diff --git a/jgibblda/.classpath b/jgibblda/.classpath
index 03f79961c13cd63e03ca08883e00ccda4e98765c..c8482de2d76dcf7fea414c4888a460cf24ddcf59 100644
--- a/jgibblda/.classpath
+++ b/jgibblda/.classpath
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
- <classpathentry kind="src" path="src"/>
+ <classpathentry kind="src" path="src/main/java"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
<attributes>
<attribute name="maven.pomderived" value="true"/>
diff --git a/jgibblda/.settings/org.eclipse.jdt.core.prefs b/jgibblda/.settings/org.eclipse.jdt.core.prefs
index 71aa314cccdc8c5610bda147357512c5a43a4d3f..92f8042339f69fb00c768e5ed3c83ebd89f2efb9 100644
--- a/jgibblda/.settings/org.eclipse.jdt.core.prefs
+++ b/jgibblda/.settings/org.eclipse.jdt.core.prefs
@@ -1,10 +1,4 @@
eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
-org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
-org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
-org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
-org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
-org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
@@ -13,89 +7,291 @@ org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=ignore
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
-org.eclipse.jdt.core.compiler.problem.comparingIdentical=ignore
-org.eclipse.jdt.core.compiler.problem.deadCode=ignore
-org.eclipse.jdt.core.compiler.problem.deprecation=ignore
-org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
-org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
-org.eclipse.jdt.core.compiler.problem.discouragedReference=ignore
-org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
-org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
-org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
-org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore
-org.eclipse.jdt.core.compiler.problem.finalParameterBound=ignore
-org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=ignore
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=ignore
-org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=ignore
-org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
-org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=ignore
-org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=ignore
-org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
-org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
-org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=ignore
-org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
-org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
-org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
-org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore
-org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore
-org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
-org.eclipse.jdt.core.compiler.problem.missingSerialVersion=ignore
-org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
-org.eclipse.jdt.core.compiler.problem.noEffectAssignment=ignore
-org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=ignore
-org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
-org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
-org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
-org.eclipse.jdt.core.compiler.problem.nullReference=ignore
-org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
-org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
-org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=ignore
-org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
-org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
-org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
-org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
-org.eclipse.jdt.core.compiler.problem.rawTypeReference=ignore
-org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
-org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
-org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
-org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
-org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
-org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
-org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
-org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=ignore
-org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
-org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
-org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
-org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
-org.eclipse.jdt.core.compiler.problem.typeParameterHiding=ignore
-org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
-org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=ignore
-org.eclipse.jdt.core.compiler.problem.unclosedCloseable=ignore
-org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
-org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
-org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
-org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
-org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
-org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
-org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
-org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
-org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
-org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
-org.eclipse.jdt.core.compiler.problem.unusedImport=ignore
-org.eclipse.jdt.core.compiler.problem.unusedLabel=ignore
-org.eclipse.jdt.core.compiler.problem.unusedLocal=ignore
-org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
-org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
-org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
-org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
-org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
-org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=ignore
-org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
-org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
-org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=ignore
org.eclipse.jdt.core.compiler.source=1.7
+org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=48
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=16
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16
+org.eclipse.jdt.core.formatter.alignment_for_assignment=0
+org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16
+org.eclipse.jdt.core.formatter.alignment_for_compact_if=16
