sphaeroforma arctica" );
 168                         t.setTaxonomyCode( "SARXX" );
 169                     }
 170                     else if ( tc.equals( "THETRA" ) ) {
 171                         t.setScientificName( "Thecamonas trahens" );
 172                         t.setTaxonomyCode( "TTRXX" );
 173                     }
 174                     else if ( tc.equals( "THITER" ) ) {
 175                         t.setScientificName( "Thielavia terrestris (strain ATCC 38088 / NRRL 8126)" );
 176                         t.setTaxonomyCode( "THITE" );
 177                     }
 178                     else if ( tc.equals( "WOLCOC" ) ) {
 179                         t.setScientificName( "Wolfiporia cocos MD-104 SS10" );
 180                         t.setTaxonomyCode( "WOLCO" );
 181                     }
 182                     else if ( tc.equals( "XANPAR" ) ) {
 183                         t.setScientificName( "Xanthoria parietina 46-1" );
 184                         t.setTaxonomyCode( "" );
 185                     }
 186                     else if ( tc.length() == 6 ) {
 187                         final Pattern p = Pattern.compile( "[A-Z9][A-Z]{2}[A-Z0-9]{2}\\d" );
 188                         if ( p.matcher( tc ).matches() ) {
 189                             t.setTaxonomyCode( tc.substring( 0, 5 ) );
 190                         }
 191                     }
 192                 }
 193             }
 194         }
 195     }
 196 }