diff --git a/build.sh b/build.sh
index 301135706f3a6999cd5cbbd955521735a76bb20a..fe85c1ddfc7b986f4c3361ca3d0e5475a3585d58 100755
--- a/build.sh
+++ b/build.sh
@@ -5,7 +5,6 @@ TOMCAT_WEBAPPS="vm/webapps"
# enable/disable (1/0) project building
BUILD_DTM=1
-BUILD_JGIBBLDA=1
BUILD_VIPRA_UTIL=1
BUILD_VIPRA_CMD=1
BUILD_VIPRA_UI=1
@@ -27,7 +26,7 @@ if [ $BUILD_DTM -eq 1 ]; then
echo using $MAKE | tee $LOG
fi
-if [ $BUILD_JGIBBLDA -eq 1 ] || [ $BUILD_VIPRA_UTIL -eq 1 ] || [ $BUILD_VIPRA_CMD -eq 1 ] || [ $BUILD_VIPRA_BACKEND -eq 1 ]; then
+if [ $BUILD_VIPRA_UTIL -eq 1 ] || [ $BUILD_VIPRA_CMD -eq 1 ] || [ $BUILD_VIPRA_BACKEND -eq 1 ]; then
JAVA=$(command -v java 2>/dev/null) || { echo >&2 "java not found"; exit 1; }
echo using $JAVA | tee $LOG
@@ -67,22 +66,6 @@ else
cd ../..
fi
-# build jgibblda
-
-echo "" >> $LOG
-echo "-------------------------------" >> $LOG
-if [ $BUILD_JGIBBLDA -ne 1 ]; then
- echo "compiling jgibblda > skipped" | tee -a $LOG
-else
- echo "compiling jgibblda" | tee -a $LOG
- echo "-------------------------------" >> $LOG
- $MVN -f ./jgibblda/pom.xml install >> $LOG 2>&1
- if [ $? -ne 0 ]; then
- echo "error"
- exit 1
- fi
-fi
-
# build vipra-util
echo "" >> $LOG
diff --git a/jgibblda/.classpath b/jgibblda/.classpath
deleted file mode 100644
index cf6dc8577b7a1ef815c8060b30722361a43c9e05..0000000000000000000000000000000000000000
--- a/jgibblda/.classpath
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="org.eclipse.jst.component.nondependency" value=""/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
- <attributes>
- <attribute name="owner.project.facets" value="java"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/jgibblda/.gitignore b/jgibblda/.gitignore
deleted file mode 100644
index 09e3bc9b241c477ea341af9ee029becad0c2148c..0000000000000000000000000000000000000000
--- a/jgibblda/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/bin/
-/target/
diff --git a/jgibblda/.project b/jgibblda/.project
deleted file mode 100644
index 2f6739e94a4f8a44417d3b5e9e2bf9db4a44913f..0000000000000000000000000000000000000000
--- a/jgibblda/.project
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>JGibbLDA</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.wst.validation.validationbuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>net.sourceforge.metrics.builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
- <nature>net.sourceforge.metrics.nature</nature>
- </natures>
-</projectDescription>
diff --git a/jgibblda/.settings/org.eclipse.core.resources.prefs b/jgibblda/.settings/org.eclipse.core.resources.prefs
deleted file mode 100644
index e9441bb123ec3e1ab029c7eac896bc45681d9a71..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.core.resources.prefs
+++ /dev/null
@@ -1,3 +0,0 @@
-eclipse.preferences.version=1
-encoding//src/main/java=UTF-8
-encoding/<project>=UTF-8
diff --git a/jgibblda/.settings/org.eclipse.jdt.core.prefs b/jgibblda/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644
index bf52a73f0cb4d7fde47825bf5e19ce3b293969af..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,298 +0,0 @@
-eclipse.preferences.version=1
-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=1.8
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.8
-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.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.8
-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=false
-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=false
-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
deleted file mode 100644
index bab1260352fa628f34603b44ab35e272a059e4b0..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.jdt.ui.prefs
+++ /dev/null
@@ -1,62 +0,0 @@
-cleanup.add_default_serial_version_id=true
-cleanup.add_generated_serial_version_id=false
-cleanup.add_missing_annotations=true
-cleanup.add_missing_deprecated_annotations=true
-cleanup.add_missing_methods=false
-cleanup.add_missing_nls_tags=false
-cleanup.add_missing_override_annotations=true
-cleanup.add_missing_override_annotations_interface_methods=true
-cleanup.add_serial_version_id=false
-cleanup.always_use_blocks=true
-cleanup.always_use_parentheses_in_expressions=false
-cleanup.always_use_this_for_non_static_field_access=false
-cleanup.always_use_this_for_non_static_method_access=false
-cleanup.convert_functional_interfaces=false
-cleanup.convert_to_enhanced_for_loop=true
-cleanup.correct_indentation=true
-cleanup.format_source_code=true
-cleanup.format_source_code_changes_only=false
-cleanup.insert_inferred_type_arguments=false
-cleanup.make_local_variable_final=true
-cleanup.make_parameters_final=true
-cleanup.make_private_fields_final=true
-cleanup.make_type_abstract_if_missing_method=false
-cleanup.make_variable_declarations_final=true
-cleanup.never_use_blocks=false
-cleanup.never_use_parentheses_in_expressions=true
-cleanup.organize_imports=true
-cleanup.qualify_static_field_accesses_with_declaring_class=false
-cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
-cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
-cleanup.qualify_static_member_accesses_with_declaring_class=true
-cleanup.qualify_static_method_accesses_with_declaring_class=false
-cleanup.remove_private_constructors=true
-cleanup.remove_redundant_type_arguments=true
-cleanup.remove_trailing_whitespaces=true
-cleanup.remove_trailing_whitespaces_all=true
-cleanup.remove_trailing_whitespaces_ignore_empty=false
-cleanup.remove_unnecessary_casts=true
-cleanup.remove_unnecessary_nls_tags=true
-cleanup.remove_unused_imports=true
-cleanup.remove_unused_local_variables=true
-cleanup.remove_unused_private_fields=true
-cleanup.remove_unused_private_members=true
-cleanup.remove_unused_private_methods=true
-cleanup.remove_unused_private_types=true
-cleanup.sort_members=false
-cleanup.sort_members_all=false
-cleanup.use_anonymous_class_creation=false
-cleanup.use_blocks=false
-cleanup.use_blocks_only_for_return_and_throw=false
-cleanup.use_lambda=true
-cleanup.use_parentheses_in_expressions=false
-cleanup.use_this_for_non_static_field_access=true
-cleanup.use_this_for_non_static_field_access_only_if_necessary=true
-cleanup.use_this_for_non_static_method_access=true
-cleanup.use_this_for_non_static_method_access_only_if_necessary=true
-cleanup.use_type_arguments=false
-cleanup_profile=_vipra
-cleanup_settings_version=2
-eclipse.preferences.version=1
-formatter_profile=_vipra
-formatter_settings_version=12
diff --git a/jgibblda/.settings/org.eclipse.m2e.core.prefs b/jgibblda/.settings/org.eclipse.m2e.core.prefs
deleted file mode 100644
index f897a7f1cb2389f85fe6381425d29f0a9866fb65..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.m2e.core.prefs
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/jgibblda/.settings/org.eclipse.wst.common.component b/jgibblda/.settings/org.eclipse.wst.common.component
deleted file mode 100644
index 245b97a8e36eb01568610dd2812fad4883b3bfaa..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.wst.common.component
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
- <wb-module deploy-name="JGibbLDA">
- <wb-resource deploy-path="/" source-path="/src/main/java"/>
- </wb-module>
-</project-modules>
diff --git a/jgibblda/.settings/org.eclipse.wst.common.project.facet.core.xml b/jgibblda/.settings/org.eclipse.wst.common.project.facet.core.xml
deleted file mode 100644
index fd0227a68279180b3dd187cfc58335b8a0914833..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.wst.common.project.facet.core.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<faceted-project>
- <fixed facet="java"/>
- <fixed facet="jst.utility"/>
- <installed facet="jst.utility" version="1.0"/>
- <installed facet="java" version="1.8"/>
-</faceted-project>
diff --git a/jgibblda/.settings/org.eclipse.wst.validation.prefs b/jgibblda/.settings/org.eclipse.wst.validation.prefs
deleted file mode 100644
index 04cad8cb752a9761c4e5167d0301d3a27674430f..0000000000000000000000000000000000000000
--- a/jgibblda/.settings/org.eclipse.wst.validation.prefs
+++ /dev/null
@@ -1,2 +0,0 @@
-disabled=06target
-eclipse.preferences.version=1
diff --git a/jgibblda/pom.xml b/jgibblda/pom.xml
deleted file mode 100644
index 6abee2d33e9a846fb25a36a86f97ca64fd63c9d8..0000000000000000000000000000000000000000
--- a/jgibblda/pom.xml
+++ /dev/null
@@ -1,39 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>jgibblda</groupId>
- <artifactId>jgibblda</artifactId>
- <version>0.0.1-SNAPSHOT</version>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.target>1.8</maven.compiler.target>
- <maven.compiler.source>1.8</maven.compiler.source>
- <log4jVersion>2.4.1</log4jVersion>
- </properties>
-
- <dependencies>
- <dependency>
- <groupId>args4j</groupId>
- <artifactId>args4j</artifactId>
- <version>2.32</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/main/java/META-INF/MANIFEST.MF b/jgibblda/src/main/java/META-INF/MANIFEST.MF
deleted file mode 100644
index 5e9495128c0376427420c4189993b3851770b702..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,3 +0,0 @@
-Manifest-Version: 1.0
-Class-Path:
-
diff --git a/jgibblda/src/main/java/jgibblda/Constants.java b/jgibblda/src/main/java/jgibblda/Constants.java
deleted file mode 100644
index 65fff358f800501ba6760de427e491b0c24f97cc..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Constants.java
+++ /dev/null
@@ -1,34 +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/main/java/jgibblda/Conversion.java b/jgibblda/src/main/java/jgibblda/Conversion.java
deleted file mode 100644
index ed310f99ed9592acbe8ce8c948d7b2f8a1ace974..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Conversion.java
+++ /dev/null
@@ -1,35 +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(final int number, final int width) {
- final 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/main/java/jgibblda/Dictionary.java b/jgibblda/src/main/java/jgibblda/Dictionary.java
deleted file mode 100644
index 335565dd190be4e05eefa2fac10a2df77ab03c54..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Dictionary.java
+++ /dev/null
@@ -1,166 +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.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.util.HashMap;
-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;
-
- // --------------------------------------------------
- // constructors
- // --------------------------------------------------
-
- public Dictionary() {
- word2id = new HashMap<String, Integer>();
- id2word = new HashMap<Integer, String>();
- }
-
- // ---------------------------------------------------
- // get/set methods
- // ---------------------------------------------------
-
- public String getWord(final int id) {
- return id2word.get(id);
- }