+org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
+org.eclipse.jdt.core.formatter.alignment_for_enum_constants=49
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
+org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
+org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
+org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
+org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
+org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=48
+org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
+org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
+org.eclipse.jdt.core.formatter.blank_lines_after_package=1
+org.eclipse.jdt.core.formatter.blank_lines_before_field=0
+org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0
+org.eclipse.jdt.core.formatter.blank_lines_before_imports=1
+org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1
+org.eclipse.jdt.core.formatter.blank_lines_before_method=1
+org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1
+org.eclipse.jdt.core.formatter.blank_lines_before_package=0
+org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1
+org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations=1
+org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_block=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_switch=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
+org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
+org.eclipse.jdt.core.formatter.comment.format_block_comments=true
+org.eclipse.jdt.core.formatter.comment.format_header=true
+org.eclipse.jdt.core.formatter.comment.format_html=true
+org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
+org.eclipse.jdt.core.formatter.comment.format_line_comments=true
+org.eclipse.jdt.core.formatter.comment.format_source_code=true
+org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
+org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
+org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
+org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
+org.eclipse.jdt.core.formatter.comment.line_length=80
+org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
+org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
+org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
+org.eclipse.jdt.core.formatter.compact_else_if=true
+org.eclipse.jdt.core.formatter.continuation_indentation=2
+org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2
+org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off
+org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on
+org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false
+org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true
+org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true
+org.eclipse.jdt.core.formatter.indent_empty_lines=false
+org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true
+org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
+org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
+org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=true
+org.eclipse.jdt.core.formatter.indentation.size=4
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_type_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert
+org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_binary_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters=insert
+org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block=insert
+org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert
+org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert=insert
+org.eclipse.jdt.core.formatter.insert_space_after_colon_in_case=insert
+org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_after_colon_in_labeled_statement=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
+org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
+org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_try=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_try_resources=insert
+org.eclipse.jdt.core.formatter.insert_space_after_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert
+org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_binary_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
+org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.join_lines_in_comments=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.lineSplit=120
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.tabulation.char=tab
+org.eclipse.jdt.core.formatter.tabulation.size=4
+org.eclipse.jdt.core.formatter.use_on_off_tags=true
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
+org.eclipse.jdt.core.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter
diff --git a/jgibblda/.settings/org.eclipse.jdt.ui.prefs b/jgibblda/.settings/org.eclipse.jdt.ui.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..5713c654549b40f76104760ab2f6cd031d71f011
--- /dev/null
+++ b/jgibblda/.settings/org.eclipse.jdt.ui.prefs
@@ -0,0 +1,3 @@
+eclipse.preferences.version=1
+formatter_profile=_vipra
+formatter_settings_version=12
diff --git a/jgibblda/pom.xml b/jgibblda/pom.xml
index 321ed5c26cb8a7c82edd5a980787899e3621d4e2..52b1475e13f9c4d5b7e7c6275a50cfd998a7d775 100644
--- a/jgibblda/pom.xml
+++ b/jgibblda/pom.xml
@@ -4,16 +4,36 @@
<groupId>JGibbLDA</groupId>
<artifactId>JGibbLDA</artifactId>
<version>0.0.1-SNAPSHOT</version>
+
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.target>1.7</maven.compiler.target>
<maven.compiler.source>1.7</maven.compiler.source>
+ <log4jVersion>2.4.1</log4jVersion>
</properties>
+
<dependencies>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
<version>2.0.6</version>
</dependency>
+
+ <!-- Logging -->
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-api</artifactId>
+ <version>${log4jVersion}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ <version>${log4jVersion}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-slf4j-impl</artifactId>
+ <version>${log4jVersion}</version>
+ </dependency>
</dependencies>
</project>
\ No newline at end of file
diff --git a/jgibblda/src/jgibblda/Constants.java b/jgibblda/src/jgibblda/Constants.java
deleted file mode 100644
index c65e53a8cd51d4ea405acdbdccd52f467195b272..0000000000000000000000000000000000000000
--- a/jgibblda/src/jgibblda/Constants.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright (C) 2007 by
- *
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
- *
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
- *
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
- *
