From: pvtroshin Date: Thu, 9 Dec 2010 12:02:15 +0000 (+0000) Subject: More javadocs X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6582e82919b0d3697fe5e96f1be6a369f90a2d93;p=jabaws.git More javadocs git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3458 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000..d386145 --- /dev/null +++ b/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,270 @@ +#Fri Nov 19 11:04:13 GMT 2010 +eclipse.preferences.version=1 +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=16 +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=52 +org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=48 +org.eclipse.jdt.core.formatter.alignment_for_enum_constants=0 +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_selector_in_method_invocation=16 +org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=64 +org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=64 +org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=64 +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.blank_lines_after_imports=0 +org.eclipse.jdt.core.formatter.blank_lines_after_package=0 +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=0 +org.eclipse.jdt.core.formatter.blank_lines_before_member_type=0 +org.eclipse.jdt.core.formatter.blank_lines_before_method=0 +org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=0 +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=0 +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_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.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_local_variable=insert +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_member=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_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_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=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=insert +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=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_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=do not 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_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_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=do not 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_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=insert +org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert +org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=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=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_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=do not 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_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_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=80 +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=false +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_outer_expressions_when_nested=true diff --git a/.settings/org.eclipse.jdt.ui.prefs b/.settings/org.eclipse.jdt.ui.prefs new file mode 100644 index 0000000..87b6dd9 --- /dev/null +++ b/.settings/org.eclipse.jdt.ui.prefs @@ -0,0 +1,4 @@ +#Fri Nov 19 11:04:13 GMT 2010 +eclipse.preferences.version=1 +formatter_profile=org.eclipse.jdt.ui.default_profile +formatter_settings_version=11 diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java index 935ce74..ddd1222 100644 --- a/datamodel/compbio/data/sequence/SequenceUtil.java +++ b/datamodel/compbio/data/sequence/SequenceUtil.java @@ -303,13 +303,23 @@ public final class SequenceUtil { } /** - * Reader for JRonn horizontal file format >Foobar M G D T T A G 0.48 0.42 - * 0.42 0.48 0.52 0.53 0.54 All values are tab delimited + * Reader for JRonn horizontal file format + * + * 
+	 * >Foobar M G D T T A G 0.48 0.42
+	 * 0.42 0.48 0.52 0.53 0.54
+	 * 
+	 * 
+	 * Where all values are tab delimited
 	 * 
 	 * @param inStream
-	 * @return
+	 *            the InputStream connected to the JRonn output file
+	 * @return List of {@link AnnotatedSequence} objects
 	 * @throws IOException
+	 *             is thrown if the inStream has problems accessing the data
 	 * @throws UnknownFileFormatException
+	 *             is thrown if the inStream represents an unknown source of
+	 * data, i.e. not a JRonn output
 	 */
 	public static List readJRonn(final InputStream inStream)
 			throws IOException, UnknownFileFormatException {
@@ -403,7 +413,7 @@ public final class SequenceUtil {
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
-	public static List> readDisembl(
+	static List> readDisembl(
 			final InputStream input) throws IOException,
 			UnknownFileFormatException {
 		Scanner scan = new Scanner(input);
diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index a76b41b..a6affb9 100644
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -80,7 +80,7 @@ public class TestAAConWS {
 			System.out.println("Pres: " + msaws.getPresets().getPresets());
 			String jobId = msaws.analize(fsl);
 			System.out.println("J: " + jobId);
-			HashSet result = msaws.getConservation(jobId);
+			HashSet result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 1);
 			assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);
@@ -92,19 +92,19 @@ public class TestAAConWS {
 			PresetManager presets = msaws.getPresets();
 			jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Quick conservation"));
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 13);
 
 			jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Slow conservation"));
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 5);
 
 			jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Complete conservation"));
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 18);
 
@@ -144,19 +144,19 @@ public class TestAAConWS {
 			PresetManager presets = msaws.getPresets();
 			String jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Quick conservation"));
-			HashSet result = msaws.getConservation(jobId);
+			HashSet result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 13);
 
 			jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Slow conservation"));
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 5);
 
 			jobId = msaws.presetAnalize(fsl,
 					presets.getPresetByName("Complete conservation"));
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 18);
 
@@ -196,7 +196,7 @@ public class TestAAConWS {
 		try {
 			options.getArgument("Calculation method").setDefaultValue("SMERFS");
 			String jobId = msaws.customAnalize(fsl, options.getArguments());
-			HashSet result = msaws.getConservation(jobId);
+			HashSet result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 1);
 			assertEquals(
@@ -207,7 +207,7 @@ public class TestAAConWS {
 			options.removeArgument("Normalize");
 			System.out.println(options);
 			jobId = msaws.customAnalize(fsl, options.getArguments());
-			result = msaws.getConservation(jobId);
+			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.size(), 1);
 			assertEquals(
diff --git a/webservices/compbio/data/msa/Annotation.java b/webservices/compbio/data/msa/Annotation.java
index 25e6ac1..27a1d55 100644
--- a/webservices/compbio/data/msa/Annotation.java
+++ b/webservices/compbio/data/msa/Annotation.java
@@ -21,18 +21,21 @@ import compbio.metadata.WrongParameterException;
 /**
  * Interface for tools that results to one or more annotation to sequence(s)
  * 
- * @author pvtroshin
- * 
- *         Date November 2010
+ * @author Peter Troshin
  * 
  * @param 
  *            executable type / web service type
+ * 
+ * @version 1.0 November 2010
  */
 @WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")
 public interface Annotation extends JABAService, JManagement, Metadata {
 
 	/**
 	 * 
+	 * Analyse the sequences. The actual analysis algorithm is defined by the
+	 * type T.
+	 * 
 	 * Any dataset containing a greater number of sequences or the average
 	 * length of the sequences are greater then defined in the default Limit
 	 * will not be accepted for an alignment operation and
@@ -56,8 +59,8 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 *             thrown if input list of fasta sequence is null or empty
 	 * @throws UnsupportedRuntimeException
 	 *             thrown if server OS does not support native executables for a
-	 *             given web service, e.g. JWS2 is deployed on Windows and Mafft
-	 *             service is called
+	 *             given web service, e.g. JABAWS is deployed on Windows and
+	 *             Mafft service is called
 	 * @throws LimitExceededException
 	 *             is throw if the input sequences number or average length
 	 *             exceeds what is defined by the limit
@@ -69,11 +72,10 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 			JobSubmissionException;
 
 	/**
-	 * 
-	 * @see Option
-	 * 
-	 *      Default Limit is used to decide whether the calculation will be
-	 *      permitted or denied
+	 * Analyse the sequences according to custom settings defined in options
+	 * list. The actual analysis algorithm is defined by the type T. Default
+	 * Limit is used to decide whether the calculation will be permitted or
+	 * denied
 	 * 
 	 * @param sequences
 	 *            List of FastaSequence objects. The programme does not perform
@@ -83,9 +85,9 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 * @param options
 	 *            A list of Options
 	 * @return jobId - unique identifier for the job
-	 * @throws JobSubmissionException. This
-	 *             exception is thrown when the job could not be submitted due
-	 *             to the following reasons: 1) The number of sequences in the
+	 * @throws JobSubmissionException
+	 *             is thrown when the job could not be submitted due to the
+	 *             following reasons: 1) The number of sequences in the
 	 *             submission or their average length is greater then defined by
 	 *             the default Limit. 2) Any problems on the server side e.g. it
 	 *             is misconfigured or malfunction, is reported via this
@@ -100,11 +102,12 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 *             thrown if input list of fasta sequence is null or empty
 	 * @throws UnsupportedRuntimeException
 	 *             thrown if server OS does not support native executables for a
-	 *             given web service, e.g. JWS2 is deployed on Windows and Mafft
-	 *             service is called
+	 *             given web service, e.g. JABAWS is deployed on Windows and
+	 *             Mafft service is called
 	 * @throws LimitExceededException
 	 *             is throw if the input sequences number or average length
 	 *             exceeds what is defined by the limit
+	 * @see Option
 	 */
 	@WebMethod
 	String customAnalize(
@@ -114,7 +117,8 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 			JobSubmissionException, WrongParameterException;
 
 	/**
-	 * 
+	 * Analyse the sequences according to the preset settings. The actual
+	 * analysis algorithm is defined by the type T.
 	 * 
 	 * Limit for a presetName is used whether the calculation will be permitted
 	 * or denied. If no Limit was defined for a presetName, than default limit
@@ -128,9 +132,9 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 * @param preset
 	 *            A list of Options
 	 * @return String - jobId - unique identifier for the job
-	 * @throws JobSubmissionException. This
-	 *             exception is thrown when the job could not be submitted due
-	 *             to the following reasons: 1) The number of sequences in the
+	 * @throws JobSubmissionException
+	 *             is thrown when the job could not be submitted due to the
+	 *             following reasons: 1) The number of sequences in the
 	 *             submission or their average length is greater then defined by
 	 *             the default Limit. 2) Any problems on the server side e.g. it
 	 *             is misconfigured or malfunction, is reported via this
@@ -145,8 +149,8 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 *             thrown if input list of fasta sequence is null or empty
 	 * @throws UnsupportedRuntimeException
 	 *             thrown if server OS does not support native executables for a
-	 *             given web service, e.g. JWS2 is deployed on Windows and Mafft
-	 *             service is called
+	 *             given web service, e.g. JABAWS is deployed on Windows and
+	 *             Mafft service is called
 	 * @throws LimitExceededException
 	 *             is throw if the input sequences number or average length
 	 *             exceeds what is defined by the limit
@@ -163,7 +167,7 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 * 
 	 * @param jobId
 	 *            a unique job identifier
-	 * @return
+	 * @return the HashSet of Score objects
 	 * @throws ResultNotAvailableException
 	 *             this exception is throw if the job execution was not
 	 *             successful or the result of the execution could not be found.
@@ -176,7 +180,7 @@ public interface Annotation extends JABAService, JManagement, Metadata {
 	 *             invalid format
 	 */
 	@WebMethod
-	HashSet getConservation(@WebParam(name = "jobId") String jobId)
+	HashSet getAnnotation(@WebParam(name = "jobId") String jobId)
 			throws ResultNotAvailableException;
 
 }
diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 5c7a879..9da8abe 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -186,7 +186,7 @@ public class Jws2Client {
 	/**
 	 * Connects to a web service by the host and the service name
 	 * 
-	 * @param 
+	 * @param T
 	 *            web service type
 	 * @param host
 	 * @param service
diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index e77c878..a32533f 100644
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -58,7 +58,7 @@ public class AAConWS implements Annotation {
 	}
 
 	@Override
-	public HashSet getConservation(String jobId)
+	public HashSet getAnnotation(String jobId)
 			throws ResultNotAvailableException {
 		WSUtil.validateJobId(jobId);
 		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
diff --git a/website/dm_javadoc/allclasses-frame.html b/website/dm_javadoc/allclasses-frame.html
new file mode 100644
index 0000000..6024adb
--- /dev/null
+++ b/website/dm_javadoc/allclasses-frame.html
@@ -0,0 +1,111 @@
+
+
+
+
+
+
+All Classes
+
+
+
+
+
+
+
+
+
+
+
+All Classes
+

+
+
+
+
+
+
Alignment
+

+AlignmentMetadata
+

+AnnotatedSequence
+

+Annotation
+

+Argument
+

+ChunkHolder
+

+ClustalAlignmentUtil
+

+DisemblResultAnnot
+

+FastaSequence
+

+IOHelper
+

+JABAService
+

+JalviewAnnotation
+

+JManagement
+

+JobExecutionException
+

+JobStatus
+

+JobSubmissionException
+

+Jws2Client
+

+Limit
+

+LimitExceededException
+

+LimitsManager
+

+Metadata
+

+MetadataHelper
+

+Method
+

+MsaWS
+

+MultiAnnotatedSequence
+

+Option
+

+Parameter
+

+Preset
+

+PresetManager
+

+Program
+

+ResultNotAvailableException
+

+RunnerConfig
+

+Score
+

+SequenceUtil
+

+Services
+

+UnknownFileFormatException
+

+UnsupportedRuntimeException
+

+ValueConstrain
+

+ValueConstrain.Type
+

+WrongParameterException
+

+WSTester
+

+

+
+
+
diff --git a/website/dm_javadoc/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html
new file mode 100644
index 0000000..9143b81
--- /dev/null
+++ b/website/dm_javadoc/allclasses-noframe.html
@@ -0,0 +1,111 @@
+
+
+
+
+
+
+All Classes
+
+
+
+
+
+
+
+
+
+
+
+All Classes
+

+
+
+
+
+
+
Alignment
+

+AlignmentMetadata
+

+AnnotatedSequence
+

+Annotation
+

+Argument
+

+ChunkHolder
+

+ClustalAlignmentUtil
+

+DisemblResultAnnot
+

+FastaSequence
+

+IOHelper
+

+JABAService
+

+JalviewAnnotation
+

+JManagement
+

+JobExecutionException
+

+JobStatus
+

+JobSubmissionException
+

+Jws2Client
+

+Limit
+

+LimitExceededException
+

+LimitsManager
+

+Metadata
+

+MetadataHelper
+

+Method
+

+MsaWS
+

+MultiAnnotatedSequence
+

+Option
+

+Parameter
+

+Preset
+

+PresetManager
+

+Program
+

+ResultNotAvailableException
+

+RunnerConfig
+

+Score
+

+SequenceUtil
+

+Services
+

+UnknownFileFormatException
+

+UnsupportedRuntimeException
+

+ValueConstrain
+

+ValueConstrain.Type
+

+WrongParameterException
+

+WSTester
+

+

+
+
+
diff --git a/website/dm_javadoc/compbio/data/msa/Annotation.html b/website/dm_javadoc/compbio/data/msa/Annotation.html
new file mode 100644
index 0000000..bf86920
--- /dev/null
+++ b/website/dm_javadoc/compbio/data/msa/Annotation.html
@@ -0,0 +1,419 @@
+
+
+
+
+
+
+Annotation
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+
    Overview     Package   Class     Use     Tree     Deprecated     Index     Help 

+		
+
+

+ PREV CLASS 
+ NEXT CLASS
+  FRAMES   
+ NO FRAMES   
+ 
+
+
+
+

+  SUMMARY: NESTED | FIELD | CONSTR | METHOD
+DETAIL: FIELD | CONSTR | METHOD

+
+
+
+

+
+

+
+compbio.data.msa
+

+Interface Annotation<T>

+

+
Type Parameters:
T - executable type / web service type

+

+
All Superinterfaces: 
JABAService, JManagement, Metadata<T>

+

+

+

+
public interface Annotation<T>
extends JABAService, JManagement, Metadata<T>

+

+
+

+Interface for tools that results to one or more annotation to sequence(s)
+

+
+

+

+
Version:

+  
1.0 November 2010

+
Author:

+  
Peter Troshin

+

+

+
+

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+Method Summary

+ Stringanalize(List<FastaSequence> sequences)
+
+

+          Analyse the sequences.

+ StringcustomAnalize(List<FastaSequence> sequences,
+              List<Option<T>> options)
+
+

+          Analyse the sequences according to custom settings defined in options
+ list.

+ HashSet<Score>getAnnotation(String jobId)
+
+

+          Return the result of the job.

+ StringpresetAnalize(List<FastaSequence> sequences,
+              Preset<T> preset)
+
+

+          Analyse the sequences according to the preset settings.

+ 
+
+
+
+
+
+
+
+
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics

+ 
+
+
+
+
+
+
+
+
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions

+ 
+

+
+
+
+
+
+
+
+
+

+Method Detail

+
+

+analize

+
+String analize(List<FastaSequence> sequences)
+               throws UnsupportedRuntimeException,
+                      LimitExceededException,
+                      JobSubmissionException

+

+
Analyse the sequences. The actual analysis algorithm is defined by the
+ type T.
+ 
+ Any dataset containing a greater number of sequences or the average
+ length of the sequences are greater then defined in the default Limit
+ will not be accepted for an alignment operation and
+ JobSubmissionException will be thrown.
+

+

+

+

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform
+            any sequence validity checks. Nor does it checks whether the
+            sequences names are unique. It is responsibility of the caller
+            to validate this information
+
Returns:
jobId - unique identifier for the job
+
Throws:
+
JobSubmissionException - is thrown when the job could not be submitted due to the
+             following reasons: 1) The number of sequences in the
+             submission or their average length is greater then defined by
+             the default Limit. 2) Any problems on the server side e.g. it
+             is misconfigured or malfunction, is reported via this
+             exception. In the first case the information on the limit
+             could be obtained from an exception.
+
InvalidParameterException - thrown if input list of fasta sequence is null or empty
+
UnsupportedRuntimeException - thrown if server OS does not support native executables for a
+             given web service, e.g. JABAWS is deployed on Windows and
+             Mafft service is called
+
LimitExceededException - is throw if the input sequences number or average length
+             exceeds what is defined by the limit

+

+

+

+
+

+customAnalize

+
+String customAnalize(List<FastaSequence> sequences,
+                     List<Option<T>> options)
+                     throws UnsupportedRuntimeException,
+                            LimitExceededException,
+                            JobSubmissionException,
+                            WrongParameterException

+

+
Analyse the sequences according to custom settings defined in options
+ list. The actual analysis algorithm is defined by the type T. Default
+ Limit is used to decide whether the calculation will be permitted or
+ denied
+

+

+

+

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform
+            any sequence validity checks. Nor does it checks whether the
+            sequences names are unique. It is responsibility of the caller
+            to validate this information
options - A list of Options
+
Returns:
jobId - unique identifier for the job
+
Throws:
+
JobSubmissionException - is thrown when the job could not be submitted due to the
+             following reasons: 1) The number of sequences in the
+             submission or their average length is greater then defined by
+             the default Limit. 2) Any problems on the server side e.g. it
+             is misconfigured or malfunction, is reported via this
+             exception. In the first case the information on the limit
+             could be obtained from an exception.
+
WrongParameterException - is throws when 1) One of the Options provided is not
+             supported, 2) The value of the option is defined outside the
+             boundaries. In both cases exception object contain the
+             information on the violating Option.
+
InvalidParameterException - thrown if input list of fasta sequence is null or empty
+
UnsupportedRuntimeException - thrown if server OS does not support native executables for a
+             given web service, e.g. JABAWS is deployed on Windows and
+             Mafft service is called
+
LimitExceededException - is throw if the input sequences number or average length
+             exceeds what is defined by the limit
See Also:
Option

+

+

+

+
+

+presetAnalize

+
+String presetAnalize(List<FastaSequence> sequences,
+                     Preset<T> preset)
+                     throws UnsupportedRuntimeException,
+                            LimitExceededException,
+                            JobSubmissionException,
+                            WrongParameterException

+

+
Analyse the sequences according to the preset settings. The actual
+ analysis algorithm is defined by the type T.
+ 
+ Limit for a presetName is used whether the calculation will be permitted
+ or denied. If no Limit was defined for a presetName, than default limit
+ is used.
+