-
- public Integer getID(final String word) {
- return word2id.get(word);
- }
-
- // ----------------------------------------------------
- // checking methods
- // ----------------------------------------------------
- /**
- * check if this dictionary contains a specified word
- */
- public boolean contains(final String word) {
- return word2id.containsKey(word);
- }
-
- public boolean contains(final int id) {
- return id2word.containsKey(id);
- }
-
- // ---------------------------------------------------
- // manupulating methods
- // ---------------------------------------------------
- /**
- * add a word into this dictionary return the corresponding id
- */
- public int addWord(final String word) {
- if (!contains(word)) {
- final int id = word2id.size();
-
- word2id.put(word, id);
- id2word.put(id, word);
-
- return id;
- } else
- return getID(word);
- }
-
- // ---------------------------------------------------
- // I/O methods
- // ---------------------------------------------------
- /**
- * read dictionary from file
- */
- public boolean readWordMap(final String wordMapFile) {
- try {
- final BufferedReader reader = new BufferedReader(
- new InputStreamReader(new FileInputStream(wordMapFile), "UTF-8"));
- String line;
-
- // read the number of words
- line = reader.readLine();
- final int nwords = Integer.parseInt(line);
-
- // read map
- for (int i = 0; i < nwords; ++i) {
- line = reader.readLine();
- final StringTokenizer tknr = new StringTokenizer(line, " \t\n\r");
-
- if (tknr.countTokens() != 2)
- continue;
-
- final String word = tknr.nextToken();
- final String id = tknr.nextToken();
- final int intID = Integer.parseInt(id);
-
- id2word.put(intID, word);
- word2id.put(word, intID);
- }
-
- reader.close();
- return true;
- } catch (final Exception e) {
- log.error("Error while reading dictionary:" + e.getMessage());
- e.printStackTrace();
- return false;
- }
- }
-
- public boolean writeWordMap(final String wordMapFile) {
- try {
- final BufferedWriter writer = new BufferedWriter(
- new OutputStreamWriter(new FileOutputStream(wordMapFile), "UTF-8"));
-
- // write number of words
- writer.write(word2id.size() + "\n");
-
- // write word to id
- final Iterator<String> it = word2id.keySet().iterator();
- while (it.hasNext()) {
- final String key = it.next();
- final Integer value = word2id.get(key);
-
- writer.write(key + " " + value + "\n");
- }
-
- writer.close();
- return true;
- } catch (final Exception e) {
- log.error("Error while writing word map " + e.getMessage());
- e.printStackTrace();
- return false;
- }
-
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/Document.java b/jgibblda/src/main/java/jgibblda/Document.java
deleted file mode 100644
index cb87aed08e12bddd5ea1223c378b55bd44bc96da..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Document.java
+++ /dev/null
@@ -1,89 +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.Vector;
-
-public class Document {
-
- // ----------------------------------------------------
- // Instance Variables
- // ----------------------------------------------------
- public int[] words;
- public String rawStr;
- public int length;
-
- // ----------------------------------------------------
- // Constructors
- // ----------------------------------------------------
- public Document() {
- words = null;
- rawStr = "";
- length = 0;
- }
-
- public Document(final int length) {
- this.length = length;
- rawStr = "";
- words = new int[length];
- }
-
- public Document(final int length, final int[] words) {
- this.length = length;
- rawStr = "";
-
- this.words = new int[length];
- for (int i = 0; i < length; ++i) {
- this.words[i] = words[i];
- }
- }
-
- public Document(final int length, final int[] words, final String rawStr) {
- this.length = length;
- this.rawStr = rawStr;
-
- this.words = new int[length];
- for (int i = 0; i < length; ++i) {
- this.words[i] = words[i];
- }
- }
-
- public Document(final Vector<Integer> doc) {
- this.length = doc.size();
- rawStr = "";
- this.words = new int[length];
- for (int i = 0; i < length; i++) {
- this.words[i] = doc.get(i);
- }
- }
-
- public Document(final Vector<Integer> doc, final String rawStr) {
- this.length = doc.size();
- this.rawStr = rawStr;
- this.words = new int[length];
- for (int i = 0; i < length; ++i) {
- this.words[i] = doc.get(i);
- }
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/Estimator.java b/jgibblda/src/main/java/jgibblda/Estimator.java
deleted file mode 100644
index 8968c09784eae25d47f73b7f34973c7e4274fda1..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Estimator.java
+++ /dev/null
@@ -1,156 +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.io.File;
-
-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;
-
- public boolean init(final LDACmdOption option) {
- this.option = option;
- trnModel = new Model();
-
- if (option.est) {
- if (!trnModel.initNewModel(option))
- return false;
- trnModel.data.localDict.writeWordMap(option.dir + File.separator + option.wordMapFileName);
- } else if (option.estc) {
- if (!trnModel.initEstimatedModel(option))
- return false;
- }
-
- return true;
- }
-
- public void estimate() {
- log.info("sampling " + trnModel.niters + " iterations");
-
- final int lastIter = trnModel.liter;
- for (trnModel.liter = lastIter + 1; trnModel.liter < trnModel.niters + lastIter; trnModel.liter++) {
- log.info("iteration " + trnModel.liter);
-
- // for all z_i
- for (int m = 0; m < trnModel.M; m++) {
- for (int n = 0; n < trnModel.data.docs[m].length; n++) {
- // z_i = z[m][n]
- // sample from p(z_i|z_-i, w)
- final int topic = sampling(m, n);
- trnModel.z[m].set(n, topic);
- } // end for each word
- } // end for each document
-
- if (option.savestep > 0) {
- if (trnModel.liter % option.savestep == 0) {
- log.info("iteration checkpoint: " + trnModel.liter);
- computeTheta();
- computePhi();
- trnModel.saveModel(option.modelName + "-" + Conversion.ZeroPad(trnModel.liter, 5));
- }
- }
- } // end iterations
-
- log.info("sampling completed, saving final model");
- computeTheta();
- computePhi();
- trnModel.liter--;
- trnModel.saveModel(option.modelName);
- }
-
- /**
- * Do sampling
- *
- * @param m
- * document number
- * @param n
- * word number
- * @return topic id
- */
- public int sampling(final int m, final int n) {
- // remove z_i from the count variable
- int topic = trnModel.z[m].get(n);
- final int w = trnModel.data.docs[m].words[n];
-
- trnModel.nw[w][topic] -= 1;
- trnModel.nd[m][topic] -= 1;
- trnModel.nwsum[topic] -= 1;
- trnModel.ndsum[m] -= 1;
-
- final double Vbeta = trnModel.V * trnModel.beta;
- final double Kalpha = trnModel.K * trnModel.alpha;
-
- // do multinominal sampling via cumulative method
- for (int k = 0; k < trnModel.K; k++) {
- trnModel.p[k] = (trnModel.nw[w][k] + trnModel.beta) / (trnModel.nwsum[k] + Vbeta)
- * (trnModel.nd[m][k] + trnModel.alpha) / (trnModel.ndsum[m] + Kalpha);
- }
-
- // cumulate multinomial parameters
- for (int k = 1; k < trnModel.K; k++) {
- trnModel.p[k] += trnModel.p[k - 1];
- }
-
- // scaled sample because of unnormalized p[]
- final double u = Math.random() * trnModel.p[trnModel.K - 1];
-
- for (topic = 0; topic < trnModel.K; topic++) {
- if (trnModel.p[topic] > u) // sample topic w.r.t distribution p
- break;
- }
-
- // add newly estimated z_i to count variables
- trnModel.nw[w][topic] += 1;
- trnModel.nd[m][topic] += 1;
- trnModel.nwsum[topic] += 1;
- trnModel.ndsum[m] += 1;
-
- return topic;
- }
-
- public void computeTheta() {
- for (int m = 0; m < trnModel.M; m++) {
- for (int k = 0; k < trnModel.K; k++) {
- trnModel.theta[m][k] = (trnModel.nd[m][k] + trnModel.alpha)
- / (trnModel.ndsum[m] + trnModel.K * trnModel.alpha);
- }
- }
- }
-
- public void computePhi() {
- for (int k = 0; k < trnModel.K; k++) {
- for (int w = 0; w < trnModel.V; w++) {
- trnModel.phi[k][w] = (trnModel.nw[w][k] + trnModel.beta)
- / (trnModel.nwsum[k] + trnModel.V * trnModel.beta);
- }
- }
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/Inferencer.java b/jgibblda/src/main/java/jgibblda/Inferencer.java
deleted file mode 100644
index 5108749dbb20812e8b3137285033ac0de1e16468..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Inferencer.java
+++ /dev/null
@@ -1,210 +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.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;
- private LDACmdOption option;
-
- private Model newModel;
- public int niters = 100;
-
- // -----------------------------------------------------
- // Init method
- // -----------------------------------------------------
- public boolean init(final LDACmdOption option) {
- this.option = option;
- trnModel = new Model();
-
- if (!trnModel.initEstimatedModel(option))
- return false;
-
- globalDict = trnModel.data.localDict;
- computeTrnTheta();
- computeTrnPhi();
-
- return true;
- }
-
- // inference new model ~ getting data from a specified dataset
- public Model inference(final LDADataset newData) {
- final Model newModel = new Model();
-
- newModel.initNewModel(option, newData, trnModel);
- this.newModel = newModel;
-
- log.info("sampling " + niters + " iterations");
- for (newModel.liter = 1; newModel.liter <= niters; newModel.liter++) {
-
- // for all newz_i
- for (int m = 0; m < newModel.M; ++m) {
- for (int n = 0; n < newModel.data.docs[m].length; n++) {
- // (newz_i = newz[m][n]
- // sample from p(z_i|z_-1,w)
- final int topic = infSampling(m, n);
- newModel.z[m].set(n, topic);
- }
- } // end foreach new doc
-
- } // end iterations
-
- log.info("sampling completed");
-
- computeNewTheta();
- computeNewPhi();
- newModel.liter--;
- return this.newModel;
- }
-
- public Model inference(final String[] strs) {
- final LDADataset dataset = LDADataset.readDataSet(strs, globalDict);
- return inference(dataset);
- }
-
- // inference new model ~ getting dataset from file specified in option
- public Model inference() {
-
- newModel = new Model();
- if (!newModel.initNewModel(option, trnModel))
- return null;
-
- log.info("sampling " + niters + " iterations");
-
- for (newModel.liter = 1; newModel.liter <= niters; newModel.liter++) {
-
- // for all newz_i
- for (int m = 0; m < newModel.M; ++m) {
- for (int n = 0; n < newModel.data.docs[m].length; n++) {
- // (newz_i = newz[m][n]
- // sample from p(z_i|z_-1,w)
- final int topic = infSampling(m, n);
- newModel.z[m].set(n, topic);
- }
- } // end foreach new doc
-
- } // end iterations
-
- log.info("sampling completed, saving final model");
-
- computeNewTheta();
- computeNewPhi();
- newModel.liter--;
- newModel.saveModel(newModel.dfile + "." + newModel.modelName);
-
- return newModel;
- }
-
- /**
- * do sampling for inference m: document number n: word number?