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-package jgibblda;
-
-public class Constants {
- public static final long BUFFER_SIZE_LONG = 1000000;
- public static final short BUFFER_SIZE_SHORT = 512;
-
- public static final int MODEL_STATUS_UNKNOWN = 0;
- public static final int MODEL_STATUS_EST = 1;
- public static final int MODEL_STATUS_ESTC = 2;
- public static final int MODEL_STATUS_INF = 3;
-}
diff --git a/jgibblda/src/jgibblda/Conversion.java b/jgibblda/src/jgibblda/Conversion.java
deleted file mode 100644
index 5834e771b429b6f240e6bf64817c6008e49cd5c7..0000000000000000000000000000000000000000
--- a/jgibblda/src/jgibblda/Conversion.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright (C) 2007 by
- *
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
- *
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
- *
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
- *
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-package jgibblda;
-
-public class Conversion {
- public static String ZeroPad(int number, int width) {
- StringBuffer result = new StringBuffer("");
- for (int i = 0; i < width - Integer.toString(number).length(); i++)
- result.append("0");
- result.append(Integer.toString(number));
-
- return result.toString();
- }
-}
diff --git a/jgibblda/src/jgibblda/LDA.java b/jgibblda/src/jgibblda/LDA.java
deleted file mode 100644
index cd950a21f259a71e626926d021b688dc68e586dd..0000000000000000000000000000000000000000
--- a/jgibblda/src/jgibblda/LDA.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*
- * Copyright (C) 2007 by
- *
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
- *
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
- *
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
- *
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-package jgibblda;
-
-import org.kohsuke.args4j.*;
-
-public class LDA {
-
- public static void main(String args[]) {
- LDACmdOption option = new LDACmdOption();
- CmdLineParser parser = new CmdLineParser(option);
-
- try {
- if (args.length == 0) {
- showHelp(parser);
- return;
- }
-
- parser.parseArgument(args);
-
- if (option.est || option.estc) {
- Estimator estimator = new Estimator();
- estimator.init(option);
- estimator.estimate();
- } else if (option.inf) {
- Inferencer inferencer = new Inferencer();
- inferencer.init(option);
-
- Model newModel = inferencer.inference();
-
- for (int i = 0; i < newModel.phi.length; ++i) {
- // phi: K * V
- System.out.println("-----------------------\ntopic" + i + " : ");
- for (int j = 0; j < 10; ++j) {
- System.out.println(inferencer.globalDict.id2word.get(j) + "\t" + newModel.phi[i][j]);
- }
- }
- }
- } catch (CmdLineException cle) {
- System.out.println("Command line error: " + cle.getMessage());
- showHelp(parser);
- return;
- } catch (Exception e) {
- System.out.println("Error in main: " + e.getMessage());
- e.printStackTrace();
- return;
- }
- }
-
- public static void showHelp(CmdLineParser parser) {
- System.out.println("LDA [options ...] [arguments...]");
- parser.printUsage(System.out);
- }
-
-}
diff --git a/jgibblda/src/jgibblda/Pair.java b/jgibblda/src/jgibblda/Pair.java
deleted file mode 100644
index 6eef0aa292cbc788947c3baa98c907f1024215db..0000000000000000000000000000000000000000
--- a/jgibblda/src/jgibblda/Pair.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright (C) 2007 by
- *
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
- *
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
- *
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
- *
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-package jgibblda;
-
-import java.util.Comparator;
-
-public class Pair implements Comparable<Pair> {
- public Object first;
- public Comparable second;
- public static boolean naturalOrder = false;
-
- public Pair(Object k, Comparable v) {
- first = k;
- second = v;
- }
-
- public Pair(Object k, Comparable v, boolean naturalOrder) {
- first = k;
- second = v;
- Pair.naturalOrder = naturalOrder;
- }
-
- public int compareTo(Pair p) {
- if (naturalOrder)
- return this.second.compareTo(p.second);
- else
- return -this.second.compareTo(p.second);
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/Constants.java b/jgibblda/src/main/java/jgibblda/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..6d1b558ac9fd8a86ade375aa48e27063934a3a31
--- /dev/null
+++ b/jgibblda/src/main/java/jgibblda/Constants.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2007 by
+ *
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
+ *
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
+ *
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ *
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package jgibblda;
+
+public class Constants {
+ public static final long BUFFER_SIZE_LONG = 1000000;
+ public static final short BUFFER_SIZE_SHORT = 512;
+
+ public static final int MODEL_STATUS_UNKNOWN = 0;
+ public static final int MODEL_STATUS_EST = 1;
+ public static final int MODEL_STATUS_ESTC = 2;
+ public static final int MODEL_STATUS_INF = 3;
+}
diff --git a/jgibblda/src/main/java/jgibblda/Conversion.java b/jgibblda/src/main/java/jgibblda/Conversion.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2bd1d7c39969459e0810d42d2b6f00380c69f3a
--- /dev/null
+++ b/jgibblda/src/main/java/jgibblda/Conversion.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright (C) 2007 by
+ *
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
+ *
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
+ *
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ *
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package jgibblda;
+
+public class Conversion {
+ public static String ZeroPad(int number, int width) {
+ StringBuffer result = new StringBuffer("");
+ for (int i = 0; i < width - Integer.toString(number).length(); i++)
+ result.append("0");
+ result.append(Integer.toString(number));
+
+ return result.toString();
+ }
+}
diff --git a/jgibblda/src/jgibblda/Dictionary.java b/jgibblda/src/main/java/jgibblda/Dictionary.java
similarity index 74%
rename from jgibblda/src/jgibblda/Dictionary.java
rename to jgibblda/src/main/java/jgibblda/Dictionary.java
index f8550fdf87649a9cca2c7b506f725b181f239a9c..90972c93b834008a6f5817d0baf39b8bec7949fe 100644
--- a/jgibblda/src/jgibblda/Dictionary.java
+++ b/jgibblda/src/main/java/jgibblda/Dictionary.java
@@ -1,29 +1,24 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
@@ -38,7 +33,13 @@ import java.util.Iterator;
