--- /dev/null
+/logs
+/distro
+/jobsout
+/JABAWSLogFilename.*
+/testsrc/testdata/*.written
+/testsrc/testdata/alirna.ps
+
+
+
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>\r
+<projectDescription>\r
+ <name>clustengine-2.5</name>\r
+ <comment></comment>\r
+ <projects>\r
+ </projects>\r
+ <buildSpec>\r
+ <buildCommand>\r
+ <name>org.eclipse.wst.jsdt.core.javascriptValidator</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>org.eclipse.jdt.core.javabuilder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>org.eclipse.wst.validation.validationbuilder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>net.sourceforge.metrics.builder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ </buildSpec>\r
+ <natures>\r
+ <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>\r
+ <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>\r
+ <nature>org.eclipse.wst.common.project.facet.core.nature</nature>\r
+ <nature>org.eclipse.jdt.core.javanature</nature>\r
+ <nature>org.eclipse.wst.jsdt.core.jsNature</nature>\r
+ <nature>net.sourceforge.metrics.nature</nature>\r
+ </natures>\r
+</projectDescription>\r
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**/binaries/*" kind="src" path=""/>
+ <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="output" path=""/>
+</classpath>
--- /dev/null
+#Thu Aug 11 15:56:45 BST 2011\r
+add_header=true\r
+eclipse.preferences.version=1\r
+header_text=/* Copyright (c) 2011 Peter Troshin\r\n * \r\n * JAva Bioinformatics Analysis Web Services (JABAWS) @version\: 2.0 \r\n * \r\n * This library is free software; you can redistribute it and/or modify it under the terms of the\r\n * Apache License version 2 as published by the Apache Software Foundation\r\n * \r\n * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r\n * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r\n * License for more details.\r\n * \r\n * A copy of the license is in apache_license.txt. It is also available here\:\r\n * @see\: http\://www.apache.org/licenses/LICENSE-2.0.txt\r\n * \r\n * Any republication or derived work distributed in source code form\r\n * must include this copyright and license notice.\r\n */\r
+project_specific_settings=true\r
+replace_header=true\r
+replacements=<?xml version\="1.0" standalone\="yes"?>\n\n<replacements>\n<replacement key\="get" scope\="1" mode\="0">Gets the</replacement>\n<replacement key\="set" scope\="1" mode\="0">Sets the</replacement>\n<replacement key\="add" scope\="1" mode\="0">Adds the</replacement>\n<replacement key\="edit" scope\="1" mode\="0">Edits the</replacement>\n<replacement key\="remove" scope\="1" mode\="0">Removes the</replacement>\n<replacement key\="init" scope\="1" mode\="0">Inits the</replacement>\n<replacement key\="parse" scope\="1" mode\="0">Parses the</replacement>\n<replacement key\="create" scope\="1" mode\="0">Creates the</replacement>\n<replacement key\="build" scope\="1" mode\="0">Builds the</replacement>\n<replacement key\="is" scope\="1" mode\="0">Checks if is</replacement>\n<replacement key\="print" scope\="1" mode\="0">Prints the</replacement>\n<replacement key\="has" scope\="1" mode\="0">Checks for</replacement>\n</replacements>\n\n\r
--- /dev/null
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.6
+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=16
+org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
+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_resources_in_try=80
+org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
+org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
+org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
+org.eclipse.jdt.core.formatter.blank_lines_after_package=1
+org.eclipse.jdt.core.formatter.blank_lines_before_field=0
+org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0
+org.eclipse.jdt.core.formatter.blank_lines_before_imports=1
+org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1
+org.eclipse.jdt.core.formatter.blank_lines_before_method=1
+org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1
+org.eclipse.jdt.core.formatter.blank_lines_before_package=0
+org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1
+org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations=1
+org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_block=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_switch=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
+org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
+org.eclipse.jdt.core.formatter.comment.format_block_comments=true
+org.eclipse.jdt.core.formatter.comment.format_header=false
+org.eclipse.jdt.core.formatter.comment.format_html=true