- */
- protected int infSampling(final int m, final int n) {
- // remove z_i from the count variables
- int topic = newModel.z[m].get(n);
- final int _w = newModel.data.docs[m].words[n];
- final int w = newModel.data.lid2gid.get(_w);
- newModel.nw[_w][topic] -= 1;
- newModel.nd[m][topic] -= 1;
- newModel.nwsum[topic] -= 1;
- newModel.ndsum[m] -= 1;
-
- final double Vbeta = trnModel.V * newModel.beta;
- final double Kalpha = trnModel.K * newModel.alpha;
-
- // do multinomial sampling via cummulative method
- for (int k = 0; k < newModel.K; k++) {
- newModel.p[k] = (trnModel.nw[w][k] + newModel.nw[_w][k] + newModel.beta)
- / (trnModel.nwsum[k] + newModel.nwsum[k] + Vbeta) * (newModel.nd[m][k] + newModel.alpha)
- / (newModel.ndsum[m] + Kalpha);
- }
-
- // cummulate multinomial parameters
- for (int k = 1; k < newModel.K; k++) {
- newModel.p[k] += newModel.p[k - 1];
- }
-
- // scaled sample because of unnormalized p[]
- final double u = Math.random() * newModel.p[newModel.K - 1];
-
- for (topic = 0; topic < newModel.K; topic++) {
- if (newModel.p[topic] > u)
- break;
- }
-
- // add newly estimated z_i to count variables
- newModel.nw[_w][topic] += 1;
- newModel.nd[m][topic] += 1;
- newModel.nwsum[topic] += 1;
- newModel.ndsum[m] += 1;
-
- return topic;
- }
-
- protected void computeNewTheta() {
- for (int m = 0; m < newModel.M; m++) {
- for (int k = 0; k < newModel.K; k++) {
- newModel.theta[m][k] = (newModel.nd[m][k] + newModel.alpha)
- / (newModel.ndsum[m] + newModel.K * newModel.alpha);
- } // end foreach topic
- } // end foreach new document
- }
-
- protected void computeNewPhi() {
- for (int k = 0; k < newModel.K; k++) {
- for (int _w = 0; _w < newModel.V; _w++) {
- final Integer id = newModel.data.lid2gid.get(_w);
-
- if (id != null) {
- newModel.phi[k][_w] = (trnModel.nw[id][k] + newModel.nw[_w][k] + newModel.beta)
- / (newModel.nwsum[k] + newModel.nwsum[k] + trnModel.V * newModel.beta);
- }
- } // end foreach word
- } // end foreach topic
- }
-
- protected void computeTrnTheta() {
- for (int m = 0; m < trnModel.M; m++) {
- for (int k = 0; k < trnModel.K; k++) {
- trnModel.theta[m][k] = (trnModel.nd[m][k] + trnModel.alpha)
- / (trnModel.ndsum[m] + trnModel.K * trnModel.alpha);
- }
- }
- }
-
- protected void computeTrnPhi() {
- for (int k = 0; k < trnModel.K; k++) {
- for (int w = 0; w < trnModel.V; w++) {
- trnModel.phi[k][w] = (trnModel.nw[w][k] + trnModel.beta)
- / (trnModel.nwsum[k] + trnModel.V * trnModel.beta);
- }
- }
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/LDA.java b/jgibblda/src/main/java/jgibblda/LDA.java
deleted file mode 100644
index 111ab000a34e447b0fbf981259125fb532024d2e..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/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.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(final String args[]) {
- final LDACmdOption option = new LDACmdOption();
- final CmdLineParser parser = new CmdLineParser(option);
-
- try {
- if (args.length == 0) {
- showHelp(parser);
- return;
- }
-
- parser.parseArgument(args);
-
- if (option.est || option.estc) {
- final Estimator estimator = new Estimator();
- estimator.init(option);
- estimator.estimate();
- } else if (option.inf) {
- final Inferencer inferencer = new Inferencer();
- inferencer.init(option);
-
- final 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 (final CmdLineException cle) {
- log.info("Command line error: " + cle.getMessage());
- showHelp(parser);
- return;
- } catch (final Exception e) {
- log.info("Error in main: " + e.getMessage());
- e.printStackTrace();
- return;
- }
- }
-
- public static void showHelp(final CmdLineParser parser) {
- log.info("LDA [options ...] [arguments...]");
- parser.printUsage(System.out);
- }
-
-}
diff --git a/jgibblda/src/main/java/jgibblda/LDACmdOption.java b/jgibblda/src/main/java/jgibblda/LDACmdOption.java
deleted file mode 100644
index 79c548a7fbf4648938ba936522be774dbf6aad28..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/LDACmdOption.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package jgibblda;
-
-import org.kohsuke.args4j.Option;
-
-public class LDACmdOption {
-
- @Option(name = "-est", usage = "Specify whether we want to estimate model from scratch")
- public boolean est = false;
-
- @Option(name = "-estc", usage = "Specify whether we want to continue the last estimation")
- public boolean estc = false;
-
- @Option(name = "-inf", usage = "Specify whether we want to do inference")
- public boolean inf = true;
-
- @Option(name = "-dir", usage = "Specify directory")
- public String dir = "";
-
- @Option(name = "-dfile", usage = "Specify data file")
- public String dfile = "";
-
- @Option(name = "-model", usage = "Specify the model name")
- public String modelName = "";
-
- @Option(name = "-alpha", usage = "Specify alpha")
- public double alpha = -1.0;
-
- @Option(name = "-beta", usage = "Specify beta")
- public double beta = -1.0;
-
- @Option(name = "-ntopics", usage = "Specify the number of topics")
- public int K = 100;
-
- @Option(name = "-niters", usage = "Specify the number of iterations")
- public int niters = 1000;
-
- @Option(name = "-savestep", usage = "Specify the number of steps to save the model since the last save")
- public int savestep = 100;
-
- @Option(name = "-twords", usage = "Specify the number of most likely words to be printed for each topic")
- public int twords = 100;
-
- @Option(name = "-withrawdata", usage = "Specify whether we include raw data in the input")
- public boolean withrawdata = false;
-
- @Option(name = "-wordmap", usage = "Specify the wordmap file")
- public String wordMapFileName = "wordmap.txt";
-}
diff --git a/jgibblda/src/main/java/jgibblda/LDADataset.java b/jgibblda/src/main/java/jgibblda/LDADataset.java
deleted file mode 100644
index f03d417a101e56ac0c14f8adf2419b62eb59b9f3..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/LDADataset.java
+++ /dev/null
@@ -1,278 +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.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
- // ---------------------------------------------------------------
-
- public Dictionary localDict; // local dictionary
- public Document[] docs; // a list of documents
- public int M; // number of documents
- public int V; // number of words
-
- // map from local coordinates (id) to global ones
- // null if the global dictionary is not set
- public Map<Integer, Integer> lid2gid;
-
- // link to a global dictionary (optional), null for train data, not null for
- // test data
- public Dictionary globalDict;
-
- // --------------------------------------------------------------
- // Constructor
- // --------------------------------------------------------------
- public LDADataset() {
- localDict = new Dictionary();
- M = 0;
- V = 0;
- docs = null;
-
- globalDict = null;
- lid2gid = null;
- }
-
- public LDADataset(final int M) {
- localDict = new Dictionary();
- this.M = M;
- this.V = 0;
- docs = new Document[M];
-
- globalDict = null;
- lid2gid = null;
- }
-
- public LDADataset(final int M, final Dictionary globalDict) {
- localDict = new Dictionary();
- this.M = M;
- this.V = 0;
- docs = new Document[M];
-
- this.globalDict = globalDict;
- lid2gid = new HashMap<Integer, Integer>();
- }
-
- // -------------------------------------------------------------
- // Public Instance Methods
- // -------------------------------------------------------------
- /**
- * set the document at the index idx if idx is greater than 0 and less than
- * M
- *
- * @param doc
- * document to be set
- * @param idx
- * index in the document array
- */
- public void setDoc(final Document doc, final int idx) {
- if (0 <= idx && idx < M) {
- docs[idx] = doc;
- }
- }
-
- /**
- * set the document at the index idx if idx is greater than 0 and less than
- * M
- *
- * @param str
- * string contains doc
- * @param idx
- * index in the document array
- */
- public void setDoc(final String str, final int idx) {
- if (0 <= idx && idx < M) {
- final String[] words = str.split("[ \\t\\n]");
-
- final Vector<Integer> ids = new Vector<Integer>();
-
- for (final String word : words) {
- int _id = localDict.word2id.size();
-
- if (localDict.contains(word))
- _id = localDict.getID(word);
-
- if (globalDict != null) {
- // get the global id
- final Integer id = globalDict.getID(word);
-
- if (id != null) {
- localDict.addWord(word);
-
- lid2gid.put(_id, id);
- ids.add(_id);
- } else { // not in global dictionary
- // do nothing currently
- }
- } else {
- localDict.addWord(word);
- ids.add(_id);
- }
- }
-
- final Document doc = new Document(ids, str);
- docs[idx] = doc;
- V = localDict.word2id.size();
- }
- }
- // ---------------------------------------------------------------
- // I/O methods
- // ---------------------------------------------------------------
-
- /**
- * read a dataset from a stream, create new dictionary
- *
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final String filename) {
- try {
- final BufferedReader reader = new BufferedReader(
- new InputStreamReader(new FileInputStream(filename), "UTF-8"));
-
- final LDADataset data = readDataSet(reader);
-
- reader.close();
- return data;
- } catch (final Exception e) {
- log.error("Read Dataset Error: " + e.getMessage());
- e.printStackTrace();
- return null;
- }
- }
-
- /**
- * read a dataset from a file with a preknown vocabulary
- *
- * @param filename
- * file from which we read dataset
- * @param dict
- * the dictionary
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final String filename, final Dictionary dict) {
- try {
- final BufferedReader reader = new BufferedReader(
- new InputStreamReader(new FileInputStream(filename), "UTF-8"));
- final LDADataset data = readDataSet(reader, dict);
-
- reader.close();
- return data;
- } catch (final Exception e) {
- log.error("Read Dataset Error: " + e.getMessage());
- e.printStackTrace();
- return null;
- }
- }
-
- /**
- * read a dataset from a stream, create new dictionary
- *
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final BufferedReader reader) {
- return readDataSet(reader, null);
- }
-
- /**
- * read a dataset from a stream with respect to a specified dictionary
- *
- * @param reader
- * stream from which we read dataset
- * @param dict
- * the dictionary
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final BufferedReader reader, final Dictionary dict) {
- try {
- final List<String> lines = new ArrayList<>();
-
- String line;
- while ((line = reader.readLine()) != null) {
- lines.add(line);
- }
-
- final LDADataset data = new LDADataset(lines.size(), dict);
-
- for (int i = 0; i < lines.size(); i++) {
- data.setDoc(lines.get(i), i);
- }
-
- return data;
- } catch (final Exception e) {
- log.error("Read Dataset Error: " + e.getMessage());
- e.printStackTrace();
- return null;
- }
- }
-
- /**
- * read a dataset from a string, create new dictionary
- *
- * @param str
- * String from which we get the dataset, documents are seperated
- * by newline character
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final String[] strs) {
- final LDADataset data = new LDADataset(strs.length);
-
- for (int i = 0; i < strs.length; ++i) {
- data.setDoc(strs[i], i);
- }
- return data;
- }
-
- /**
- * read a dataset from a string with respect to a specified dictionary
- *
- * @param str
- * String from which we get the dataset, documents are seperated
- * by newline character
- * @param dict
- * the dictionary
- * @return dataset if success and null otherwise
- */
- public static LDADataset readDataSet(final String[] strs, final Dictionary dict) {
- final LDADataset data = new LDADataset(strs.length, dict);
-
- for (int i = 0; i < strs.length; ++i) {
- data.setDoc(strs[i], i);
- }
- return data;
- }
-}
diff --git a/jgibblda/src/main/java/jgibblda/Model.java b/jgibblda/src/main/java/jgibblda/Model.java
deleted file mode 100644
index fbdb5b9bfde95d94b0903b8b9e0b99bd7fe6e3a3..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Model.java
+++ /dev/null
@@ -1,719 +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.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-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.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
- // ---------------------------------------------------------------
-
- public static String tassignSuffix; // suffix for topic assignment file
- public static String thetaSuffix; // suffix for theta (topic - document
- // distribution) file
- public static String phiSuffix; // suffix for phi file (topic - word
- // distribution) file
- public static String othersSuffix; // suffix for containing other parameters
- public static String twordsSuffix; // suffix for file containing
- // words-per-topics
-
- // ---------------------------------------------------------------
- // Model Parameters and Variables
- // ---------------------------------------------------------------
-
- public String wordMapFile; // file that contain word to id map
- public String trainlogFile; // training log file
-
- public String dir;
- public String dfile;
- public String modelName;
- public int modelStatus; // see Constants class for status of model
- public LDADataset data; // link to a dataset
-
- public int M; // dataset size (i.e., number of docs)
- public int V; // vocabulary size
- public int K; // number of topics
- public double alpha, beta; // LDA hyperparameters
- public int niters; // number of Gibbs sampling iteration
- public int liter; // the iteration at which the model was saved
- public int savestep; // saving period
- public int twords; // print out top words per each topic
- public int withrawdata;
-
- // Estimated/Inferenced parameters
- public double[][] theta; // theta: document - topic distributions, size M x
- // K
- public double[][] phi; // phi: topic-word distributions, size K x V
-
- // Temp variables while sampling
- public Vector<Integer>[] z; // topic assignments for words, size M x
- // doc.size()
- protected int[][] nw; // nw[i][j]: number of instances of word/term i
- // assigned to topic j, size V x K
- protected int[][] nd; // nd[i][j]: number of words in document i assigned to
- // topic j, size M x K
- protected int[] nwsum; // nwsum[j]: total number of words assigned to topic
- // j, size K
- protected int[] ndsum; // ndsum[i]: total number of words in document i,
- // size M
-
- // temp variables for sampling
- protected double[] p;
-
- // ---------------------------------------------------------------
- // Constructors
- // ---------------------------------------------------------------
-
- public Model() {
- setDefaultValues();
- }
-
- /**
- * Set default values for variables
- */
- public void setDefaultValues() {
- wordMapFile = "wordmap.txt";
- trainlogFile = "trainlog.txt";
- tassignSuffix = ".tassign";
- thetaSuffix = ".theta";
- phiSuffix = ".phi";
- othersSuffix = ".others";
- twordsSuffix = ".twords";
-
- dir = "./";
- dfile = "trndocs.dat";
- modelName = "model-final";
- modelStatus = Constants.MODEL_STATUS_UNKNOWN;
-
- M = 0;
- V = 0;
- K = 100;
- alpha = 50.0 / K;
- beta = 0.1;
- niters = 2000;
- liter = 0;
-
- z = null;
- nw = null;
- nd = null;
- nwsum = null;
- ndsum = null;
- theta = null;
- phi = null;
- }
-
- // ---------------------------------------------------------------
- // I/O Methods
- // ---------------------------------------------------------------
- /**
- * read other file to get parameters
- */
- protected boolean readOthersFile(final String otherFile) {
- // open file <model>.others to read:
-
- try {
- final BufferedReader reader = new BufferedReader(new FileReader(otherFile));
- String line;
- while ((line = reader.readLine()) != null) {
- final StringTokenizer tknr = new StringTokenizer(line, "= \t\r\n");
-
- final int count = tknr.countTokens();
- if (count != 2)
- continue;
-
- final String optstr = tknr.nextToken();
- final String optval = tknr.nextToken();
-
- if (optstr.equalsIgnoreCase("alpha")) {
- alpha = Double.parseDouble(optval);
- } else if (optstr.equalsIgnoreCase("beta")) {
- beta = Double.parseDouble(optval);
- } else if (optstr.equalsIgnoreCase("ntopics")) {
- K = Integer.parseInt(optval);
- } else if (optstr.equalsIgnoreCase("liter")) {
- liter = Integer.parseInt(optval);
- } else if (optstr.equalsIgnoreCase("nwords")) {
- V = Integer.parseInt(optval);
- } else if (optstr.equalsIgnoreCase("ndocs")) {
- M = Integer.parseInt(optval);
- } else {
- // any more?
