in progress

[jalview.git] / forester / java / src / org / forester / io / parsers / nhx / NHXParser.java

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 c373104..c1cfa40 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -39,6 +39,7 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.Phylogeny;
@@ -60,17 +61,16 @@ import org.forester.util.ForesterUtil;
 
 public final class NHXParser implements PhylogenyParser {
 
-    public static final boolean                              LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = false;
-    public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT       = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
-    final static private boolean                             GUESS_ROOTEDNESS_DEFAULT          = true;
-    final static private boolean                             GUESS_IF_SUPPORT_VALUES           = true;
-    final static private boolean                             IGNORE_QUOTES_DEFAULT             = false;
-    final static public boolean                              REPLACE_UNDERSCORES_DEFAULT       = false;
+    public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
+    final static private boolean                             GUESS_ROOTEDNESS_DEFAULT    = true;
+    final static private boolean                             GUESS_IF_SUPPORT_VALUES     = true;
+    final static private boolean                             IGNORE_QUOTES_DEFAULT       = false;
+    final static public boolean                              REPLACE_UNDERSCORES_DEFAULT = false;
     private boolean                                          _saw_closing_paren;
-    final static private byte                                STRING                            = 0;
-    final static private byte                                STRING_BUFFER                     = 1;
-    final static private byte                                CHAR_ARRAY                        = 2;
-    final static private byte                                BUFFERED_READER                   = 3;
+    final static private byte                                STRING                      = 0;
+    final static private byte                                STRING_BUFFER               = 1;
+    final static private byte                                CHAR_ARRAY                  = 2;
+    final static private byte                                BUFFERED_READER             = 3;
     private boolean                                          _guess_rootedness;
     private boolean                                          _has_next;
     private boolean                                          _ignore_quotes;
@@ -84,16 +84,16 @@ public final class NHXParser implements PhylogenyParser {
     private Phylogeny                                        _current_phylogeny;
     private PhylogenyMethods.TAXONOMY_EXTRACTION             _taxonomy_extraction;
     private boolean                                          _replace_underscores;
-    public final static Pattern                              UC_LETTERS_NUMBERS_PATTERN        = Pattern
-                                                                                                       .compile( "^[A-Z0-9]+$" );
-    public final static Pattern                              NUMBERS_ONLY_PATTERN              = Pattern
-                                                                                                       .compile( "^[0-9\\.]+$" );
-    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_BL_PATTERN                     = Pattern
-                                                                                                       .compile( "length_median=([^,]+)" );
+    public final static Pattern                              UC_LETTERS_NUMBERS_PATTERN  = Pattern
+                                                                                                 .compile( "^[A-Z0-9]+$" );
+    public final static Pattern                              NUMBERS_ONLY_PATTERN        = Pattern
+                                                                                                 .compile( "^[0-9\\.]+$" );
+    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_BL_PATTERN               = Pattern
+                                                                                                 .compile( "length_median=([^,]+)" );
 
     public NHXParser() {
         init();
@@ -118,8 +118,9 @@ public final class NHXParser implements PhylogenyParser {
      * 
      * @throws PhylogenyParserException
      * @throws NHXFormatException
+     * @throws PhyloXmlDataFormatException 
      */
-    private void finishPhylogeny() throws PhylogenyParserException, NHXFormatException {
+    private void finishPhylogeny() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
         setCladeLevel( 0 );
         if ( getCurrentPhylogeny() != null ) {
             parseNHX( getCurrentAnotation().toString(),
@@ -142,7 +143,8 @@ public final class NHXParser implements PhylogenyParser {
         }
     }
 
-    private void finishSingleNodePhylogeny() throws PhylogenyParserException, NHXFormatException {
+    private void finishSingleNodePhylogeny() throws PhylogenyParserException, NHXFormatException,
+            PhyloXmlDataFormatException {
         setCladeLevel( 0 );
         final PhylogenyNode new_node = new PhylogenyNode();
         parseNHX( getCurrentAnotation().toString(), new_node, getTaxonomyExtraction(), isReplaceUnderscores() );
@@ -408,8 +410,9 @@ public final class NHXParser implements PhylogenyParser {
      * 
      * @throws PhylogenyParserException
      * @throws NHXFormatException
+     * @throws PhyloXmlDataFormatException 
      */
-    private void processCloseParen() throws PhylogenyParserException, NHXFormatException {
+    private void processCloseParen() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
         decreaseCladeLevel();
         if ( !isSawClosingParen() ) {
             final PhylogenyNode new_node = new PhylogenyNode();
@@ -435,8 +438,9 @@ public final class NHXParser implements PhylogenyParser {
      * 
      * @throws PhylogenyParserException
      * @throws NHXFormatException
+     * @throws PhyloXmlDataFormatException 
      */
-    private void processComma() throws PhylogenyParserException, NHXFormatException {
+    private void processComma() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
         if ( !isSawClosingParen() ) {
             final PhylogenyNode new_node = new PhylogenyNode();
             parseNHX( getCurrentAnotation().toString(), new_node, getTaxonomyExtraction(), isReplaceUnderscores() );
@@ -460,8 +464,9 @@ public final class NHXParser implements PhylogenyParser {
      * 
      * @throws PhylogenyParserException
      * @throws NHXFormatException
+     * @throws PhyloXmlDataFormatException 
      */
-    private void processOpenParen() throws PhylogenyParserException, NHXFormatException {
+    private void processOpenParen() throws PhylogenyParserException, NHXFormatException, PhyloXmlDataFormatException {
         final PhylogenyNode new_node = new PhylogenyNode();
         if ( getCladeLevel() == 0 ) {
             if ( getCurrentPhylogeny() != null ) {
@@ -643,7 +648,8 @@ public final class NHXParser implements PhylogenyParser {
     public static void parseNHX( String s,
                                  final PhylogenyNode node_to_annotate,
                                  final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
-                                 final boolean replace_underscores ) throws NHXFormatException {
+                                 final boolean replace_underscores ) throws NHXFormatException,
+            PhyloXmlDataFormatException {
         if ( ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.NO ) && replace_underscores ) {
             throw new IllegalArgumentException( "cannot extract taxonomies and replace under scores at the same time" );
         }
@@ -685,10 +691,8 @@ public final class NHXParser implements PhylogenyParser {
                     node_to_annotate.setName( t.nextToken() );
                     if ( !replace_underscores
                             && ( !is_nhx && ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.NO ) ) ) {
-                        final String tax = ParserUtils
-                                .extractTaxonomyCodeFromNodeName( node_to_annotate.getName(),
-                                                                  LIMIT_SPECIES_NAMES_TO_FIVE_CHARS,
-                                                                  taxonomy_extraction );
+                        final String tax = ParserUtils.extractTaxonomyCodeFromNodeName( node_to_annotate.getName(),
+                                                                                        taxonomy_extraction );
                         if ( !ForesterUtil.isEmpty( tax ) ) {
                             if ( !node_to_annotate.getNodeData().isHasTaxonomy() ) {
                                 node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() );