+org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
+org.eclipse.jdt.core.formatter.comment.format_line_comments=true
+org.eclipse.jdt.core.formatter.comment.format_source_code=true
+org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
+org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
+org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
+org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
+org.eclipse.jdt.core.formatter.comment.line_length=80
+org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
+org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
+org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
+org.eclipse.jdt.core.formatter.compact_else_if=true
+org.eclipse.jdt.core.formatter.continuation_indentation=2
+org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2
+org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off
+org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on
+org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false
+org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true
+org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true
+org.eclipse.jdt.core.formatter.indent_empty_lines=false
+org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true
+org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
+org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
+org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
+org.eclipse.jdt.core.formatter.indentation.size=4
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_member=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_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=insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_try=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_try_resources=insert
+org.eclipse.jdt.core.formatter.insert_space_after_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert
+org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_binary_operator=insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
+org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.join_lines_in_comments=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.lineSplit=140
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.tabulation.char=tab
+org.eclipse.jdt.core.formatter.tabulation.size=4
+org.eclipse.jdt.core.formatter.use_on_off_tags=false
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
--- /dev/null
+eclipse.preferences.version=1
+formatter_profile=_my
+formatter_settings_version=12
--- /dev/null
+XDOCLETBUILDERACTIVE=true
+XDOCLETHOME=
+XDOCLETUSEGLOBAL=true
+XDOCLETVERSION=1.2.1
+eclipse.preferences.version=1
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+ <wb-module deploy-name="jaba">
+ <wb-resource deploy-path="/" source-path="/website" tag="defaultRootSource"/>
+ <wb-resource deploy-path="/binaries" source-path="binaries"/>
+ <wb-resource deploy-path="/jobsout" source-path="jobsout"/>
+ <wb-resource deploy-path="/ExecutionStatistic" source-path="ExecutionStatistic"/>
+ <wb-resource deploy-path="/conf" source-path="conf"/>
+ <wb-resource deploy-path="/statpages" source-path="statpages"/>
+ <wb-resource deploy-path="/WEB-INF" source-path="WEB-INF"/>
+ <wb-resource deploy-path="/META-INF" source-path="META-INF"/>
+ <wb-resource deploy-path="/WEB-INF/classes" source-path="/log"/>
+<!-- <dependent-module archiveName="jaba-client.jar" deploy-path="/WEB-INF/lib/" handle="module:/resource/jaba-client/jaba-client">
+ <dependency-type>uses</dependency-type>
+ </dependent-module> -->
+ <property name="java-output-path" value="WEB-INF/classes"/>
+ <property name="context-root" value="jabaws"/>
+ </wb-module>
+</project-modules>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+ <runtime name="Apache Tomcat v7.0 (v.41)"/>
+ <fixed facet="wst.jsdt.web"/>
+ <fixed facet="java"/>
+ <fixed facet="jst.web"/>
+ <installed facet="java" version="1.6"/>
+ <installed facet="jst.web" version="2.4"/>
+ <installed facet="wst.jsdt.web" version="1.0"/>
+</faceted-project>
--- /dev/null
+org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file
--- /dev/null
+Window
\ No newline at end of file
--- /dev/null
+DELEGATES_PREFERENCE=delegateValidatorList
+USER_BUILD_PREFERENCE=enabledBuildValidatorListorg.eclipse.jst.j2ee.internal.classpathdep.ClasspathDependencyValidator;org.eclipse.jst.j2ee.internal.web.validation.UIWarValidator;
+USER_MANUAL_PREFERENCE=enabledManualValidatorListorg.eclipse.jst.j2ee.internal.classpathdep.ClasspathDependencyValidator;org.eclipse.jst.j2ee.internal.web.validation.UIWarValidator;
+USER_PREFERENCE=overrideGlobalPreferencestruedisableAllValidationfalseversion1.2.402.v201212031633