- }
- }
-
- reader.close();
- } catch (final Exception e) {
- log.error("Error while reading other file:" + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- @SuppressWarnings("unchecked")
- protected boolean readTAssignFile(final String tassignFile) {
- BufferedReader reader = null;
- try {
- int i, j;
- reader = new BufferedReader(new InputStreamReader(new FileInputStream(tassignFile), "UTF-8"));
-
- String line;
- z = new Vector[M];
- data = new LDADataset(M);
- data.V = V;
- for (i = 0; i < M; i++) {
- line = reader.readLine();
- final StringTokenizer tknr = new StringTokenizer(line, " \t\r\n");
-
- final int length = tknr.countTokens();
-
- final Vector<Integer> words = new Vector<Integer>();
- final Vector<Integer> topics = new Vector<Integer>();
-
- for (j = 0; j < length; j++) {
- final String token = tknr.nextToken();
-
- final StringTokenizer tknr2 = new StringTokenizer(token, ":");
- if (tknr2.countTokens() != 2) {
- log.warn("Invalid word-topic assignment line\n");
- return false;
- }
-
- words.add(Integer.parseInt(tknr2.nextToken()));
- topics.add(Integer.parseInt(tknr2.nextToken()));
- } // end for each topic assignment
-
- // allocate and add new document to the corpus
- final Document doc = new Document(words);
- data.setDoc(doc, i);
-
- // assign values for z
- z[i] = new Vector<Integer>();
- for (j = 0; j < topics.size(); j++) {
- z[i].add(topics.get(j));
- }
-
- } // end for each doc
- } catch (final Exception e) {
- log.error("Error while loading model: " + e.getMessage());
- e.printStackTrace();
- return false;
- } finally {
- if (reader != null)
- try {
- reader.close();
- } catch (final IOException e) {}
- }
- return true;
- }
-
- /**
- * load saved model
- */
- public boolean loadModel() {
- if (!readOthersFile(dir + File.separator + modelName + othersSuffix))
- return false;
-
- if (!readTAssignFile(dir + File.separator + modelName + tassignSuffix))
- return false;
-
- // read dictionary
- final Dictionary dict = new Dictionary();
- if (!dict.readWordMap(dir + File.separator + wordMapFile))
- return false;
-
- data.localDict = dict;
-
- return true;
- }
-
- /**
- * Save word-topic assignments for this model
- */
- public boolean saveModelTAssign(final String filename) {
- int i, j;
-
- try {
- final BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
-
- // write docs with topic assignments for words
- for (i = 0; i < data.M; i++) {
- for (j = 0; j < data.docs[i].length; ++j) {
- writer.write(data.docs[i].words[j] + ":" + z[i].get(j) + " ");
- }
- writer.write("\n");
- }
-
- writer.close();
- } catch (final Exception e) {
- log.error("Error while saving model tassign: " + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /**
- * Save theta (topic distribution) for this model
- */
- public boolean saveModelTheta(final String filename) {
- try {
- final BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
- for (int i = 0; i < M; i++) {
- for (int j = 0; j < K; j++) {
- writer.write(theta[i][j] + " ");
- }
- writer.write("\n");
- }
- writer.close();
- } catch (final Exception e) {
- log.error("Error while saving topic distribution file for this model: " + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /**
- * Save word-topic distribution
- */
-
- public boolean saveModelPhi(final String filename) {
- try {
- final BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
-
- for (int i = 0; i < K; i++) {
- for (int j = 0; j < V; j++) {
- writer.write(phi[i][j] + " ");
- }
- writer.write("\n");
- }
- writer.close();
- } catch (final Exception e) {
- log.error("Error while saving word-topic distribution:" + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /**
- * Save other information of this model
- */
- public boolean saveModelOthers(final String filename) {
- try {
- final BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
-
- writer.write("alpha=" + alpha + "\n");
- writer.write("beta=" + beta + "\n");
- writer.write("ntopics=" + K + "\n");
- writer.write("ndocs=" + M + "\n");
- writer.write("nwords=" + V + "\n");
- writer.write("liters=" + liter + "\n");
-
- writer.close();
- } catch (final Exception e) {
- log.error("Error while saving model others:" + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /**
- * Save model the most likely words for each topic
- */
- public boolean saveModelTwords(final String filename) {
- try {
- final BufferedWriter writer = new BufferedWriter(
- new OutputStreamWriter(new FileOutputStream(filename), "UTF-8"));
-
- if (twords > V) {
- twords = V;
- }
-
- for (int k = 0; k < K; k++) {
- final List<Pair> wordsProbsList = new ArrayList<Pair>();
- for (int w = 0; w < V; w++) {
- final Pair p = new Pair(w, phi[k][w], false);
-
- wordsProbsList.add(p);
- } // end foreach word
-
- // print topic
- writer.write("Topic " + k + "th:\n");
- Collections.sort(wordsProbsList);
-
- for (int i = 0; i < twords; i++) {
- if (data.localDict.contains((Integer) wordsProbsList.get(i).first)) {
- final String word = data.localDict.getWord((Integer) wordsProbsList.get(i).first);
-
- writer.write("\t" + word + " " + wordsProbsList.get(i).second + "\n");
- }
- }
- } // end foreach topic
-
- writer.close();
- } catch (final Exception e) {
- log.error("Error while saving model twords: " + e.getMessage());
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /**
- * Save model
- */
- public boolean saveModel(final String modelName) {
- if (!saveModelTAssign(dir + File.separator + modelName + tassignSuffix)) {
- return false;
- }
-
- if (!saveModelOthers(dir + File.separator + modelName + othersSuffix)) {
- return false;
- }
-
- if (!saveModelTheta(dir + File.separator + modelName + thetaSuffix)) {
- return false;
- }
-
- if (!saveModelPhi(dir + File.separator + modelName + phiSuffix)) {
- return false;
- }
-
- if (twords > 0) {
- if (!saveModelTwords(dir + File.separator + modelName + twordsSuffix))
- return false;
- }
- return true;
- }
-
- // ---------------------------------------------------------------
- // Init Methods
- // ---------------------------------------------------------------
- /**
- * initialize the model
- */
- protected boolean init(final LDACmdOption option) {
- if (option == null)
- return false;
-
- modelName = option.modelName;
- K = option.K;
-
- alpha = option.alpha;
- if (alpha < 0.0)
- alpha = 50.0 / K;
-
- if (option.beta >= 0)
- beta = option.beta;
-
- niters = option.niters;
-
- dir = option.dir;
- if (dir.endsWith(File.separator))
- dir = dir.substring(0, dir.length() - 1);
-
- dfile = option.dfile;
- twords = option.twords;
- wordMapFile = option.wordMapFileName;
-
- return true;
- }
-
- /**
- * Init parameters for estimation
- */
- @SuppressWarnings("unchecked")
- public boolean initNewModel(final LDACmdOption option) {
- if (!init(option))
- return false;
-
- int m, n, w, k;
- p = new double[K];
-
- data = LDADataset.readDataSet(dir + File.separator + dfile);
- if (data == null) {
- log.error("Fail to read training data!\n");
- return false;
- }
-
- // + allocate memory and assign values for variables
- M = data.M;
- V = data.V;
- dir = option.dir;
- savestep = option.savestep;
-
- // K: from command line or default value
- // alpha, beta: from command line or default values
- // niters, savestep: from command line or default values
-
- nw = new int[V][K];
- for (w = 0; w < V; w++) {
- for (k = 0; k < K; k++) {
- nw[w][k] = 0;
- }
- }
-
- nd = new int[M][K];
- for (m = 0; m < M; m++) {
- for (k = 0; k < K; k++) {
- nd[m][k] = 0;
- }
- }
-
- nwsum = new int[K];
- for (k = 0; k < K; k++) {
- nwsum[k] = 0;
- }
-
- ndsum = new int[M];
- for (m = 0; m < M; m++) {
- ndsum[m] = 0;
- }
-
- z = new Vector[M];
- for (m = 0; m < data.M; m++) {
- final int N = data.docs[m].length;
- z[m] = new Vector<Integer>();
-
- // initilize for z
- for (n = 0; n < N; n++) {
- final int topic = (int) Math.floor(Math.random() * K);
- z[m].add(topic);
-
- // number of instances of word assigned to topic j
- nw[data.docs[m].words[n]][topic] += 1;
- // number of words in document i assigned to topic j
- nd[m][topic] += 1;
- // total number of words assigned to topic j
- nwsum[topic] += 1;
- }
- // total number of words in document i
- ndsum[m] = N;
- }
-
- theta = new double[M][K];
- phi = new double[K][V];
-
- return true;
- }
-
- /**
- * Init parameters for inference
- *
- * @param newData
- * DataSet for which we do inference
- */
- @SuppressWarnings("unchecked")
- public boolean initNewModel(final LDACmdOption option, final LDADataset newData, final Model trnModel) {
- if (!init(option))
- return false;
-
- int m, n, w, k;
-
- K = trnModel.K;
- alpha = trnModel.alpha;
- beta = trnModel.beta;
-
- p = new double[K];
- log.info("K:" + K);
-
- data = newData;
-
- // + allocate memory and assign values for variables
- M = data.M;
- V = data.V;
- dir = option.dir;
- savestep = option.savestep;
- log.info("M:" + M);
- log.info("V:" + V);
-
- // K: from command line or default value
- // alpha, beta: from command line or default values
- // niters, savestep: from command line or default values
-
- nw = new int[V][K];
- for (w = 0; w < V; w++) {
- for (k = 0; k < K; k++) {
- nw[w][k] = 0;
- }
- }
-
- nd = new int[M][K];
- for (m = 0; m < M; m++) {
- for (k = 0; k < K; k++) {
- nd[m][k] = 0;
- }
- }
-
- nwsum = new int[K];
- for (k = 0; k < K; k++) {
- nwsum[k] = 0;
- }
-
- ndsum = new int[M];
- for (m = 0; m < M; m++) {
- ndsum[m] = 0;
- }
-
- z = new Vector[M];
- for (m = 0; m < data.M; m++) {
- final int N = data.docs[m].length;
- z[m] = new Vector<Integer>();
-
- // initilize for z
- for (n = 0; n < N; n++) {
- final int topic = (int) Math.floor(Math.random() * K);
- z[m].add(topic);
-
- // number of instances of word assigned to topic j
- nw[data.docs[m].words[n]][topic] += 1;
- // number of words in document i assigned to topic j
- nd[m][topic] += 1;
- // total number of words assigned to topic j
- nwsum[topic] += 1;
- }
- // total number of words in document i
- ndsum[m] = N;
- }
-
- theta = new double[M][K];
- phi = new double[K][V];
-
- return true;
- }
-
- /**
- * Init parameters for inference reading new dataset from file
- */
- public boolean initNewModel(final LDACmdOption option, final Model trnModel) {
- if (!init(option))
- return false;
-
- final LDADataset dataset = LDADataset.readDataSet(dir + File.separator + dfile, trnModel.data.localDict);
- if (dataset == null) {
- log.error("Fail to read dataset!\n");
- return false;
- }
-
- return initNewModel(option, dataset, trnModel);
- }
-
- /**
- * init parameter for continue estimating or for later inference
- */
- public boolean initEstimatedModel(final LDACmdOption option) {
- if (!init(option))
- return false;
-
- int m, n, w, k;
-
- p = new double[K];
-
- // load model, i.e., read z and trndata
- if (!loadModel()) {
- log.error("Fail to load word-topic assignment file of the model!\n");
- return false;
- }
-
- 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++) {
- for (k = 0; k < K; k++) {
- nw[w][k] = 0;
- }
- }
-
- nd = new int[M][K];
- for (m = 0; m < M; m++) {
- for (k = 0; k < K; k++) {
- nd[m][k] = 0;
- }
- }
-
- nwsum = new int[K];
- for (k = 0; k < K; k++) {
- nwsum[k] = 0;
- }
-
- ndsum = new int[M];
- for (m = 0; m < M; m++) {
- ndsum[m] = 0;
- }
-
- for (m = 0; m < data.M; m++) {
- final int N = data.docs[m].length;
-
- // assign values for nw, nd, nwsum, and ndsum
- for (n = 0; n < N; n++) {
- w = data.docs[m].words[n];
- final int topic = z[m].get(n);
-
- // number of instances of word i assigned to topic j
- nw[w][topic] += 1;
- // number of words in document i assigned to topic j
- nd[m][topic] += 1;
- // total number of words assigned to topic j
- nwsum[topic] += 1;
- }
- // total number of words in document i
- ndsum[m] = N;
- }
-
- theta = new double[M][K];
- phi = new double[K][V];
- dir = option.dir;
- savestep = option.savestep;
-
- return true;
- }
-
-}
diff --git a/jgibblda/src/main/java/jgibblda/Pair.java b/jgibblda/src/main/java/jgibblda/Pair.java
deleted file mode 100644
