<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="java/resources/itextpdf-5.1.0.jar"/>
<classpathentry kind="lib" path="java/resources/commons-codec-1.5.jar"/>
+ <classpathentry kind="lib" path="java/resources/openchart.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
-#Mon Feb 09 15:19:35 PST 2009
eclipse.preferences.version=1
org.eclipse.jdt.core.codeComplete.argumentPrefixes=
org.eclipse.jdt.core.codeComplete.argumentSuffixes=
org.eclipse.jdt.core.codeComplete.staticFieldSuffixes=
org.eclipse.jdt.core.formatter.align_type_members_on_columns=true
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=82
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=82
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=82
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=82
org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
org.eclipse.jdt.core.formatter.alignment_for_enum_constants=50
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=82
org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=82
+org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=48
org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
org.eclipse.jdt.core.formatter.blank_lines_after_package=1
org.eclipse.jdt.core.formatter.blank_lines_before_field=0
org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=end_of_line
org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=end_of_line
org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=end_of_line
+org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line
org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=end_of_line
org.eclipse.jdt.core.formatter.brace_position_for_switch=end_of_line
org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
org.eclipse.jdt.core.formatter.comment.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_switchstatements_compare_to_cases=true
org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=true
org.eclipse.jdt.core.formatter.indentation.size=4
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_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_after_type_annotation=do not insert
org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=do not insert
org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=insert
org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer=do not insert
org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert
org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
+org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=do not insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=insert
org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=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=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_closing_paren_in_parenthesized_expression=insert
org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=insert
org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=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=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_comma_in_type_arguments=do not insert
org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert
org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert
org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
org.eclipse.jdt.core.formatter.insert_space_before_opening_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_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_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.put_empty_statement_on_new_line=true
org.eclipse.jdt.core.formatter.tabulation.char=space
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
-#Thu Mar 03 10:19:18 PST 2011
cleanup.add_default_serial_version_id=false
cleanup.add_generated_serial_version_id=true
cleanup.add_missing_annotations=true
cleanup.always_use_parentheses_in_expressions=true
cleanup.always_use_this_for_non_static_field_access=false
cleanup.always_use_this_for_non_static_method_access=false
+cleanup.convert_functional_interfaces=false
cleanup.convert_to_enhanced_for_loop=true
cleanup.correct_indentation=true
cleanup.format_source_code=true
cleanup.format_source_code_changes_only=false
+cleanup.insert_inferred_type_arguments=false
cleanup.make_local_variable_final=true
cleanup.make_parameters_final=true
cleanup.make_private_fields_final=true
cleanup.qualify_static_member_accesses_with_declaring_class=true
cleanup.qualify_static_method_accesses_with_declaring_class=false
cleanup.remove_private_constructors=true
+cleanup.remove_redundant_type_arguments=true
cleanup.remove_trailing_whitespaces=true
cleanup.remove_trailing_whitespaces_all=true
cleanup.remove_trailing_whitespaces_ignore_empty=false
cleanup.remove_unused_private_types=true
cleanup.sort_members=false
cleanup.sort_members_all=false
+cleanup.use_anonymous_class_creation=false
cleanup.use_blocks=true
cleanup.use_blocks_only_for_return_and_throw=false
+cleanup.use_lambda=true
cleanup.use_parentheses_in_expressions=true
cleanup.use_this_for_non_static_field_access=true
cleanup.use_this_for_non_static_field_access_only_if_necessary=true
cleanup.use_this_for_non_static_method_access=true
cleanup.use_this_for_non_static_method_access_only_if_necessary=true