+eclipse.preferences.version=1
+override=true
+suspend=false
+vals/org.eclipse.jst.jsp.core.JSPBatchValidator/groups=0107include01113projectNature131org.eclipse.jdt.core.javanature0107include110111contentType134org.eclipse.jst.jsp.core.jspsourceT111contentType142org.eclipse.jst.jsp.core.jspfragmentsourceT111contentType134org.eclipse.jst.jsp.core.tagsourceT07fileext03jspF07fileext04jspfF07fileext03jsfF07fileext03tagF07fileext04tagfF07fileext03jsvF07fileext04jtplF0107exclude0104file08binariesF02
+vals/org.eclipse.jst.jsp.core.JSPContentValidator/groups=0107include09111contentType134org.eclipse.jst.jsp.core.jspsourceT111contentType142org.eclipse.jst.jsp.core.jspfragmentsourceT07fileext03jspF07fileext04jspfF07fileext03jsfF07fileext03tagF07fileext04tagfF07fileext03jsvF07fileext04jtplF0107exclude0104file08binariesF02
+vals/org.eclipse.wst.dtd.core.dtdDTDValidator/global=FF01
+vals/org.eclipse.wst.html.core.HTMLValidator/groups=0107include06111contentType136org.eclipse.wst.html.core.htmlsourceT07fileext04htmlF07fileext05xhtmlF07fileext03htmF07fileext04htplF07fileext03wmlF0107exclude0604file08binariesF0204file118website/dm_javadocF0204file120website/full_javadocF0204file117website/prog_docsF0204file115website/archiveF0204file113website/testsF02
+vals/org.eclipse.wst.xml.core.xml/groups=0107include05111contentType128org.eclipse.core.runtime.xmlT111contentType134org.eclipse.wst.xml.core.xmlsourceT111contentType134org.eclipse.wst.xml.core.xslsourceT111contentType134org.eclipse.jst.jsp.core.tldsourceT07fileext03xmlF0107exclude08113projectNature134org.eclipse.jst.j2ee.ejb.EJBNature113projectNature130org.eclipse.jst.j2ee.EARNature04file08.projectT0104file110.classpathT0104file110.settings/T0204file116testsrc/testdataF0204file113website/testsF02111contentType134org.eclipse.wst.dtd.core.dtdsourceF
+vals/org.eclipse.wst.xsd.core.xsd/groups=0107include0107fileext03xsdF0107exclude01111contentType134org.eclipse.wst.dtd.core.dtdsourceF
+vf.version=3
--- /dev/null
+Runtime dependency for web services. They are required to run a web service \r
+within servlet container e.g. tomcat\r
+\r
+webservices-rt.jar\r
+webservices-tools.jar \r
+webservices-api.jar \r
+\r
+JABAWS Statistics web application dependencies: \r
+\r
+- Display Tag 1.2 dependencies\r
+\r
+commons-beanutils-1.7.0.jar\r
+commons-collections-3.2.jar\r
+commons-lang-2.3.jar\r
+commons-logging-1.1.jar\r
+displaytag-1.2.jar\r
+displaytag-export-poi-1.2.jar\r
+itext-1.4.7.jar\r
+jstl-1.1.2.jar\r
+poi-3.2-FINAL-20081019.jar\r
+standard-1.1.2.jar\r
+\r
+- Derby database driver for statistics database \r
+derby.jar
\ No newline at end of file
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>\r
+<endpoints xmlns='http://java.sun.com/xml/ns/jax-ws/ri/runtime' version='2.0'>\r
+ <endpoint name='RegistryWS'\r
+ implementation='compbio.ws.server.RegistryWS'\r
+ url-pattern='/RegistryWS'/>\r
+ <endpoint name='ClustalWS'\r
+ implementation='compbio.ws.server.ClustalWS'\r
+ url-pattern='/ClustalWS'/>\r
+ <endpoint name='ClustalOWS'\r
+ implementation='compbio.ws.server.ClustalOWS'\r
+ url-pattern='/ClustalOWS'/>\r
+ <endpoint name='MuscleWS'\r
+ implementation='compbio.ws.server.MuscleWS'\r
+ url-pattern='/MuscleWS'/>\r
+ <endpoint name='TcoffeeWS'\r
+ implementation='compbio.ws.server.TcoffeeWS'\r
+ url-pattern='/TcoffeeWS'/>\r
+ <endpoint name='MafftWS'\r
+ implementation='compbio.ws.server.MafftWS'\r
+ url-pattern='/MafftWS'/>\r
+ <endpoint name='ProbconsWS'\r
+ implementation='compbio.ws.server.ProbconsWS'\r
+ url-pattern='/ProbconsWS'/>\r
+ <endpoint name='MSAprobsWS'\r
+ implementation='compbio.ws.server.MSAprobsWS'\r
+ url-pattern='/MSAprobsWS'/>\r
+ <endpoint name='GLprobsWS'\r
+ implementation='compbio.ws.server.GLprobsWS'\r
+ url-pattern='/GLprobsWS'/>\r
+ <endpoint name='AAConWS'\r
+ implementation='compbio.ws.server.AAConWS'\r
+ url-pattern='/AAConWS'/>\r
+ <endpoint name='JronnWS'\r
+ implementation='compbio.ws.server.JronnWS'\r
+ url-pattern='/JronnWS'/>\r
+ <endpoint name='DisemblWS'\r
+ implementation='compbio.ws.server.DisemblWS'\r
+ url-pattern='/DisemblWS'/>\r
+ <endpoint name='GlobPlotWS'\r
+ implementation='compbio.ws.server.GlobPlotWS'\r
+ url-pattern='/GlobPlotWS'/>\r
+ <endpoint name='IUPredWS'\r
+ implementation='compbio.ws.server.IUPredWS'\r
+ url-pattern='/IUPredWS'/>\r
+ <endpoint name='JpredWS'\r
+ implementation='compbio.ws.server.JpredWS'\r
+ url-pattern='/JpredWS'/>\r
+ <endpoint name='RNAalifoldWS'\r
+ implementation='compbio.ws.server.RNAalifoldWS'\r
+ url-pattern='/RNAalifoldWS'/>\r
+</endpoints>\r
--- /dev/null
+<web-app xmlns="http://java.sun.com/xml/ns/j2ee"\r
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"\r