index 887b90694bf140315407c44e1416beb5798d6b2c..0000000000000000000000000000000000000000
--- a/jgibblda/src/main/java/jgibblda/Pair.java
+++ /dev/null
@@ -1,51 +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;
-
-@SuppressWarnings("rawtypes")
-public class Pair implements Comparable<Pair> {
- public Object first;
- public Comparable second;
- public static boolean naturalOrder = false;
-
- public Pair(final Object k, final Comparable v) {
- first = k;
- second = v;
- }
-
- public Pair(final Object k, final Comparable v, final boolean naturalOrder) {
- first = k;
- second = v;
- Pair.naturalOrder = naturalOrder;
- }
-
- @Override
- @SuppressWarnings("unchecked")
- public int compareTo(final Pair p) {
- if (naturalOrder)
- return this.second.compareTo(p.second);
- else
- return -this.second.compareTo(p.second);
- }
-}
diff --git a/vipra-backend/src/main/java/de/vipra/rest/resource/SequenceResource.java b/vipra-backend/src/main/java/de/vipra/rest/resource/SequenceResource.java
index 170570f728616d07ba4b4f3e91d71271ae228355..4960daef6c84e8b73cbbdb14a3bc8bfab9202ad9 100644
--- a/vipra-backend/src/main/java/de/vipra/rest/resource/SequenceResource.java
+++ b/vipra-backend/src/main/java/de/vipra/rest/resource/SequenceResource.java
@@ -39,8 +39,7 @@ public class SequenceResource {
@GET
@Produces(MediaType.APPLICATION_JSON)
public Response getSequences(@QueryParam("skip") final Integer skip, @QueryParam("limit") final Integer limit,
- @QueryParam("sort") @DefaultValue("startDate") final String sortBy,
- @QueryParam("fields") final String fields) {
+ @QueryParam("sort") @DefaultValue("id") final String sortBy, @QueryParam("fields") final String fields) {
final ResponseWrapper<List<SequenceFull>> res = new ResponseWrapper<>();
if (res.hasErrors())
diff --git a/vipra-cmd/pom.xml b/vipra-cmd/pom.xml
index ccacb04b64992fe250634dcba7b7686d246cfedc..5c87afc82927589f029ac08340756eddef4b1e08 100644
--- a/vipra-cmd/pom.xml
+++ b/vipra-cmd/pom.xml
@@ -87,11 +87,6 @@
<artifactId>util</artifactId>
<version>0.0.1-SNAPSHOT</version>
</dependency>
- <dependency>
- <groupId>jgibblda</groupId>
- <artifactId>jgibblda</artifactId>
- <version>0.0.1-SNAPSHOT</version>
- </dependency>
</dependencies>
<build>
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 dc5e26555ecaccd1de04888d0caf2f6173e679af..9a8db6e34714d258e09e64f75ba63d3857778800 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
@@ -86,8 +86,6 @@ public abstract class Filebase implements Closeable {
switch (Constants.ANALYZER) {
case DTM:
return new DTMFilebase(dataDir);
- case JGIBB:
- return new JGibbFilebase(dataDir);
default:
return null;
}
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
deleted file mode 100644
index 0e42682aee43f9ccdbb953e8459296e0176801cb..0000000000000000000000000000000000000000
--- a/vipra-cmd/src/main/java/de/vipra/cmd/file/JGibbFilebase.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package de.vipra.cmd.file;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.List;
-
-import de.vipra.cmd.ex.FilebaseException;
-import de.vipra.util.model.ArticleFull;
-import edu.stanford.nlp.util.StringUtils;
-
-public class JGibbFilebase extends Filebase {
-
- private final File modelFile;
-
- public JGibbFilebase(final File dataDir) throws FilebaseException {
- super(dataDir, "jgibb");
- modelFile = getModelFile(null);
- }
-
- @Override
- public synchronized void write(final List<ArticleFull> articles) throws IOException {
- if (!articles.isEmpty()) {
- final BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(modelFile)));
- for (final ArticleFull article : articles)
- writer.write(StringUtils.join(article.getProcessedText()) + "\n");
- writer.close();
- }
- }
-
-}
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/lda/Analyzer.java b/vipra-cmd/src/main/java/de/vipra/cmd/lda/Analyzer.java
index 88a31bcfe7827cb6be81cf04491abe79bda6c2d8..b62453ce717e9c4751305301abd7027f89b975cc 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/lda/Analyzer.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/lda/Analyzer.java
@@ -26,9 +26,6 @@ public abstract class Analyzer {
case DTM:
analyzer = new DTMAnalyzer();
break;
- case JGIBB:
- analyzer = new JGibbAnalyzer();
- break;
default:
return null;
}
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/lda/DTMAnalyzer.java b/vipra-cmd/src/main/java/de/vipra/cmd/lda/DTMAnalyzer.java
index 5ac5d47406ce5e251cbcb08196665ca885aca35d..9287f12beb9aeeaa452fced3ecc8723d82eb0dce 100644
--- a/vipra-cmd/src/main/java/de/vipra/cmd/lda/DTMAnalyzer.java
+++ b/vipra-cmd/src/main/java/de/vipra/cmd/lda/DTMAnalyzer.java
@@ -201,7 +201,6 @@ public class DTMAnalyzer extends Analyzer {
final TopicFull newTopic = new TopicFull();
final List<Sequence> newTopicSequences = new ArrayList<>(sequencesCount);
newTopic.setSequences(newTopicSequences);
- newTopic.setDynamic(true);
newTopics.add(newTopic);
in = new BufferedReader(new InputStreamReader(new FileInputStream(seqFile)));
@@ -332,7 +331,7 @@ public class DTMAnalyzer extends Analyzer {
// update article
if (!newTopicRefs.isEmpty()) {
// renormalize share
- for (TopicRef newTopicRef : newTopicRefs)
+ for (final TopicRef newTopicRef : newTopicRefs)
newTopicRef.setShare(newTopicRef.getShare() / reducedShare);
Collections.sort(newTopicRefs, Comparator.reverseOrder());
diff --git a/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbAnalyzer.java b/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbAnalyzer.java
deleted file mode 100644
index 7f94afc67fafb02e4a145d00811826816fe196cd..0000000000000000000000000000000000000000
--- a/vipra-cmd/src/main/java/de/vipra/cmd/lda/JGibbAnalyzer.java
+++ /dev/null
@@ -1,252 +0,0 @@
-package de.vipra.cmd.lda;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.bson.types.ObjectId;
-
-import de.vipra.cmd.ex.AnalyzerException;
-import de.vipra.cmd.file.FilebaseIndex;
-import de.vipra.util.Config;
-import de.vipra.util.Constants;
-import de.vipra.util.CountMap;
-import de.vipra.util.FileUtils;
-import de.vipra.util.ex.ConfigException;
-import de.vipra.util.ex.DatabaseException;
-import de.vipra.util.model.ArticleFull;
-import de.vipra.util.model.Topic;
-import de.vipra.util.model.TopicFull;
-import de.vipra.util.model.TopicRef;
-import de.vipra.util.model.TopicWord;
-import de.vipra.util.model.Word;
-import de.vipra.util.service.MongoService;
-import jgibblda.Estimator;
-import jgibblda.LDACmdOption;
-
-public class JGibbAnalyzer extends Analyzer {
-
- public static final Logger log = LogManager.getLogger(JGibbAnalyzer.class);
- public static final String NAME = "jgibb";
-
- private File dataDir;
- private File modelDir;
- private File modelFile;
- private LDACmdOption options;
- private MongoService<ArticleFull, ObjectId> dbArticles;
- private MongoService<TopicFull, ObjectId> dbTopics;
- private MongoService<Word, String> dbWords;
- private FilebaseIndex index;
-
- protected JGibbAnalyzer() {
- super("JGibb Analyzer");
- }
-
- @Override
- public void init(Config config) throws AnalyzerException {
- options = new LDACmdOption();
-
- try {
- dataDir = config.getDataDirectory();
- } catch (final ConfigException e) {
- throw new AnalyzerException(e);
- }
-
- modelDir = new File(dataDir, NAME);
- options.dir = modelDir.getAbsolutePath();
- options.estc = new File(modelDir, NAME + ".tassign").exists();
- options.est = !options.estc;
- options.K = Constants.K_TOPICS;
- options.twords = Constants.K_TOPIC_WORDS;
- options.niters = Constants.STATIC_ITER;
-
- modelFile = new File(modelDir, NAME);
- options.dfile = modelFile.getName();
-
- options.modelName = NAME;
-
- try {
- config = Config.getConfig();
- dbArticles = MongoService.getDatabaseService(config, ArticleFull.class);
- dbTopics = MongoService.getDatabaseService(config, TopicFull.class);
- dbWords = MongoService.getDatabaseService(config, Word.class);
- index = new FilebaseIndex(modelDir);
- } catch (final Exception e) {
- throw new AnalyzerException(e);
- }
- }
-
- @Override
- public void analyze(final boolean reread) throws AnalyzerException {
- if (!modelFile.exists()) {
- throw new AnalyzerException("model file does not exist: " + modelFile.getAbsolutePath());
- }
-
- if (!reread) {
- final Estimator estimator = new Estimator();
- estimator.init(options);
- estimator.estimate();
- }
-
- final boolean seqRelativeCutoff = Constants.MINIMUM_RELATIVE_PROB > 0;
-
- // read topic definitions and save
-
- final File twords = new File(modelDir, NAME + ".twords");
- List<String> lines;
- try {
- lines = FileUtils.readFile(twords);
- } catch (final IOException e) {
- throw new AnalyzerException(e);
- }
-
- // the list of new topics
- final List<TopicFull> newTopics = new ArrayList<>(options.K);
- // set of new words
- final Set<Word> newWords = new HashSet<>();
-
- List<TopicWord> topicWords = null;
- int topicIndex = -1;
- final double[] maxLikelinesses = new double[Constants.K_TOPICS];
-
- // create topics and determine maximum likeliness for each topic
- for (final String line : lines) {
- if (!line.startsWith("\t")) {
- topicIndex++;
- topicWords = new ArrayList<>(Constants.K_TOPIC_WORDS);
- final TopicFull newTopic = new TopicFull();
- newTopic.setWords(topicWords);
- newTopics.add(newTopic);
- continue;
- }
-
- final String[] parts = line.trim().split("\\s+");
- final double likeliness = Double.parseDouble(parts[1]);
-
- // determine maximum likeliness of this topic
- if (likeliness > maxLikelinesses[topicIndex])
- maxLikelinesses[topicIndex] = likeliness;
-
- // check word likeliness
- topicWords.add(new TopicWord(new Word(parts[0]), likeliness));
- }
-
- // filter out words below minimum relative likeliness, add accepted
- // words to list of new words
- for (topicIndex = 0; topicIndex < newTopics.size(); topicIndex++) {
- final TopicFull topic = newTopics.get(topicIndex);
- final double maxLikeliness = maxLikelinesses[topicIndex];
- final ArrayList<TopicWord> filteredTopicWords = new ArrayList<>(topic.getWords().size());
- for (final TopicWord word : topic.getWords()) {
- if (!seqRelativeCutoff || word.getLikeliness() >= Constants.MINIMUM_RELATIVE_PROB * maxLikeliness) {
- filteredTopicWords.add(word);
- newWords.add(word.getWord());
- }
- }
- topic.setWords(filteredTopicWords);
-
- if (!filteredTopicWords.isEmpty()) {
- Collections.sort(filteredTopicWords, Collections.reverseOrder());
-
- topic.setName(TopicFull.getNameFromWords(filteredTopicWords));
- }
- }
-
- // recreate topics and words
- dbTopics.drop();
- dbWords.drop();
- try {
- dbTopics.createMultiple(newTopics);
- dbWords.createMultiple(newWords);
- } catch (final DatabaseException e) {
- throw new AnalyzerException(e);
- }
-
- // read documents and reference topics
-
- final File tassign = new File(modelDir, NAME + ".tassign");
- final Pattern topicIndexPattern = Pattern.compile(":(\\d+)");
- BufferedReader in = null;
-
- try {
- in = new BufferedReader(new InputStreamReader(new FileInputStream(tassign)));
- String line;
- int articleIndex = 0;
-
- // each line in the tassign file is a document, formatted with
- // <word-id>:<topic-id>
- while ((line = in.readLine()) != null) {
- // extract topic ids and count them
- final CountMap<String> countMap = new CountMap<>();
- final Matcher matcher = topicIndexPattern.matcher(line);
- while (matcher.find())
- countMap.count(matcher.group(1));
-
- int maxCount = 0;
- for (final Entry<String, Integer> entry : countMap.entrySet())
- if (entry.getValue() > maxCount)
- maxCount = entry.getValue();
- final double minShare = maxCount * Constants.MINIMUM_RELATIVE_PROB;
-
- // create list of topics refs referencing topics with counted
- // occurrences, sum accepted topic word count
- long reducedCount = 0;
- final List<TopicRef> newTopicRefs = new ArrayList<>(countMap.size());
- for (final Entry<String, Integer> entry : countMap.entrySet()) {
- // check if topic above threshold
- if (entry.getValue() >= minShare) {
- reducedCount += entry.getValue();
- final TopicFull topic = newTopics.get(Integer.parseInt(entry.getKey()));
- // TODO words with low relative likeliness are ignored.