import java.util.Map;
import java.util.StringTokenizer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class Dictionary {
+
+ public static final Logger log = LoggerFactory.getLogger(Dictionary.class);
+
public Map<String, Integer> word2id;
public Map<Integer, String> id2word;
@@ -130,7 +131,7 @@ public class Dictionary {
reader.close();
return true;
} catch (Exception e) {
- System.out.println("Error while reading dictionary:" + e.getMessage());
+ log.error("Error while reading dictionary:" + e.getMessage());
e.printStackTrace();
return false;
}
@@ -156,7 +157,7 @@ public class Dictionary {
writer.close();
return true;
} catch (Exception e) {
- System.out.println("Error while writing word map " + e.getMessage());
+ log.error("Error while writing word map " + e.getMessage());
e.printStackTrace();
return false;
}
diff --git a/jgibblda/src/jgibblda/Document.java b/jgibblda/src/main/java/jgibblda/Document.java
similarity index 65%
rename from jgibblda/src/jgibblda/Document.java
rename to jgibblda/src/main/java/jgibblda/Document.java
index c9faf020f3fff5b48802a265e11c98c2557c2aa9..bc5ce78c4473cc6309c996bea9e8467b2f23780e 100644
--- a/jgibblda/src/jgibblda/Document.java
+++ b/jgibblda/src/main/java/jgibblda/Document.java
@@ -1,29 +1,24 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
diff --git a/jgibblda/src/jgibblda/Estimator.java b/jgibblda/src/main/java/jgibblda/Estimator.java
similarity index 69%
rename from jgibblda/src/jgibblda/Estimator.java
rename to jgibblda/src/main/java/jgibblda/Estimator.java
index c26a3ecdeb36a677098c46ac4824afa21ff562f7..b59b77a02c2637a93c5645b6f7e9ce53f9538bfe 100644
--- a/jgibblda/src/jgibblda/Estimator.java
+++ b/jgibblda/src/main/java/jgibblda/Estimator.java
@@ -1,38 +1,37 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
import java.io.File;
-import java.util.Vector;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
public class Estimator {
+ public static final Logger log = LoggerFactory.getLogger(Estimator.class);
+
// output model
protected Model trnModel;
LDACmdOption option;
@@ -54,11 +53,11 @@ public class Estimator {
}
public void estimate() {
- System.out.println("Sampling " + trnModel.niters + " iteration!");
+ log.info("Sampling " + trnModel.niters + " iteration!");
int lastIter = trnModel.liter;
for (trnModel.liter = lastIter + 1; trnModel.liter < trnModel.niters + lastIter; trnModel.liter++) {
- System.out.println("Iteration " + trnModel.liter + " ...");
+ log.info("Iteration " + trnModel.liter + " ...");
// for all z_i
for (int m = 0; m < trnModel.M; m++) {
@@ -72,20 +71,20 @@ public class Estimator {
if (option.savestep > 0) {
if (trnModel.liter % option.savestep == 0) {
- System.out.println("Saving the model at iteration " + trnModel.liter + " ...");
+ log.info("Saving the model at iteration " + trnModel.liter + " ...");
computeTheta();
computePhi();
- trnModel.saveModel("model-" + Conversion.ZeroPad(trnModel.liter, 5));
+ trnModel.saveModel(option.modelName + "-" + Conversion.ZeroPad(trnModel.liter, 5));
}
}
} // end iterations
- System.out.println("Gibbs sampling completed!\n");
- System.out.println("Saving the final model!\n");
+ log.info("Gibbs sampling completed");
+ log.info("Saving the final model");
computeTheta();
computePhi();
trnModel.liter--;
- trnModel.saveModel("model-final");
+ trnModel.saveModel(option.modelName);
}
/**
diff --git a/jgibblda/src/jgibblda/Inferencer.java b/jgibblda/src/main/java/jgibblda/Inferencer.java
similarity index 73%
rename from jgibblda/src/jgibblda/Inferencer.java
rename to jgibblda/src/main/java/jgibblda/Inferencer.java
index 3811c582e7f1db4bf50671a8e89beb5334a233a0..25bfa07fd0abb543ea31fdc23d4d85c33c63a076 100644
--- a/jgibblda/src/jgibblda/Inferencer.java
+++ b/jgibblda/src/main/java/jgibblda/Inferencer.java
@@ -1,41 +1,35 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
public class Inferencer {
+
+ public static final Logger log = LoggerFactory.getLogger(Inferencer.class);
+
// Train model
public Model trnModel;
public Dictionary globalDict;
@@ -63,15 +57,14 @@ public class Inferencer {
// inference new model ~ getting data from a specified dataset
public Model inference(LDADataset newData) {
- System.out.println("init new model");
+ log.info("init new model");
Model newModel = new Model();
newModel.initNewModel(option, newData, trnModel);
this.newModel = newModel;
- System.out.println("Sampling " + niters + " iteration for inference!");
+ log.info("Sampling " + niters + " iteration for inference!");
for (newModel.liter = 1; newModel.liter <= niters; newModel.liter++) {
- // System.out.println("Iteration " + newModel.liter + " ...");
// for all newz_i
for (int m = 0; m < newModel.M; ++m) {
@@ -85,7 +78,7 @@ public class Inferencer {
} // end iterations
- System.out.println("Gibbs sampling for inference completed!");
+ log.info("Gibbs sampling for inference completed!");
computeNewTheta();
computeNewPhi();
@@ -94,27 +87,20 @@ public class Inferencer {
}
public Model inference(String[] strs) {
- // System.out.println("inference");
- Model newModel = new Model();
-
- // System.out.println("read dataset");
LDADataset dataset = LDADataset.readDataSet(strs, globalDict);
-
return inference(dataset);
}
// inference new model ~ getting dataset from file specified in option
public Model inference() {
- // System.out.println("inference");
newModel = new Model();
if (!newModel.initNewModel(option, trnModel))
return null;
- System.out.println("Sampling " + niters + " iteration for inference!");
+ log.info("Sampling " + niters + " iteration for inference!");
for (newModel.liter = 1; newModel.liter <= niters; newModel.liter++) {
- // System.out.println("Iteration " + newModel.liter + " ...");
// for all newz_i
for (int m = 0; m < newModel.M; ++m) {
@@ -128,8 +114,8 @@ public class Inferencer {
} // end iterations
- System.out.println("Gibbs sampling for inference completed!");
- System.out.println("Saving the inference outputs!");
+ log.info("Gibbs sampling for inference completed!");
+ log.info("Saving the inference outputs!");
computeNewTheta();
computeNewPhi();
diff --git a/jgibblda/src/main/java/jgibblda/LDA.java b/jgibblda/src/main/java/jgibblda/LDA.java
new file mode 100644
index 0000000000000000000000000000000000000000..808b7e27d168f42b429f76ebf3f41636062c3da3
--- /dev/null
+++ b/jgibblda/src/main/java/jgibblda/LDA.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright (C) 2007 by
+ *
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