+ version="2.4">\r
+\r
+<display-name>JABAWS</display-name>\r
+<description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>\r
+\r
+\r
+ <!-- JABAWS listeners -->\r
+ <listener>\r
+ <listener-class>compbio.ws.server.MainManager</listener-class>\r
+ </listener>\r
+ <listener>\r
+ <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>\r
+ </listener>\r
+ <listener>\r
+ <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>\r
+ </listener>\r
+ <listener>\r
+ <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>\r
+ </listener>\r
+\r
+\r
+ <!-- Session timeout in minutes -->\r
+ <session-config>\r
+ <session-timeout>20</session-timeout>\r
+ </session-config>\r
+\r
+\r
+ <servlet>\r
+ <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>\r
+ <servlet-name>listings</servlet-name>\r
+ <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>\r
+ <init-param>\r
+ <param-name>debug</param-name>\r
+ <param-value>0</param-value>\r
+ </init-param>\r
+ <init-param>\r
+ <param-name>readonly</param-name>\r
+ <param-value>true</param-value>\r
+ </init-param>\r
+ <init-param>\r
+ <param-name>listings</param-name>\r
+ <param-value>true</param-value>\r
+ </init-param>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+\r
+ <!-- JABAWS servlets -->\r
+ <servlet>\r
+ <description>Display pre-calculated accounting info</description>\r
+ <servlet-name>DisplayStat</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <description>WebServices Status</description>\r
+ <servlet-name>ServiceStatus</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>DownloadRedirector</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <description>WebService Status with no UI. Accepts web service name as a parameter</description>\r
+ <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <description>Display job list</description>\r
+ <servlet-name>Joblist</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.Joblist</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <description>Display monthly summary statistics</description>\r
+ <servlet-name>AnnualStat</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <description>Display monthly summary statistics with no links to details</description>\r
+ <servlet-name>PublicAnnualStat</servlet-name>\r
+ <servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>RegistryWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>ClustalWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>ClustalOWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>MuscleWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>MafftWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>TcoffeeWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>ProbconsWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>MSAprobsWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>GLprobsWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>AAConWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>JronnWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>DisemblWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>GlobPlotWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>IUPredWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>JpredWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+ <servlet>\r
+ <servlet-name>RNAalifoldWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <!-- JABAWS servlet mappings -->\r
+ <servlet-mapping>\r
+ <servlet-name>listings</servlet-name>\r
+ <url-pattern>/</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>DownloadRedirector</servlet-name>\r
+ <url-pattern>/download</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>DisplayStat</servlet-name>\r
+ <url-pattern>/DisplayStat</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>ServiceStatus</servlet-name>\r
+ <url-pattern>/ServiceStatus</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>HttpCodeResponseServiceStatus</servlet-name>\r
+ <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>AnnualStat</servlet-name>\r
+ <url-pattern>/AnnualStat</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>PublicAnnualStat</servlet-name>\r
+ <url-pattern>/PublicAnnualStat</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>Joblist</servlet-name>\r
+ <url-pattern>/Joblist</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>RegistryWS</servlet-name>\r
+ <url-pattern>/RegistryWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>ClustalWS</servlet-name>\r
+ <url-pattern>/ClustalWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>ClustalOWS</servlet-name>\r
+ <url-pattern>/ClustalOWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>MuscleWS</servlet-name>\r