- // topic references from this file are possibly wrong.
- // fix this by checking if the word is actually accepted
- // by the referenced topic.
- final TopicRef ref = new TopicRef();
- ref.setCount(entry.getValue());
- ref.setTopic(new Topic(topic.getId()));
- newTopicRefs.add(ref);
- }
- }
-
- // calculate each accepted topic share
- for (final TopicRef ref : newTopicRefs)
- ref.setShare((double) ref.getCount() / reducedCount);
-
- if (!newTopicRefs.isEmpty()) {
- Collections.sort(newTopicRefs, Comparator.reverseOrder());
-
- // update article with topic references (partial update)
- final ArticleFull article = new ArticleFull();
- article.setId(index.get(articleIndex++));
- article.setTopics(newTopicRefs);
-
- try {
- // TODO: using field name here. Hard to refactor
- dbArticles.updateSingle(article, "topics");
- } catch (final DatabaseException e) {
- log.error(e);
- }
- }
- }
-
- in.close();
-
- } catch (final Exception e) {
- throw new AnalyzerException(e);
- }
- }
-
-}
diff --git a/vipra-ui/app/html/directives/alert.html b/vipra-ui/app/html/directives/alert.html
deleted file mode 100644
index 97d850995dbbfd2b1c6e65dd2eb0da4c49a62cb0..0000000000000000000000000000000000000000
--- a/vipra-ui/app/html/directives/alert.html
+++ /dev/null
@@ -1,6 +0,0 @@
-<div ng-attr-class="{{classes}}" role="alert">
- <button type="button" class="close" data-dismiss="alert" aria-label="Close" ng-show="dismissible">
- <span aria-hidden="true">×</span>
- </button>
- <ng-transclude/>
-</div>
diff --git a/vipra-ui/app/html/directives/dropdown.html b/vipra-ui/app/html/directives/dropdown.html
deleted file mode 100644
index 70c61a654a796ba0d342a3c2e70ca164a472525b..0000000000000000000000000000000000000000
--- a/vipra-ui/app/html/directives/dropdown.html
+++ /dev/null
@@ -1,7 +0,0 @@
-<div class="dropdown">
- <button class="btn btn-default dropdown-toggle" type="button" ng-attr-id="{{dropdownId}}" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
- <span ng-bind="label"></span>
- <span class="caret"></span>
- </button>
- <ul ng-attr-class="{{'dropdown-menu ' + align}}" ng-attr-aria-labelledby="{{dropdownId}}" ng-transclude></ul>
-</div>
diff --git a/vipra-ui/app/html/explorer.html b/vipra-ui/app/html/explorer.html
index 961e0f9d437afb9f7d99e5d334a393da120e53c3..ad539a64615ae34b6a4815a5710b97789e7624a0 100644
--- a/vipra-ui/app/html/explorer.html
+++ b/vipra-ui/app/html/explorer.html
@@ -1,10 +1,24 @@
<div class="fullsize navpadding explorer" ng-cloak ng-hide="$state.current.name !== 'explorer'">
<div class="sidebar">
- <button class="btn btn-sm btn-default" ng-click="checkTopics(true)">All</button>
- <button class="btn btn-sm btn-default" ng-click="checkTopics(false)">None</button>
- <button class="btn btn-sm btn-default" ng-click="checkTopics()">Toggle</button>
+ <div class="btn-group btn-group-justified" role="group" aria-label="...">
+ <a class="btn btn-sm btn-default" ng-click="checkTopics(true)" title="Select all topics">All</a>
+ <a class="btn btn-sm btn-default" ng-click="checkTopics(false)" title="Deselect all topics">None</a>
+ <a class="btn btn-sm btn-default" ng-click="checkTopics()" title="Toggle all topics">Toggle</a>
+ </div>
+ <div class="btn-group btn-group-justified">
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'name'" title="Sort by name">α</a>
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'avgRelevance'" title="Sort by relevance average">μ</a>
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'varRelevance'" title="Sort by relevance variance">σ</a>
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'frel'" title="Sort by falling relevance">↘</a>
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'rrel'" title="Sort by rising relevance">↗</a>
+ <a class="btn btn-sm btn-default" ng-model="opts.sorttopics" ng-model-store bs-radio="'rreld'" title="Sort by rising relevance with decay">↝</a>
+ </div>
+ <div class="btn-group btn-group-justified">
+ <input type="text" class="form-control" ng-model="search.$" ng-model-store placeholder="Filter">
+ <span class="glyphicon glyphicon-remove-circle searchclear" ng-click="search=''"></span>
+ </div>
<ul class="list-unstyled topic-choice">
- <li ng-repeat="topic in topics">
+ <li ng-repeat="topic in topics | orderBy:opts.sorttopics | filter:search">
<div class="checkbox checkbox-condensed" ng-attr-title="{{::topic.name}}" ng-class="{selected:opts.selectedTopics[topic.id]}">
<input type="checkbox" ng-model="opts.selectedTopics[topic.id]" ng-attr-id="{{::topic.id}}" ng-model-store="selectedTopics-{{::topic.id}}">
<label class="check" ng-attr-for="{{::topic.id}}">
@@ -15,7 +29,19 @@
</li>
</ul>
</div>
- <div class="chart">
-
+ <div class="chart message-container">
+ <div class="topbar">
+ Display relevances:
+ <div class="radio radio-inline">
+ <input type="radio" id="seqAbsolute" ng-model="opts.seqstyle" value="absolute" ng-model-store ng-model-default="'absolute'">
+ <label for="seqAbsolute">Absolute</label>
+ </div>
+ <div class="radio radio-inline">
+ <input type="radio" id="seqRelative" ng-model="opts.seqstyle" value="relative" ng-model-store>
+ <label for="seqRelative">Relative</label>
+ </div>
+ </div>
+ <div class="area-chart" id="topic-seq" highcharts="topicSeq"></div>
+ <div class="message" ng-show="!topicsSelected">No topic selected</div>
</div>
</div>
\ No newline at end of file
diff --git a/vipra-ui/app/html/index.html b/vipra-ui/app/html/index.html
index 260825fac09599e9678a420d1a014b80e9eea49d..5798ff160834e05c92b0b70edcaeac3984d94aee 100644
--- a/vipra-ui/app/html/index.html
+++ b/vipra-ui/app/html/index.html
@@ -54,4 +54,4 @@
</div>
</div>
</div>
-<div ng-cloak ui-view></div>
+<div ng-cloak ui-view></div>
\ No newline at end of file
diff --git a/vipra-ui/app/html/network.html b/vipra-ui/app/html/network.html
index 6d933364f6742036cddb10b081943f04c15dd159..1fbf495530f2289088d6bb1fced3aec6698f3b0c 100644
--- a/vipra-ui/app/html/network.html
+++ b/vipra-ui/app/html/network.html
@@ -1,15 +1,18 @@
<div ng-cloak ng-hide="$state.current.name !== 'network'">
<div class="fullsize navpadding">
<div class="graph-legend overlay">
- <label style="color:{{colors.articles}}">
- <input type="checkbox" ng-model="shown.articles" ng-model-store="showArticles" ng-model-default="type == 'articles'" ng-disabled="type == 'articles'"> Articles
- </label>
- <label style="color:{{colors.topics}}">
- <input type="checkbox" ng-model="shown.topics" ng-model-store="showTopics" ng-model-default="true" ng-disabled="type == 'topics'"> Topics
- </label>
- <label style="color:{{colors.words}}">
- <input type="checkbox" ng-model="shown.words" ng-model-store="showWords" ng-model-default="true" ng-disabled="type == 'words'"> Words
- </label>
+ <div class="checkbox">
+ <input type="checkbox" id="showArticles" ng-model="shown.articles" ng-model-store="showArticles" ng-model-default="type == 'articles'" ng-disabled="type == 'articles'">
+ <label for="showArticles" style="color:{{colors.articles}}">Articles</label>
+ </div>
+ <div class="checkbox">
+ <input type="checkbox" id="showTopics" ng-model="shown.topics" ng-model-store="showTopics" ng-model-default="true" ng-disabled="type == 'topics'">
+ <label for="showTopics" style="color:{{colors.topics}}">Topics</label>
+ </div>
+ <div class="checkbox">
+ <input type="checkbox" id="showWords" ng-model="shown.words" ng-model-store="showWords" ng-model-default="true" ng-disabled="type == 'words'">
+ <label for="showWords" style="color:{{colors.words}}">Words</label>
+ </div>
</div>
<div class="fullsize navpadding" id="visgraph"></div>
</div>
diff --git a/vipra-ui/app/html/topics/show.html b/vipra-ui/app/html/topics/show.html
index 6dd31fad7b18a8ce006f64d88a0e3fa1ed7c7ced..599aa2085117dc5536e04a8faf8d42a1cf6df177 100644
--- a/vipra-ui/app/html/topics/show.html
+++ b/vipra-ui/app/html/topics/show.html
@@ -14,15 +14,18 @@
</div>
</div>
</h1>
- <bs-alert type="danger" ng-if="renameErrors">
- <span ng-bind-html="renameErrors"></span>
- </bs-alert>
<table class="item-actions">
<tr>
<td>
- <bs-dropdown label="Actions">
- <li><a ng-click="startRename()">Rename</a></li>
- </bs-dropdown>
+ <div class="dropdown">
+ <button class="btn btn-default dropdown-toggle" type="button" id="actionsDropdown" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
+ Actions
+ <span class="caret"></span>
+ </button>
+ <ul class="dropdown-menu" aria-labelledby="actionsDropdown">
+ <li><a ng-click="startRename()">Rename</a></li>
+ </ul>
+ </div>
</td>
<td>
<a class="btn btn-default" ui-sref="network({type:'topics', id:topic.id})">Network graph</a>
@@ -54,53 +57,26 @@
</table>
</div>
</div>
- <div ng-if="!topic.dynamic">
- <h3>Words</h3>
- <div class="row">
- <div class="col-md-12">
- <table class="table table-bordered table-condensed table-fixed">
- <thead>
- <tr>
- <th sort-by="id" ng-model="opts.wordSort" sort-reverse="opts.wordSortRev">
- Word
- </th>
- <th sort-by="likeliness" ng-model="opts.wordSort" sort-reverse="opts.wordSortRev">
- Likeliness
- </th>
- </tr>
- </thead>
- <tbody>
- <tr ng-repeat="word in topic.words | orderBy:opts.wordSort:opts.wordSortRev">
- <td>
- <a ui-sref="words.show({id:word.id})" ng-bind="word.id"></a>
- </td>
- <td ng-bind-template="{{word.likeliness.toFixed(6)}}"></td>
- </tr>
- </tbody>
- </table>
- </div>
- </div>
- </div>
- <div ng-if="topic.dynamic">
- <h3>Relevance over time</h3>
- <div class="row">
- <div class="col-md-12">
- <div class="well well-sm">
- <label class="radio-inline">
- <input type="radio" ng-model="opts.seqstyle" value="absolute" ng-model-store="seqStyle" ng-model-default="'absolute'" ng-change="changeSeqStyle()">Absolute
- </label>
- <label class="radio-inline">
- <input type="radio" ng-model="opts.seqstyle" value="relative" ng-model-store="seqStyle" ng-change="changeSeqStyle()">Relative