+ *
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
+ *
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ *
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package jgibblda;
+
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class LDA {
+
+ public static final Logger log = LoggerFactory.getLogger(LDA.class);
+
+ public static void main(String args[]) {
+ LDACmdOption option = new LDACmdOption();
+ CmdLineParser parser = new CmdLineParser(option);
+
+ try {
+ if (args.length == 0) {
+ showHelp(parser);
+ return;
+ }
+
+ parser.parseArgument(args);
+
+ if (option.est || option.estc) {
+ Estimator estimator = new Estimator();
+ estimator.init(option);
+ estimator.estimate();
+ } else if (option.inf) {
+ Inferencer inferencer = new Inferencer();
+ inferencer.init(option);
+
+ Model newModel = inferencer.inference();
+
+ for (int i = 0; i < newModel.phi.length; ++i) {
+ // phi: K * V
+ log.info("-----------------------\ntopic" + i + " : ");
+ for (int j = 0; j < 10; ++j) {
+ log.info(inferencer.globalDict.id2word.get(j) + "\t" + newModel.phi[i][j]);
+ }
+ }
+ }
+ } catch (CmdLineException cle) {
+ log.info("Command line error: " + cle.getMessage());
+ showHelp(parser);
+ return;
+ } catch (Exception e) {
+ log.info("Error in main: " + e.getMessage());
+ e.printStackTrace();
+ return;
+ }
+ }
+
+ public static void showHelp(CmdLineParser parser) {
+ log.info("LDA [options ...] [arguments...]");
+ parser.printUsage(System.out);
+ }
+
+}
diff --git a/jgibblda/src/jgibblda/LDACmdOption.java b/jgibblda/src/main/java/jgibblda/LDACmdOption.java
similarity index 94%
rename from jgibblda/src/jgibblda/LDACmdOption.java
rename to jgibblda/src/main/java/jgibblda/LDACmdOption.java
index 6d29a5e572cc61b454a21d084fac9c95cb6c3294..79c548a7fbf4648938ba936522be774dbf6aad28 100644
--- a/jgibblda/src/jgibblda/LDACmdOption.java
+++ b/jgibblda/src/main/java/jgibblda/LDACmdOption.java
@@ -1,6 +1,6 @@
package jgibblda;
-import org.kohsuke.args4j.*;
+import org.kohsuke.args4j.Option;
public class LDACmdOption {
diff --git a/jgibblda/src/jgibblda/LDADataset.java b/jgibblda/src/main/java/jgibblda/LDADataset.java
similarity index 74%
rename from jgibblda/src/jgibblda/LDADataset.java
rename to jgibblda/src/main/java/jgibblda/LDADataset.java
index d820974505abade6554247324afeabbc28fb967e..7b11caa8595207884c2033ceee3b995b1a579436 100644
--- a/jgibblda/src/jgibblda/LDADataset.java
+++ b/jgibblda/src/main/java/jgibblda/LDADataset.java
@@ -1,40 +1,43 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.InputStreamReader;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Vector;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class LDADataset {
+
+ public static final Logger log = LoggerFactory.getLogger(LDADataset.class);
+
// ---------------------------------------------------------------
// Instance Variables
// ---------------------------------------------------------------
@@ -127,7 +130,6 @@ public class LDADataset {
if (globalDict != null) {
// get the global id
Integer id = globalDict.getID(word);
- // System.out.println(id);
if (id != null) {
localDict.addWord(word);
@@ -166,7 +168,7 @@ public class LDADataset {
reader.close();
return data;
} catch (Exception e) {
- System.out.println("Read Dataset Error: " + e.getMessage());
+ log.error("Read Dataset Error: " + e.getMessage());
e.printStackTrace();
return null;
}
@@ -189,7 +191,7 @@ public class LDADataset {
reader.close();
return data;
} catch (Exception e) {
- System.out.println("Read Dataset Error: " + e.getMessage());
+ log.error("Read Dataset Error: " + e.getMessage());
e.printStackTrace();
return null;
}
@@ -201,25 +203,7 @@ public class LDADataset {
* @return dataset if success and null otherwise
*/
public static LDADataset readDataSet(BufferedReader reader) {
- try {
- // read number of document
- String line;
- line = reader.readLine();
- int M = Integer.parseInt(line);
-
- LDADataset data = new LDADataset(M);
- for (int i = 0; i < M; ++i) {
- line = reader.readLine();
-
- data.setDoc(line, i);
- }
-
- return data;
- } catch (Exception e) {
- System.out.println("Read Dataset Error: " + e.getMessage());
- e.printStackTrace();
- return null;
- }
+ return readDataSet(reader, null);
}
/**
@@ -233,22 +217,22 @@ public class LDADataset {
*/
public static LDADataset readDataSet(BufferedReader reader, Dictionary dict) {
try {
- // read number of document
+ List<String> lines = new ArrayList<>();
+
String line;
- line = reader.readLine();
- int M = Integer.parseInt(line);
- System.out.println("NewM:" + M);
+ while ((line = reader.readLine()) != null) {
+ lines.add(line);
+ }
- LDADataset data = new LDADataset(M, dict);
- for (int i = 0; i < M; ++i) {
- line = reader.readLine();
+ LDADataset data = new LDADataset(lines.size(), dict);
- data.setDoc(line, i);
+ for (int i = 0; i < lines.size(); i++) {
+ data.setDoc(lines.get(i), i);
}
return data;
} catch (Exception e) {
- System.out.println("Read Dataset Error: " + e.getMessage());
+ log.error("Read Dataset Error: " + e.getMessage());
e.printStackTrace();
return null;
}
@@ -282,11 +266,9 @@ public class LDADataset {
* @return dataset if success and null otherwise
*/
public static LDADataset readDataSet(String[] strs, Dictionary dict) {
- // System.out.println("readDataset...");
LDADataset data = new LDADataset(strs.length, dict);
for (int i = 0; i < strs.length; ++i) {
- // System.out.println("set doc " + i);
data.setDoc(strs[i], i);
}
return data;
diff --git a/jgibblda/src/jgibblda/Model.java b/jgibblda/src/main/java/jgibblda/Model.java
similarity index 84%
rename from jgibblda/src/jgibblda/Model.java
rename to jgibblda/src/main/java/jgibblda/Model.java
index b8669df055afabd7e3ab7b97f8a53b93caafce10..4303d74a33855a18a67352801b6804397f51b752 100644
--- a/jgibblda/src/jgibblda/Model.java
+++ b/jgibblda/src/main/java/jgibblda/Model.java
@@ -1,29 +1,24 @@
/*
* Copyright (C) 2007 by
*
- * Xuan-Hieu Phan
- * hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
- * Graduate School of Information Sciences
- * Tohoku University
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
*
- * Cam-Tu Nguyen
- * ncamtu@gmail.com
- * College of Technology
- * Vietnam National University, Hanoi
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
*
- * JGibbsLDA is a free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published
- * by the Free Software Foundation; either version 2 of the License,
- * or (at your option) any later version.