+ <url-pattern>/MuscleWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>MafftWS</servlet-name>\r
+ <url-pattern>/MafftWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>TcoffeeWS</servlet-name>\r
+ <url-pattern>/TcoffeeWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>ProbconsWS</servlet-name>\r
+ <url-pattern>/ProbconsWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>MSAprobsWS</servlet-name>\r
+ <url-pattern>/MSAprobsWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>GLprobsWS</servlet-name>\r
+ <url-pattern>/GLprobsWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>AAConWS</servlet-name>\r
+ <url-pattern>/AAConWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>JronnWS</servlet-name>\r
+ <url-pattern>/JronnWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>DisemblWS</servlet-name>\r
+ <url-pattern>/DisemblWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>GlobPlotWS</servlet-name>\r
+ <url-pattern>/GlobPlotWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>IUPredWS</servlet-name>\r
+ <url-pattern>/IUPredWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>JpredWS</servlet-name>\r
+ <url-pattern>/JpredWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>RNAalifoldWS</servlet-name>\r
+ <url-pattern>/RNAalifoldWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+\r
+ <!-- JABAWS security constraints -->\r
+ <security-constraint>\r
+ <web-resource-collection>\r
+ <web-resource-name>Administrator pages</web-resource-name>\r
+ <!-- Prohibit access to any resources -->\r
+ <url-pattern>/DisplayStat</url-pattern>\r
+ <url-pattern>/Joblist</url-pattern>\r
+ <url-pattern>/AnnualStat</url-pattern>\r
+ <url-pattern>/conf/*</url-pattern>\r
+ <url-pattern>/binaries/*</url-pattern>\r
+ <url-pattern>/jobsout/*</url-pattern>\r
+ <url-pattern>/testsrc/*</url-pattern>\r
+ <url-pattern>/lib/*</url-pattern>\r
+ <url-pattern>/test-output/*</url-pattern>\r
+ <!-- Uncomment this to secure services status checker \r
+ <url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>\r
+ <url-pattern>/ServiceStatus</url-pattern>\r
+ -->\r
+ <!-- No http-method means all methods are constrained -->\r
+ </web-resource-collection>\r
+ <auth-constraint>\r
+ <role-name>admin</role-name>\r
+ </auth-constraint>\r
+ </security-constraint>\r
+\r
+\r
+ <!-- unsupported HTTP methods -->\r
+ <security-constraint>\r
+ <web-resource-collection>\r
+ <web-resource-name>unsupported HTTP methods</web-resource-name>\r
+ <url-pattern>/*</url-pattern>\r
+ <http-method>PUT</http-method>\r
+ <http-method>DELETE</http-method>\r
+ <http-method>TRACE</http-method>\r
+ <http-method>OPTIONS</http-method>\r
+ </web-resource-collection>\r
+ <auth-constraint/>\r
+ </security-constraint>\r
+\r
+\r
+ <!-- Define the Login Configuration for this Application -->\r
+ <login-config>\r
+ <auth-method>BASIC</auth-method>\r
+ <realm-name>JABAWS administrators</realm-name>\r
+ </login-config>\r
+\r
+\r
+ <!-- Security roles referenced by this web application -->\r
+ <security-role>\r
+ <description>The role that is required to log in and view JABAWS internals</description>\r
+ <role-name>admin</role-name>\r
+ </security-role>\r
+\r
+</web-app>\r
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+
+<project default="proteocache" name="Build ProteoCache - Results repository for the Dundee Resource" basedir=".">
+
+ <property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
+
+ <!-- Distributive file names-->
+ <property name="distdir" value="distro"/>
+ <mkdir dir="${distdir}" />
+
+ <!-- projects details -->
+ <property name="project.url" value="http://www.compbio.dundee.ac.uk/proteocache"/>
+ <property name="product" value="ProteoCache"/>
+ <property name="author" value="Alexander Sherstnev"/>
+
+ <!-- dependencies on other compbio projects -->
+ <property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>
+ <property name="compbio-util" value="compbio-util-1.4.jar"/>
+ <property name="compbio-ga" value="compbio-ga-1.0.jar"/>
+
+ <!-- products -->
+ <property name="proteocache_version" value="2.1.0"/>
+ <property name="datamodel" value="${distdir}/datamodel-${proteocache_version}.jar"/>
+ <property name="datamodel-src" value="${distdir}/datamodel-src-${proteocache_version}.jar"/>
+ <property name="min-proteocache-client" value="${distdir}/min-proteocache-client-${proteocache_version}.jar"/>
+ <property name="min-proteocache-client-nolog" value="${distdir}/min-proteocache-client-nolog-${proteocache_version}.jar"/>
+ <property name="proteocache-client-src" value="${distdir}/proteocache-client-src-${proteocache_version}.jar"/>
+ <property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