+cleanup.use_type_arguments=false
cleanup_profile=_forester_java_profile
cleanup_settings_version=2
eclipse.preferences.version=1
formatter_profile=_forester
-formatter_settings_version=11
+formatter_settings_version=12
org.eclipse.jdt.ui.exception.name=e
org.eclipse.jdt.ui.gettersetter.use.is=true
org.eclipse.jdt.ui.keywordthis=false
}
}
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ .getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
final boolean internal_numbers_are_confidences,
final TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean midpoint_reroot )
- throws FileNotFoundException, IOException {
+ throws FileNotFoundException, IOException {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
final public static void showErrorMessage( final Component parent, final String error_msg ) {
printAppletMessage( Constants.PRG_NAME, error_msg );
JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
- + "] Error", JOptionPane.ERROR_MESSAGE );
+ + "] Error", JOptionPane.ERROR_MESSAGE );
}
public static void writePhylogenyToGraphicsFile( final File intree,
phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
+ .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
mf.end();
}
}
final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
- SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
- InvocationTargetException, InterruptedException {
+ SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
+ InvocationTargetException, InterruptedException {
final String os = System.getProperty( "os.name" );
final Runtime runtime = Runtime.getRuntime();
if ( os.toLowerCase().startsWith( "win" ) ) {
final MainPanel main_panel ) {
if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
- + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
- + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
+ + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
+ + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
}
int i = 1;
for( final Phylogeny phy : phys ) {
JOptionPane.showMessageDialog( null,
"Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+ "\n\nError: " + e.getLocalizedMessage(),
- "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
sb.append( s + "\n" );
}
JOptionPane
- .showMessageDialog( null,
- "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
- + sb,
+ .showMessageDialog( null,
+ "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
+ + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+ + sb,
"Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
"An unexpected exception has occured. \nPlease contact: "
+ Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ "\n" + sb,
- "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
}
final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
}
boolean nhx_or_nexus = false;
final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
- .isValidatePhyloXmlAgainstSchema() );
+ .isValidatePhyloXmlAgainstSchema() );
if ( p instanceof NHXParser ) {
nhx_or_nexus = true;
final NHXParser nhx = ( NHXParser ) p;
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9908 experimental";
- final static String PRG_DATE = "150312";
+ final static String VERSION = "0.9909 experimental";
+ final static String PRG_DATE = "150513";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
- "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
+ "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
final static boolean VERBOSE_DEFAULT = false;
final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100;
final static String AUTHOR_EMAIL = "phyloxml@gmail.com";
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
my_panel,\r
"Enter the sequence annotation(s) for the "\r
+ nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
+ JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
String ref = ref_field.getText();\r
String desc = desc_filed.getText();\r
for( final PhylogenyNode n : nodes ) {\r
ForesterUtil.ensurePresenceOfSequence( n );\r
final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
+ : new Annotation( ref );\r
if ( !ForesterUtil.isEmpty( desc ) ) {\r
ann.setDesc( desc );\r
}\r
.showInputDialog( this,\r
"Please enter the minimum for confidence values to be displayed.\n"\r
+ "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final int todo = nodes.size();\r
return;\r
}\r
final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
if ( !delete ) {\r
final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
"Please enter the default line width for PDF export.\n"\r
+ "[current value: "\r
+ getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
float f = 0.0f;\r
+ Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ Constants.US_LETTER_SIZE_X + ", "\r
+ Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
boolean success = true;\r
int x = 0;\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
_mainpanel.getCurrentTreePanel(),\r
_mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
+ .copy() );\r
new Thread( inferrer ).start();\r
}\r
\r
if ( getCurrentTreePanel() != null ) {\r
if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
return true;\r
}\r
}\r
void updateOptions( final Options options ) {\r
