inprogress

[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 5f1a5b1..d40e3f8 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -46,7 +46,6 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Confidence;
-import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
@@ -58,7 +57,6 @@ import org.forester.util.ForesterUtil;
 public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParser {
 
     public static final TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT = TAXONOMY_EXTRACTION.NO;
-    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=([^,]+)" );
@@ -292,6 +290,9 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     }
 
     private final void getNext() throws IOException, NHXFormatException {
+        if ( _source == null ) {
+            throw new IOException( "source is not set" );
+        }
         while ( true ) {
             char c = '\b';
             if ( _input_type == BUFFERED_READER ) {
@@ -594,13 +595,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
                         }
                         node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
                     }
-                    else if ( s.startsWith( NHXtags.DOMAIN_STRUCTURE ) ) {
-                        if ( !node_to_annotate.getNodeData().isHasSequence() ) {
-                            node_to_annotate.getNodeData().setSequence( new Sequence() );
-                        }
-                        node_to_annotate.getNodeData().getSequence()
-                                .setDomainArchitecture( new DomainArchitecture( s.substring( 3 ) ) );
-                    }
                     else if ( s.startsWith( NHXtags.SEQUENCE_ACCESSION ) ) {
                         if ( !node_to_annotate.getNodeData().isHasSequence() ) {
                             node_to_annotate.getNodeData().setSequence( new Sequence() );
@@ -709,6 +703,6 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse
     }
 
     public static enum TAXONOMY_EXTRACTION {
-        NO, YES, PFAM_STYLE_ONLY;
+        NO, PFAM_STYLE_RELAXED, PFAM_STYLE_STRICT, AGGRESSIVE;
     }
 }