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
*
- * JGibbsLDA is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with JGibbsLDA; if not, write to the Free Software Foundation,
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package jgibblda;
@@ -34,17 +29,22 @@ import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.HashMap;
import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class Model {
+ public static final Logger log = LoggerFactory.getLogger(Model.class);
+
// ---------------------------------------------------------------
// Class Variables
// ---------------------------------------------------------------
@@ -184,18 +184,19 @@ public class Model {
reader.close();
} catch (Exception e) {
- System.out.println("Error while reading other file:" + e.getMessage());
+ log.error("Error while reading other file:" + e.getMessage());
e.printStackTrace();
return false;
}
return true;
}
+ @SuppressWarnings("unchecked")
protected boolean readTAssignFile(String tassignFile) {
+ BufferedReader reader = null;
try {
int i, j;
- BufferedReader reader = new BufferedReader(
- new InputStreamReader(new FileInputStream(tassignFile), "UTF-8"));
+ reader = new BufferedReader(new InputStreamReader(new FileInputStream(tassignFile), "UTF-8"));
String line;
z = new Vector[M];
@@ -215,7 +216,7 @@ public class Model {
StringTokenizer tknr2 = new StringTokenizer(token, ":");
if (tknr2.countTokens() != 2) {
- System.out.println("Invalid word-topic assignment line\n");
+ log.warn("Invalid word-topic assignment line\n");
return false;
}
@@ -234,12 +235,15 @@ public class Model {
}
} // end for each doc
-
- reader.close();
} catch (Exception e) {
- System.out.println("Error while loading model: " + e.getMessage());
+ log.error("Error while loading model: " + e.getMessage());
e.printStackTrace();
return false;
+ } finally {
+ if (reader != null)
+ try {
+ reader.close();
+ } catch (IOException e) {}
}
return true;
}
@@ -283,7 +287,7 @@ public class Model {
writer.close();
} catch (Exception e) {
- System.out.println("Error while saving model tassign: " + e.getMessage());
+ log.error("Error while saving model tassign: " + e.getMessage());
e.printStackTrace();
return false;
}
@@ -304,7 +308,7 @@ public class Model {
}
writer.close();
} catch (Exception e) {
- System.out.println("Error while saving topic distribution file for this model: " + e.getMessage());
+ log.error("Error while saving topic distribution file for this model: " + e.getMessage());
e.printStackTrace();
return false;
}
@@ -327,7 +331,7 @@ public class Model {
}
writer.close();
} catch (Exception e) {
- System.out.println("Error while saving word-topic distribution:" + e.getMessage());
+ log.error("Error while saving word-topic distribution:" + e.getMessage());
e.printStackTrace();
return false;
}
@@ -350,7 +354,7 @@ public class Model {
writer.close();
} catch (Exception e) {
- System.out.println("Error while saving model others:" + e.getMessage());
+ log.error("Error while saving model others:" + e.getMessage());
e.printStackTrace();
return false;
}
@@ -391,7 +395,7 @@ public class Model {
writer.close();
} catch (Exception e) {
- System.out.println("Error while saving model twords: " + e.getMessage());
+ log.error("Error while saving model twords: " + e.getMessage());
e.printStackTrace();
return false;
}
@@ -461,6 +465,7 @@ public class Model {
/**
* Init parameters for estimation
*/
+ @SuppressWarnings("unchecked")
public boolean initNewModel(LDACmdOption option) {
if (!init(option))
return false;
@@ -470,7 +475,7 @@ public class Model {
data = LDADataset.readDataSet(dir + File.separator + dfile);
if (data == null) {
- System.out.println("Fail to read training data!\n");
+ log.error("Fail to read training data!\n");
return false;
}
@@ -541,6 +546,7 @@ public class Model {
* @param newData
* DataSet for which we do inference
*/
+ @SuppressWarnings("unchecked")
public boolean initNewModel(LDACmdOption option, LDADataset newData, Model trnModel) {
if (!init(option))
return false;
@@ -552,7 +558,7 @@ public class Model {
beta = trnModel.beta;
p = new double[K];
- System.out.println("K:" + K);
+ log.info("K:" + K);
data = newData;
@@ -561,8 +567,8 @@ public class Model {
V = data.V;
dir = option.dir;
savestep = option.savestep;
- System.out.println("M:" + M);
- System.out.println("V:" + V);
+ log.info("M:" + M);
+ log.info("V:" + V);
// K: from command line or default value
// alpha, beta: from command line or default values
@@ -628,7 +634,7 @@ public class Model {
LDADataset dataset = LDADataset.readDataSet(dir + File.separator + dfile, trnModel.data.localDict);
if (dataset == null) {
- System.out.println("Fail to read dataset!\n");
+ log.error("Fail to read dataset!\n");
return false;
}
@@ -648,15 +654,15 @@ public class Model {
// load model, i.e., read z and trndata
if (!loadModel()) {