+

+

+

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform
+            any sequence validity checks. Nor does it checks whether the
+            sequences names are unique. It is responsibility of the caller
+            to validate this information
preset - A list of Options
+
Returns:
String - jobId - unique identifier for the job
+
Throws:
+
JobSubmissionException - is thrown when the job could not be submitted due to the
+             following reasons: 1) The number of sequences in the
+             submission or their average length is greater then defined by
+             the default Limit. 2) Any problems on the server side e.g. it
+             is misconfigured or malfunction, is reported via this
+             exception. In the first case the information on the limit
+             could be obtained from an exception.
+
WrongParameterException - is throws when 1) One of the Options provided is not
+             supported, 2) The value of the option is defined outside the
+             boundaries. In both cases exception object contain the
+             information on the violating Option.
+
InvalidParameterException - thrown if input list of fasta sequence is null or empty
+
UnsupportedRuntimeException - thrown if server OS does not support native executables for a
+             given web service, e.g. JABAWS is deployed on Windows and
+             Mafft service is called
+
LimitExceededException - is throw if the input sequences number or average length
+             exceeds what is defined by the limit

+

+

+

+
+

+getAnnotation

+
+HashSet<Score> getAnnotation(String jobId)
+                             throws ResultNotAvailableException

+

+
Return the result of the job.
+

+

+

+

+

+
Parameters:
jobId - a unique job identifier
+
Returns:
the HashSet of Score objects
+
Throws:
+
ResultNotAvailableException - this exception is throw if the job execution was not
+             successful or the result of the execution could not be found.
+             (e.g. removed). Exception could also be thrown is dues to the
+             lower level problems on the server i.e. IOException,
+             FileNotFoundException problems as well as
+             UnknownFileFormatException.
+
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in
+             invalid format

+

+

+
+

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+
    Overview     Package   Class     Use     Tree     Deprecated     Index     Help 

+		
+
+

+ PREV CLASS 
+ NEXT CLASS
+  FRAMES   
+ NO FRAMES   
+ 
+
+
+
+

+  SUMMARY: NESTED | FIELD | CONSTR | METHOD
+DETAIL: FIELD | CONSTR | METHOD

+
+
+
+

+
+
+
diff --git a/website/dm_javadoc/compbio/data/msa/JABAService.html b/website/dm_javadoc/compbio/data/msa/JABAService.html
new file mode 100644
index 0000000..03f6b80
--- /dev/null
+++ b/website/dm_javadoc/compbio/data/msa/JABAService.html
@@ -0,0 +1,179 @@
+
+
+
+
+
+
+JABAService
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+
    Overview     Package   Class     Use     Tree     Deprecated     Index     Help 

+		
+
+

+ PREV CLASS 
+ NEXT CLASS
+  FRAMES   
+ NO FRAMES   
+ 
+
+
+
+

+  SUMMARY: NESTED | FIELD | CONSTR | METHOD
+DETAIL: FIELD | CONSTR | METHOD

+
+
+
+

+
+

+
+compbio.data.msa
+

+Interface JABAService

+

+
All Known Subinterfaces: 
Annotation<T>, MsaWS<T>

+

+

+

+
public interface JABAService

+
+ +

+This is a marker interface, contains no methods +

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

+ +

+ +

+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/JManagement.html b/website/dm_javadoc/compbio/data/msa/JManagement.html new file mode 100644 index 0000000..b78648c --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/JManagement.html @@ -0,0 +1,272 @@ + + + + + + +JManagement + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.msa +
+Interface JManagement

+
+
All Known Subinterfaces:
Annotation<T>, MsaWS<T>
+
+
+
+
public interface JManagement
+ + +

+

+ +

+ + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleancancelJob(String jobId) + +
+          Stop running the job jobId but leave its output untouched
+ JobStatusgetJobStatus(String jobId) + +
+          Return the status of the job.
+ ChunkHolderpullExecStatistics(String jobId, + long position) + +
+          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
+  +

+ + + + + + + + +
+Method Detail
+ +

+cancelJob

+
+boolean cancelJob(String jobId)
+
+
Stop running the job jobId but leave its output untouched +

+

+ +
Returns:
true if job was cancelled successfully, false otherwise +
Throws: +
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
+
+
+
+ +

+getJobStatus

+
+JobStatus getJobStatus(String jobId)
+
+
Return the status of the job. +

+

+
Parameters:
jobId - - unique job identifier +
Returns:
JobStatus - status of the job +
Throws: +
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
See Also:
JobStatus
+
+
+
+ +

+pullExecStatistics

+
+ChunkHolder pullExecStatistics(String jobId,
+                               long position)
+
+
Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file. +

+

+
Parameters:
jobId - - unique job identifier
position - - next position within the file to read +
Returns:
ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read +
Throws: +
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format and also if the position value is negative
See Also:
ChunkHolder
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/Metadata.html b/website/dm_javadoc/compbio/data/msa/Metadata.html new file mode 100644 index 0000000..c028b24 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/Metadata.html @@ -0,0 +1,282 @@ + + + + + + +Metadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.msa +
+Interface Metadata<T>

+
+
All Known Subinterfaces:
Annotation<T>, MsaWS<T>
+
+
+
+
public interface Metadata<T>
+ + +

+

+ +

+ + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Limit<T>getLimit(String presetName) + +
+          Get a Limit for a preset.
+ LimitsManager<T>getLimits() + +
+          List Limits supported by a web service.
+ PresetManager<T>getPresets() + +
+          Get presets supported by a web service
+ RunnerConfig<T>getRunnerOptions() + +
+          Get options supported by a web service
+  +

+ + + + + + + + +
+Method Detail
+ +

+getRunnerOptions

+
+RunnerConfig<T> getRunnerOptions()
+
+
Get options supported by a web service +

+

+ +
Returns:
RunnerConfig the list of options and parameters supported by a + web service.
+
+
+
+ +

+getPresets

+
+PresetManager<T> getPresets()
+
+
Get presets supported by a web service +

+

+ +
Returns:
PresetManager the object contains information about presets + supported by a web service
+
+
+
+ +

+getLimit

+
+Limit<T> getLimit(String presetName)
+
+
Get a Limit for a preset. +

+

+
Parameters:
presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
Returns:
Limit
+
+
+
+ +

+getLimits

+
+LimitsManager<T> getLimits()
+
+
List Limits supported by a web service. +

+

+ +
Returns:
LimitManager
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..5f059e1 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,415 @@ + + + + + + +MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.msa +
+Interface MsaWS<T>

+
+
Type Parameters:
T - executable type / web service type
+
+
All Superinterfaces:
JABAService, JManagement, Metadata<T>
+
+
+
+
public interface MsaWS<T>
extends JABAService, JManagement, Metadata<T>
+ + +

+Multiple Sequence Alignment (MSA) Web Services Interface +

+ +

+

+
Author:
+
pvtroshin + + Date November 2010
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Stringalign(List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ StringcustomAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Align a list of sequences with options.
+ AlignmentgetResult(String jobId) + +
+          Return the result of the job.
+ StringpresetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
+  +

+ + + + + + + + +
+Method Detail
+ +

+align

+
+String align(List<FastaSequence> sequences)
+             throws UnsupportedRuntimeException,
+                    LimitExceededException,
+                    JobSubmissionException
+
+
Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

+

+
+
+
+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this +
Returns:
jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
InvalidParameterException - thrown if input list of FASTA sequences is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
+
+
+
+ +

+customAlign

+
+String customAlign(List<FastaSequence> sequences,
+                   List<Option<T>> options)
+                   throws UnsupportedRuntimeException,
+                          LimitExceededException,
+                          JobSubmissionException,
+                          WrongParameterException
+
+
Align a list of sequences with options. +

+

+
+
+
+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
options - A list of Options +
Returns:
jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
See Also:
Default Limit is used to decide whether the calculation will be + permitted or denied
+
+
+
+ +

+presetAlign

+
+String presetAlign(List<FastaSequence> sequences,
+                   Preset<T> preset)
+                   throws UnsupportedRuntimeException,
+                          LimitExceededException,
+                          JobSubmissionException,
+                          WrongParameterException
+
+
Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

+

+
+
+
+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
preset - A list of Options +
Returns:
String - jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
See Also:
Preset
+
+
+
+ +

+getResult

+
+Alignment getResult(String jobId)
+                    throws ResultNotAvailableException
+
+
Return the result of the job. This method waits for the job + jobId to complete before return. +

+

+
+
+
+
Parameters:
jobId - a unique job identifier +
Returns:
Alignment +
Throws: +
ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid + format
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/Annotation.html b/website/dm_javadoc/compbio/data/msa/class-use/Annotation.html new file mode 100644 index 0000000..45615ff --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/Annotation.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Interface compbio.data.msa.Annotation + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.Annotation

+
+No usage of compbio.data.msa.Annotation +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/JABAService.html b/website/dm_javadoc/compbio/data/msa/class-use/JABAService.html new file mode 100644 index 0000000..f2b185b --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/JABAService.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Interface compbio.data.msa.JABAService + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.JABAService

+
+ + + + + + + + + + + + + +
+Packages that use JABAService
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + +
+Uses of JABAService in compbio.data.msa
+  +

+ + + + + + + + + + + + + +
Subinterfaces of JABAService in compbio.data.msa
+ interfaceAnnotation<T> + +
+          Interface for tools that results to one or more annotation to sequence(s)
+ interfaceMsaWS<T> + +
+          Multiple Sequence Alignment (MSA) Web Services Interface
+  +

+ + + + + +
+Uses of JABAService in compbio.ws.client
+  +

+ + + + + + + + + +
Methods in compbio.ws.client that return JABAService
+static JABAServiceJws2Client.connect(String host, + Services service) + +
+          Connects to a web service by the host and the service name
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html b/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html new file mode 100644 index 0000000..d760285 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html @@ -0,0 +1,188 @@ + + + + + + +Uses of Interface compbio.data.msa.JManagement + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.JManagement

+
+ + + + + + + + + +
+Packages that use JManagement
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + +
+Uses of JManagement in compbio.data.msa
+  +

+ + + + + + + + + + + + + +
Subinterfaces of JManagement in compbio.data.msa
+ interfaceAnnotation<T> + +
+          Interface for tools that results to one or more annotation to sequence(s)
+ interfaceMsaWS<T> + +
+          Multiple Sequence Alignment (MSA) Web Services Interface
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html b/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html new file mode 100644 index 0000000..a2a2167 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html @@ -0,0 +1,188 @@ + + + + + + +Uses of Interface compbio.data.msa.Metadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.Metadata

+
+ + + + + + + + + +
+Packages that use Metadata
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + +
+Uses of Metadata in compbio.data.msa
+  +

+ + + + + + + + + + + + + +
Subinterfaces of Metadata in compbio.data.msa
+ interfaceAnnotation<T> + +
+          Interface for tools that results to one or more annotation to sequence(s)
+ interfaceMsaWS<T> + +
+          Multiple Sequence Alignment (MSA) Web Services Interface
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html new file mode 100644 index 0000000..f853c02 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Interface compbio.data.msa.MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.MsaWS

+
+No usage of compbio.data.msa.MsaWS +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-frame.html b/website/dm_javadoc/compbio/data/msa/package-frame.html new file mode 100644 index 0000000..e1ed1f7 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-frame.html @@ -0,0 +1,40 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + +compbio.data.msa + + + + +
+Interfaces  + +
+Annotation +
+JABAService +
+JManagement +
+Metadata +
+MsaWS
+ + + + diff --git a/website/dm_javadoc/compbio/data/msa/package-summary.html b/website/dm_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..ea2a21c --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,192 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+Package compbio.data.msa +

+Web Service interfaces for JAva Bioinformatics Analysis Web Services. +

+See: +
+          Description +

+ + + + + + + + + + + + + + + + + + + + + + + + + +
+Interface Summary
Annotation<T>Interface for tools that results to one or more annotation to sequence(s)
JABAServiceThis is a marker interface, contains no methods
JManagement 
Metadata<T> 
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
+  + +

+

+Package compbio.data.msa Description +

+ +

+Web Service interfaces for JAva Bioinformatics Analysis Web Services. +

+ +

+

+
Version:
+
1.0 April 2010
+
Author:
+
Peter Troshin
+
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-tree.html b/website/dm_javadoc/compbio/data/msa/package-tree.html new file mode 100644 index 0000000..4cea3c0 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-tree.html @@ -0,0 +1,163 @@ + + + + + + +compbio.data.msa Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Hierarchy For Package compbio.data.msa +

+
+
+
Package Hierarchies:
All Packages
+
+

+Interface Hierarchy +

+ +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-use.html b/website/dm_javadoc/compbio/data/msa/package-use.html new file mode 100644 index 0000000..65545a3 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-use.html @@ -0,0 +1,202 @@ + + + + + + +Uses of Package compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Package
compbio.data.msa

+
+ + + + + + + + + + + + + +
+Packages that use compbio.data.msa
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + + + + + + + + + + +
+Classes in compbio.data.msa used by compbio.data.msa
JABAService + +
+          This is a marker interface, contains no methods
JManagement + +
+           
Metadata + +
+           
+  +

+ + + + + + + + +
+Classes in compbio.data.msa used by compbio.ws.client
JABAService + +
+          This is a marker interface, contains no methods
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..3ac11c6 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,403 @@ + + + + + + +Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class Alignment

+
+java.lang.Object
+  extended by compbio.data.sequence.Alignment
+
+
+
+
@Immutable
+public final class Alignment
extends Object
+ + +

+Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. It does not guarantee neither the uniqueness of the names of + sequences nor it guarantees the uniqueness of the sequences. +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
See Also:
FastaSequence, +AlignmentMetadata
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+          Please note that this implementation does not take the order of sequences + into account!
+ AlignmentMetadatagetMetadata() + +
+           
+ List<FastaSequence>getSequences() + +
+           
+ intgetSize() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Alignment

+
+public Alignment(List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
+
+
+
Parameters:
sequences -
program -
gapchar -
+
+
+ +

+Alignment

+
+public Alignment(List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
+
+
+
Parameters:
sequences -
metadata -
+
+ + + + + + + + +
+Method Detail
+ +

+getSequences

+
+public List<FastaSequence> getSequences()
+
+
+ +
Returns:
list of FastaSequence records
+
+
+
+ +

+getSize

+
+public int getSize()
+
+
+ +
Returns:
a number of sequence in the alignment
+
+
+
+ +

+getMetadata

+
+public AlignmentMetadata getMetadata()
+
+
+ +
Returns:
AlignmentMetadata object
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
Please note that this implementation does not take the order of sequences + into account! +

+

+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..231bca9 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,329 @@ + + + + + + +AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class AlignmentMetadata

+
+java.lang.Object
+  extended by compbio.data.sequence.AlignmentMetadata
+
+
+
+
@Immutable
+public class AlignmentMetadata
extends Object
+ + +

+Alignment metadata e.g. method/program being used to generate the alignment + and its parameters +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
AlignmentMetadata(Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ chargetGapchar() + +
+           
+ ProgramgetProgram() + +
+           
+ inthashCode() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+AlignmentMetadata

+
+public AlignmentMetadata(Program program,
+                         char gapchar)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getProgram

+
+public Program getProgram()
+
+
+
+
+
+
+ +

+getGapchar

+
+public char getGapchar()
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/AnnotatedSequence.html b/website/dm_javadoc/compbio/data/sequence/AnnotatedSequence.html new file mode 100644 index 0000000..7d57ba0 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/AnnotatedSequence.html @@ -0,0 +1,351 @@ + + + + + + +AnnotatedSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class AnnotatedSequence

+
+java.lang.Object
+  extended by compbio.data.sequence.FastaSequence
+      extended by compbio.data.sequence.AnnotatedSequence
+
+
+
+
public class AnnotatedSequence
extends FastaSequence
+ + +

+

+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
AnnotatedSequence(FastaSequence fsequence, + float[] annotation) + +
+           
AnnotatedSequence(String id, + String sequence, + float[] annotation) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ float[]getAnnotation() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+          Same as oneLineFasta
+  + + + + + + + +
Methods inherited from class compbio.data.sequence.FastaSequence
countMatchesInSequence, getFormatedSequence, getFormattedFasta, getId, getLength, getOnelineFasta, getSequence
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+AnnotatedSequence

+
+public AnnotatedSequence(String id,
+                         String sequence,
+                         float[] annotation)
+
+
+
+ +

+AnnotatedSequence

+
+public AnnotatedSequence(FastaSequence fsequence,
+                         float[] annotation)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getAnnotation

+
+public float[] getAnnotation()
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class FastaSequence
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class FastaSequence
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
Description copied from class: FastaSequence
+
Same as oneLineFasta +

+

+
Overrides:
toString in class FastaSequence
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..62738e1 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,387 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class ClustalAlignmentUtil

+
+java.lang.Object
+  extended by compbio.data.sequence.ClustalAlignmentUtil
+
+
+
+
public final class ClustalAlignmentUtil
extends Object
+ + +

+Tools to read and write clustal formated files +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
Petr Troshin based on jimp class
+
+
+ +

+ + + + + + + + + + + +
+Field Summary
+static chargapchar + +
+          Dash char to be used as gap char in the alignments
+  + + + + + + + + + + +
+Constructor Summary
ClustalAlignmentUtil() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static booleanisValidClustalFile(InputStream input) + +
+          Please note this method closes the input stream provided as a parameter
+static AlignmentreadClustalFile(File file) + +
+           
+static AlignmentreadClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+static voidwriteClustalAlignment(OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+gapchar

+
+public static final char gapchar
+
+
Dash char to be used as gap char in the alignments +

+

+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+ClustalAlignmentUtil

+
+public ClustalAlignmentUtil()
+
+
+ + + + + + + + +
+Method Detail
+ +

+readClustalFile

+
+public static Alignment readClustalFile(InputStream instream)
+                                 throws IOException,
+                                        UnknownFileFormatException
+
+
Read Clustal formatted alignment. Limitations: Does not read consensus + + Sequence names as well as the sequences are not guaranteed to be unique! +

+

+ +
Throws: +
{@link - IOException} +
{@link - UnknownFileFormatException} +
IOException +
UnknownFileFormatException
+
+
+
+ +

+isValidClustalFile

+
+public static boolean isValidClustalFile(InputStream input)
+
+
Please note this method closes the input stream provided as a parameter +

+

+
Parameters:
input - +
Returns:
true if the file is recognised as Clustal formatted alignment, + false otherwise
+
+
+
+ +

+writeClustalAlignment

+
+public static void writeClustalAlignment(OutputStream outStream,
+                                         Alignment alignment)
+                                  throws IOException
+
+
Write Clustal formatted alignment Limitations: does not record the + consensus. Potential bug - records 60 chars length alignment where + Clustal would have recorded 50 chars. +

+

+
Parameters:
outStream -
alignment - +
Throws: +
IOException
+
+
+
+ +

+readClustalFile

+
+public static Alignment readClustalFile(File file)
+                                 throws UnknownFileFormatException,
+                                        IOException
+
+
+ +
Throws: +
UnknownFileFormatException +
IOException
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/DisemblResultAnnot.html b/website/dm_javadoc/compbio/data/sequence/DisemblResultAnnot.html new file mode 100644 index 0000000..61d9f9f --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/DisemblResultAnnot.html @@ -0,0 +1,338 @@ + + + + + + +DisemblResultAnnot + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Enum DisemblResultAnnot

