From 5608ffe84b2c541f79adaf498063906a9804a9db Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 9 Apr 2013 02:30:25 +0000 Subject: [PATCH] inprogress --- .../org/forester/io/parsers/util/ParserUtils.java | 6 ++---- forester/java/src/org/forester/test/Test.java | 22 ++++++++++---------- 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java index 975e558..92275ad 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -58,10 +58,8 @@ public final class ParserUtils { final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP"; final public static Pattern TAXOMONY_SN_PATTERN = Pattern .compile( "[A-Z0-9]{2,}_([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)\\b" ); - final public static Pattern TAXOMONY_CODE_PATTERN_R1 = Pattern.compile( "[A-Z0-9]+_(" + TAX_CODE - + ")(?:\\b|_)" ); - final public static Pattern TAXOMONY_CODE_PATTERN_R2 = Pattern.compile( "(?:\\b|_)(" + TAX_CODE - + ")(?:\\b|_)" ); + final public static Pattern TAXOMONY_CODE_PATTERN_R1 = Pattern.compile( "[A-Z0-9]+_(" + TAX_CODE + ")\\b" ); + final public static Pattern TAXOMONY_CODE_PATTERN_R2 = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")\\b" ); final private static Pattern TAXOMONY_CODE_PATTERN_PF = Pattern.compile( "[A-Z0-9]{2,}_(" + TAX_CODE + ")/\\d+-\\d+" ); final public static Pattern TAXOMONY_CODE_PATTERN_4 = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" ); diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index dc1d14f..cbd304d 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -1148,11 +1148,11 @@ public final class Test { if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN_", TAXONOMY_EXTRACTION.AGGRESSIVE ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE ) .equals( "SOYBN" ) ) { return false; } @@ -1180,7 +1180,7 @@ public final class Test { .equals( "SOYBN" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "SOYBN" ) ) { return false; } @@ -1188,7 +1188,7 @@ public final class Test { .equals( "SOYBN" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN_qwerty", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN qwerty", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "SOYBN" ) ) { return false; } @@ -1203,7 +1203,7 @@ public final class Test { if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "SOYBN" ) ) { return false; } @@ -1221,7 +1221,7 @@ public final class Test { .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; @@ -1243,7 +1243,7 @@ public final class Test { TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) { return false; } @@ -1276,18 +1276,18 @@ public final class Test { .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE^", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } - if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) != null ) { + if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE*", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) != null ) { return false; } - if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "x_MOUSE_x", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) + if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "x_MOUSE=x", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) .equals( "MOUSE" ) ) { return false; } -- 1.7.10.2