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
+ && _background_gradient_cbmi.isSelected() );\r
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
+ && _show_annotation_ref_source.isSelected() );\r
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
+ && _abbreviate_scientific_names.isSelected() );\r
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
}\r
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
+ && _search_case_senstive_cbmi.isSelected() );\r
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
options.setShowScale( _show_scale_cbmi.isSelected() );\r
}\r
}\r
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
&& _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
+ && _print_black_and_white_cbmi.isSelected() );\r
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
}\r
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
+ && _replace_underscores_cbmi.isSelected() );\r
options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
+ && _inverse_search_result_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi != null ) {\r
options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
}\r
showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
}\r
}\r
\r
*/\r
static void about() {\r
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
+ about.append( "Copyright (C) 2015 Christian M Zmasek\n" );\r
about.append( "All Rights Reserved\n" );\r
about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
"Please enter the default size for node shapes.\n"\r
+ "[current value: "\r
+ options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to PDF file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
if ( !opts.isPrintUsingActualSize() ) {\r
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
+ + ")" );\r
}\r
else {\r
mi.setText( "Select Color Scheme..." );\r
JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to an image file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
contentpane.repaint();\r
public class TestPhylogenyReconstruction {
- private final static double ZERO_DIFF = 1.0E-9;
+ private final static double ZERO_DIFF = 1.0E-9;
+ private final static boolean VERBOSE = false;
public static boolean isEqual( final double a, final double b ) {
return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
public static void main( final String[] args ) {
System.out.println( "NJ" );
- if ( testNeighborJoining() ) {
+ if ( testNeighborJoining( VERBOSE ) ) {
System.out.println( " OK." );
}
else {
}
System.out.println( "OK." );
System.out.print( " Neighbor Joining: " );
- if ( !testNeighborJoining() ) {
+ if ( !testNeighborJoining( VERBOSE ) ) {
System.out.println( "failed." );
return false;
}
private static boolean testDistanceCalculationMethods( final File test_dir ) {
try {
final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
- + "bcl.aln" ) );
+ + "bcl.aln" ) );
final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
if ( pwd0.getSize() != 120 ) {
return false;
final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
- 1 );
+ 1 );
m1.setIdentifier( 0, "a" );
m1.setIdentifier( 1, "b" );
m1.setIdentifier( 2, "c" );
final String p2_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root";
final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 18,
- 4 );
+ 4 );
m2.setIdentifier( 0, "a" );
m2.setIdentifier( 1, "b" );
m2.setIdentifier( 2, "c" );
final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m10 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
- 1 );
+ 1 );
m10.setIdentifier( 0, "a" );
m10.setIdentifier( 1, "b" );
m10.setIdentifier( 2, "c" );
final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
- 1 );
+ 1 );
m1.setIdentifier( 0, "a" );
m1.setIdentifier( 1, "b" );
m1.setIdentifier( 2, "y" );
final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r";
final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
- 1 );
+ 1 );
m2.setIdentifier( 0, "a" );
m2.setIdentifier( 1, "b" );
m2.setIdentifier( 2, "y" );
return true;
}
- private static boolean testNeighborJoining() {
+ private static boolean testNeighborJoining( final boolean verbose ) {
try {
NeighborJoining nj = NeighborJoining.createInstance();
final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 );
m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
//NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
- nj = NeighborJoining.createInstance( true, 6 );
+ nj = NeighborJoining.createInstance( verbose, 6 );
final Phylogeny p2 = nj.execute( m );
//Archaeopteryx.createApplication( p2 );
p2.reRoot( p2.getNode( "Bovine" ) );
return false;
}
if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
m = new BasicSymmetricalDistanceMatrix( 4 );
m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 );
- njf = NeighborJoiningF.createInstance( true, 5 );
+ njf = NeighborJoiningF.createInstance( verbose, 5 );
final Phylogeny p2f = njf.execute( m );
p2f.reRoot( p2f.getNode( "Bovine" ) );
if ( isUnequal( p2f.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) {
return false;
}
if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.42027 ) ) {
+ .getDistanceToParent(), 0.42027 ) ) {
return false;
}