+
+java.lang.Object
+  extended by java.lang.Enum<DisemblResultAnnot>
+      extended by compbio.data.sequence.DisemblResultAnnot
+
+
+
All Implemented Interfaces:
Serializable, Comparable<DisemblResultAnnot>
+
+
+
+
public enum DisemblResultAnnot
extends Enum<DisemblResultAnnot>
+ + +

+

+ +

+ + + + + + + + + + + + + + + + +
+Enum Constant Summary
COILS + +
+           
HOTLOOPS + +
+           
REM465 + +
+           
+  + + + + + + + + + + + + + + + +
+Method Summary
+static DisemblResultAnnotvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static DisemblResultAnnot[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+COILS

+
+public static final DisemblResultAnnot COILS
+
+
+
+
+
+ +

+REM465

+
+public static final DisemblResultAnnot REM465
+
+
+
+
+
+ +

+HOTLOOPS

+
+public static final DisemblResultAnnot HOTLOOPS
+
+
+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static DisemblResultAnnot[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (DisemblResultAnnot c : DisemblResultAnnot.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static DisemblResultAnnot valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..4147b34 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,474 @@ + + + + + + +FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class FastaSequence

+
+java.lang.Object
+  extended by compbio.data.sequence.FastaSequence
+
+
+
Direct Known Subclasses:
AnnotatedSequence
+
+
+
+
@Immutable
+public class FastaSequence
extends Object
+ + +

+A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it stores e.g. it could be nucleotide, + protein or even gapped alignment sequence! The only guarantee it makes is + that the sequence does not contain white space characters e.g. spaces, new + lines etc +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
FastaSequence(String id, + String sequence) + +
+          Upon construction the any whitespace characters are removed from the + sequence
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static intcountMatchesInSequence(String theString, + String theRegExp) + +
+           
+ booleanequals(Object obj) + +
+           
+ StringgetFormatedSequence(int width) + +
+          Format sequence per width letter in one string.
+ StringgetFormattedFasta() + +
+           
+ StringgetId() + +
+          Gets the value of id
+ intgetLength() + +
+           
+ StringgetOnelineFasta() + +
+           
+ StringgetSequence() + +
+          Gets the value of sequence
+ inthashCode() + +
+           
+ StringtoString() + +
+          Same as oneLineFasta
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+FastaSequence

+
+public FastaSequence(String id,
+                     String sequence)
+
+
Upon construction the any whitespace characters are removed from the + sequence +

+

+
Parameters:
id -
sequence -
+
+ + + + + + + + +
+Method Detail
+ +

+getId

+
+public String getId()
+
+
Gets the value of id +

+

+ +
Returns:
the value of id
+
+
+
+ +

+getSequence

+
+public String getSequence()
+
+
Gets the value of sequence +

+

+ +
Returns:
the value of sequence
+
+
+
+ +

+countMatchesInSequence

+
+public static int countMatchesInSequence(String theString,
+                                         String theRegExp)
+
+
+
+
+
+
+ +

+getFormattedFasta

+
+public String getFormattedFasta()
+
+
+
+
+
+
+ +

+getOnelineFasta

+
+public String getOnelineFasta()
+
+
+ +
Returns:
one line name, next line sequence, no matter what the sequence + length is
+
+
+
+ +

+getFormatedSequence

+
+public String getFormatedSequence(int width)
+
+
Format sequence per width letter in one string. Without spaces. +

+

+ +
Returns:
multiple line formated sequence, one line width letters length
+
+
+
+ +

+getLength

+
+public int getLength()
+
+
+ +
Returns:
sequence length
+
+
+
+ +

+toString

+
+public String toString()
+
+
Same as oneLineFasta +

+

+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/JalviewAnnotation.html b/website/dm_javadoc/compbio/data/sequence/JalviewAnnotation.html new file mode 100644 index 0000000..539bceb --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/JalviewAnnotation.html @@ -0,0 +1,224 @@ + + + + + + +JalviewAnnotation + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class JalviewAnnotation

+
+java.lang.Object
+  extended by compbio.data.sequence.JalviewAnnotation
+
+
+
+
public class JalviewAnnotation
extends Object
+ + +

+

+ +

+ + + + + + + + + + + +
+Constructor Summary
JalviewAnnotation() + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JalviewAnnotation

+
+public JalviewAnnotation()
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Method.html b/website/dm_javadoc/compbio/data/sequence/Method.html new file mode 100644 index 0000000..0ea97fa --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Method.html @@ -0,0 +1,605 @@ + + + + + + +Method + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Enum Method

+
+java.lang.Object
+  extended by java.lang.Enum<Method>
+      extended by compbio.data.sequence.Method
+
+
+
All Implemented Interfaces:
Serializable, Comparable<Method>
+
+
+
+
public enum Method
extends Enum<Method>
+ + +

+Enumeration listing of all the supported methods. +

+ +

+

+
Author:
+
Agnieszka Golicz & Peter Troshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Enum Constant Summary
ARMON + +
+           
GERSTEIN + +
+           
JORES + +
+           
KABAT + +
+           
KARLIN + +
+           
LANDGRAF + +
+           
MIRNY + +
+           
NOT_LANCET + +
+           
SANDER + +
+           
SCHNEIDER + +
+           
SHENKIN + +
+           
SMERFS + +
+           
TAYLOR_GAPS + +
+           
TAYLOR_NO_GAPS + +
+           
THOMPSON + +
+           
VALDAR + +
+           
WILLIAMSON + +
+           
ZVELIBIL + +
+           
+  + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static MethodgetMethod(String meth) + +
+           
+static MethodvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Method[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+KABAT

+
+public static final Method KABAT
+
+
+
+
+
+ +

+JORES

+
+public static final Method JORES
+
+
+
+
+
+ +

+SCHNEIDER

+
+public static final Method SCHNEIDER
+
+
+
+
+
+ +

+SHENKIN

+
+public static final Method SHENKIN
+
+
+
+
+
+ +

+GERSTEIN

+
+public static final Method GERSTEIN
+
+
+
+
+
+ +

+TAYLOR_GAPS

+
+public static final Method TAYLOR_GAPS
+
+
+
+
+
+ +

+TAYLOR_NO_GAPS

+
+public static final Method TAYLOR_NO_GAPS
+
+
+
+
+
+ +

+ZVELIBIL

+
+public static final Method ZVELIBIL
+
+
+
+
+
+ +

+KARLIN

+
+public static final Method KARLIN
+
+
+
+
+
+ +

+ARMON

+
+public static final Method ARMON
+
+
+
+
+
+ +

+THOMPSON

+
+public static final Method THOMPSON
+
+
+
+
+
+ +

+NOT_LANCET

+
+public static final Method NOT_LANCET
+
+
+
+
+
+ +

+MIRNY

+
+public static final Method MIRNY
+
+
+
+
+
+ +

+WILLIAMSON

+
+public static final Method WILLIAMSON
+
+
+
+
+
+ +

+LANDGRAF

+
+public static final Method LANDGRAF
+
+
+
+
+
+ +

+SANDER

+
+public static final Method SANDER
+
+
+
+
+
+ +

+VALDAR

+
+public static final Method VALDAR
+
+
+
+
+
+ +

+SMERFS

+
+public static final Method SMERFS
+
+
+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static Method[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (Method c : Method.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static Method valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+
+ +

+getMethod

+
+public static Method getMethod(String meth)
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/MultiAnnotatedSequence.html b/website/dm_javadoc/compbio/data/sequence/MultiAnnotatedSequence.html new file mode 100644 index 0000000..79ac315 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/MultiAnnotatedSequence.html @@ -0,0 +1,369 @@ + + + + + + +MultiAnnotatedSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class MultiAnnotatedSequence<T extends Enum<T>>

+
+java.lang.Object
+  extended by compbio.data.sequence.MultiAnnotatedSequence<T>
+
+
+
Type Parameters:
T - enum type
+
+
+
@NotThreadSafe
+public class MultiAnnotatedSequence<T extends Enum<T>>
extends Object
+ + +

+TODO complete +

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
MultiAnnotatedSequence(Class<T> enumeration) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ voidaddAnnotation(T type, + ArrayList<Float> annotation) + +
+           
+ booleanequals(Object obj) + +
+           
+ Map<T,List<Float>>getAnnotations() + +
+           
+ inthashCode() + +
+           
+ JalviewAnnotationtoJalviewAnnotation() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+MultiAnnotatedSequence

+
+public MultiAnnotatedSequence(Class<T> enumeration)
+
+
+ + + + + + + + +
+Method Detail
+ +

+addAnnotation

+
+public void addAnnotation(T type,
+                          ArrayList<Float> annotation)
+
+
+
+
+
+
+ +

+getAnnotations

+
+public Map<T,List<Float>> getAnnotations()
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+toJalviewAnnotation

+
+public JalviewAnnotation toJalviewAnnotation()
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..f1a55bf --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,388 @@ + + + + + + +Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Enum Program

+
+java.lang.Object
+  extended by java.lang.Enum<Program>
+      extended by compbio.data.sequence.Program
+
+
+
All Implemented Interfaces:
Serializable, Comparable<Program>
+
+
+
+
public enum Program
extends Enum<Program>
+ + +

+The list of programmes that can produce alignments +

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + +
+Enum Constant Summary
CLUSTAL + +
+          ClustalW
MAFFT + +
+          Mafft
MUSCLE + +
+          Muscle
Probcons + +
+          Probcons
Tcoffee + +
+          Tcoffee
+  + + + + + + + + + + + + + + + +
+Method Summary
+static ProgramvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Program[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+CLUSTAL

+
+public static final Program CLUSTAL
+
+
ClustalW +

+

+
+
+
+ +

+MAFFT

+
+public static final Program MAFFT
+
+
Mafft +

+

+
+
+
+ +

+MUSCLE

+
+public static final Program MUSCLE
+
+
Muscle +

+

+
+
+
+ +

+Tcoffee

+
+public static final Program Tcoffee
+
+
Tcoffee +

+

+
+
+
+ +

+Probcons

+
+public static final Program Probcons
+
+
Probcons +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static Program[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (Program c : Program.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static Program valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Score.html b/website/dm_javadoc/compbio/data/sequence/Score.html new file mode 100644 index 0000000..ceffe94 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Score.html @@ -0,0 +1,340 @@ + + + + + + +Score + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class Score

+
+java.lang.Object
+  extended by compbio.data.sequence.Score
+
+
+
+
@Immutable
+public class Score
extends Object
+ + +

+

+ +

+ + + + + + + + + + + +
+Constructor Summary
Score(Method method, + List<Float> scores) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ MethodgetMethod() + +
+           
+ List<Float>getScores() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Score

+
+public Score(Method method,
+             List<Float> scores)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getMethod

+
+public Method getMethod()
+
+
+
+
+
+
+ +

+getScores

+
+public List<Float> getScores()
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..1cd3c3a --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,755 @@ + + + + + + +SequenceUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class SequenceUtil

+
+java.lang.Object
+  extended by compbio.data.sequence.SequenceUtil
+
+
+
+
public final class SequenceUtil
extends Object
+ + +

+Utility class for operations on sequences +

+ +

+

+
Version:
+
1.0
+
Author:
+
Petr Troshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Field Summary
+static PatternAA + +
+          Valid Amino acids
+static PatternAMBIGUOUS_AA + +
+          Same as AA pattern but with two additional letters - XU
+static PatternAMBIGUOUS_NUCLEOTIDE + +
+          Ambiguous nucleotide
+static PatternDIGIT + +
+          A digit
+static PatternNON_AA + +
+          inversion of AA pattern
+static PatternNON_NUCLEOTIDE + +
+          Non nucleotide
+static PatternNONWORD + +
+          Non word
+static PatternNUCLEOTIDE + +
+          Nucleotides a, t, g, c, u
+static PatternWHITE_SPACE + +
+          A whitespace character: [\t\n\x0B\f\r]
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static StringcleanSequence(String sequence) + +
+          Removes all whitespace chars in the sequence string
+static voidcloseSilently(Logger log, + Closeable stream) + +
+          Closes the Closable and logs the exception if any
+static StringdeepCleanSequence(String sequence) + +
+          Removes all special characters and digits as well as whitespace chars + from the sequence
+static booleanisAmbiguosProtein(String sequence) + +
+          Check whether the sequence confirms to amboguous protein sequence
+static booleanisNonAmbNucleotideSequence(String sequence) + +
+          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
+static booleanisNucleotideSequence(FastaSequence s) + +
+           
+static booleanisProteinSequence(String sequence) + +
+           
+static HashSet<Score>readAAConResults(InputStream results) + +
+          Read AACon result with no alignment files.
+static List<FastaSequence>readFasta(InputStream inStream) + +
+          Reads fasta sequences from inStream into the list of FastaSequence + objects
+static List<AnnotatedSequence>readJRonn(File result) + +
+           
+static List<AnnotatedSequence>readJRonn(InputStream inStream) + +
+          Reader for JRonn horizontal file format
+static voidwriteFasta(OutputStream os, + List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidwriteFasta(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
+static voidwriteFastaKeepTheStream(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+WHITE_SPACE

+
+public static final Pattern WHITE_SPACE
+
+
A whitespace character: [\t\n\x0B\f\r] +

+

+
+
+
+ +

+DIGIT

+
+public static final Pattern DIGIT
+
+
A digit +

+

+
+
+
+ +

+NONWORD

+
+public static final Pattern NONWORD
+
+
Non word +

+

+
+
+
+ +

+AA

+
+public static final Pattern AA
+
+
Valid Amino acids +

+

+
+
+
+ +

+NON_AA

+
+public static final Pattern NON_AA
+
+
inversion of AA pattern +

+

+
+
+
+ +

+AMBIGUOUS_AA

+
+public static final Pattern AMBIGUOUS_AA
+
+
Same as AA pattern but with two additional letters - XU +

+

+
+
+
+ +

+NUCLEOTIDE

+
+public static final Pattern NUCLEOTIDE
+
+
Nucleotides a, t, g, c, u +

+

+
+
+
+ +

+AMBIGUOUS_NUCLEOTIDE

+
+public static final Pattern AMBIGUOUS_NUCLEOTIDE
+
+
Ambiguous nucleotide +

+

+
+
+
+ +

+NON_NUCLEOTIDE

+
+public static final Pattern NON_NUCLEOTIDE
+
+
Non nucleotide +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+isNucleotideSequence

+
+public static boolean isNucleotideSequence(FastaSequence s)
+
+
+ +
Returns:
true is the sequence contains only letters a,c, t, g, u
+
+
+
+ +

+isNonAmbNucleotideSequence

+
+public static boolean isNonAmbNucleotideSequence(String sequence)
+
+
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +

+

+
+
+
+
+ +

+cleanSequence

+
+public static String cleanSequence(String sequence)
+
+
Removes all whitespace chars in the sequence string +

+

+
Parameters:
sequence - +
Returns:
cleaned up sequence
+
+
+
+ +

+deepCleanSequence

+
+public static String deepCleanSequence(String sequence)
+
+
Removes all special characters and digits as well as whitespace chars + from the sequence +

+

+
Parameters:
sequence - +
Returns:
cleaned up sequence
+
+
+
+ +

+isProteinSequence

+
+public static boolean isProteinSequence(String sequence)
+
+
+
Parameters:
sequence - +
Returns:
true is the sequence is a protein sequence, false overwise
+
+
+
+ +

+isAmbiguosProtein

+
+public static boolean isAmbiguosProtein(String sequence)
+
+
Check whether the sequence confirms to amboguous protein sequence +

+

+
Parameters:
sequence - +
Returns:
return true only if the sequence if ambiguous protein sequence + Return false otherwise. e.g. if the sequence is non-ambiguous + protein or DNA
+
+
+
+ +

+writeFasta

+
+public static void writeFasta(OutputStream outstream,
+                              List<FastaSequence> sequences,
+                              int width)
+                       throws IOException
+
+
Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +

+

+
Parameters:
outstream -
sequences -
width - - the maximum number of characters to write in one line +
Throws: +
IOException
+
+
+
+ +

+writeFastaKeepTheStream

+
+public static void writeFastaKeepTheStream(OutputStream outstream,
+                                           List<FastaSequence> sequences,
+                                           int width)
+                                    throws IOException
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+readFasta

+
+public static List<FastaSequence> readFasta(InputStream inStream)
+                                     throws IOException
+
+
Reads fasta sequences from inStream into the list of FastaSequence + objects +

+

+
Parameters:
inStream - from +
Returns:
list of FastaSequence objects +
Throws: +
IOException
+
+
+
+ +

+writeFasta

+
+public static void writeFasta(OutputStream os,
+                              List<FastaSequence> sequences)
+                       throws IOException
+
+
Writes FastaSequence in the file, each sequence will take one line only +

+

+
Parameters:
os -
sequences - +
Throws: +
IOException
+
+
+
+ +

+readJRonn

+
+public static List<AnnotatedSequence> readJRonn(File result)
+                                         throws IOException,
+                                                UnknownFileFormatException
+
+
+ +
Throws: +
IOException +
UnknownFileFormatException
+
+
+
+ +

+readJRonn

+
+public static List<AnnotatedSequence> readJRonn(InputStream inStream)
+                                         throws IOException,
+                                                UnknownFileFormatException
+
+
Reader for JRonn horizontal file format + + 
+ >Foobar M G D T T A G 0.48 0.42
+ 0.42 0.48 0.52 0.53 0.54
+ 
+ 
+ Where all values are tab delimited
+

+

+
Parameters:
inStream - the InputStream connected to the JRonn output file
+
Returns:
List of AnnotatedSequence objects
+
Throws:
+
IOException - is thrown if the inStream has problems accessing the data
+
UnknownFileFormatException - is thrown if the inStream represents an unknown source of
+ data, i.e. not a JRonn output

+

+
+
+ +

+closeSilently

+
+public static final void closeSilently(Logger log,
+                                       Closeable stream)
+
+
Closes the Closable and logs the exception if any +

+

+
Parameters:
log -
stream -
+
+
+
+ +

+readAAConResults

+
+public static HashSet<Score> readAAConResults(InputStream results)
+
+
Read AACon result with no alignment files. This method leaves incoming + the InputStream results open! +

+

+
Parameters:
results - output file of AAConservation +
Returns:
Map with keys Method -> float[]
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..e3136e5 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,300 @@ + + + + + + +UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class UnknownFileFormatException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.data.sequence.UnknownFileFormatException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class UnknownFileFormatException
extends Exception
+ + +

+

+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + +
+Constructor Summary
UnknownFileFormatException() + +
+           
UnknownFileFormatException(File file, + Throwable cause) + +
+           
UnknownFileFormatException(String message) + +
+           
UnknownFileFormatException(String message, + Throwable cause) + +
+           
UnknownFileFormatException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException()
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(File file,
+                                  Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(String message,
+                                  Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(String message)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..05b6478 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,236 @@ + + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Alignment

+
+ + + + + + + + + + + + + +
+Packages that use Alignment
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Alignment in compbio.data.msa
+  +

+ + + + + + + + + +
Methods in compbio.data.msa that return Alignment
+ AlignmentMsaWS.getResult(String jobId) + +
+          Return the result of the job.
+  +