- System.out.println("Fail to load word-topic assignment file of the model!\n");
+ log.error("Fail to load word-topic assignment file of the model!\n");
return false;
}
- System.out.println("Model loaded:");
- System.out.println("\talpha:" + alpha);
- System.out.println("\tbeta:" + beta);
- System.out.println("\tM:" + M);
- System.out.println("\tV:" + V);
+ log.info("Model loaded:");
+ log.info("\talpha:" + alpha);
+ log.info("\tbeta:" + beta);
+ log.info("\tM:" + M);
+ log.info("\tV:" + V);
nw = new int[V][K];
for (w = 0; w < V; w++) {
diff --git a/jgibblda/src/main/java/jgibblda/Pair.java b/jgibblda/src/main/java/jgibblda/Pair.java
new file mode 100644
index 0000000000000000000000000000000000000000..7753f6597a558e474ba44defc33ebb0705154a9e
--- /dev/null
+++ b/jgibblda/src/main/java/jgibblda/Pair.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright (C) 2007 by
+ *
+ * Xuan-Hieu Phan hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com Graduate School
+ * of Information Sciences Tohoku University
+ *
+ * Cam-Tu Nguyen ncamtu@gmail.com College of Technology Vietnam National
+ * University, Hanoi
+ *
+ * JGibbsLDA is a free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ *
+ * JGibbsLDA is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * JGibbsLDA; if not, write to the Free Software Foundation, Inc., 59 Temple
+ * Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package jgibblda;
+
+@SuppressWarnings("rawtypes")
+public class Pair implements Comparable<Pair> {
+ public Object first;
+ public Comparable second;
+ public static boolean naturalOrder = false;
+
+ public Pair(Object k, Comparable v) {
+ first = k;
+ second = v;
+ }
+
+ public Pair(Object k, Comparable v, boolean naturalOrder) {
+ first = k;
+ second = v;
+ Pair.naturalOrder = naturalOrder;
+ }
+
+ @SuppressWarnings("unchecked")
+ public int compareTo(Pair p) {
+ if (naturalOrder)
+ return this.second.compareTo(p.second);
+ else
+ return -this.second.compareTo(p.second);
+ }
+}
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/file/Filebase.java b/vipra-cmd/src/main/java/de/vipra/cmd/file/Filebase.java
index 320290eccea12b7ab706b9712fc0ca8587be5be6..02dcda7b2cc00e2b780f5f956086a81324729cc8 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/file/Filebase.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/file/Filebase.java
@@ -13,28 +13,29 @@ import de.vipra.util.ex.ConfigException;
public abstract class Filebase implements Closeable {
- private final File dataDir;
- private final File dataFile;
+ private final File modelDir;
+ private final File modelFile;
private final FilebaseIndex index;
private final FilebaseVocabulary vocab;
- public Filebase(File dataDir, String fileName) throws FilebaseException {
- this.dataDir = dataDir;
+ public Filebase(File dataDir, String modelName) throws FilebaseException {
+ this.modelDir = new File(dataDir, modelName);
+ if (!modelDir.exists()) {
+ if (!modelDir.mkdirs()) {
+ throw new FilebaseException("could not create model directory: " + modelDir.getAbsolutePath());
+ }
+ }
try {
- this.dataFile = new File(dataDir, fileName);
- this.index = new FilebaseIndex(new File(dataDir, Constants.INDEX_FILE));
- this.vocab = new FilebaseVocabulary(new File(dataDir, Constants.VOCAB_FILE));
+ this.modelFile = new File(modelDir, modelName);
+ this.index = new FilebaseIndex(new File(modelDir, Constants.INDEX_FILE));
+ this.vocab = new FilebaseVocabulary(new File(modelDir, Constants.VOCAB_FILE));
} catch (IOException e) {
throw new FilebaseException("could not read index: " + e.getMessage());
}
}
- public File getDataDir() {
- return dataDir;
- }
-
- public File getDataFile() {
- return dataFile;
+ public File getModelFile() {
+ return modelFile;
}
public FilebaseIndex getIndex() {
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/file/JGibbFilebase.java b/vipra-cmd/src/main/java/de/vipra/cmd/file/JGibbFilebase.java
index 18f6a5d5b96133fd871dc72bb1501c888876bddd..b92fcf9a1d1ada9daf0251a7b50f75b36bd7441e 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/file/JGibbFilebase.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/file/JGibbFilebase.java
@@ -8,19 +8,18 @@ import java.util.List;
import de.vipra.cmd.ex.FilebaseException;
import de.vipra.cmd.model.Article;
-import de.vipra.util.StringUtils;
import de.vipra.util.ex.NotImplementedException;
public class JGibbFilebase extends Filebase {
- private final File dataFile;
+ private final File modelFile;
private final FilebaseIndex index;
private final FilebaseVocabulary vocab;
private final List<Article> articles;
public JGibbFilebase(File dataDir) throws FilebaseException {
super(dataDir, "jgibb");
- this.dataFile = getDataFile();
+ this.modelFile = getModelFile();
this.index = getIndex();
this.vocab = getVocab();
this.articles = new ArrayList<>();
@@ -41,28 +40,16 @@ public class JGibbFilebase extends Filebase {
@Override
public void write() throws IOException {