if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
}
return false;
}
if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
//
throw new PhyloXmlDataFormatException( "failed to parse element [" + element + "]: " + e.getMessage() );
}
name = element.getValueAsString();
- if ( ( f == -1 ) || ( t == -1 ) || ( conf == ProteinDomain.CONFIDENCE_DEFAULT ) ) {
- throw new PhyloXmlDataFormatException( "from, to, or confidence attribute not set in: " + element );
+ if ( f == -1 ) {
+ throw new PhyloXmlDataFormatException( "\"" + PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM
+ + "\" attribute not set in: " + element );
+ }
+ if ( t == -1 ) {
+ throw new PhyloXmlDataFormatException( "\"" + PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO
+ + "\" attribute not set in: " + element );
+ }
+ if ( conf < 0 ) {
+ throw new PhyloXmlDataFormatException( "\""
+ + PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE
+ + "\" attribute either negative or not set in: " + element );
}
return new ProteinDomain( name, f, t, id, conf );
}
public class ProteinDomain implements PhylogenyData {
- final public static double CONFIDENCE_DEFAULT = 0.0;
+ final public static double CONFIDENCE_DEFAULT = -1;
final public static String IDENTIFIER_DEFAULT = "";
final private String _name;
final private int _from;
sb.append( " " );
sb.append( getId() );
}
- if ( getConfidence() != CONFIDENCE_DEFAULT ) {
+ if ( getConfidence() >= 0 ) {
sb.append( " " );
sb.append( getConfidence() );
}
public final class Test {
private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
- + ForesterUtil.getFileSeparator() + "resources"
- + ForesterUtil.getFileSeparator();
+ + ForesterUtil.getFileSeparator() + "resources"
+ + ForesterUtil.getFileSeparator();
private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
- + ForesterUtil.getFileSeparator() + "test_data"
- + ForesterUtil.getFileSeparator();
+ + ForesterUtil.getFileSeparator() + "test_data"
+ + ForesterUtil.getFileSeparator();
private final static boolean PERFORM_DB_TESTS = true;
private static final boolean PERFORM_WEB_TREE_ACCESS = true;
private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
- + ForesterConstants.PHYLO_XML_VERSION + "/"
- + ForesterConstants.PHYLO_XML_XSD;
+ + ForesterConstants.PHYLO_XML_VERSION + "/"
+ + ForesterConstants.PHYLO_XML_XSD;
private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
- + ForesterConstants.PHYLO_XML_VERSION + "/"
- + ForesterConstants.PHYLO_XML_XSD;
+ + ForesterConstants.PHYLO_XML_VERSION + "/"
+ + ForesterConstants.PHYLO_XML_XSD;
private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
private final static double ZERO_DIFF = 1.0E-9;
public static void main( final String[] args ) {
System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION
- + "]" );
+ + "]" );
Locale.setDefault( Locale.US );
System.out.println( "[Locale: " + Locale.getDefault() + "]" );
int failed = 0;
System.exit( -1 );
}
final long start_time = new Date().getTime();
- System.out.print( "MSA entropy: " );
- if ( Test.testMsaEntropy() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
System.out.print( "Basic node methods: " );
if ( Test.testBasicNodeMethods() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "MSA entropy: " );
+ if ( Test.testMsaEntropy() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
if ( PERFORM_DB_TESTS ) {
System.out.print( "Uniprot Entry Retrieval: " );
if ( Test.testUniprotEntryRetrieval() ) {
return false;
}
if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getConfidence() != 2144 ) {
+ .getConfidence() != 0 ) {
return false;
}
if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
}
if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ .equals( "MOUSE" ) ) {
return false;
}
if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
final String test_dir = Test.PATH_TO_TEST_DATA;
try {
final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
+ + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
parser1.parse();
final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir
- + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
+ + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE );
final List<Protein> proteins = parser2.parse();
if ( parser2.getProteinsEncountered() != 4 ) {
return false;
l.add( s2 );
l.add( s3 );
final Msa msa = BasicMsa.createInstance( l );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
+ //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ //FIXME
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
final Msa msa2 = BasicMsa.createInstance( l2 );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return false;
}
if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" )
- .getDistanceToParent() ) ) {
+ .getDistanceToParent() ) ) {
return false;
}
if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" )
- .getDistanceToParent() ) ) {
+ .getDistanceToParent() ) ) {
return false;
}
if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) {
final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() );
final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() );
final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;"
- + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
- + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
- new NHXParser() );
+ + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; "
+ + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;",
+ new NHXParser() );
if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
return false;
}
if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
.equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) {
System.out.println( n7
- .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
+ .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) );
return false;
}
}
if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
- final Phylogeny p12 = factory
- .create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
- new NHXParser() )[ 0 ];
+ final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
+ new NHXParser() )[ 0 ];
if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
-
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
final Phylogeny p2 = factory
.create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00,"
- + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
- + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
- + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
- + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
- + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
- + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
- + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
- + "7.369400000000000e-02}])",
- new NHXParser() )[ 0 ];
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02,"
+ + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02,"
+ + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00,"
+ + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\","
+ + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02,"
+ + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02,"
+ + "7.369400000000000e-02}])",
+ new NHXParser() )[ 0 ];
if ( p2.getNode( "1" ) == null ) {
return false;
}
// J. of Comput Bio. Vol. 4, No 2, pp.177-187
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1,"
- + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
- new NHXParser() )[ 0 ];
+ + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1,"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;",
+ new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
final SDI sdi6 = new SDI( gene6, species6 );
}
final Phylogeny species6 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene6 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species6.setRooted( true );
gene6.setRooted( true );
Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 );
p6 = null;
final Phylogeny species7 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene7 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species7.setRooted( true );
gene7.setRooted( true );
Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 );
p7 = null;
final Phylogeny species8 = factory
.create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2,"
- + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
- new NHXParser() )[ 0 ];
+ + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)",
+ new NHXParser() )[ 0 ];
final Phylogeny gene8 = factory
.create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4],"
- + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
- + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
- + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
- + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
- new NHXParser() )[ 0 ];
+ + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2],"
+ + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],"
+ + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])"
+ + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])",
+ new NHXParser() )[ 0 ];
species8.setRooted( true );
gene8.setRooted( true );
Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))"
- + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
- + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
- + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
- + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
- new NHXParser() );
+ + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))"
+ + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))"
+ + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))"
+ + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))",
+ new NHXParser() );
SupportCount.count( t0_1, phylogenies_1, true, false );
final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ];
final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),((F,G),X))"
- + "(((((A,Y),B),C),D),((F,G),E))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G))"
- + "(((((A,B),C),D),E),(F,G),Z)"
- + "(((((A,B),C),D),E),(F,G))"
- + "((((((A,B),C),D),E),F),G)"
- + "(((((X,Y),F,G),E),((A,B),C)),D)",
- new NHXParser() );
+ + "(((((A,B),C),D),E),((F,G),X))"
+ + "(((((A,Y),B),C),D),((F,G),E))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "(((((A,B),C),D),E),(F,G),Z)"
+ + "(((((A,B),C),D),E),(F,G))"
+ + "((((((A,B),C),D),E),F),G)"
+ + "(((((X,Y),F,G),E),((A,B),C)),D)",
+ new NHXParser() );