+ + + + + +
+Uses of Alignment in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Alignment
+static AlignmentClustalAlignmentUtil.readClustalFile(File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence with parameters of type Alignment
+static voidClustalAlignmentUtil.writeClustalAlignment(OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html new file mode 100644 index 0000000..288fa94 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html @@ -0,0 +1,196 @@ + + + + + + +Uses of Class compbio.data.sequence.AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.AlignmentMetadata

+
+ + + + + + + + + +
+Packages that use AlignmentMetadata
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of AlignmentMetadata in compbio.data.sequence
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence that return AlignmentMetadata
+ AlignmentMetadataAlignment.getMetadata() + +
+           
+  +

+ + + + + + + + +
Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AnnotatedSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/AnnotatedSequence.html new file mode 100644 index 0000000..18521f2 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/AnnotatedSequence.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data.sequence.AnnotatedSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.AnnotatedSequence

+
+ + + + + + + + + +
+Packages that use AnnotatedSequence
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of AnnotatedSequence in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type AnnotatedSequence
+static List<AnnotatedSequence>SequenceUtil.readJRonn(File result) + +
+           
+static List<AnnotatedSequence>SequenceUtil.readJRonn(InputStream inStream) + +
+          Reader for JRonn horizontal file format
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html new file mode 100644 index 0000000..60045ad --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

+
+No usage of compbio.data.sequence.ClustalAlignmentUtil +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/DisemblResultAnnot.html b/website/dm_javadoc/compbio/data/sequence/class-use/DisemblResultAnnot.html new file mode 100644 index 0000000..d7ffb00 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/DisemblResultAnnot.html @@ -0,0 +1,190 @@ + + + + + + +Uses of Class compbio.data.sequence.DisemblResultAnnot + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.DisemblResultAnnot

+
+ + + + + + + + + +
+Packages that use DisemblResultAnnot
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of DisemblResultAnnot in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return DisemblResultAnnot
+static DisemblResultAnnotDisemblResultAnnot.valueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static DisemblResultAnnot[]DisemblResultAnnot.values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..4664dc9 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,420 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.FastaSequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
+  +

+ + + + + +
+Uses of FastaSequence in compbio.data.msa
+  +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.msa with type arguments of type FastaSequence
+ StringMsaWS.align(List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ StringAnnotation.analize(List<FastaSequence> sequences) + +
+          Analyse the sequences.
+ StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Align a list of sequences with options.
+ StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Analyse the sequences according to custom settings defined in options + list.
+ StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+ StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Analyse the sequences according to the preset settings.
+  +

+ + + + + +
+Uses of FastaSequence in compbio.data.sequence
+  +

+ + + + + + + + + +
Subclasses of FastaSequence in compbio.data.sequence
+ classAnnotatedSequence + +
+           
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
+ List<FastaSequence>Alignment.getSequences() + +
+           
+static List<FastaSequence>SequenceUtil.readFasta(InputStream inStream) + +
+          Reads fasta sequences from inStream into the list of FastaSequence + objects
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence with parameters of type FastaSequence
+static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) + +
+           
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.sequence with type arguments of type FastaSequence
+static voidSequenceUtil.writeFasta(OutputStream os, + List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidSequenceUtil.writeFasta(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
+static voidSequenceUtil.writeFastaKeepTheStream(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+           
+  +

+ + + + + + + + +
Constructors in compbio.data.sequence with parameters of type FastaSequence
AnnotatedSequence(FastaSequence fsequence, + float[] annotation) + +
+           
+  +

+ + + + + + + + + + + +
Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  +

+ + + + + +
+Uses of FastaSequence in compbio.metadata
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.metadata with type arguments of type FastaSequence
+static intLimit.getAvgSequenceLength(List<FastaSequence> data) + +
+          Calculates an average sequence length of the dataset
+ booleanLimit.isExceeded(List<FastaSequence> data) + +
+          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
+static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/JalviewAnnotation.html b/website/dm_javadoc/compbio/data/sequence/class-use/JalviewAnnotation.html new file mode 100644 index 0000000..ebf4f70 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/JalviewAnnotation.html @@ -0,0 +1,181 @@ + + + + + + +Uses of Class compbio.data.sequence.JalviewAnnotation + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.JalviewAnnotation

+
+ + + + + + + + + +
+Packages that use JalviewAnnotation
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of JalviewAnnotation in compbio.data.sequence
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence that return JalviewAnnotation
+ JalviewAnnotationMultiAnnotatedSequence.toJalviewAnnotation() + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Method.html b/website/dm_javadoc/compbio/data/sequence/class-use/Method.html new file mode 100644 index 0000000..7a7be38 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Method.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Method + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Method

+
+ + + + + + + + + +
+Packages that use Method
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Method in compbio.data.sequence
+  +

+ + + + + + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Method
+ MethodScore.getMethod() + +
+           
+static MethodMethod.getMethod(String meth) + +
+           
+static MethodMethod.valueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Method[]Method.values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  +

+ + + + + + + + +
Constructors in compbio.data.sequence with parameters of type Method
Score(Method method, + List<Float> scores) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/MultiAnnotatedSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/MultiAnnotatedSequence.html new file mode 100644 index 0000000..fe1f667 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/MultiAnnotatedSequence.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.MultiAnnotatedSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.MultiAnnotatedSequence

+
+No usage of compbio.data.sequence.MultiAnnotatedSequence +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Program.html b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html new file mode 100644 index 0000000..52ca248 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Program

+
+ + + + + + + + + +
+Packages that use Program
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Program in compbio.data.sequence
+  +

+ + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Program
+ ProgramAlignmentMetadata.getProgram() + +
+           
+static ProgramProgram.valueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Program[]Program.values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  +

+ + + + + + + + + + + +
Constructors in compbio.data.sequence with parameters of type Program
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
AlignmentMetadata(Program program, + char gapchar) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Score.html b/website/dm_javadoc/compbio/data/sequence/class-use/Score.html new file mode 100644 index 0000000..1d7be0c --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Score.html @@ -0,0 +1,210 @@ + + + + + + +Uses of Class compbio.data.sequence.Score + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Score

+
+ + + + + + + + + + + + + +
+Packages that use Score
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Score in compbio.data.msa
+  +

+ + + + + + + + + +
Methods in compbio.data.msa that return types with arguments of type Score
+ HashSet<Score>Annotation.getAnnotation(String jobId) + +
+          Return the result of the job.
+  +

+ + + + + +
+Uses of Score in compbio.data.sequence
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type Score
+static HashSet<Score>SequenceUtil.readAAConResults(InputStream results) + +
+          Read AACon result with no alignment files.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..425273a --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.SequenceUtil

+
+No usage of compbio.data.sequence.SequenceUtil +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..8d8d77b --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,205 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.UnknownFileFormatException

+
+ + + + + + + + + +
+Packages that use UnknownFileFormatException
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of UnknownFileFormatException in compbio.data.sequence
+  +

+ + + + + + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that throw UnknownFileFormatException
+static AlignmentClustalAlignmentUtil.readClustalFile(File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+static List<AnnotatedSequence>SequenceUtil.readJRonn(File result) + +
+           
+static List<AnnotatedSequence>SequenceUtil.readJRonn(InputStream inStream) + +
+          Reader for JRonn horizontal file format
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-frame.html b/website/dm_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..206baf7 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,74 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + +compbio.data.sequence + + + + +
+Classes  + +
+Alignment +
+AlignmentMetadata +
+AnnotatedSequence +
+ClustalAlignmentUtil +
+FastaSequence +
+JalviewAnnotation +
+MultiAnnotatedSequence +
+Score +
+SequenceUtil
+ + + + + + +
+Enums  + +
+DisemblResultAnnot +
+Method +
+Program
+ + + + + + +
+Exceptions  + +
+UnknownFileFormatException
+ + + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-summary.html b/website/dm_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..993d80a --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,248 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+Package compbio.data.sequence +

+A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. +

+See: +
+          Description +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Class Summary
AlignmentMultiple sequence alignment.
AlignmentMetadataAlignment metadata e.g.
AnnotatedSequence 
ClustalAlignmentUtilTools to read and write clustal formated files
FastaSequenceA FASTA formatted sequence.
JalviewAnnotation 
MultiAnnotatedSequence<T extends Enum<T>>TODO complete
Score 
SequenceUtilUtility class for operations on sequences
+  + +

+ + + + + + + + + + + + + + + + + +
+Enum Summary
DisemblResultAnnot 
MethodEnumeration listing of all the supported methods.
ProgramThe list of programmes that can produce alignments
+  + +

+ + + + + + + + + +
+Exception Summary
UnknownFileFormatException 
+  + +

+

+Package compbio.data.sequence Description +

+ +

+A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services. +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
Petr Troshin
+
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-tree.html b/website/dm_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..9fbb608 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,170 @@ + + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Hierarchy For Package compbio.data.sequence +

+
+
+
Package Hierarchies:
All Packages
+
+

+Class Hierarchy +

+ +

+Enum Hierarchy +

+ +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-use.html b/website/dm_javadoc/compbio/data/sequence/package-use.html new file mode 100644 index 0000000..c6aacdc --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-use.html @@ -0,0 +1,276 @@ + + + + + + +Uses of Package compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Package
compbio.data.sequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use compbio.data.sequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
+  +

+ + + + + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.msa
Alignment + +
+          Multiple sequence alignment.
FastaSequence + +
+          A FASTA formatted sequence.
Score + +
+           
+  +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.sequence
Alignment + +
+          Multiple sequence alignment.
AlignmentMetadata + +
+          Alignment metadata e.g.
AnnotatedSequence + +
+           
DisemblResultAnnot + +
+           
FastaSequence + +
+          A FASTA formatted sequence.
JalviewAnnotation + +
+           
Method + +
+          Enumeration listing of all the supported methods.
Program + +
+          The list of programmes that can produce alignments
Score + +
+           
UnknownFileFormatException + +
+           
+  +

+ + + + + + + + +
+Classes in compbio.data.sequence used by compbio.metadata
FastaSequence + +
+          A FASTA formatted sequence.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Argument.html b/website/dm_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..1ac5610 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,327 @@ + + + + + + +Argument + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Interface Argument<T>

+
+
Type Parameters:
T - executable type
+
+
All Known Implementing Classes:
Option, Parameter
+
+
+
+
public interface Argument<T>
+ + +

+An unmodifiable view for the options and parameters, with one exception - it + allows to set a value +

+ +

+

+
Author:
+
pvtroshin + + Date December 2009
+
See Also:
Parameter, +Option
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ StringgetDefaultValue() + +
+           
+ StringgetDescription() + +
+           
+ URLgetFurtherDetails() + +
+           
+ StringgetName() + +
+           
+ List<String>getPossibleValues() + +
+           
+ voidsetValue(String defaultValue) + +
+          Set default values for the parameter or an option
+  +

+ + + + + + + + +
+Method Detail
+ +

+getFurtherDetails

+
+URL getFurtherDetails()
+
+
+
+
+
+
+ +

+getDefaultValue

+
+String getDefaultValue()
+
+
+
+
+
+
+ +

+getDescription

+
+String getDescription()
+
+
+
+
+
+
+ +

+getName

+
+String getName()
+
+
+
+
+
+
+ +

+getPossibleValues

+
+List<String> getPossibleValues()
+
+
+ +
Returns:
List of values allowed for an Argument
+
+
+
+ +

+setValue

+
+void setValue(String defaultValue)
+              throws WrongParameterException
+
+
Set default values for the parameter or an option +

+

+
Parameters:
defaultValue - the value to be set +
Throws: +
WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
See Also:
ValueConstrain
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..13f176d --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,350 @@ + + + + + + +ChunkHolder + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class ChunkHolder

+
+java.lang.Object
+  extended by compbio.metadata.ChunkHolder
+
+
+
+
public class ChunkHolder
extends Object
+ + +

+Represents a chunk of a string data together with the position in a file for + the next read operation. +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
ChunkHolder(String chunk, + long position) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ StringgetChunk() + +
+           
+ longgetNextPosition() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ChunkHolder

+
+public ChunkHolder(String chunk,
+                   long position)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getChunk

+
+public String getChunk()
+
+
+
+
+
+
+ +

+getNextPosition

+
+public long getNextPosition()
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..cdd30d6 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,279 @@ + + + + + + +JobExecutionException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class JobExecutionException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobExecutionException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class JobExecutionException
extends Exception
+ + +

+JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
JobExecutionException(String message) + +
+           
JobExecutionException(String message, + Throwable cause) + +
+           
JobExecutionException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobExecutionException

+
+public JobExecutionException(String message)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(Throwable cause)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(String message,
+                             Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..c7d67aa --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,465 @@ + + + + + + +JobStatus + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Enum JobStatus

+
+java.lang.Object
+  extended by java.lang.Enum<JobStatus>
+      extended by compbio.metadata.JobStatus
+
+
+
All Implemented Interfaces:
Serializable, Comparable<JobStatus>
+
+
+
+
public enum JobStatus
extends Enum<JobStatus>
+ + +

+The status of the job. +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Enum Constant Summary
CANCELLED + +
+          Jobs that has been cancelled
COLLECTED + +
+          Results has been collected
FAILED + +
+          Failed jobs
FINISHED + +
+          Finished jobs
PENDING + +
+          Jobs which are in the queue and awaiting execution reported for cluster + jobs only
RUNNING + +
+          Jobs that are running
STARTED + +
+          Job calculation has been started.
SUBMITTED + +
+          Job has been submitted.
UNDEFINED + +
+          Represents jobs with unknown status
+  + + + + + + + + + + + + + + + +
+Method Summary
+static JobStatusvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static JobStatus[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+PENDING

+
+public static final JobStatus PENDING
+
+
Jobs which are in the queue and awaiting execution reported for cluster + jobs only +

+

+
+
+
+ +

+RUNNING

+
+public static final JobStatus RUNNING
+
+
Jobs that are running +

+

+
+
+
+ +

+CANCELLED

+
+public static final JobStatus CANCELLED
+
+
Jobs that has been cancelled +

+

+
+
+
+ +

+FINISHED

+
+public static final JobStatus FINISHED
+
+
Finished jobs +

+

+
+
+
+ +

+FAILED

+
+public static final JobStatus FAILED
+
+
Failed jobs +

+

+
+
+
+ +

+UNDEFINED

+
+public static final JobStatus UNDEFINED
+
+
Represents jobs with unknown status +

+

+
+
+
+ +

+STARTED

+
+public static final JobStatus STARTED
+
+
Job calculation has been started. First status reported by the local + engine +

+

+
+
+
+ +

+SUBMITTED

+
+public static final JobStatus SUBMITTED
+
+
Job has been submitted. This status is only set for cluster jobs +

+

+
+
+
+ +

+COLLECTED

+
+public static final JobStatus COLLECTED
+
+
Results has been collected +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static JobStatus[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (JobStatus c : JobStatus.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static JobStatus valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..93688e0 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,283 @@ + + + + + + +JobSubmissionException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class JobSubmissionException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
+
+
+
+
public class JobSubmissionException
extends Exception
+ + +

+Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException. If + this exception is thrown the task has not been calculated +

+ +

+

+
Author:
+
pvtroshin + + Date December 2009
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
JobSubmissionException(String message) + +
+           
JobSubmissionException(String message, + Throwable cause) + +
+           
JobSubmissionException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobSubmissionException

+
+public JobSubmissionException(String message)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(Throwable cause)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(String message,
+                              Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..537f064 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,478 @@ + + + + + + +Limit + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Limit<T>

+
+java.lang.Object
+  extended by compbio.metadata.Limit<T>
+
+
+
Type Parameters:
T - the type of an executable for which this limit is defined.
+
+
+
public class Limit<T>
extends Object
+ + +

+A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. Also contains static method for determining the + number of sequence and their average length in the List +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
pvtroshin
+
See Also:
LimitsManager
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Limit(int seqNumber, + int seqLength, + String preset) + +
+          Instantiate the limit
Limit(int seqNumber, + int seqLength, + String preset, + boolean isDefault) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ intgetAvgSeqLength() + +
+           
+static intgetAvgSequenceLength(List<FastaSequence> data) + +
+          Calculates an average sequence length of the dataset
+ StringgetPreset() + +
+           
+ intgetSeqNumber() + +
+           
+ inthashCode() + +
+           
+ booleanisDefault() + +
+           
+ booleanisExceeded(List<FastaSequence> data) + +
+          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             String preset)
+
+
Instantiate the limit +

+

+
Parameters:
seqNumber - the maximum number of sequences allowed for calculation. + Required
seqLength - the average length of the sequence, optional
preset - the name of preset if any, optional +
Throws: +
IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
+
+
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             String preset,
+             boolean isDefault)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPreset

+
+public String getPreset()
+
+
+
+
+
+
+ +

+getAvgSeqLength

+
+public int getAvgSeqLength()
+
+
+ +
Returns:
the allowed average sequence length
+
+
+
+ +

+getSeqNumber

+
+public int getSeqNumber()
+
+
+ +
Returns:
the maximum number of sequences allowed
+
+
+
+ +

+isDefault

+
+public boolean isDefault()
+
+
+ +
Returns:
true is this is a default limit to be used, false otherwise
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+isExceeded

+
+public boolean isExceeded(List<FastaSequence> data)
+
+
Checks if the number of sequences or their average length in the dataset + exceeds this limit. +

+

+
Parameters:
data - the dataset to measure +
Returns:
true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise. First check the number of sequences + in the dataset and if it exceeds the limit return true + irrespective of the average length. If the number of sequences in + the dataset is less than the limit and average length is defined, + then check whether the total number of letters (number of + sequence multiplied by the average sequence length) is greater + then the total number of letters in the dataset. Returns true if + the total number of letters in the dataset is greater than the + limit, false otherwise.
+
+
+
+ +

+getAvgSequenceLength

+
+public static int getAvgSequenceLength(List<FastaSequence> data)
+
+
Calculates an average sequence length of the dataset +

+

+
Parameters:
data - +
Returns:
an average sequence length in the input dataset
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..8006005 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,357 @@ + + + + + + +LimitExceededException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class LimitExceededException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.LimitExceededException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class LimitExceededException
extends JobSubmissionException
+ + +

+This exception is thrown if the task larger in size that the limit that + applies to the calculation. +

+ +

+

+
Version:
+
1.0 February 2010
+
Author:
+
pvtroshin
+
See Also:
Limit, +Serialized Form
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
LimitExceededException(String message) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ intgetActualNumberofSequences() + +
+           
+ intgetNumberOfSequencesAllowed() + +
+           
+ intgetSequenceLenghtActual() + +
+           
+ intgetSequenceLenghtAllowed() + +
+           
+static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitExceededException

+
+public LimitExceededException(String message)
+
+
+ + + + + + + + +
+Method Detail
+ +

+newLimitExceeded

+
+public static LimitExceededException newLimitExceeded(Limit<?> limit,
+                                                      List<FastaSequence> seqs)
+
+
+
+
+
+
+ +

