From e14e8c06907c1bb35de6c3c21986e1e32e520d82 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 20 Jul 2012 22:03:23 +0000 Subject: [PATCH] in progress --- .../io/parsers/HmmscanPerDomainTableParser.java | 5 +++ .../AdjactantDirectedBinaryDomainCombination.java | 5 ++- .../surfacing/BasicBinaryDomainCombination.java | 39 ++++++++++++-------- .../surfacing/DirectedBinaryDomainCombination.java | 5 ++- 4 files changed, 34 insertions(+), 20 deletions(-) diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java index 0bb224c..2aa4497 100644 --- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java @@ -64,6 +64,7 @@ public final class HmmscanPerDomainTableParser { private static final ReturnType RETURN_TYPE_DEFAULT = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN; private static final boolean IGNORE_DUFS_DEFAULT = false; private static final int MAX_ALLOWED_OVERLAP_DEFAULT = -1; + private static final boolean IGNORE_REPLACED_RRMS = true; private final Set _filter; private final FilterType _filter_type; private final File _input_file; @@ -447,6 +448,10 @@ public final class HmmscanPerDomainTableParser { else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) { ++_domains_ignored_due_to_duf; } + else if ( IGNORE_REPLACED_RRMS + && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id + .contains( "RRM_6" ) ) ) { + } else if ( isIgnoreVirusLikeIds() && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO ) || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG ) diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java index 6e6da35..3da8ed4 100644 --- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java @@ -36,8 +36,9 @@ public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainC if ( ( n_terminal == null ) || ( c_terminal == null ) ) { throw new IllegalArgumentException( "attempt to create binary domain combination using null" ); } - _id_0 = n_terminal.getId(); - _id_1 = c_terminal.getId(); + // _id_0 = n_terminal.getId(); + // _id_1 = c_terminal.getId(); + _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId(); } public AdjactantDirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) { diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java index 6516903..67e5ffd 100644 --- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java @@ -32,14 +32,16 @@ import org.forester.util.ForesterUtil; public class BasicBinaryDomainCombination implements BinaryDomainCombination { - String _id_0; - String _id_1; + String _data; + //String _id_0; + // String _id_1; //DomainId _id_0; //DomainId _id_1; BasicBinaryDomainCombination() { - _id_0 = null; - _id_1 = null; + //_id_0 = null; + // _id_1 = null; + _data = null; } public BasicBinaryDomainCombination( final String id_0, final String id_1 ) { @@ -49,12 +51,14 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { final String my_id_0 = id_0.trim(); final String my_id_1 = id_1.trim(); if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) { - _id_0 = my_id_0; - _id_1 = my_id_1; + //_id_0 = my_id_0; + //_id_1 = my_id_1; + _data = my_id_0 + BinaryDomainCombination.SEPARATOR + my_id_1; } else { - _id_0 = my_id_1; - _id_1 = my_id_0; + //_id_0 = my_id_1; + // _id_1 = my_id_0; + _data = my_id_1 + BinaryDomainCombination.SEPARATOR + my_id_0; } } @@ -100,18 +104,20 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { @Override public DomainId getId0() { - return new DomainId( _id_0 ); + return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 0 ] ); } @Override public DomainId getId1() { - return new DomainId( _id_1 ); + // return new DomainId( _id_1 ); + return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] ); } @Override public int hashCode() { // return getId0().hashCode() + ( 19 * getId1().hashCode() ); - return ( _id_0 + _id_1 ).hashCode(); + // return ( _id_0 + _id_1 ).hashCode(); + return _data.hashCode(); } @Override @@ -160,11 +166,12 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { @Override public String toString() { - final StringBuffer sb = new StringBuffer(); - sb.append( _id_0 ); - sb.append( BinaryDomainCombination.SEPARATOR ); - sb.append( _id_1 ); - return sb.toString(); + return _data; + // final StringBuffer sb = new StringBuffer(); + // sb.append( _id_0 ); + // sb.append( BinaryDomainCombination.SEPARATOR ); + // sb.append( _id_1 ); + // return sb.toString(); } public static BinaryDomainCombination createInstance( final String ids ) { diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java index 237bb67..e57e137 100644 --- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java @@ -36,8 +36,9 @@ public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombinatio if ( ( n_terminal == null ) || ( c_terminal == null ) ) { throw new IllegalArgumentException( "attempt to create binary domain combination using null" ); } - _id_0 = n_terminal.getId(); - _id_1 = c_terminal.getId(); + //_id_0 = n_terminal.getId(); + //_id_1 = c_terminal.getId(); + _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId(); } public DirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) { -- 1.7.10.2