SupportCount.count( t0_2, phylogenies_2, true, false );
final PhylogenyNodeIterator it = t0_2.iteratorPostorder();
while ( it.hasNext() ) {
private static boolean testUniprotEntryRetrieval() {
try {
- final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
+ if ( entry.getMolecularSequence() == null ) {
+ return false;
+ }
if ( !entry
.getMolecularSequence()
.getMolecularSequenceAsString()
.startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
|| !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
- System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
+ System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() );
+ System.out.println( "expected something else." );
return false;
}
}
e.printStackTrace( System.out );
return true;
}
+ catch ( final NullPointerException f ) {
+ f.printStackTrace( System.out );
+ return false;
+ }
catch ( final Exception e ) {
return false;
}
public final class ForesterConstants {
- public final static String FORESTER_VERSION = "1.038";
- public final static String FORESTER_DATE = "141014";
+ public final static String FORESTER_VERSION = "1.039";
+ public final static String FORESTER_DATE = "150513";
public final static String PHYLO_XML_VERSION = "1.10";
public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org";
public final static String PHYLO_XML_XSD = "phyloxml.xsd";
//Protein: 3 letters + 5 numerals\r
//http://www.ncbi.nlm.nih.gov/Sequin/acc.html\r
public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
public final static Pattern GENBANK_PROT_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
public final static Pattern GI_PATTERN = Pattern\r
- .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
+ .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
public final static String UNIPROT_KB_BASE_PATTERN_STR = "((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))";\r
public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "(?:\\b|_)"\r
- + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+ + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]"\r
- + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+ + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern\r
- .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"\r
- + UNIPROT_KB_BASE_PATTERN_STR\r
- + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
+ .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"\r
+ + UNIPROT_KB_BASE_PATTERN_STR\r
+ + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );\r
// RefSeq accession numbers can be distinguished from GenBank accessions\r
// by their distinct prefix format of 2 characters followed by an\r
// underscore character ('_'). For example, a RefSeq protein accession is NP_015325.\r
private final static Pattern REFSEQ_PATTERN = Pattern\r
- .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
+ .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
\r
private SequenceAccessionTools() {\r
// Hiding the constructor.\r
public final class EbiDbEntry implements SequenceDatabaseEntry {
+ private final static boolean DEBUG = false;
private SortedSet<Annotation> _annotations;
private String _chromosome;
private SortedSet<Accession> _cross_references;
if ( _cross_references == null ) {
_cross_references = new TreeSet<Accession>();
}
- System.out.println( "XREF ADDED: " + accession );
+ if ( DEBUG ) {
+ System.out.println( "XREF ADDED: " + accession );
+ }
_cross_references.add( accession );
}
public final static String EMBL_GENBANK = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
public final static String EMBL_REFSEQ = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
public final static String EMBL_EMBL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
- private final static boolean DEBUG = true;
+ private final static boolean DEBUG = false;
private final static String URL_ENC = "UTF-8";
private final static int SLEEP = 200;
private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false;
public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
*/
public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict( final String sn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return );
if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final String my_code = new String( code );
final List<String> result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
if ( result.size() > 0 ) {
final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str );
if ( acc == null ) {
throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str
- + "\"" );
+ + "\"" );
}
if ( acc.getSource().equals( Source.REFSEQ.toString() ) || acc.getSource().equals( Source.EMBL.toString() )
|| acc.getSource().equals( Source.NCBI.toString() ) ) {
}
else {
throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource()
- + "\"" );
+ + "\"" );
}
}
public static List<String> queryEmblDb( final Accession acc, final int max_lines_to_return ) throws IOException {
final StringBuilder url_sb = new StringBuilder();
// url_sb.append( BASE_EMBL_DB_URL );
- System.out.println( "source: " + acc.getSource() );
+ if ( DEBUG ) {
+ System.out.println( "source: " + acc.getSource() );
+ }
if ( acc.getSource().equals( Source.NCBI.toString() ) ) {