+getNumberOfSequencesAllowed

+
+public int getNumberOfSequencesAllowed()
+
+
+
+
+
+
+ +

+getActualNumberofSequences

+
+public int getActualNumberofSequences()
+
+
+
+
+
+
+ +

+getSequenceLenghtAllowed

+
+public int getSequenceLenghtAllowed()
+
+
+
+
+
+
+ +

+getSequenceLenghtActual

+
+public int getSequenceLenghtActual()
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..2bb5171 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,363 @@ + + + + + + +LimitsManager + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class LimitsManager<T>

+
+java.lang.Object
+  extended by compbio.metadata.LimitsManager<T>
+
+
+
Type Parameters:
T - executable type
+
+
+
public class LimitsManager<T>
extends Object
+ + +

+A collection of Limits +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
pvtroshin
+
See Also:
Limit
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
LimitsManager() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Limit<T>getDefaultLimit() + +
+           
+ Limit<T>getLimitByName(String presetName) + +
+           
+ List<Limit<T>>getLimits() + +
+           
+ StringtoString() + +
+           
+ voidvalidate(PresetManager<T> presets) + +
+          Validate Limits
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitsManager

+
+public LimitsManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getLimits

+
+public List<Limit<T>> getLimits()
+
+
+ +
Returns:
all limits defined for an executable T
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+getLimitByName

+
+public Limit<T> getLimitByName(String presetName)
+
+
+
Parameters:
presetName - +
Returns:
Limit defined for the executable T and presetName. If no limit is + defined for the presetName then default Limit is returned. If + presetName is empty or null than the default Limit will be + returned. If not limit defined for the type T than NULL will be + returned
+
+
+
+ +

+getDefaultLimit

+
+public Limit<T> getDefaultLimit()
+
+
+ +
Returns:
the default Limit for an executable type T
+
+
+
+ +

+validate

+
+public void validate(PresetManager<T> presets)
+              throws ValidationException
+
+
Validate Limits +

+

+
Parameters:
presets - +
Throws: +
ValidationException - if any of the Limit defined is found to be invalid. That is + when + + 1) No default limit is defined + + 2) More than 1 default limit is defined + + 3) Limit's preset name does not match any presets for type T
See Also:
Limit, +Preset
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..2eaf582 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Option.html @@ -0,0 +1,714 @@ + + + + + + +Option + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Option<T>

+
+java.lang.Object
+  extended by compbio.metadata.Option<T>
+
+
+
Type Parameters:
T - type of executable
+
+
All Implemented Interfaces:
Argument<T>
+
+
+
Direct Known Subclasses:
Parameter
+
+
+
+
public class Option<T>
extends Object
implements Argument<T>
+ + +

+Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
Option(String name, + String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Set<String>addOptionNames(String... value) + +
+          Adds an option to the optionName list
+ booleanequals(Object obj) + +
+           
+ StringgetDefaultValue() + +
+          A default value of the option.
+ StringgetDescription() + +
+          A long description of the Option
+ URLgetFurtherDetails() + +
+          The URL where further details about the option can be found
+ StringgetName() + +
+          Human readable name of the option
+ List<String>getOptionNames() + +
+           
+ List<String>getPossibleValues() + +
+          List of possible optionNames
+ inthashCode() + +
+           
+ booleanisRequired() + +
+          Flag that indicated that this option must be specified in the command + line for an executable to run
+ voidsetDefaultValue(String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetDescription(String description) + +
+           
+ voidsetFurtherDetails(URL furtherDetails) + +
+           
+ voidsetName(String name) + +
+           
+ voidsetOptionNames(Set<String> optionNames) + +
+           
+ voidsetRequired(boolean isRequired) + +
+           
+ voidsetValue(String dValue) + +
+          Set default values for the parameter or an option
+ StringtoCommand(String nameValueSeparator) + +
+          Convert the option to the command string.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Option

+
+public Option(String name,
+              String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getName

+
+public String getName()
+
+
Human readable name of the option +

+

+
Specified by:
getName in interface Argument<T>
+
+
+
+
+
+
+ +

+setName

+
+public void setName(String name)
+
+
+
+
+
+
+
+
+
+ +

+getDescription

+
+public String getDescription()
+
+
A long description of the Option +

+

+
Specified by:
getDescription in interface Argument<T>
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(String description)
+
+
+
+
+
+
+
+
+
+ +

+getFurtherDetails

+
+public URL getFurtherDetails()
+
+
The URL where further details about the option can be found +

+

+
Specified by:
getFurtherDetails in interface Argument<T>
+
+
+
+
+
+
+ +

+setFurtherDetails

+
+public void setFurtherDetails(URL furtherDetails)
+
+
+
+
+
+
+
+
+
+ +

+getDefaultValue

+
+public String getDefaultValue()
+
+
A default value of the option. Defaults to command line argument name + e.g. -auto +

+

+
Specified by:
getDefaultValue in interface Argument<T>
+
+
+
+
+
+
+ +

+setDefaultValue

+
+public void setDefaultValue(String defaultVal)
+                     throws WrongParameterException
+
+
Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

+

+
+
+
+
Parameters:
defaultVal - +
Throws: +
WrongParameterException - is thrown if the defaultValue is not found in optionList
+
+
+
+ +

+isRequired

+
+public boolean isRequired()
+
+
Flag that indicated that this option must be specified in the command + line for an executable to run +

+

+
+
+
+ +
Returns:
true is the option is required, false otherwise
+
+
+
+ +

+setRequired

+
+public void setRequired(boolean isRequired)
+
+
+
+
+
+
+
+
+
+ +

+getOptionNames

+
+public List<String> getOptionNames()
+
+
+
+
+
+ +
Returns:
List of option names
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(Set<String> optionNames)
+
+
+
+
+
+
+
+
+
+ +

+addOptionNames

+
+public Set<String> addOptionNames(String... value)
+
+
Adds an option to the optionName list +

+

+
+
+
+
Parameters:
value - +
Returns:
modified optionName list
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+toCommand

+
+public String toCommand(String nameValueSeparator)
+
+
Convert the option to the command string. +

+

+
+
+
+ +
Returns:
If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public List<String> getPossibleValues()
+
+
List of possible optionNames +

+

+
Specified by:
getPossibleValues in interface Argument<T>
+
+
+ +
Returns:
List of values allowed for an Argument
+
+
+
+ +

+setValue

+
+public void setValue(String dValue)
+              throws WrongParameterException
+
+
Description copied from interface: Argument
+
Set default values for the parameter or an option +

+

+
Specified by:
setValue in interface Argument<T>
+
+
+
Parameters:
dValue - the value to be set +
Throws: +
WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
See Also:
ValueConstrain
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..a863ed3 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,572 @@ + + + + + + +Parameter + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Parameter<T>

+
+java.lang.Object
+  extended by compbio.metadata.Option<T>
+      extended by compbio.metadata.Parameter<T>
+
+
+
All Implemented Interfaces:
Argument<T>
+
+
+
+
public class Parameter<T>
extends Option<T>
+ + +

+A single value containing an option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues +

+ +

+

+
Version:
+
1.0 November 2009
+
Author:
+
pvtroshin
+
See Also:
Option, +Argument
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
Parameter(String name, + String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Set<String>addOptionNames(String... value) + +
+          Adds an option to the optionName list
+ Set<String>addPossibleValues(String... value) + +
+           
+ booleanequals(Object obj) + +
+           
+ StringgetOptionName() + +
+           
+ List<String>getPossibleValues() + +
+          List is more convenient to work with
+ ValueConstraingetValidValue() + +
+           
+ inthashCode() + +
+           
+ voidsetDefaultValue(String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetOptionName(String optionName) + +
+           
+ voidsetOptionNames(Set<String> optionName) + +
+           
+ voidsetPossibleValues(Set<String> possibleValues) + +
+           
+ voidsetValidValue(ValueConstrain validValue) + +
+           
+ StringtoCommand(String nameValueSeparator) + +
+          Convert the option to the command string.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class compbio.metadata.Option
getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Parameter

+
+public Parameter(String name,
+                 String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getValidValue

+
+public ValueConstrain getValidValue()
+
+
+
+
+
+
+ +

+setValidValue

+
+public void setValidValue(ValueConstrain validValue)
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Option<T>
+
+
+
+
+
+
+ +

+toCommand

+
+public String toCommand(String nameValueSeparator)
+
+
Description copied from class: Option
+
Convert the option to the command string. +

+

+
Overrides:
toCommand in class Option<T>
+
+
+ +
Returns:
If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Option<T>
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public List<String> getPossibleValues()
+
+
List is more convenient to work with +

+

+
Specified by:
getPossibleValues in interface Argument<T>
Overrides:
getPossibleValues in class Option<T>
+
+
+ +
Returns:
List of String
+
+
+
+ +

+setPossibleValues

+
+public void setPossibleValues(Set<String> possibleValues)
+
+
+
+
+
+
+ +

+addPossibleValues

+
+public Set<String> addPossibleValues(String... value)
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Option<T>
+
+
+
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(Set<String> optionName)
+
+
+
Overrides:
setOptionNames in class Option<T>
+
+
+
+
+
+
+ +

+addOptionNames

+
+public Set<String> addOptionNames(String... value)
+
+
Description copied from class: Option
+
Adds an option to the optionName list +

+

+
Overrides:
addOptionNames in class Option<T>
+
+
+ +
Returns:
modified optionName list
+
+
+
+ +

+getOptionName

+
+public String getOptionName()
+
+
+
+
+
+
+ +

+setOptionName

+
+public void setOptionName(String optionName)
+
+
+
+
+
+
+ +

+setDefaultValue

+
+public void setDefaultValue(String defaultVal)
+                     throws WrongParameterException
+
+
Description copied from class: Option
+
Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

+

+
Overrides:
setDefaultValue in class Option<T>
+
+
+ +
Throws: +
WrongParameterException - is thrown if the defaultValue is not found in optionList
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..3951f2c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,455 @@ + + + + + + +Preset + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Preset<T>

+
+java.lang.Object
+  extended by compbio.metadata.Preset<T>
+
+
+
Type Parameters:
T - executable type
+
+
+
public class Preset<T>
extends Object
+ + +

+Collection of Options and Parameters with their values +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
See Also:
Option, +Parameter
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
Preset() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ List<Option<T>>getArguments(RunnerConfig<T> rconfig) + +
+          Converts list of options as String to type Option
+ StringgetDescription() + +
+           
+ StringgetName() + +
+           
+ List<String>getOptions() + +
+           
+ inthashCode() + +
+           
+ voidsetDescription(String description) + +
+           
+ voidsetName(String name) + +
+           
+ voidsetOptions(List<String> option) + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Preset

+
+public Preset()
+
+
+ + + + + + + + +
+Method Detail
+ +

+setOptions

+
+public void setOptions(List<String> option)
+
+
+
+
+
+
+ +

+setName

+
+public void setName(String name)
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(String description)
+
+
+
+
+
+
+ +

+getOptions

+
+public List<String> getOptions()
+
+
+ +
Returns:
a List of Options as a String
+
+
+
+ +

+getName

+
+public String getName()
+
+
+ +
Returns:
- name of the Preset
+
+
+
+ +

+getDescription

+
+public String getDescription()
+
+
+ +
Returns:
- a long description of the Preset
+
+
+
+ +

+getArguments

+
+public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
+                             throws WrongParameterException
+
+
Converts list of options as String to type Option +

+

+
Parameters:
rconfig - +
Returns:
List of Options +
Throws: +
WrongParameterException - if the value of the parameter is invalid @see + Parameter
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..d0c21c7 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,428 @@ + + + + + + +PresetManager + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class PresetManager<T>

+
+java.lang.Object
+  extended by compbio.metadata.PresetManager<T>
+
+
+
Type Parameters:
T - type of executable.
+
+
+
public class PresetManager<T>
extends Object
+ + +

+Collection of presets and methods to manipulate them @see Preset +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Field Summary
+static StringLOCAL_ENGINE_LIMIT_PRESET + +
+           
+  + + + + + + + + + + +
+Constructor Summary
PresetManager() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Preset<T>getPresetByName(String presetName) + +
+           
+ List<Preset<T>>getPresets() + +
+           
+ StringgetRunnerClassName() + +
+           
+ voidsetPresets(List<Preset<T>> presets) + +
+           
+ voidsetRunnerClassName(String runnerClassName) + +
+           
+ StringtoString() + +
+           
+ voidvalidate(RunnerConfig<T> options) + +
+          Checks whether preset option and parameter are defined in RunnerConfig + object.
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+LOCAL_ENGINE_LIMIT_PRESET

+
+public static final String LOCAL_ENGINE_LIMIT_PRESET
+
+
+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+PresetManager

+
+public PresetManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPresets

+
+public List<Preset<T>> getPresets()
+
+
+
+
+
+
+ +

+setPresets

+
+public void setPresets(List<Preset<T>> presets)
+
+
+
+
+
+
+ +

+getRunnerClassName

+
+public String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name of type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(String runnerClassName)
+
+
+
+
+
+
+ +

+getPresetByName

+
+public Preset<T> getPresetByName(String presetName)
+
+
+
Parameters:
presetName - +
Returns:
preset by its name, null if no preset found
+
+
+
+ +

+validate

+
+public void validate(RunnerConfig<T> options)
+              throws ValidationException
+
+
Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly! +

+

+ +
Throws: +
ValidationException - if preset is found to be invalid.
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..6d42c1e --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,280 @@ + + + + + + +ResultNotAvailableException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class ResultNotAvailableException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.ResultNotAvailableException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class ResultNotAvailableException
extends Exception
+ + +

+ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides lower level exceptions + like DrmaaException +

+ +

+

+
Author:
+
pvtroshin + + Date October 2009
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
ResultNotAvailableException(String message) + +
+           
ResultNotAvailableException(String message, + Throwable cause) + +
+           
ResultNotAvailableException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(String message)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(Throwable cause)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(String message,
+                                   Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..01c7b2c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,706 @@ + + + + + + +RunnerConfig + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class RunnerConfig<T>

+
+java.lang.Object
+  extended by compbio.metadata.RunnerConfig<T>
+
+
+
Type Parameters:
T - type of an Executable
+
+
+
@NotThreadSafe
+public class RunnerConfig<T>
extends Object
+ + +

+The list of Parameters and Options supported by executable. + The lists is defined in and loaded from Parameters.xml file. +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
RunnerConfig() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ voidaddOption(Option<T> option) + +
+          Adds Option to the internal list of options
+ voidaddParameter(Parameter<T> param) + +
+          Adds parameter to the internal parameter list
+ RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
+           
+ booleanequals(Object obj) + +
+           
+ Option<T>getArgument(String name) + +
+          Returns the argument by its name if found, NULL otherwise.
+ Option<T>getArgumentByOptionName(String optionName) + +
+          Returns the argument by option name, NULL if the argument is not found
+ List<Option<T>>getArguments() + +
+          Returns list of Parameter and Option supported by current + runner
+ List<Option<T>>getOptions() + +
+          Returns the list of the Options supported by the executable of type T
+ List<Parameter<T>>getParameters() + +
+          Returns the list of parameters supported executable of type T.
+ StringgetPrmSeparator() + +
+           
+ StringgetRunnerClassName() + +
+           
+ booleanremoveArgument(String name) + +
+          Removes the argument Argument if found.
+ booleanremoveArgumentByOptionName(String optionName) + +
+          Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
+ voidsetOptions(List<Option<T>> parameters) + +
+          Adds the list of options or parameters to the internal list of options
+ voidsetParameters(List<Parameter<T>> parameters) + +
+          Sets the list of parameters as internal list
+ voidsetPrmSeparator(String prmSeparator) + +
+          Sets name value separator character
+ voidsetRunnerClassName(String runnerClassName) + +
+          Set the name of a runner class
+ StringtoString() + +
+           
+ voidvalidate() + +
+          Validate the value of the argument.
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+RunnerConfig

+
+public RunnerConfig()
+
+
+ + + + + + + + +
+Method Detail
+ +

+copyAndValidateRConfig

+
+public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
+
+
+
+
+
+
+ +

+getOptions

+
+public List<Option<T>> getOptions()
+
+
Returns the list of the Options supported by the executable of type T +

+

+ +
Returns:
list of Option supported by type T
See Also:
Option
+
+
+
+ +

+addParameter

+
+public void addParameter(Parameter<T> param)
+
+
Adds parameter to the internal parameter list +

+

+
Parameters:
param - the Parameter to add
See Also:
Parameter
+
+
+
+ +

+addOption

+
+public void addOption(Option<T> option)
+
+
Adds Option to the internal list of options +

+

+
Parameters:
option - the Option to add
+
+
+
+ +

+getArguments

+
+public List<Option<T>> getArguments()
+
+
Returns list of Parameter and Option supported by current + runner +

+

+ +
Returns:
list of Option and Parameter supported by type T
+
+
+
+ +

+getPrmSeparator

+
+public String getPrmSeparator()
+
+
+ +
Returns:
name value separator character
+
+
+
+ +

+setPrmSeparator

+
+public void setPrmSeparator(String prmSeparator)
+
+
Sets name value separator character +

+

+
Parameters:
prmSeparator - the separator char
+
+
+
+ +

+setOptions

+
+public void setOptions(List<Option<T>> parameters)
+
+
Adds the list of options or parameters to the internal list of options +

+

+
Parameters:
parameters - the list of parameters to add
+
+
+
+ +

+getRunnerClassName

+
+public String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name for type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(String runnerClassName)
+
+
Set the name of a runner class +

+

+
Parameters:
runnerClassName - the name of the executable wrapping class
+
+
+
+ +

+setParameters

+
+public void setParameters(List<Parameter<T>> parameters)
+
+
Sets the list of parameters as internal list +

+

+
Parameters:
parameters - the list of parameters
+
+
+
+ +

+getParameters

+
+public List<Parameter<T>> getParameters()
+
+
Returns the list of parameters supported executable of type T. Where + Parameter is an Option with value. +

+

+ +
Returns:
List of Parameter supported by type T.
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+getArgument

+
+public Option<T> getArgument(String name)
+
+
Returns the argument by its name if found, NULL otherwise. Where the + Argument is a common interface for Option and Parameter + therefore this method can return either. If you need to retrieve the + Option by its optionNames use @link + getArgumentByOptionName(String) method. The + difference between option name and optionName is explained by the + following example: + + 
+ Sequence type
+         
+         --nuc - Assume the sequences are nucleotide.
+         --amino - Assume the sequences are amino acid. 
+         --amino
+         --nuc
+         --auto
+
+ + In the example, the "Sequence type" is a name whereas --amino, --nuc and + --auto are all optionNames. This dichotomy only manifests in + Option never in Parameters as the latter can + only have single element +

+

+
Parameters:
name - the Parameter of Option name +
Returns:
Argument
+
+
+
+ +

+removeArgument

+
+public boolean removeArgument(String name)
+
+
Removes the argument Argument if found. Where Argument is either + Option or Parameter. +

+

+
Parameters:
name - of the argument +
Returns:
true if argument was removed, false otherwise
+
+
+
+ +

+getArgumentByOptionName

+
+public Option<T> getArgumentByOptionName(String optionName)
+
+
Returns the argument by option name, NULL if the argument is not found +