+ <property name="full-proteocache-client" value="${distdir}/full-proteocache-client-${proteocache_version}.jar"/>
+ <property name="proteocache-source-jar" value="${distdir}/proteocache-src-${proteocache_version}.jar"/>
+ <property name="full-proteocache-client-pack" value="${distdir}/full-proteocache-client-${proteocache_version}-pack.zip"/>
+ <property name="proteocache" value="${distdir}/proteocache.war"/>
+ <!-- TODO
+ <property name="proteocache-dundee" value="${distdir}/proteocache-dundee.war"/>
+ -->
+ <property name="proteocache-no-binaries" value="${distdir}/proteocache-no-binaries.war"/>
+ <property name="binaries" value="${distdir}/binaries.zip"/>
+ <property name="proteocache-devel-web" value="${distdir}/proteocache-devel-website.zip"/>
+
+ <!--Whole project archive -->
+ <property name="proteocache-project" value="${distdir}/proteocache-project.zip"/>
+
+ <!-- java -->
+ <property name="test.src" location="${basedir}/testsrc" />
+ <property name="classes" location="${basedir}/WEB-INF/classes" />
+ <property name="lib.path" location="${basedir}/lib" />
+ <property name="web.lib.path" location="${basedir}/WEB-INF/lib" />
+ <property name="test.lib.path" location="${basedir}/testsrc/lib" />
+ <property name="activity.log" location="${basedir}/activity.log" />
+
+ <!-- add libraries -->
+ <path id="project.classpath">
+ <fileset dir="${lib.path}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${web.lib.path}">
+ <include name="*.jar" />
+ </fileset>
+ </path>
+
+ <!-- add test classes -->
+ <path id="test.classpath">
+ <fileset dir="${test.lib.path}">
+ <include name="*.jar" />
+ </fileset>
+ <pathelement location="${classes}" />
+ </path>
+
+ <fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
+ <!-- Datamodel -->
+ <include name="compbio/data/**"/>
+ <include name="compbio/metadata/**"/>
+ <!-- Engine -->
+ <include name="compbio/engine/**"/>
+ <!-- Casscode -->
+ <include name="compbio/casscode/**"/>
+ <!-- Logging configuration -->
+ </fileset>
+
+ <!-- Clean temp directories -->
+ <target name="clean">
+ <delete dir="${classes}" />
+ <delete dir="${basedir}/logs" />
+ <delete file="${distdir}/binaries.zip" />
+ <delete file="${basedir}/activity.log" />
+ <delete file="${basedir}/derby.log" />
+ <mkdir dir="${classes}" />
+ <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+ </target>
+
+ <!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
+ <target name="full-clean" depends="clean">
+ <delete>
+ <fileset dir="${distdir}">
+ <include name="*.jar"/>
+ <include name="*.zip"/>
+ <include name="*.war"/>
+ </fileset>
+ </delete>
+ </target>
+
+ <target name="clearStatDB" description="Remove all records from statistics database">
+ <echo>Cleaning Statistics database</echo>
+ <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
+ <jvmarg value="-Dlog4j.configuration=file:log/log4j.properties.statdb" />
+ <classpath refid="project.classpath" />
+ </java>
+ </target>
+
+ <!--
+ The compilation order is
+ 1. datamodel
+ 2. engine
+ 3. casscode
+ 4. testscr
+ 5. webservices
+ Packages of the lower order could not have dependencies on the packages on the next layer.
+ So, casscode (layer 3) depends on the enginesand the datamodel but engine does not depend on
+ anything in casscode or any other layers above. Testsrc is not allowed to test webservices.
+ -->
+ <target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
+ <!-- copy files to class path-->
+ <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+ <!-- Complile the datamodel first -->
+ <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6"
+ source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the engines -->
+ <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6"
+ source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the casscode -->
+ <javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6"
+ source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the webservices -->
+ <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"
+ source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the tests -->
+ <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"
+ source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ <classpath refid="test.classpath" />
+ </javac>
+ </target>
+
+ <!--
+ Compile with optimisation. Do not compile testsrc
+ The compilation order is
+ 1. datamodel
+ 2. engine
+ 3. casscode
+ 4. webservices
+ Packages of the lower order could not have dependencies on the packages on the next layer.
+ So casscode (layer 3) depends on the engine and the datamodel but engine does not depend
+ on anything in casscode or any other layers above.