- </label>
+ <h3>Relevance over time</h3>
+ <div class="row">
+ <div class="col-md-12">
+ <div class="well well-sm">
+ <div class="radio radio-inline">
+ <input type="radio" id="seqAbsolute" ng-model="opts.seqstyle" value="absolute" ng-model-store="seqStyle" ng-model-default="'absolute'">
+ <label for="seqAbsolute">Absolute</label>
+ </div>
+ <div class="radio radio-inline">
+ <input type="radio" id="seqRelative" ng-model="opts.seqstyle" value="relative" ng-model-store="seqStyle">
+ <label for="seqRelative">Relative</label>
</div>
</div>
</div>
- <br>
- <div class="row">
- <div class="col-md-12">
- <div class="area-chart" id="topic-seq" highcharts="topicSeq"></div>
- </div>
+ </div>
+ <br>
+ <div class="row">
+ <div class="col-md-12">
+ <div class="area-chart" id="topic-seq" highcharts="topicSeq"></div>
</div>
- </div>
+ </div>
</div>
<div ng-cloak ui-view></div>
diff --git a/vipra-ui/app/js/app.js b/vipra-ui/app/js/app.js
index 515882f4e578d6bc16fc36a1554b5a5da97d825b..cfa37ff395f75cd560a4a2ac1842f6e1b02f8312 100644
--- a/vipra-ui/app/js/app.js
+++ b/vipra-ui/app/js/app.js
@@ -10,6 +10,7 @@
var app = angular.module('vipra.app', [
'ngResource',
'ngSanitize',
+ 'ngAnimate',
'ui.router',
'nya.bootstrap.select',
'vipra.controllers',
diff --git a/vipra-ui/app/js/controllers.js b/vipra-ui/app/js/controllers.js
index bf42c96a245e1d81dd22bd94502f1282ccba027d..6bfbe8838dc0f79391847a9ded297a5cd7186435 100644
--- a/vipra-ui/app/js/controllers.js
+++ b/vipra-ui/app/js/controllers.js
@@ -293,9 +293,13 @@
app.controller('ExplorerController', ['$scope', 'TopicFactory',
function($scope, TopicFactory) {
- $scope.opts = {};
+ $scope.opts = {
+ sorttopics: 'name'
+ };
- TopicFactory.query({}, function(data) {
+ TopicFactory.query({
+ fields: 'name,sequences,avgRelevance,varRelevance'
+ }, function(data) {
$scope.topics = data;
var colors = Vipra.generateColors($scope.topics.length);
for (var i = 0; i < $scope.topics.length; i++)
@@ -306,17 +310,70 @@
$scope.checkTopics = function(to) {
var toggle = typeof to === 'undefined';
- if(!$scope.opts.selectedTopics)
+ if (!$scope.opts.selectedTopics)
$scope.opts.selectedTopics = {};
- for(var i = 0, t; i < $scope.topics.length; i++) {
+ for (var i = 0, t; i < $scope.topics.length; i++) {
t = $scope.topics[i];
- if(toggle)
+ if (toggle)
$scope.opts.selectedTopics[t.id] = !$scope.opts.selectedTopics[t.id];
else
$scope.opts.selectedTopics[t.id] = to;
}
};
+ $scope.redrawGraph = function() {
+ if (!$scope.topics || !$scope.opts.selectedTopics) return;
+ var series = [];
+
+ // create series of selected topics
+ for (var i = 0; i < $scope.topics.length; i++) {
+ if ($scope.opts.selectedTopics[$scope.topics[i].id]) {
+ var topic = $scope.topics[i],
+ min = 0,
+ max = 0,
+ relevances = [];
+
+ // data array with relevances and min/max
+ for (var j = 0, sequence, relevance; j < topic.sequences.length; j++) {
+ sequence = topic.sequences[j];
+ relevance = $scope.opts.seqstyle === 'relative' ? sequence.relevanceChange : sequence.relevance;
+ relevances.push({
+ x: new Date(sequence.window.startDate).getTime(),
+ y: relevance,
+ id: topic.id,
+ seq: sequence
+ });
+ if (relevances[j].y > relevances[max].y)
+ max = j;
+ else if (relevances[j].y < relevances[min].y)
+ min = j;
+ }
+
+ // mark maximum and minimum value
+ relevances[max].marker = { symbol: 'triangle', fillColor: '#f00' };
+ relevances[min].marker = { symbol: 'triangle-down', fillColor: '#f00' };
+
+ series.push({
+ name: topic.name,
+ data: relevances,
+ color: 'rgb(' + topic.color.join() + ')'
+ });
+ }
+ }
+
+ // highcharts configuration
+ $scope.topicSeq = areaRelevanceChart(series, $scope.selectSequence);
+ $scope.topicsSelected = series.length;
+ };
+
+ $scope.selectSequence = function(node) {
+ $scope.$apply(function() {
+
+ });
+ };
+
+ $scope.$watchCollection('opts.selectedTopics', $scope.redrawGraph);
+ $scope.$watch('opts.seqstyle', $scope.redrawGraph);
}
]);
@@ -377,22 +434,11 @@
}
// highcharts data
- var topicShare = {
- chart: { type: 'pie' },
- credits: { enabled: false },
- plotOptions: {
- pie: { allowPointSelect: true }
- },
- title: { text: '' },
- tooltip: { pointFormat: '{series.name}: <b>{point.percentage:.1f}%</b>' },
- series: [{
- name: 'Topic Share',
- colorByPoint: true,
- data: topicShareSeries
- }]
- };
-
- $scope.topicShare = topicShare;
+ $scope.topicShare = topicShareChart([{
+ name: 'Topic Share',
+ colorByPoint: true,
+ data: topicShareSeries
+ }]);
}
}, function(err) {
$scope.errors = err;
@@ -467,6 +513,40 @@
$scope.topic = data;
$scope.topicCreated = Vipra.formatDateTime($scope.topic.created);
$scope.topicModified = Vipra.formatDateTime($scope.topic.modified);
+
+ $scope.$watch('opts.seqstyle', function(style) {
+ if (!style || !$scope.topic || !$scope.topic.sequences) return;
+ console.log('redraw relevance chart');
+ var min = 0,
+ max = 0,
+ relevances = [];
+
+ // create series
+ for (var i = 0, sequence, relevance; i < $scope.topic.sequences.length; i++) {
+ sequence = $scope.topic.sequences[i];
+ relevance = $scope.opts.seqstyle === 'relative' ? sequence.relevanceChange : sequence.relevance;
+ relevances.push([new Date(sequence.window.startDate).getTime(), relevance]);
+ if (relevances[i][1] > relevances[max][1])
+ max = i;
+ else if (relevances[i][1] < relevances[min][1])
+ min = i;
+ }
+
+ // mark maximum and minimum value
+ relevances[max] = {
+ x: relevances[max][0],
+ y: relevances[max][1],
+ marker: { symbol: 'triangle', fillColor: '#f00' }
+ };
+ relevances[min] = {
+ x: relevances[min][0],
+ y: relevances[min][1],
+ marker: { symbol: 'triangle-down', fillColor: '#f00' }
+ };
+
+ // highcharts configuration
+ $scope.topicSeq = areaRelevanceChart([{ name: $scope.topic.name, data: relevances }]);
+ });
}, function(err) {
$scope.errors = err;
});
@@ -500,60 +580,6 @@
$event.preventDefault();
}
};
-
- $scope.$watch('opts.seqstyle', function(style) {
- if (!style) return;
- console.log('redraw relevance chart');
- var min = 0,
- max = 0,
- relevances = [];
- // create series
- for (var i = 0, sequence, relevance; i < $scope.topic.sequences.length; i++) {
- sequence = $scope.topic.sequences[i];
- relevance = $scope.opts.seqstyle === 'relative' ? sequence.relevanceChange : sequence.relevance;
- relevances.push([new Date(sequence.window.startDate).getTime(), relevance]);
- if (relevances[i][1] > relevances[max][1])
- max = i;
- else if (relevances[i][1] < relevances[min][1])
- min = i;
- }
-
- // mark maximum and minimum value
- relevances[max] = {
- x: relevances[max][0],
- y: relevances[max][1],
- marker: { symbol: 'triangle', fillColor: '#f00' }
- };
- relevances[min] = {
- x: relevances[min][0],
- y: relevances[min][1],
- marker: { symbol: 'triangle-down', fillColor: '#f00' }
- };
-
- // highcharts configuration
- $scope.topicSeq = {
- chart: {
- type: 'areaspline',
- zoomType: 'x',
- spacingLeft: 0,
- spacingRight: 0
- },
- title: { text: '' },
- xAxis: {
- type: 'datetime',
- title: { text: '' }
- },
- yAxis: { title: { text: 'Relevance' } },
- tooltip: {
- headerFormat: '',
- pointFormat: '{point.x:%Y}: {point.y:.4f}'
- },
- legend: { enabled: false },
- credits: { enabled: false },
- plotOptions: { areaspline: { fillOpacity: 0.5 } },
- series: [{ name: $scope.topic.name, data: relevances }]
- };
- });
}
]);
@@ -633,4 +659,59 @@
}
]);
+ /****************************************************************************
+ * Shared Highcharts configurations
+ ****************************************************************************/
+
+ function areaRelevanceChart(series, clickCallback) {
+ return {
+ chart: {
+ type: 'areaspline',
+ zoomType: 'x',
+ spacingLeft: 0,
+ spacingRight: 0
+ },
+ title: { text: '' },
+ xAxis: {
+ type: 'datetime',
+ title: { text: '' }
+ },
+ yAxis: { title: { text: 'Relevance' } },
+ tooltip: {
+ headerFormat: '',
+ pointFormat: '{point.x:%Y}: {point.y:.4f}'
+ },
+ legend: { enabled: false },
+ credits: { enabled: false },
+ plotOptions: {
+ areaspline: { fillOpacity: 0.5 },
+ series: {
+ cursor: 'pointer',
+ allowPointSelect: true,
+ point: {
+ events: {
+ click: function(e) {
+ clickCallback(e.point);
+ }
+ }
+ }
+ }
+ },
+ series: series
+ };
+ }
+
+ function topicShareChart(series) {
+ return {
+ chart: { type: 'pie' },
+ credits: { enabled: false },
+ plotOptions: {
+ pie: { allowPointSelect: true }
+ },
+ title: { text: '' },
+ tooltip: { pointFormat: '{series.name}: <b>{point.percentage:.1f}%</b>' },
+ series: series
+ };
+ }
+
})();
diff --git a/vipra-ui/app/js/directives.js b/vipra-ui/app/js/directives.js
index d790879ba8a00a2fbd85f584fb80f8ac96b4fbf4..754ef28f055d8ba21d4e7289a2b111cebced0eb8 100644
--- a/vipra-ui/app/js/directives.js
+++ b/vipra-ui/app/js/directives.js
@@ -2,7 +2,7 @@
* Vipra Application
* Directives
******************************************************************************/
-/* globals angular, $, console, Vipra */
+/* globals angular, console */
(function() {
"use strict";
@@ -65,16 +65,6 @@
};
});
- app.directive('toggleLink', function() {
- return {
- link: function($scope, $elem, $attrs) {
- $elem.click(function() {
- $($attrs.target).slideToggle();
- });
- }
- };
- });
-
app.directive('ngModelStore', ['Store', function(Store) {
return {
restrict: 'A',
@@ -88,7 +78,7 @@
console.log('no store key given');
return;
}
- var key = $attrs.ngModelStore;
+ var key = $attrs.ngModelStore || $attrs.ngModel;
var value = Store(key);
if (value !== null) {
$ctrl.$setViewValue(value);
@@ -104,49 +94,6 @@
};
}]);
- app.directive('bsDropdown', function() {
- return {
- scope: {
- label: '@',
- align: '@'
- },
- templateUrl: 'html/directives/dropdown.html',
- transclude: true,
- replace: true,
- link: function($scope) {
- $scope.dropdownId = Vipra.randomId();
- $scope.align = 'dropdown-menu-left';