+

+
Parameters:
optionName - - the optionName. This is not the same as an Option name. + + For example: + + 
+            Output sequences order
+                          --inputorder - Output order: same as input. 
+                           --reorder - Output order: aligned. Default: same as input
+                          --inputorder
+                          --reorder
+
+ + The name of the option in the example is + "Output sequences order" whereas optionNames are + "--inputorder" and "--reorder". If you need to retrieve the + Option or Parameter by its names use + getArgument(String) method +
Returns:
Option
+
+
+
+ +

+removeArgumentByOptionName

+
+public boolean removeArgumentByOptionName(String optionName)
+
+
Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor. +

+

+
Parameters:
optionName - the optionName of the option, do not confuse with the name! +
Returns:
true if argument with optionName exists and was removed, false + otherwise
See Also:
for destinctions + between optionNames and the name of the Option
+
+
+
+ +

+validate

+
+public void validate()
+              throws ValidationException
+
+
Validate the value of the argument. Checks whether the argument value is + in the valid values range. +

+

+ +
Throws: +
ValidationException - if any of the arguments found invalid which is when +
+
  • Parameter value outside ValueConstrain boundary
    • +
  • Parameter name is not listed in possible values
    • +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..b699aeb --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,265 @@ + + + + + + +UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class UnsupportedRuntimeException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.UnsupportedRuntimeException
+
    +
    +
    All Implemented Interfaces:
    Serializable
    +
    +
    +
    +
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    + + +

    +Indicates that the server could not execute native executables. e.g. If Mafft + (unix executable) is asked to be run on Windows. In context of JABAWS this + exception indicates that the service is deployed but is not able to run. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    UnsupportedRuntimeException(String message) + +
    +           
    UnsupportedRuntimeException(Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(String message)
    +
    +
    +
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..af4673f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,325 @@ + + + + + + +ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Enum ValueConstrain.Type

    +
    +java.lang.Object
+  extended by java.lang.Enum<ValueConstrain.Type>
+      extended by compbio.metadata.ValueConstrain.Type
+
    +
    +
    All Implemented Interfaces:
    Serializable, Comparable<ValueConstrain.Type>
    +
    +
    +
    Enclosing class:
    ValueConstrain
    +
    +
    +
    +
    public static enum ValueConstrain.Type
    extends Enum<ValueConstrain.Type>
    + + +

    +

    + +

    + + + + + + + + + + + + + +
    +Enum Constant Summary
    Float + +
    +           
    Integer + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ValueConstrain.TypevalueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +Integer

    +
    +public static final ValueConstrain.Type Integer
    +
    +
    +
    +
    +
    + +

    +Float

    +
    +public static final ValueConstrain.Type Float
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static ValueConstrain.Type[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (ValueConstrain.Type c : ValueConstrain.Type.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static ValueConstrain.Type valueOf(String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    IllegalArgumentException - if this enum type has no constant +with the specified name +
    NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..e90af5f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,440 @@ + + + + + + +ValueConstrain + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class ValueConstrain

    +
    +java.lang.Object
+  extended by compbio.metadata.ValueConstrain
+
    +
    +
    +
    public class ValueConstrain
    extends Object
    + + +

    +The type and the lower and upper boundaries for numerical value. +

    + +

    +

    +
    Version:
    +
    1.0 November 2009
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classValueConstrain.Type + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ValueConstrain() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(Object obj) + +
    +           
    + NumbergetMax() + +
    +           
    + NumbergetMin() + +
    +           
    + ValueConstrain.TypegetType() + +
    +           
    + inthashCode() + +
    +           
    + voidsetMax(String max) + +
    +           
    + voidsetMin(String min) + +
    +           
    + voidsetType(ValueConstrain.Type type) + +
    +           
    + StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ValueConstrain

    +
    +public ValueConstrain()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getType

    +
    +public ValueConstrain.Type getType()
    +
    +
    +
    +
    +
    +
    + +

    +setType

    +
    +public void setType(ValueConstrain.Type type)
    +
    +
    +
    +
    +
    +
    + +

    +getMax

    +
    +public Number getMax()
    +
    +
    +
    +
    +
    +
    + +

    +setMax

    +
    +public void setMax(String max)
    +
    +
    +
    +
    +
    +
    + +

    +getMin

    +
    +public Number getMin()
    +
    +
    +
    +
    +
    +
    + +

    +setMin

    +
    +public void setMin(String min)
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(Object obj)
    +
    +
    +
    Overrides:
    equals in class Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public String toString()
    +
    +
    +
    Overrides:
    toString in class Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..90b5837 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,294 @@ + + + + + + +WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class WrongParameterException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.WrongParameterException
+
    +
    +
    All Implemented Interfaces:
    Serializable
    +
    +
    +
    +
    public class WrongParameterException
    extends Exception
    + + +

    +WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value. +

    + +

    +

    +
    Version:
    +
    1.0 October 2009
    +
    Author:
    +
    pvtroshin
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterException(Option<?> option) + +
    +           
    WrongParameterException(String message) + +
    +           
    WrongParameterException(String message, + Throwable cause) + +
    +           
    WrongParameterException(Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Option<?> option)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(String message)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Throwable cause)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(String message,
+                               Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html new file mode 100644 index 0000000..912b100 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Argument.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.metadata.Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.metadata.Argument

    +
    + + + + + + + + + +
    +Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Argument in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Classes in compbio.metadata that implement Argument
    + classOption<T> + +
    +          Command line option/flag or multiple exclusive options with no value.
    + classParameter<T> + +
    +          A single value containing an option supported by the web service e.g.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html new file mode 100644 index 0000000..42c605f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html @@ -0,0 +1,182 @@ + + + + + + +Uses of Class compbio.metadata.ChunkHolder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ChunkHolder

    +
    + + + + + + + + + +
    +Packages that use ChunkHolder
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return ChunkHolder
    + ChunkHolderJManagement.pullExecStatistics(String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html new file mode 100644 index 0000000..f44464f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.metadata.JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobExecutionException

    +
    +No usage of compbio.metadata.JobExecutionException +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html new file mode 100644 index 0000000..1836c3c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Class compbio.metadata.JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobStatus

    +
    + + + + + + + + + + + + + +
    +Packages that use JobStatus
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return JobStatus
    + JobStatusJManagement.getJobStatus(String jobId) + +
    +          Return the status of the job.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return JobStatus
    +static JobStatusJobStatus.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JobStatus[]JobStatus.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html new file mode 100644 index 0000000..a665022 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html @@ -0,0 +1,264 @@ + + + + + + +Uses of Class compbio.metadata.JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobSubmissionException

    +
    + + + + + + + + + + + + + +
    +Packages that use JobSubmissionException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw JobSubmissionException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringAnnotation.analize(List<FastaSequence> sequences) + +
    +          Analyse the sequences.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Analyse the sequences according to custom settings defined in options + list.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Analyse the sequences according to the preset settings.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Subclasses of JobSubmissionException in compbio.metadata
    + classLimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    + classUnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Limit.html b/website/dm_javadoc/compbio/metadata/class-use/Limit.html new file mode 100644 index 0000000..a5c6546 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Limit.html @@ -0,0 +1,251 @@ + + + + + + +Uses of Class compbio.metadata.Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Limit

    +
    + + + + + + + + + + + + + +
    +Packages that use Limit
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Limit
    + Limit<T>Metadata.getLimit(String presetName) + +
    +          Get a Limit for a preset.
    +  +

    + + + + + +
    +Uses of Limit in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Limit
    + Limit<T>LimitsManager.getDefaultLimit() + +
    +           
    + Limit<T>LimitsManager.getLimitByName(String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Limit
    + List<Limit<T>>LimitsManager.getLimits() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html new file mode 100644 index 0000000..d2158c5 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html @@ -0,0 +1,256 @@ + + + + + + +Uses of Class compbio.metadata.LimitExceededException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.LimitExceededException

    +
    + + + + + + + + + + + + + +
    +Packages that use LimitExceededException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw LimitExceededException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringAnnotation.analize(List<FastaSequence> sequences) + +
    +          Analyse the sequences.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Analyse the sequences according to custom settings defined in options + list.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Analyse the sequences according to the preset settings.
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return LimitExceededException
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html new file mode 100644 index 0000000..ffcd79f --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.metadata.LimitsManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.LimitsManager

    +
    + + + + + + + + + +
    +Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return LimitsManager
    + LimitsManager<T>Metadata.getLimits() + +
    +          List Limits supported by a web service.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Option.html b/website/dm_javadoc/compbio/metadata/class-use/Option.html new file mode 100644 index 0000000..9f1c8d7 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Option.html @@ -0,0 +1,324 @@ + + + + + + +Uses of Class compbio.metadata.Option + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Option

    +
    + + + + + + + + + + + + + +
    +Packages that use Option
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.data.msa with type arguments of type Option
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Analyse the sequences according to custom settings defined in options + list.
    +  +

    + + + + + +
    +Uses of Option in compbio.metadata
    +  +

    + + + + + + + + + +
    Subclasses of Option in compbio.metadata
    + classParameter<T> + +
    +          A single value containing an option supported by the web service e.g.
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Option
    + Option<T>RunnerConfig.getArgument(String name) + +
    +          Returns the argument by its name if found, NULL otherwise.
    + Option<T>RunnerConfig.getArgumentByOptionName(String optionName) + +
    +          Returns the argument by option name, NULL if the argument is not found
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Option
    + List<Option<T>>RunnerConfig.getArguments() + +
    +          Returns list of Parameter and Option supported by current + runner
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + List<Option<T>>RunnerConfig.getOptions() + +
    +          Returns the list of the Options supported by the executable of type T
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Option
    + voidRunnerConfig.addOption(Option<T> option) + +
    +          Adds Option to the internal list of options
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Option
    + voidRunnerConfig.setOptions(List<Option<T>> parameters) + +
    +          Adds the list of options or parameters to the internal list of options
    +  +

    + + + + + + + + +
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Parameter.html b/website/dm_javadoc/compbio/metadata/class-use/Parameter.html new file mode 100644 index 0000000..23fd7ed --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Parameter.html @@ -0,0 +1,213 @@ + + + + + + +Uses of Class compbio.metadata.Parameter + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Parameter

    +
    + + + + + + + + + +
    +Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Parameter in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Parameter
    + List<Parameter<T>>RunnerConfig.getParameters() + +
    +          Returns the list of parameters supported executable of type T.
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Parameter
    + voidRunnerConfig.addParameter(Parameter<T> param) + +
    +          Adds parameter to the internal parameter list
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Parameter
    + voidRunnerConfig.setParameters(List<Parameter<T>> parameters) + +
    +          Sets the list of parameters as internal list
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Preset.html b/website/dm_javadoc/compbio/metadata/class-use/Preset.html new file mode 100644 index 0000000..8e434ce --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Preset.html @@ -0,0 +1,252 @@ + + + + + + +Uses of Class compbio.metadata.Preset + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Preset

    +
    + + + + + + + + + + + + + +
    +Packages that use Preset
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa with parameters of type Preset
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Analyse the sequences according to the preset settings.
    +  +

    + + + + + +
    +Uses of Preset in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return Preset
    + Preset<T>PresetManager.getPresetByName(String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Preset
    + List<Preset<T>>PresetManager.getPresets() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Preset
    + voidPresetManager.setPresets(List<Preset<T>> presets) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html b/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html new file mode 100644 index 0000000..283d3b7 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html @@ -0,0 +1,210 @@ + + + + + + +Uses of Class compbio.metadata.PresetManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.PresetManager

    +
    + + + + + + + + + + + + + +
    +Packages that use PresetManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return PresetManager
    + PresetManager<T>Metadata.getPresets() + +
    +          Get presets supported by a web service
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type PresetManager
    + voidLimitsManager.validate(PresetManager<T> presets) + +
    +          Validate Limits
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html new file mode 100644 index 0000000..098d736 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ResultNotAvailableException.html @@ -0,0 +1,188 @@ + + + + + + +Uses of Class compbio.metadata.ResultNotAvailableException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ResultNotAvailableException

    +
    + + + + + + + + + +
    +Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw ResultNotAvailableException
    + HashSet<Score>Annotation.getAnnotation(String jobId) + +
    +          Return the result of the job.
    + AlignmentMsaWS.getResult(String jobId) + +
    +          Return the result of the job.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html new file mode 100644 index 0000000..b149947 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/RunnerConfig.html @@ -0,0 +1,243 @@ + + + + + + +Uses of Class compbio.metadata.RunnerConfig + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.RunnerConfig

    +
    + + + + + + + + + + + + + +
    +Packages that use RunnerConfig
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return RunnerConfig
    + RunnerConfig<T>Metadata.getRunnerOptions() + +
    +          Get options supported by a web service
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata with parameters of type RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidPresetManager.validate(RunnerConfig<T> options) + +
    +          Checks whether preset option and parameter are defined in RunnerConfig + object.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html new file mode 100644 index 0000000..7df3169 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/UnsupportedRuntimeException.html @@ -0,0 +1,225 @@ + + + + + + +Uses of Class compbio.metadata.UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.UnsupportedRuntimeException

    +
    + + + + + + + + + +
    +Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringAnnotation.analize(List<FastaSequence> sequences) + +
    +          Analyse the sequences.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Analyse the sequences according to custom settings defined in options + list.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Analyse the sequences according to the preset settings.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html new file mode 100644 index 0000000..6a195a4 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html @@ -0,0 +1,214 @@ + + + + + + +Uses of Class compbio.metadata.ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ValueConstrain.Type

    +
    + + + + + + + + + +
    +Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain.Type in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain.Type
    + ValueConstrain.TypeValueConstrain.getType() + +
    +           
    +static ValueConstrain.TypeValueConstrain.Type.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]ValueConstrain.Type.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    + voidValueConstrain.setType(ValueConstrain.Type type) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.html new file mode 100644 index 0000000..9653c7c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ValueConstrain.html @@ -0,0 +1,197 @@ + + + + + + +Uses of Class compbio.metadata.ValueConstrain + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ValueConstrain

    +
    + + + + + + + + + +
    +Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain
    + ValueConstrainParameter.getValidValue() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain
    + voidParameter.setValidValue(ValueConstrain validValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html new file mode 100644 index 0000000..728332b --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html @@ -0,0 +1,271 @@ + + + + + + +Uses of Class compbio.metadata.WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.WrongParameterException

    +
    + + + + + + + + + + + + + +
    +Packages that use WrongParameterException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw WrongParameterException
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringAnnotation.customAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Analyse the sequences according to custom settings defined in options + list.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + StringAnnotation.presetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Analyse the sequences according to the preset settings.
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that throw WrongParameterException
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidOption.setDefaultValue(String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidParameter.setDefaultValue(String defaultVal) + +
    +           
    + voidArgument.setValue(String defaultValue) + +
    +          Set default values for the parameter or an option
    + voidOption.setValue(String dValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-frame.html b/website/dm_javadoc/compbio/metadata/package-frame.html new file mode 100644 index 0000000..659e54d --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-frame.html @@ -0,0 +1,93 @@ + + + + + + +compbio.metadata + + + + + + + + + + + +compbio.metadata + + + + +
    +Interfaces  + +
    +Argument
    + + + + + + +
    +Classes  + +
    +ChunkHolder +
    +Limit +
    +LimitsManager +
    +Option +
    +Parameter +
    +Preset +
    +PresetManager +
    +RunnerConfig +
    +ValueConstrain
    + + + + + + +
    +Enums  + +
    +JobStatus +
    +ValueConstrain.Type
    + + + + + + +
    +Exceptions  + +
    +JobExecutionException +
    +JobSubmissionException +
    +LimitExceededException +
    +ResultNotAvailableException +
    +UnsupportedRuntimeException +
    +WrongParameterException
    + + + + diff --git a/website/dm_javadoc/compbio/metadata/package-summary.html b/website/dm_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..be1cc91 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,286 @@ + + + + + + +compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.metadata +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. +

    +See: +
    +          Description +

    + + + + + + + + + +
    +Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    ChunkHolderRepresents a chunk of a string data together with the position in a file for + the next read operation.
    Limit<T>A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing an option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    +  + +

    + + + + + + + + + + + + + +
    +Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThis exception is thrown if the task larger in size that the limit that + applies to the calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  + +

    +

    +Package compbio.metadata Description +

    + +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) +

    + +

    +

    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-tree.html b/website/dm_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..5818861 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,178 @@ + + + + + + +compbio.metadata Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.metadata +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-use.html b/website/dm_javadoc/compbio/metadata/package-use.html new file mode 100644 index 0000000..5ffdc11 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-use.html @@ -0,0 +1,347 @@ + + + + + + +Uses of Package compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Package
    compbio.metadata

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder + +
    +          Represents a chunk of a string data together with the position in a file for + the next read operation.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.metadata
    Argument + +
    +          An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Parameter + +
    +          A single value containing an option supported by the web service e.g.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    ValueConstrain + +
    +          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type + +
    +           
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/IOHelper.html b/website/dm_javadoc/compbio/ws/client/IOHelper.html new file mode 100644 index 0000000..6ab87de --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/IOHelper.html @@ -0,0 +1,224 @@ + + + + + + +IOHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class IOHelper

    +
    +java.lang.Object
+  extended by compbio.ws.client.IOHelper
+
    +
    +
    +
    public class IOHelper
    extends Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    IOHelper() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +IOHelper

    +
    +public IOHelper()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..aeb0b07 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,309 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class Jws2Client

    +
    +java.lang.Object
+  extended by compbio.ws.client.Jws2Client
+
    +
    +
    +
    public class Jws2Client
    extends Object
    + + +

    +A command line client for JAva Bioinformatics Analysis Web Services +

    + +

    +

    +
    Version:
    +
    1.0
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static JABAServiceconnect(String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +static voidmain(String[] args) + +
    +          Starts command line client, if no parameter are supported print help.
    +static booleanvalidURL(String urlstr) + +
    +          Attempt to construct the URL object from the string
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +validURL

    +
    +public static boolean validURL(String urlstr)
    +
    +
    Attempt to construct the URL object from the string +

    +

    +
    Parameters:
    urlstr - +
    Returns:
    true if it succeed false otherwise
    +
    +
    +
    + +

    +connect

    +
    +public static JABAService connect(String host,
+                                  Services service)
+                           throws WebServiceException
    +
    +
    Connects to a web service by the host and the service name +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - +
    Returns:
    MsaWS +
    Throws: +
    WebServiceException
    +
    +
    +
    + +

    +main

    +
    +public static void main(String[] args)
    +
    +
    Starts command line client, if no parameter are supported print help. Two + parameters are required for successfull call the JWS2 host name and a + service name. +

    +

    +
    Parameters:
    args - Usage: -h=host_and_context + -s=serviceName ACTION [OPTIONS] + + -h= - a full URL to the JWS2 web server + including context path e.g. http://10.31.1.159:8080/ws + + -s= - one of [MafftWS, MuscleWS, ClustalWS, + TcoffeeWS, ProbconsWS] ACTIONS: + + -i= - full path to fasta formatted sequence file, + from which to align sequences + + -parameters - lists parameters supported by web service + + -presets - lists presets supported by web service + + -limits - lists web services limits Please note that if input + file is specified other actions are ignored + + OPTIONS: (only for use with -i action): + + -r= - name of the preset to use + + -o= - full path to the file where to write an + alignment -f= - the name of the file with + the list of parameters to use. Please note that -r and -f + options cannot be used together. Alignment is done with either + preset or a parameters from the file, but not both!
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/MetadataHelper.html b/website/dm_javadoc/compbio/ws/client/MetadataHelper.html new file mode 100644 index 0000000..8dd31e7 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/MetadataHelper.html @@ -0,0 +1,224 @@ + + + + + + +MetadataHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class MetadataHelper