+ -->
+ <target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
+ <!-- copy files to class path-->
+ <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+ <!-- Complile the datamodel -->
+ <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <compilerarg value="-Xlint:-unchecked" />
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the engine -->
+ <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <compilerarg value="-Xlint:-all" />
+ <compilerarg value="-Xlint:-unchecked" />
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the casscode -->
+ <javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <compilerarg value="-Xlint:-unchecked" />
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the webservices -->
+ <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <compilerarg value="-Xlint:-unchecked" />
+ <classpath refid="project.classpath" />
+ </javac>
+ </target>
+
+ <target name="datamodel-jar" depends="compile" description="Pack data model classes">
+ <echo>Jar file: Minimal WS client jar</echo>
+ <delete file="${basedir}/${datamodel}">
+ </delete>
+ <jar jarfile="${basedir}/${datamodel}">
+ <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
+ <include name="${compbio-util}"/>
+ <include name="${compbio-annotation}"/>
+ </zipgroupfileset>
+ <fileset dir="${basedir}/WEB-INF/classes/">
+ <include name="compbio/data/sequence/*.class"/>
+ <include name="compbio/metadata/*.class"/>
+ </fileset>
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Implementation-Title" value="Datamodel for ${product} " />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="minimal-proteocache-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
+ <echo>Jar file: Minimal WS client jar</echo>
+ <delete file="${basedir}/${min-proteocache-client}"></delete>
+ <jar jarfile="${basedir}/${min-proteocache-client}">
+ <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
+ <fileset dir="${basedir}/WEB-INF/classes/">
+ <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
+ <include name="compbio/data/msa/**"/>
+ <include name="compbio/ws/client/**"/>
+ </fileset>
+ <zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Implementation-Title" value="Minimal ${product} Client" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ <delete file="${basedir}/${min-proteocache-client-nolog}"></delete>
+ <jar jarfile="${basedir}/${min-proteocache-client-nolog}">
+ <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
+ <fileset dir="${basedir}/WEB-INF/classes/">
+ <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
+ <include name="compbio/data/msa/**"/>
+ <include name="compbio/ws/client/**"/>
+ </fileset>
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Implementation-Title" value="Minimal ${product} Client" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="full-proteocache-client-jar" depends="compile" description="Pack datamodel, engine and casscode">
+ <echo>Jar file: Full ProteoCache client jar</echo>
+ <delete file="${full-proteocache-client}">
+ </delete>
+ <jar jarfile="${full-proteocache-client}">
+ <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
+ <include name="${compbio-util}"/>
+ <include name="${compbio-annotation}"/>
+ <include name="drmaa.jar"/>
+ </zipgroupfileset>
+ <fileset refid="fullclient"/>
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Implementation-Title" value="Full ${product} Client" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="full-proteocache-client" depends="full-proteocache-client-jar" description="Pack sources and configuration files">
+ <echo>Packing binaries, and configuration files</echo>
+ <zip destfile="${full-proteocache-client-pack}" >
+ <zipgroupfileset file="${binaries}" />
+ <zipfileset dir="conf" prefix="conf" >
+ <exclude name="**/temp/**"/>
+ </zipfileset>
+ <fileset file="${full-proteocache-client}" />
+ </zip>
+ </target>
+
+
+ <target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
+ <delete file="${basedir}/${proteocache-source-jar}">
+ </delete>
+ <jar jarfile="${basedir}/${proteocache-source-jar}">
+ <zipgroupfileset excludes="META-INF/*.MF" file="${datamodel-src}"/>
+ <fileset dir="${basedir}/casscode">
+ <include name="**"/>
+ </fileset>
+ <fileset dir="${basedir}/engine">
+ <include name="**"/>
+ </fileset>
+ <fileset dir="${basedir}/webservices/">
+ <include name="**"/>
+ </fileset>
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Implementation-Title" value="${product} Source Code Archive" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="datamodel-source-jar" depends="compile" description="Pack java sources">
+ <delete file="${datamodel-src}">
+ </delete>
+ <jar jarfile="${datamodel-src}">
+ <fileset dir="${basedir}/datamodel">
+ <include name="**"/>
+ </fileset>
+ <zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
+ <include name="**"/>
+ </zipgroupfileset>
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="full-proteocache-jar" depends="compile" description="Pack datamodel, engine, casscode, configuration, binaries and webservices">
+ <echo>Jar file: Full WS client jar</echo>
+ <delete file="${full-proteocache-client}">
+ </delete>
+ <jar jarfile="${full-proteocache-client}">
+ <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
+ <include name="log4j-1.2.15.jar"/>
+ <include name="${compbio-util}"/>
+ <include name="${compbio-annotation}"/>
+ <include name="drmaa.jar"/>
+ </zipgroupfileset>
+ <fileset refid="fullclient">
+ </fileset>
+ <fileset dir="${basedir}/WEB-INF/classes/">
+ <!-- Statistics web application -->
+ <include name="compbio/stat/**"/>
+ <!-- Web services-->
+ <include name="compbio/ws/**"/>
+ </fileset>
+ <!-- Set WSTester as main to help user to test their deployments -->
+ <manifest>
+ <attribute name="Built-By" value="${author}" />