- if ($scope.align === 'right')
- $scope.align = 'dropdown-menu-right';
- }
- };
- });
-
- app.directive('bsAlert', function() {
- return {
- scope: {
- type: '@',
- dismissible: '@'
- },
- transclude: true,
- replace: true,
- templateUrl: 'html/directives/alert.html',
- link: function($scope) {
- if (!$scope.type) {
- console.log('no alert type given');
- return;
- }
-
- $scope.dismissible = $scope.dismissible !== 'false';
-
- var classes = 'alert alert-' + $scope.type;
- if ($scope.dismissible)
- classes += ' alert-dismissible';
- $scope.classes = classes;
- }
- };
- });
-
app.directive('sortBy', ['Store', function(Store) {
return {
scope: {
@@ -179,46 +126,27 @@
};
}]);
- app.directive('revolveSelect', function() {
+ app.directive('bsRadio', function() {
return {
scope: {
- ngModel: '=',
- values: '='
+ bsRadio: '=',
+ ngModel: '='
},
- template: '<span ng-bind-html="label" ng-click="next()"></span>',
- link: function($scope) {
- var hasObjects = false;
- if ($scope.values && $scope.values.length)
- hasObjects = angular.isObject($scope.values[0]);
-
- var index = function() {
- if (hasObjects) {
- for (var i = 0; i < $scope.values.length; i++) {
- if ($scope.values[i].value == $scope.ngModel)
- return i;
- }
- return 0;
- } else {
- return $scope.values.indexOf($scope.ngModel);
- }
- };
-
- var select = function(i) {
- if (i < 0 || i >= $scope.values.length) return;
- if (hasObjects) {
- $scope.ngModel = $scope.values[i].value;
- $scope.label = $scope.values[i].label;
- } else {
- $scope.ngModel = $scope.label = $scope.values[i];
- }
+ restrict: 'A',
+ link: function($scope, $elem) {
+ var setActive = function() {
+ $elem.parent().children().removeClass("active");
+ $elem.addClass("active");
};
- $scope.next = function() {
- select((index() + 1) % $scope.values.length);
- };
+ if ($scope.ngModel === $scope.bsRadio)
+ setActive();
- $scope.$watch('ngModel', function() {
- select(index());
+ $elem.click(function() {
+ $scope.$apply(function() {
+ $scope.ngModel = $scope.bsRadio;
+ setActive();
+ });
});
}
};
diff --git a/vipra-ui/app/js/factories.js b/vipra-ui/app/js/factories.js
index b745096610a111a512ce565689efbb72070ce12d..55742067640b97be968a89604692dadabe956ccc 100644
--- a/vipra-ui/app/js/factories.js
+++ b/vipra-ui/app/js/factories.js
@@ -28,6 +28,10 @@
});
}]);
+ app.factory('SequenceFactory', ['$resource', function($resource) {
+ return $resource(Vipra.config.restUrl + '/sequences/:id');
+ }]);
+
app.factory('SearchFactory', ['$resource', function($resource) {
return $resource(Vipra.config.restUrl + '/search');
}]);
diff --git a/vipra-ui/app/less/app.less b/vipra-ui/app/less/app.less
index 3613090040c9e81e772571fb81fba09265b60ceb..b2789ca044a4f67eccf1045b538d7ee4fcd0216d 100644
--- a/vipra-ui/app/less/app.less
+++ b/vipra-ui/app/less/app.less
@@ -106,7 +106,7 @@ ul.dashed {
.graph-legend {
position: absolute;
- top: 60px;
+ top: 50px;
left: 10px;
font-weight: bold;
padding: 10px;
@@ -287,17 +287,34 @@ revolve-select, [revolve-select] {
.explorer {
display: flex;
flex-direction: row;
+ flex-wrap: wrap;
.sidebar {
flex: 0 0 250px;
width: 250px;
background: #f9f9f9;
height: 100%;
- padding: 5px 0 5px 5px;
+ padding: 5px;
+
+ > * + * {
+ margin-top: 5px;
+ }
+ }
+
+ .topbar {
+ background: #f9f9f9;
+ width: 100%;
+ padding: 5px;
+ vertical-align: middle;
}
.chart {
flex: 1 0 0;
+ padding: 5px;
+ }
+
+ .sequence {
+ flex: 1 0 0;
}
.topic-choice {
@@ -330,6 +347,49 @@ input[type=checkbox],
cursor: pointer;
}
+.radio-inline {
+ vertical-align: bottom;
+}
+
+.btn-groups {
+ .btn-group:not(:first-child) {
+ .btn {
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+ }
+ }
+
+ .btn-group:not(:last-child) {
+ .btn {
+ border-bottom-left-radius: 0;
+ border-bottom-right-radius: 0;
+ }
+ }
+}
+
+.message-container {
+ position: relative;
+}
+
+.message {
+ position: absolute;
+ top: 50%;
+ left: 50%;
+ transform: translate(-50%, -50%);
+}
+
+.searchclear {
+ position: absolute;
+ right: 5px;
+ top: 0;
+ bottom: 0;
+ height: 14px;
+ margin: auto;
+ font-size: 14px;
+ cursor: pointer;
+ color: #ccc;
+}
+
@-moz-keyframes spin { 100% { -moz-transform: rotateY(360deg); } }
@-webkit-keyframes spin { 100% { -webkit-transform: rotateY(360deg); } }
@keyframes spin { 100% { -webkit-transform: rotateY(360deg); transform:rotateY(360deg); } }
diff --git a/vipra-ui/bower.json b/vipra-ui/bower.json
index c484899bfc46e5503535d8c4ab4646278594e2e6..f45e1e27a253877a749b43b3f68067bbf6d214de 100644
--- a/vipra-ui/bower.json
+++ b/vipra-ui/bower.json
@@ -28,6 +28,8 @@
"moment": "^2.x",
"nya-bootstrap-select": "^2.x",
"font-awesome": "^4.x",
- "awesome-bootstrap-checkbox": "^0.3.7"
+ "awesome-bootstrap-checkbox": "^0.3.7",
+ "angular-bootstrap": "^1.x",
+ "angular-animate": "^1.5.0"
}
}
diff --git a/vipra-ui/gulpfile.js b/vipra-ui/gulpfile.js
index 3cfe64cac2daa164bce78064dfa23023e01ff701..e520fc6108a569b06372ca9480d7d885ce14834e 100644
--- a/vipra-ui/gulpfile.js
+++ b/vipra-ui/gulpfile.js
@@ -15,9 +15,11 @@ var assets = {
'bower_components/jquery/dist/jquery.min.js',
'bower_components/angular/angular.min.js',
'bower_components/angular-resource/angular-resource.min.js',
+ 'bower_components/angular-animate/angular-animate.min.js',
'bower_components/angular-sanitize/angular-sanitize.min.js',
'bower_components/angular-ui-router/release/angular-ui-router.min.js',
'bower_components/bootstrap/dist/js/bootstrap.min.js',
+ //'bower_components/angular-bootstrap/ui-bootstrap-tpls.min.js',
'bower_components/highcharts/highcharts.js',
'bower_components/vis/dist/vis.min.js',
'bower_components/moment/min/moment.min.js',
diff --git a/vipra-util/src/main/java/de/vipra/util/Constants.java b/vipra-util/src/main/java/de/vipra/util/Constants.java
index d245aa3eef31f41056a76a75a4553d1b7447da45..49a56366bbb062c79934803248bee976e4d3bc33 100644
--- a/vipra-util/src/main/java/de/vipra/util/Constants.java
+++ b/vipra-util/src/main/java/de/vipra/util/Constants.java
@@ -312,7 +312,6 @@ public class Constants {
* The topic modeling analyzers available, including the default analyzer.
*/
public static enum Analyzer {
- JGIBB("jgibb"),
DTM("dtm");
public final String name;
diff --git a/vipra-util/src/main/java/de/vipra/util/model/Sequence.java b/vipra-util/src/main/java/de/vipra/util/model/Sequence.java
index 96f9538d1da691221027be1b483a8210b07f5fdf..784f0b233d0db496091040525a561439d7200d69 100644
--- a/vipra-util/src/main/java/de/vipra/util/model/Sequence.java
+++ b/vipra-util/src/main/java/de/vipra/util/model/Sequence.java
@@ -57,7 +57,7 @@ public class Sequence implements Model<ObjectId>, Comparable<Sequence>, Serializ
return relevanceChange;
}
- public void setRelevanceChange(Double relevanceChange) {
+ public void setRelevanceChange(final Double relevanceChange) {
this.relevanceChange = relevanceChange;
}
diff --git a/vipra-util/src/main/java/de/vipra/util/model/SequenceFull.java b/vipra-util/src/main/java/de/vipra/util/model/SequenceFull.java
index 91b576f8f38cedfc78b9aa32cae51e938d5c3d60..9f43e31d3b53dd95c94c57fe12dc7a7e5a88eaba 100644
--- a/vipra-util/src/main/java/de/vipra/util/model/SequenceFull.java
+++ b/vipra-util/src/main/java/de/vipra/util/model/SequenceFull.java
@@ -63,7 +63,7 @@ public class SequenceFull implements Model<ObjectId>, Comparable<SequenceFull>,
return relevanceChange;
}
- public void setRelevanceChange(Double relevanceChange) {
+ public void setRelevanceChange(final Double relevanceChange) {
this.relevanceChange = relevanceChange;
}
diff --git a/vipra-util/src/main/java/de/vipra/util/model/TopicFull.java b/vipra-util/src/main/java/de/vipra/util/model/TopicFull.java
index cb1d99dc52c4d37a0794ab498a8568ac53cb47f3..f206b6ade3644ef0d38abb1931931ca6a81bb3a5 100644
--- a/vipra-util/src/main/java/de/vipra/util/model/TopicFull.java
+++ b/vipra-util/src/main/java/de/vipra/util/model/TopicFull.java
@@ -6,7 +6,6 @@ import java.util.Date;
import java.util.List;
import org.bson.types.ObjectId;
-import org.mongodb.morphia.annotations.Embedded;
import org.mongodb.morphia.annotations.Entity;
import org.mongodb.morphia.annotations.Id;
import org.mongodb.morphia.annotations.PrePersist;
@@ -26,10 +25,6 @@ public class TopicFull implements Model<ObjectId>, Serializable {
private String name;
- @Embedded
- @QueryIgnore(multi = true)
- private List<TopicWord> words;
-
@Reference
@QueryIgnore(multi = true)
private List<Sequence> sequences;
@@ -40,8 +35,6 @@ public class TopicFull implements Model<ObjectId>, Serializable {
@QueryIgnore(multi = true)
private Double varRelevance;
- private boolean dynamic = false;
-
private Date created;
private Date modified;
@@ -68,14 +61,6 @@ public class TopicFull implements Model<ObjectId>, Serializable {
this.name = name;
}
- public List<TopicWord> getWords() {
- return words;
- }
-
- public void setWords(final List<TopicWord> topicWords) {
- words = topicWords;
- }
-
public List<Sequence> getSequences() {
return sequences;
}
@@ -100,14 +85,6 @@ public class TopicFull implements Model<ObjectId>, Serializable {
this.varRelevance = varRelevance;
}
- public boolean isDynamic() {
- return dynamic;
- }
-
- public void setDynamic(final boolean dynamic) {
- this.dynamic = dynamic;
- }
-
public Date getCreated() {
return created;
}
@@ -165,9 +142,8 @@ public class TopicFull implements Model<ObjectId>, Serializable {
@Override
public String toString() {
- return "TopicFull [id=" + id + ", name=" + name + ", words=" + words + ", sequences=" + sequences
- + ", avgRelevance=" + avgRelevance + ", varRelevance=" + varRelevance + ", created=" + created
- + ", modified=" + modified + "]";
+ return "TopicFull [id=" + id + ", name=" + name + ", sequences=" + sequences + ", avgRelevance=" + avgRelevance
+ + ", varRelevance=" + varRelevance + ", created=" + created + ", modified=" + modified + "]";
}
}