    +
    +java.lang.Object
+  extended by compbio.ws.client.MetadataHelper
+
    +
    +
    +
    public class MetadataHelper
    extends Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    MetadataHelper() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +MetadataHelper

    +
    +public MetadataHelper()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/Services.html b/website/dm_javadoc/compbio/ws/client/Services.html new file mode 100644 index 0000000..43be079 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Services.html @@ -0,0 +1,409 @@ + + + + + + +Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Enum Services

    +
    +java.lang.Object
+  extended by java.lang.Enum<Services>
+      extended by compbio.ws.client.Services
+
    +
    +
    All Implemented Interfaces:
    Serializable, Comparable<Services>
    +
    +
    +
    +
    public enum Services
    extends Enum<Services>
    + + +

    +List of web services currently supported by JABAWS version 2 +

    + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    AAConWS + +
    +           
    ClustalWS + +
    +           
    MafftWS + +
    +           
    MuscleWS + +
    +           
    ProbconsWS + +
    +           
    TcoffeeWS + +
    +           
    +  + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static ServicesgetService(String servName) + +
    +           
    +static ServicesvalueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Services[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +MafftWS

    +
    +public static final Services MafftWS
    +
    +
    +
    +
    +
    + +

    +MuscleWS

    +
    +public static final Services MuscleWS
    +
    +
    +
    +
    +
    + +

    +ClustalWS

    +
    +public static final Services ClustalWS
    +
    +
    +
    +
    +
    + +

    +TcoffeeWS

    +
    +public static final Services TcoffeeWS
    +
    +
    +
    +
    +
    + +

    +ProbconsWS

    +
    +public static final Services ProbconsWS
    +
    +
    +
    +
    +
    + +

    +AAConWS

    +
    +public static final Services AAConWS
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Services[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (Services c : Services.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static Services valueOf(String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    IllegalArgumentException - if this enum type has no constant +with the specified name +
    NullPointerException - if the argument is null
    +
    +
    +
    + +

    +getService

    +
    +public static Services getService(String servName)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..f7f4383 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,278 @@ + + + + + + +WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class WSTester

    +
    +java.lang.Object
+  extended by compbio.ws.client.WSTester
+
    +
    +
    +
    public class WSTester
    extends Object
    + + +

    +Class for testing web services +

    + +

    +

    +
    Version:
    +
    1.0 February 2010
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSTester() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> void
    +    		main(String[] args) + +
    +          Test JWS2 web services
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WSTester

    +
    +public WSTester()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static <T> void main(String[] args)
+                 throws IOException
    +
    +
    Test JWS2 web services +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= + + -s= which is optional. If service name is not + provided then all known JWS2 web services are tested +
    Throws: +
    IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/class-use/IOHelper.html b/website/dm_javadoc/compbio/ws/client/class-use/IOHelper.html new file mode 100644 index 0000000..fb5f000 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/class-use/IOHelper.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.IOHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.IOHelper

    +
    +No usage of compbio.ws.client.IOHelper +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/class-use/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/class-use/Jws2Client.html new file mode 100644 index 0000000..9a40441 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/class-use/Jws2Client.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.Jws2Client

    +
    +No usage of compbio.ws.client.Jws2Client +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/class-use/MetadataHelper.html b/website/dm_javadoc/compbio/ws/client/class-use/MetadataHelper.html new file mode 100644 index 0000000..2061a54 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/class-use/MetadataHelper.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.MetadataHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.MetadataHelper

    +
    +No usage of compbio.ws.client.MetadataHelper +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/class-use/Services.html b/website/dm_javadoc/compbio/ws/client/class-use/Services.html new file mode 100644 index 0000000..91b63bb --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/class-use/Services.html @@ -0,0 +1,215 @@ + + + + + + +Uses of Class compbio.ws.client.Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.Services

    +
    + + + + + + + + + +
    +Packages that use Services
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of Services in compbio.ws.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.client that return Services
    +static ServicesServices.getService(String servName) + +
    +           
    +static ServicesServices.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Services[]Services.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client with parameters of type Services
    +static JABAServiceJws2Client.connect(String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/class-use/WSTester.html b/website/dm_javadoc/compbio/ws/client/class-use/WSTester.html new file mode 100644 index 0000000..c184955 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/class-use/WSTester.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.WSTester

    +
    +No usage of compbio.ws.client.WSTester +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/package-frame.html b/website/dm_javadoc/compbio/ws/client/package-frame.html new file mode 100644 index 0000000..fce656d --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/package-frame.html @@ -0,0 +1,49 @@ + + + + + + +compbio.ws.client + + + + + + + + + + + +compbio.ws.client + + + + +
    +Classes  + +
    +IOHelper +
    +Jws2Client +
    +MetadataHelper +
    +WSTester
    + + + + + + +
    +Enums  + +
    +Services
    + + + + diff --git a/website/dm_javadoc/compbio/ws/client/package-summary.html b/website/dm_javadoc/compbio/ws/client/package-summary.html new file mode 100644 index 0000000..58328a6 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/package-summary.html @@ -0,0 +1,204 @@ + + + + + + +compbio.ws.client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.ws.client +

    +A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    IOHelper 
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    MetadataHelper 
    WSTesterClass for testing web services
    +  + +

    + + + + + + + + + +
    +Enum Summary
    ServicesList of web services currently supported by JABAWS version 2
    +  + +

    +

    +Package compbio.ws.client Description +

    + +

    +A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. +

    + +

    +

    +
    Version:
    +
    1.0 April 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/package-tree.html b/website/dm_javadoc/compbio/ws/client/package-tree.html new file mode 100644 index 0000000..7c64c46 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/package-tree.html @@ -0,0 +1,163 @@ + + + + + + +compbio.ws.client Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.ws.client +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/package-use.html b/website/dm_javadoc/compbio/ws/client/package-use.html new file mode 100644 index 0000000..a3524b3 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/package-use.html @@ -0,0 +1,171 @@ + + + + + + +Uses of Package compbio.ws.client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Package
    compbio.ws.client

    +
    + + + + + + + + + +
    +Packages that use compbio.ws.client
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + + + + +
    +Classes in compbio.ws.client used by compbio.ws.client
    Services + +
    +          List of web services currently supported by JABAWS version 2
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/constant-values.html b/website/dm_javadoc/constant-values.html new file mode 100644 index 0000000..410b7d3 --- /dev/null +++ b/website/dm_javadoc/constant-values.html @@ -0,0 +1,202 @@ + + + + + + +Constant Field Values + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Constant Field Values

    +
    +
    +Contents + + + + + + +
    +compbio.data.*
    + +

    + + + + + + + + + + + + +
    compbio.data.sequence.ClustalAlignmentUtil
    +public static final chargapchar45
    + +

    + +

    + + + + + +
    +compbio.metadata.*
    + +

    + + + + + + + + + + + + +
    compbio.metadata.PresetManager<T>
    +public static final StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    + +

    + +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/deprecated-list.html b/website/dm_javadoc/deprecated-list.html new file mode 100644 index 0000000..5c8268f --- /dev/null +++ b/website/dm_javadoc/deprecated-list.html @@ -0,0 +1,146 @@ + + + + + + +Deprecated List + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree   Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Deprecated API

    +
    +
    +Contents + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree   Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/help-doc.html b/website/dm_javadoc/help-doc.html new file mode 100644 index 0000000..c90cd5d --- /dev/null +++ b/website/dm_javadoc/help-doc.html @@ -0,0 +1,223 @@ + + + + + + +API Help + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index   Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +How This API Document Is Organized

    +
    +This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.

    +Overview

    +
    + +

    +The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.

    +

    +Package

    +
    + +

    +Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:

    +
    +

    +Class/Interface

    +
    + +

    +Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:

    +Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.
    + +

    +Annotation Type

    +
    + +

    +Each annotation type has its own separate page with the following sections:

    +
    + +

    +Enum

    +
    + +

    +Each enum has its own separate page with the following sections:

    +
    +

    +Use

    +
    +Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.
    +

    +Tree (Class Hierarchy)

    +
    +There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with java.lang.Object. The interfaces do not inherit from java.lang.Object. +
    +

    +Deprecated API

    +
    +The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.
    +

    +Index

    +
    +The Index contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.
    +

    +Prev/Next

    +These links take you to the next or previous class, interface, package, or related page.

    +Frames/No Frames

    +These links show and hide the HTML frames. All pages are available with or without frames. +

    +

    +Serialized Form

    +Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description. +

    +

    +Constant Field Values

    +The Constant Field Values page lists the static final fields and their values. +

    + + +This help file applies to API documentation generated using the standard doclet. + +
    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index   Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/index-files/index-1.html b/website/dm_javadoc/index-files/index-1.html new file mode 100644 index 0000000..6ef2aba --- /dev/null +++ b/website/dm_javadoc/index-files/index-1.html @@ -0,0 +1,191 @@ + + + + + + +A-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +A

    +
    +
    AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Valid Amino acids +
    addAnnotation(T, ArrayList<Float>) - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    addOption(Option<T>) - +Method in class compbio.metadata.RunnerConfig +
    Adds Option to the internal list of options +
    addOptionNames(String...) - +Method in class compbio.metadata.Option +
    Adds an option to the optionName list +
    addOptionNames(String...) - +Method in class compbio.metadata.Parameter +
      +
    addParameter(Parameter<T>) - +Method in class compbio.metadata.RunnerConfig +
    Adds parameter to the internal parameter list +
    addPossibleValues(String...) - +Method in class compbio.metadata.Parameter +
      +
    align(List<FastaSequence>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with default settings. +
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - +Constructor for class compbio.data.sequence.Alignment +
      +
    Alignment(List<FastaSequence>, AlignmentMetadata) - +Constructor for class compbio.data.sequence.Alignment +
      +
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - +Constructor for class compbio.data.sequence.AlignmentMetadata +
      +
    AMBIGUOUS_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Same as AA pattern but with two additional letters - XU +
    AMBIGUOUS_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Ambiguous nucleotide +
    analize(List<FastaSequence>) - +Method in interface compbio.data.msa.Annotation +
    Analyse the sequences. +
    AnnotatedSequence - Class in compbio.data.sequence
     
    AnnotatedSequence(String, String, float[]) - +Constructor for class compbio.data.sequence.AnnotatedSequence +
      +
    AnnotatedSequence(FastaSequence, float[]) - +Constructor for class compbio.data.sequence.AnnotatedSequence +
      +
    Annotation<T> - Interface in compbio.data.msa
    Interface for tools that results to one or more annotation to sequence(s)
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-10.html b/website/dm_javadoc/index-files/index-10.html new file mode 100644 index 0000000..b3ec57f --- /dev/null +++ b/website/dm_javadoc/index-files/index-10.html @@ -0,0 +1,159 @@ + + + + + + +L-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +L

    +
    +
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    Limit(int, int, String) - +Constructor for class compbio.metadata.Limit +
    Instantiate the limit +
    Limit(int, int, String, boolean) - +Constructor for class compbio.metadata.Limit +
      +
    LimitExceededException - Exception in compbio.metadata
    This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    LimitExceededException(String) - +Constructor for exception compbio.metadata.LimitExceededException +
      +
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - +Constructor for class compbio.metadata.LimitsManager +
      +
    LOCAL_ENGINE_LIMIT_PRESET - +Static variable in class compbio.metadata.PresetManager +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-11.html b/website/dm_javadoc/index-files/index-11.html new file mode 100644 index 0000000..1d2f972 --- /dev/null +++ b/website/dm_javadoc/index-files/index-11.html @@ -0,0 +1,154 @@ + + + + + + +M-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +M

    +
    +
    main(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Starts command line client, if no parameter are supported print help. +
    main(String[]) - +Static method in class compbio.ws.client.WSTester +
    Test JWS2 web services +
    Metadata<T> - Interface in compbio.data.msa
     
    MetadataHelper - Class in compbio.ws.client
     
    MetadataHelper() - +Constructor for class compbio.ws.client.MetadataHelper +
      +
    Method - Enum in compbio.data.sequence
    Enumeration listing of all the supported methods.
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    MultiAnnotatedSequence<T extends Enum<T>> - Class in compbio.data.sequence
    TODO complete
    MultiAnnotatedSequence(Class<T>) - +Constructor for class compbio.data.sequence.MultiAnnotatedSequence +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-12.html b/website/dm_javadoc/index-files/index-12.html new file mode 100644 index 0000000..6a91f76 --- /dev/null +++ b/website/dm_javadoc/index-files/index-12.html @@ -0,0 +1,157 @@ + + + + + + +N-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +N

    +
    +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - +Static method in exception compbio.metadata.LimitExceededException +
      +
    NON_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    inversion of AA pattern +
    NON_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non nucleotide +
    NONWORD - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non word +
    NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Nucleotides a, t, g, c, u +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-13.html b/website/dm_javadoc/index-files/index-13.html new file mode 100644 index 0000000..2a88977 --- /dev/null +++ b/website/dm_javadoc/index-files/index-13.html @@ -0,0 +1,145 @@ + + + + + + +O-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +O

    +
    +
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - +Constructor for class compbio.metadata.Option +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-14.html b/website/dm_javadoc/index-files/index-14.html new file mode 100644 index 0000000..5273a79 --- /dev/null +++ b/website/dm_javadoc/index-files/index-14.html @@ -0,0 +1,161 @@ + + + + + + +P-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +P

    +
    +
    Parameter<T> - Class in compbio.metadata
    A single value containing an option supported by the web service e.g.
    Parameter(String, String) - +Constructor for class compbio.metadata.Parameter +
      +
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - +Constructor for class compbio.metadata.Preset +
      +
    presetAlign(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with preset. +
    presetAnalize(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.Annotation +
    Analyse the sequences according to the preset settings. +
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - +Constructor for class compbio.metadata.PresetManager +
      +
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    pullExecStatistics(String, long) - +Method in interface compbio.data.msa.JManagement +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-15.html b/website/dm_javadoc/index-files/index-15.html new file mode 100644 index 0000000..d71c79e --- /dev/null +++ b/website/dm_javadoc/index-files/index-15.html @@ -0,0 +1,182 @@ + + + + + + +R-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +R

    +
    +
    readAAConResults(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Read AACon result with no alignment files. +
    readClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Read Clustal formatted alignment. +
    readClustalFile(File) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    readFasta(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +
    readJRonn(File) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    readJRonn(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reader for JRonn horizontal file format +
    removeArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument Argument if found. +
    removeArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor. +
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    ResultNotAvailableException(String) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(String, Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - +Constructor for class compbio.metadata.RunnerConfig +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-16.html b/website/dm_javadoc/index-files/index-16.html new file mode 100644 index 0000000..0c6ba55 --- /dev/null +++ b/website/dm_javadoc/index-files/index-16.html @@ -0,0 +1,220 @@ + + + + + + +S-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +S

    +
    +
    Score - Class in compbio.data.sequence
     
    Score(Method, List<Float>) - +Constructor for class compbio.data.sequence.Score +
      +
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 2
    setDefaultValue(String) - +Method in class compbio.metadata.Option +
    Sets one of the values defined in optionList as default. +
    setDefaultValue(String) - +Method in class compbio.metadata.Parameter +
      +
    setDescription(String) - +Method in class compbio.metadata.Option +
      +
    setDescription(String) - +Method in class compbio.metadata.Preset +
      +
    setFurtherDetails(URL) - +Method in class compbio.metadata.Option +
      +
    setMax(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setMin(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setName(String) - +Method in class compbio.metadata.Option +
      +
    setName(String) - +Method in class compbio.metadata.Preset +
      +
    setOptionName(String) - +Method in class compbio.metadata.Parameter +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Option +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setOptions(List<String>) - +Method in class compbio.metadata.Preset +
      +
    setOptions(List<Option<T>>) - +Method in class compbio.metadata.RunnerConfig +
    Adds the list of options or parameters to the internal list of options +
    setParameters(List<Parameter<T>>) - +Method in class compbio.metadata.RunnerConfig +
    Sets the list of parameters as internal list +
    setPossibleValues(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setPresets(List<Preset<T>>) - +Method in class compbio.metadata.PresetManager +
      +
    setPrmSeparator(String) - +Method in class compbio.metadata.RunnerConfig +
    Sets name value separator character +
    setRequired(boolean) - +Method in class compbio.metadata.Option +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.PresetManager +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.RunnerConfig +
    Set the name of a runner class +
    setType(ValueConstrain.Type) - +Method in class compbio.metadata.ValueConstrain +
      +
    setValidValue(ValueConstrain) - +Method in class compbio.metadata.Parameter +
      +
    setValue(String) - +Method in interface compbio.metadata.Argument +
    Set default values for the parameter or an option +
    setValue(String) - +Method in class compbio.metadata.Option +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-17.html b/website/dm_javadoc/index-files/index-17.html new file mode 100644 index 0000000..bcedbe3 --- /dev/null +++ b/website/dm_javadoc/index-files/index-17.html @@ -0,0 +1,193 @@ + + + + + + +T-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +T

    +
    +
    toCommand(String) - +Method in class compbio.metadata.Option +
    Convert the option to the command string. +
    toCommand(String) - +Method in class compbio.metadata.Parameter +
      +
    toJalviewAnnotation() - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    toString() - +Method in class compbio.data.sequence.Alignment +
      +
    toString() - +Method in class compbio.data.sequence.AnnotatedSequence +
      +
    toString() - +Method in class compbio.data.sequence.FastaSequence +
    Same as oneLineFasta +
    toString() - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    toString() - +Method in class compbio.data.sequence.Score +
      +
    toString() - +Method in class compbio.metadata.ChunkHolder +
      +
    toString() - +Method in class compbio.metadata.Limit +
      +
    toString() - +Method in class compbio.metadata.LimitsManager +
      +
    toString() - +Method in class compbio.metadata.Option +
      +
    toString() - +Method in class compbio.metadata.Parameter +
      +
    toString() - +Method in class compbio.metadata.Preset +
      +
    toString() - +Method in class compbio.metadata.PresetManager +
      +
    toString() - +Method in class compbio.metadata.RunnerConfig +
      +
    toString() - +Method in class compbio.metadata.ValueConstrain +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-18.html b/website/dm_javadoc/index-files/index-18.html new file mode 100644 index 0000000..c63c760 --- /dev/null +++ b/website/dm_javadoc/index-files/index-18.html @@ -0,0 +1,163 @@ + + + + + + +U-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +U

    +
    +
    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(File, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    UnsupportedRuntimeException(Throwable) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-19.html b/website/dm_javadoc/index-files/index-19.html new file mode 100644 index 0000000..ca042cf --- /dev/null +++ b/website/dm_javadoc/index-files/index-19.html @@ -0,0 +1,200 @@ + + + + + + +V-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +V