- boolean exists = dataFile.exists();
-
- RandomAccessFile raf = new RandomAccessFile(dataFile, "rw");
-
- // read count if exists
- int articleCount = 0;
- if (exists) {
- byte[] count = new byte[10];
- raf.read(count);
- articleCount = Integer.parseInt(new String(count));
- }
-
- // write count
- // count is padded to allow replacement with bigger numbers
- articleCount += articles.size();
- raf.seek(0);
- raf.writeBytes(StringUtils.padNumber(articleCount));
+ boolean linesep = modelFile.exists();
+ RandomAccessFile raf = new RandomAccessFile(modelFile, "rw");
// write articles
raf.seek(raf.length());
for (Article a : articles) {
- raf.writeBytes(System.lineSeparator());
+ if (linesep)
+ raf.writeBytes(System.lineSeparator());
+ else
+ linesep = true;
raf.writeBytes(a.getProcessedText().getText());
}
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbLDAAnalyzer.java b/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbLDAAnalyzer.java
index 1d1f3e9a00ba76d0aeaa27b67995a2a9f38981ad..4ba727279719b170efaa826dea86fa06482316bc 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbLDAAnalyzer.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbLDAAnalyzer.java
@@ -1,38 +1,71 @@
package de.vipra.cmd.lda;
+import java.io.File;
+
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import de.vipra.cmd.ex.LDAAnalyzerException;
import de.vipra.util.Config;
+import de.vipra.util.ex.ConfigException;
+import jgibblda.Estimator;
import jgibblda.Inferencer;
import jgibblda.LDACmdOption;
+import jgibblda.Model;
public class JGibbLDAAnalyzer extends LDAAnalyzer {
public static final Logger log = LoggerFactory.getLogger(JGibbLDAAnalyzer.class);
- private final LDACmdOption ldaOption;
- private final Inferencer inferencer;
+ private File dataDir;
+ private File modelDir;
+ private File modelFile;
+ private LDACmdOption options;
protected JGibbLDAAnalyzer() {
super("JGibb Analyzer");
- this.ldaOption = new LDACmdOption();
- this.inferencer = new Inferencer();
}
@Override
public void init(Config config) throws LDAAnalyzerException {
- try {
+ options = new LDACmdOption();
- } catch (Exception e) {
+ try {
+ dataDir = config.getDataDirectory();
+ } catch (ConfigException e) {
throw new LDAAnalyzerException(e);
}
+
+ modelDir = new File(dataDir, "jgibb");
+ options.dir = modelDir.getAbsolutePath();
+ options.estc = new File(modelDir, "model-final.tassign").exists();
+ options.est = !options.estc;
+
+ modelFile = new File(modelDir, "jgibb");
+ options.dfile = modelFile.getName();
+
+ options.modelName = "jgibb";
}
@Override
public void analyze() throws LDAAnalyzerException {
+ if (!modelFile.exists()) {
+ throw new LDAAnalyzerException("model file does not exist: " + modelFile.getAbsolutePath());
+ }
+ estimate();
+ inference();
+ }
+
+ private void estimate() {
+ Estimator estimator = new Estimator();
+ estimator.init(options);
+ estimator.estimate();
+ }
+ private void inference() {
+ Inferencer inferencer = new Inferencer();
+ inferencer.init(options);
+ Model newModel = inferencer.inference();
}
}
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/option/ImportCommand.java b/vipra-cmd/src/main/java/de/vipra/cmd/option/ImportCommand.java
index f6b20130aed5c92e0c0205b318a371f0c9b2e14d..34869e1b4fa2684b49dab0f01aacd80748707239 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/option/ImportCommand.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/option/ImportCommand.java
@@ -146,7 +146,7 @@ public class ImportCommand implements Command {
preprocessor = Processor.getPreprocessor(config);
analyzer = LDAAnalyzer.getAnalyzer(config);
- out.info("using data directory: " + filebase.getDataDir().getAbsolutePath());
+ out.info("using data directory: " + config.getDataDirectory().getAbsolutePath());
out.info("using preprocessor: " + preprocessor.getName());
out.info("using analyzer: " + analyzer.getName());
@@ -160,14 +160,14 @@ public class ImportCommand implements Command {
}
long durImport = timer.lap();
- // do topic modeling
- analyzer.analyze();
- long durAnalyze = timer.lap();
-
// write filebase
filebase.close();
long durIndex = timer.lap();
+ // do topic modeling
+ analyzer.analyze();
+ long durAnalyze = timer.lap();
+
out.info("imported " + articles.size() + " " + (articles.size() == 1 ? "article" : "articles"));
out.info("import: " + StringUtils.timeString(durImport) + ", analyze: " + StringUtils.timeString(durAnalyze)
+ ", reindex: " + StringUtils.timeString(durIndex));
diff --git a/vipra-rest/.settings/org.eclipse.jdt.ui.prefs b/vipra-rest/.settings/org.eclipse.jdt.ui.prefs
index a7f8de8ef5b0d043d6e4ba0446e4ea440514af27..fe89f28bca5900b59ebe3dc0ed0745189fa9e153 100644
--- a/vipra-rest/.settings/org.eclipse.jdt.ui.prefs
+++ b/vipra-rest/.settings/org.eclipse.jdt.ui.prefs
@@ -1,3 +1,2 @@
eclipse.preferences.version=1
-formatter_profile=_Vipra
formatter_settings_version=12