+ <attribute name="Class-Path" value="." />
+ <attribute name="Main-Class" value="compbio.ws.client.WSTester" />
+ <attribute name="Implementation-Title" value="${product}" />
+ <attribute name="Implementation-Vendor" value="${author}" />
+ <attribute name="Implementation-URL" value="${project.url}" />
+ </manifest>
+ </jar>
+ </target>
+
+ <target name="proteocache-no-binaries" depends="full-proteocache-jar, clearStatDB" description="Prepare proteocache war file without native binaries">
+ <echo>Preparing a war file without binaries</echo>
+ <delete file="${proteocache-no-binaries}">
+ </delete>
+ <zip destfile="${proteocache-no-binaries}" whenempty="create">
+ <zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
+ <exclude name="classes"/>
+ <!-- These are included into JABA client so exclude the jars -->
+ <exclude name="lib/drmaa.jar"/>
+ <exclude name="lib/log4j-1.2.15.jar"/>
+ <exclude name="lib/${compbio-annotation}"/>
+ <exclude name="lib/${compbio-util}"/>
+
+ <include name="web.xml"/>
+ <include name="sun-jaxws.xml"/>
+ <include name="lib/*"/>
+ </zipfileset>
+ <zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
+ <zipfileset dir="${basedir}/statpages" prefix="statpages" />
+ <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
+ <zipfileset dir="conf" prefix="conf" >
+ <exclude name="**/temp/**"/>
+ </zipfileset>
+ <!-- Add proteocache web site apart from the binary archive -->
+ <zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
+ <zipfileset dir="." includes="${full-proteocache-client}" fullpath="WEB-INF/lib/proteocache-client.jar"/>
+ <!-- Put a copy of log4j configuration file where it can be used -->
+ <zipfileset dir="log" includes="log4j.properties" prefix="WEB-INF/classes"/>
+ </zip>
+ </target>
+
+ <target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >
+ <echo>Packing data for internal web site</echo>
+ <delete file="${proteocache-devel-web}">
+ </delete>
+ <zip destfile="${proteocache-devel-web}" whenempty="create">
+ <!-- Add proteocache web site apart from the binary archive -->
+ <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
+ </zip>
+ </target>
+
+ <target name="proteocache-complete" depends="proteocache-no-binaries" description="Prepare proteocache war file without runtime dependency - JAXWS jars">
+ <echo>Preparing a complete war file</echo>
+ <delete file="${proteocache}">
+ </delete>
+ <copy tofile="${proteocache}" file="${proteocache-no-binaries}"/>
+ <zip destfile="${proteocache}" update="true" >
+ <zipgroupfileset file="${binaries}" />
+ </zip>
+ </target>
+
+ <target name="build-all" depends="full-proteocache-client, minimal-proteocache-client-jar, proteocache-no-binaries, proteocache-complete, datamodel-jar, datamodel-source-jar, source-jar" description="Build-all the distributives"/>
+
+ <!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->
+ <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">
+ <delete file="${proteocache-project}">
+ </delete>
+ <zip destfile="${proteocache-project}" whenempty="create" >
+ <fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>
+ <!-- Add jobsout directory but no content -->
+ <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="*/**"/>
+ </zip>
+ </target>
+
+<!-- Test targets -->
+ <taskdef name="testNG" classname="org.testng.TestNGAntTask">
+ <classpath refid="test.classpath">
+ </classpath>
+ </taskdef>
+
+ <target name="CustomTest" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG haltonfailure="true" enableassert="true" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <xmlfileset dir="." includes="temp-testng-customsuite.xml"/>
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Run_cluster_dependent_test" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG groups="cluster" haltonfailure="true" enableassert="true" parallel="false" verbose="3">
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Test" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance, webservices" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Performance_tests" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG haltonfailure="true" enableassert="true" verbose="3" groups="performance" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Test_casscode" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG groups="casscode" haltonfailure="true" verbose="3" enableassert="true" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Test_engines" depends="compile_with_debug">
+ <delete file="${activity.log}"/>
+ <testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="All_cluster_independent_windows_only_tests" depends="compile_with_debug">
+ <delete file="${activity.log}" failonerror="false"/>
+ <testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="All_cluster_independent_tests" depends="compile_with_debug">
+ <delete file="${activity.log}" failonerror="false"/>
+ <testNG excludedgroups="cluster, performance" haltonfailure="true" verbose="3" enableassert="true" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <classfileset dir="${classes}" includes="**/*.class" />
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+
+ <target name="Rerun_failed_tests" depends="compile_with_debug">
+ <delete file="${activity.log}" failonerror="false"/>
+ <testNG haltonfailure="true" enableassert="true" verbose="9" >
+ <jvmarg value="-server" />
+ <jvmarg value="-enableassertions" />
+ <jvmarg value="-Xms1024m" />
+ <jvmarg value="-Xmx1024m" />
+ <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
+ <classpath refid="test.classpath" />
+ <classpath refid="project.classpath" />
+ <xmlfileset dir="." includes="test-output/testng-failed.xml"/>
+ <sysproperty key="TestingDataPath" value="${data.src}"/>
+ </testNG>
+ </target>
+</project>
git://source.jalview.org / proteocache.git / commitdiff