    +
    +
    validate(PresetManager<T>) - +Method in class compbio.metadata.LimitsManager +
    Validate Limits +
    validate(RunnerConfig<T>) - +Method in class compbio.metadata.PresetManager +
    Checks whether preset option and parameter are defined in RunnerConfig + object. +
    validate() - +Method in class compbio.metadata.RunnerConfig +
    Validate the value of the argument. +
    validURL(String) - +Static method in class compbio.ws.client.Jws2Client +
    Attempt to construct the URL object from the string +
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - +Constructor for class compbio.metadata.ValueConstrain +
      +
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - +Static method in enum compbio.data.sequence.DisemblResultAnnot +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.data.sequence.Method +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.data.sequence.Program +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.JobStatus +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.ws.client.Services +
    Returns the enum constant of this type with the specified name. +
    values() - +Static method in enum compbio.data.sequence.DisemblResultAnnot +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.data.sequence.Method +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.data.sequence.Program +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.JobStatus +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.ws.client.Services +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-2.html b/website/dm_javadoc/index-files/index-2.html new file mode 100644 index 0000000..04176ac --- /dev/null +++ b/website/dm_javadoc/index-files/index-2.html @@ -0,0 +1,174 @@ + + + + + + +C-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +C

    +
    +
    cancelJob(String) - +Method in interface compbio.data.msa.JManagement +
    Stop running the job jobId but leave its output untouched +
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of a string data together with the position in a file for + the next read operation.
    ChunkHolder(String, long) - +Constructor for class compbio.metadata.ChunkHolder +
      +
    cleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all whitespace chars in the sequence string +
    closeSilently(Logger, Closeable) - +Static method in class compbio.data.sequence.SequenceUtil +
    Closes the Closable and logs the exception if any +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - +Constructor for class compbio.data.sequence.ClustalAlignmentUtil +
      +
    compbio.data.msa - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    connect(String, Services) - +Static method in class compbio.ws.client.Jws2Client +
    Connects to a web service by the host and the service name +
    copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +
      +
    countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +
      +
    customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with options. +
    customAnalize(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.Annotation +
    Analyse the sequences according to custom settings defined in options + list. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-20.html b/website/dm_javadoc/index-files/index-20.html new file mode 100644 index 0000000..473d4a4 --- /dev/null +++ b/website/dm_javadoc/index-files/index-20.html @@ -0,0 +1,176 @@ + + + + + + +W-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +W

    +
    +
    WHITE_SPACE - +Static variable in class compbio.data.sequence.SequenceUtil +
    A whitespace character: [\t\n\x0B\f\r] +
    writeClustalAlignment(OutputStream, Alignment) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Write Clustal formatted alignment Limitations: does not record the + consensus. +
    writeFasta(OutputStream, List<FastaSequence>, int) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +
    writeFasta(OutputStream, List<FastaSequence>) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes FastaSequence in the file, each sequence will take one line only +
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    WrongParameterException(Option<?>) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String, Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - +Constructor for class compbio.ws.client.WSTester +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-3.html b/website/dm_javadoc/index-files/index-3.html new file mode 100644 index 0000000..454eebc --- /dev/null +++ b/website/dm_javadoc/index-files/index-3.html @@ -0,0 +1,149 @@ + + + + + + +D-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +D

    +
    +
    deepCleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all special characters and digits as well as whitespace chars + from the sequence +
    DIGIT - +Static variable in class compbio.data.sequence.SequenceUtil +
    A digit +
    DisemblResultAnnot - Enum in compbio.data.sequence
     
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-4.html b/website/dm_javadoc/index-files/index-4.html new file mode 100644 index 0000000..1e0a8b5 --- /dev/null +++ b/website/dm_javadoc/index-files/index-4.html @@ -0,0 +1,182 @@ + + + + + + +E-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +E

    +
    +
    equals(Object) - +Method in class compbio.data.sequence.Alignment +
    Please note that this implementation does not take the order of sequences + into account! +
    equals(Object) - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    equals(Object) - +Method in class compbio.data.sequence.AnnotatedSequence +
      +
    equals(Object) - +Method in class compbio.data.sequence.FastaSequence +
      +
    equals(Object) - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    equals(Object) - +Method in class compbio.data.sequence.Score +
      +
    equals(Object) - +Method in class compbio.metadata.ChunkHolder +
      +
    equals(Object) - +Method in class compbio.metadata.Limit +
      +
    equals(Object) - +Method in class compbio.metadata.Option +
      +
    equals(Object) - +Method in class compbio.metadata.Parameter +
      +
    equals(Object) - +Method in class compbio.metadata.Preset +
      +
    equals(Object) - +Method in class compbio.metadata.RunnerConfig +
      +
    equals(Object) - +Method in class compbio.metadata.ValueConstrain +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-5.html b/website/dm_javadoc/index-files/index-5.html new file mode 100644 index 0000000..8cc9c72 --- /dev/null +++ b/website/dm_javadoc/index-files/index-5.html @@ -0,0 +1,146 @@ + + + + + + +F-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +F

    +
    +
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - +Constructor for class compbio.data.sequence.FastaSequence +
    Upon construction the any whitespace characters are removed from the + sequence +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-6.html b/website/dm_javadoc/index-files/index-6.html new file mode 100644 index 0000000..f39621d --- /dev/null +++ b/website/dm_javadoc/index-files/index-6.html @@ -0,0 +1,350 @@ + + + + + + +G-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +G

    +
    +
    gapchar - +Static variable in class compbio.data.sequence.ClustalAlignmentUtil +
    Dash char to be used as gap char in the alignments +
    getActualNumberofSequences() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getAnnotation(String) - +Method in interface compbio.data.msa.Annotation +
    Return the result of the job. +
    getAnnotation() - +Method in class compbio.data.sequence.AnnotatedSequence +
      +
    getAnnotations() - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    getArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by its name if found, NULL otherwise. +
    getArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by option name, NULL if the argument is not found +
    getArguments(RunnerConfig<T>) - +Method in class compbio.metadata.Preset +
    Converts list of options as String to type Option +
    getArguments() - +Method in class compbio.metadata.RunnerConfig +
    Returns list of Parameter and Option supported by current + runner +
    getAvgSeqLength() - +Method in class compbio.metadata.Limit +
      +
    getAvgSequenceLength(List<FastaSequence>) - +Static method in class compbio.metadata.Limit +
    Calculates an average sequence length of the dataset +
    getChunk() - +Method in class compbio.metadata.ChunkHolder +
      +
    getDefaultLimit() - +Method in class compbio.metadata.LimitsManager +
      +
    getDefaultValue() - +Method in interface compbio.metadata.Argument +
      +
    getDefaultValue() - +Method in class compbio.metadata.Option +
    A default value of the option. +
    getDescription() - +Method in interface compbio.metadata.Argument +
      +
    getDescription() - +Method in class compbio.metadata.Option +
    A long description of the Option +
    getDescription() - +Method in class compbio.metadata.Preset +
      +
    getFormatedSequence(int) - +Method in class compbio.data.sequence.FastaSequence +
    Format sequence per width letter in one string. +
    getFormattedFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getFurtherDetails() - +Method in interface compbio.metadata.Argument +
      +
    getFurtherDetails() - +Method in class compbio.metadata.Option +
    The URL where further details about the option can be found +
    getGapchar() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getId() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of id +
    getJobStatus(String) - +Method in interface compbio.data.msa.JManagement +
    Return the status of the job. +
    getLength() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getLimit(String) - +Method in interface compbio.data.msa.Metadata +
    Get a Limit for a preset. +
    getLimitByName(String) - +Method in class compbio.metadata.LimitsManager +
      +
    getLimits() - +Method in interface compbio.data.msa.Metadata +
    List Limits supported by a web service. +
    getLimits() - +Method in class compbio.metadata.LimitsManager +
      +
    getMax() - +Method in class compbio.metadata.ValueConstrain +
      +
    getMetadata() - +Method in class compbio.data.sequence.Alignment +
      +
    getMethod(String) - +Static method in enum compbio.data.sequence.Method +
      +
    getMethod() - +Method in class compbio.data.sequence.Score +
      +
    getMin() - +Method in class compbio.metadata.ValueConstrain +
      +
    getName() - +Method in interface compbio.metadata.Argument +
      +
    getName() - +Method in class compbio.metadata.Option +
    Human readable name of the option +
    getName() - +Method in class compbio.metadata.Preset +
      +
    getNextPosition() - +Method in class compbio.metadata.ChunkHolder +
      +
    getNumberOfSequencesAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getOnelineFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getOptionName() - +Method in class compbio.metadata.Parameter +
      +
    getOptionNames() - +Method in class compbio.metadata.Option +
      +
    getOptions() - +Method in class compbio.metadata.Preset +
      +
    getOptions() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of the Options supported by the executable of type T +
    getParameters() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of parameters supported executable of type T. +
    getPossibleValues() - +Method in interface compbio.metadata.Argument +
      +
    getPossibleValues() - +Method in class compbio.metadata.Option +
    List of possible optionNames +
    getPossibleValues() - +Method in class compbio.metadata.Parameter +
    List is more convenient to work with +
    getPreset() - +Method in class compbio.metadata.Limit +
      +
    getPresetByName(String) - +Method in class compbio.metadata.PresetManager +
      +
    getPresets() - +Method in interface compbio.data.msa.Metadata +
    Get presets supported by a web service +
    getPresets() - +Method in class compbio.metadata.PresetManager +
      +
    getPrmSeparator() - +Method in class compbio.metadata.RunnerConfig +
      +
    getProgram() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getResult(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the result of the job. +
    getRunnerClassName() - +Method in class compbio.metadata.PresetManager +
      +
    getRunnerClassName() - +Method in class compbio.metadata.RunnerConfig +
      +
    getRunnerOptions() - +Method in interface compbio.data.msa.Metadata +
    Get options supported by a web service +
    getScores() - +Method in class compbio.data.sequence.Score +
      +
    getSeqNumber() - +Method in class compbio.metadata.Limit +
      +
    getSequence() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of sequence +
    getSequenceLenghtActual() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequenceLenghtAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequences() - +Method in class compbio.data.sequence.Alignment +
      +
    getService(String) - +Static method in enum compbio.ws.client.Services +
      +
    getSize() - +Method in class compbio.data.sequence.Alignment +
      +
    getType() - +Method in class compbio.metadata.ValueConstrain +
      +
    getValidValue() - +Method in class compbio.metadata.Parameter +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-7.html b/website/dm_javadoc/index-files/index-7.html new file mode 100644 index 0000000..bf07be6 --- /dev/null +++ b/website/dm_javadoc/index-files/index-7.html @@ -0,0 +1,178 @@ + + + + + + +H-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +H

    +
    +
    hashCode() - +Method in class compbio.data.sequence.Alignment +
      +
    hashCode() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    hashCode() - +Method in class compbio.data.sequence.AnnotatedSequence +
      +
    hashCode() - +Method in class compbio.data.sequence.FastaSequence +
      +
    hashCode() - +Method in class compbio.data.sequence.MultiAnnotatedSequence +
      +
    hashCode() - +Method in class compbio.data.sequence.Score +
      +
    hashCode() - +Method in class compbio.metadata.ChunkHolder +
      +
    hashCode() - +Method in class compbio.metadata.Limit +
      +
    hashCode() - +Method in class compbio.metadata.Option +
      +
    hashCode() - +Method in class compbio.metadata.Parameter +
      +
    hashCode() - +Method in class compbio.metadata.Preset +
      +
    hashCode() - +Method in class compbio.metadata.ValueConstrain +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-8.html b/website/dm_javadoc/index-files/index-8.html new file mode 100644 index 0000000..0ef4eb0 --- /dev/null +++ b/website/dm_javadoc/index-files/index-8.html @@ -0,0 +1,172 @@ + + + + + + +I-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +I

    +
    +
    IOHelper - Class in compbio.ws.client
     
    IOHelper() - +Constructor for class compbio.ws.client.IOHelper +
      +
    isAmbiguosProtein(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Check whether the sequence confirms to amboguous protein sequence +
    isDefault() - +Method in class compbio.metadata.Limit +
      +
    isExceeded(List<FastaSequence>) - +Method in class compbio.metadata.Limit +
    Checks if the number of sequences or their average length in the dataset + exceeds this limit. +
    isNonAmbNucleotideSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +
    isNucleotideSequence(FastaSequence) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isProteinSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isRequired() - +Method in class compbio.metadata.Option +
    Flag that indicated that this option must be specified in the command + line for an executable to run +
    isValidClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Please note this method closes the input stream provided as a parameter +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index-files/index-9.html b/website/dm_javadoc/index-files/index-9.html new file mode 100644 index 0000000..ac849c7 --- /dev/null +++ b/website/dm_javadoc/index-files/index-9.html @@ -0,0 +1,165 @@ + + + + + + +J-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    +

    +J

    +
    +
    JABAService - Interface in compbio.data.msa
    This is a marker interface, contains no methods
    JalviewAnnotation - Class in compbio.data.sequence
     
    JalviewAnnotation() - +Constructor for class compbio.data.sequence.JalviewAnnotation +
      +
    JManagement - Interface in compbio.data.msa
     
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobExecutionException(String) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(String, Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(String, Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
    + PREV LETTER  + NEXT LETTER + FRAMES   + NO FRAMES   +  + + + +
    + + + +A C D E F G H I J L M N O P R S T U V W
    + + + diff --git a/website/dm_javadoc/index.html b/website/dm_javadoc/index.html new file mode 100644 index 0000000..6750bba --- /dev/null +++ b/website/dm_javadoc/index.html @@ -0,0 +1,39 @@ + + + + + + +Generated Documentation (Untitled) + + + + + + + + + + + +<H2> +Frame Alert</H2> + +<P> +This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client. +<BR> +Link to<A HREF="overview-summary.html">Non-frame version.</A> + + + diff --git a/website/dm_javadoc/overview-frame.html b/website/dm_javadoc/overview-frame.html new file mode 100644 index 0000000..bab78a1 --- /dev/null +++ b/website/dm_javadoc/overview-frame.html @@ -0,0 +1,48 @@ + + + + + + +Overview List + + + + + + + + + + + + + + + +
    +
    + + + + + +
    All Classes +

    + +Packages +
    +compbio.data.msa +
    +compbio.data.sequence +
    +compbio.metadata +
    +compbio.ws.client +
    +

    + +

    +  + + diff --git a/website/dm_javadoc/overview-summary.html b/website/dm_javadoc/overview-summary.html new file mode 100644 index 0000000..ad61afd --- /dev/null +++ b/website/dm_javadoc/overview-summary.html @@ -0,0 +1,171 @@ + + + + + + +Overview + + + + + + + + + + + + +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
     Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +JABAWS datamodel and web services client Javadoc +

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    + +

    + 

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
     Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/overview-tree.html b/website/dm_javadoc/overview-tree.html new file mode 100644 index 0000000..cf09d8a --- /dev/null +++ b/website/dm_javadoc/overview-tree.html @@ -0,0 +1,191 @@ + + + + + + +Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For All Packages

    +
    +
    +
    Package Hierarchies:
    compbio.data.msa, compbio.data.sequence, compbio.metadata, compbio.ws.client
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/package-list b/website/dm_javadoc/package-list new file mode 100644 index 0000000..897043a --- /dev/null +++ b/website/dm_javadoc/package-list @@ -0,0 +1,4 @@ +compbio.data.msa +compbio.data.sequence +compbio.metadata +compbio.ws.client diff --git a/website/dm_javadoc/resources/inherit.gif b/website/dm_javadoc/resources/inherit.gif new file mode 100644 index 0000000..c814867 Binary files /dev/null and b/website/dm_javadoc/resources/inherit.gif differ diff --git a/website/dm_javadoc/serialized-form.html b/website/dm_javadoc/serialized-form.html new file mode 100644 index 0000000..410c949 --- /dev/null +++ b/website/dm_javadoc/serialized-form.html @@ -0,0 +1,317 @@ + + + + + + +Serialized Form + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Serialized Form

    +
    +
    + + + + + +
    +Package compbio.data.sequence
    + +

    + + + + + +
    +Class compbio.data.sequence.UnknownFileFormatException extends Exception implements Serializable
    + +

    +serialVersionUID: 196629543695636854L + +

    + + + + + +
    +Serialized Fields
    + +

    +file

    +
    +File file
    +
    +
    +
    +
    +
    + + + + + +
    +Package compbio.metadata
    + +

    + + + + + +
    +Class compbio.metadata.JobExecutionException extends Exception implements Serializable
    + +

    +serialVersionUID: -5477751361755778769L + +

    + +

    + + + + + +
    +Class compbio.metadata.JobSubmissionException extends Exception implements Serializable
    + +

    +serialVersionUID: 607986894357895572L + +

    + +

    + + + + + +
    +Class compbio.metadata.LimitExceededException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: 15066952180013505L + +

    + + + + + +
    +Serialized Fields
    + +

    +numberOfSequencesAllowed

    +
    +int numberOfSequencesAllowed
    +
    +
    +
    +
    +
    +

    +actualNumberofSequences

    +
    +int actualNumberofSequences
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtAllowed

    +
    +int aSequenceLenghtAllowed
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtActual

    +
    +int aSequenceLenghtActual
    +
    +
    +
    +
    + +

    + + + + + +
    +Class compbio.metadata.ResultNotAvailableException extends Exception implements Serializable
    + +

    +serialVersionUID: -5475613614578761L + +

    + +

    + + + + + +
    +Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: -86624836785110293L + +

    + +

    + + + + + +
    +Class compbio.metadata.WrongParameterException extends Exception implements Serializable
    + +

    +serialVersionUID: -547775417557345769L + +

    + +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/stylesheet.css b/website/dm_javadoc/stylesheet.css new file mode 100644 index 0000000..cbd3428 --- /dev/null +++ b/website/dm_javadoc/stylesheet.css @@ -0,0 +1,29 @@ +/* Javadoc style sheet */ + +/* Define colors, fonts and other style attributes here to override the defaults */ + +/* Page background color */ +body { background-color: #FFFFFF; color:#000000 } + +/* Headings */ +h1 { font-size: 145% } + +/* Table colors */ +.TableHeadingColor { background: #CCCCFF; color:#000000 } /* Dark mauve */ +.TableSubHeadingColor { background: #EEEEFF; color:#000000 } /* Light mauve */ +.TableRowColor { background: #FFFFFF; color:#000000 } /* White */ + +/* Font used in left-hand frame lists */ +.FrameTitleFont { font-size: 100%; font-family: Helvetica, Arial, sans-serif; color:#000000 } +.FrameHeadingFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 } +.FrameItemFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 } + +/* Navigation bar fonts and colors */ +.NavBarCell1 { background-color:#EEEEFF; color:#000000} /* Light mauve */ +.NavBarCell1Rev { background-color:#00008B; color:#FFFFFF} /* Dark Blue */ +.NavBarFont1 { font-family: Arial, Helvetica, sans-serif; color:#000000;color:#000000;} +.NavBarFont1Rev { font-family: Arial, Helvetica, sans-serif; color:#FFFFFF;color:#FFFFFF;} + +.NavBarCell2 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000} +.NavBarCell3 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000} +