url_sb.append( EMBL_GENBANK );
//url_sb.append( '/' );
private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
final int max_taxonomies_return )
- throws IOException {
+ throws IOException {
final List<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
if ( result.size() > 0 ) {
return parseUniProtTaxonomy( result );
return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc
.getSource().equals( Source.UNIPROT.toString() ) )
&& ( acc.getSource().toString().equals( Source.EMBL.toString() ) ) && ( acc.getSource().toString()
- .equals( Source.REFSEQ.toString() ) ) ) ) );
+ .equals( Source.REFSEQ.toString() ) ) ) ) );
}
private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result ) throws IOException {
public final class UniProtEntry implements SequenceDatabaseEntry {
- public final static Pattern BindingDB_PATTERN = Pattern.compile( "BindingDB;\\s+([0-9A-Z]+);" );
- public final static Pattern CTD_PATTERN = Pattern.compile( "CTD;\\s+(\\d+);" );
- public final static Pattern DrugBank_PATTERN = Pattern.compile( "DrugBank;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
- public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PFC]):([^;]+);" );
- public final static Pattern KEGG_PATTERN = Pattern.compile( "KEGG;\\s+([a-z]+:[0-9]+);" );
- public final static Pattern MIM_PATTERN = Pattern.compile( "MIM;\\s+(\\d+);" );
- public final static Pattern NextBio_PATTERN = Pattern.compile( "NextBio;\\s+(\\d+);" );
- public final static Pattern Orphanet_PATTERN = Pattern.compile( "Orphanet;\\s+(\\d+);\\s+([^\\.]+)" );
- public final static Pattern PDB_PATTERN = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
- public final static Pattern PharmGKB_PATTERN = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
- public final static Pattern Reactome_PATTERN = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
- public final static Pattern HGNC_PATTERN = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
- public final static Pattern NCBI_TAXID_PATTERN= Pattern.compile( "NCBI_TaxID=(\\d+)" );
-
+ public final static Pattern BindingDB_PATTERN = Pattern.compile( "BindingDB;\\s+([0-9A-Z]+);" );
+ public final static Pattern CTD_PATTERN = Pattern.compile( "CTD;\\s+(\\d+);" );
+ public final static Pattern DrugBank_PATTERN = Pattern.compile( "DrugBank;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ public final static Pattern GO_PATTERN = Pattern.compile( "GO;\\s+(GO:\\d+);\\s+([PFC]):([^;]+);" );
+ public final static Pattern KEGG_PATTERN = Pattern.compile( "KEGG;\\s+([a-z]+:[0-9]+);" );
+ public final static Pattern MIM_PATTERN = Pattern.compile( "MIM;\\s+(\\d+);" );
+ public final static Pattern NextBio_PATTERN = Pattern.compile( "NextBio;\\s+(\\d+);" );
+ public final static Pattern Orphanet_PATTERN = Pattern.compile( "Orphanet;\\s+(\\d+);\\s+([^\\.]+)" );
+ public final static Pattern PDB_PATTERN = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
+ public final static Pattern PharmGKB_PATTERN = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
+ public final static Pattern Reactome_PATTERN = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+ public final static Pattern HGNC_PATTERN = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
+ public final static Pattern NCBI_TAXID_PATTERN = Pattern.compile( "NCBI_TaxID=(\\d+)" );
private String _ac;
private SortedSet<Accession> _cross_references;
private String _gene_name;
&& ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
&& ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() )
&& ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences()
- .isEmpty() ) );
+ .isEmpty() ) );
}
private void addCrossReference( final Accession accession ) {
final StringBuffer sq_buffer = new StringBuffer();
boolean is_aa = false;
for( final String line : lines ) {
- //System.out.println( line );
if ( line.startsWith( "AC" ) ) {
e.setAc( SequenceDbWsTools.extractFromTo( line, "AC", ";" ) );
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- if ( line.indexOf( "{" ) > 0 ) {
+ if ( line.indexOf( "{" ) > 0 ) {
e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
}
else {
}
}
else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- if ( line.indexOf( "{" ) > 0 ) {
+ if ( line.indexOf( "{" ) > 0 ) {
e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
}
else {
e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
}
-
}
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
-
if ( line.indexOf( "Short=" ) > 0 ) {
- if ( line.indexOf( "{" ) > 0 ) {
+ if ( line.indexOf( "{" ) > 0 ) {
e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", "{" ) );
}
else {
e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
}
-
}
}
else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
if ( line.indexOf( "Name=" ) > 0 ) {
- if ( line.indexOf( "{" ) > 0 ) {
+ if ( line.indexOf( "{" ) > 0 ) {
e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", "{" ) );
}
else {
sq_buffer.append( line.replaceAll( "\\s+", "" ) );
}
}
- if ( ( sq_buffer.length() > 0 ) && is_aa ) {
- e.setMolecularSequence( BasicSequence.createAaSequence( e.getAccession(), sq_buffer.toString() ) );
+ if ( sq_buffer.length() > 0 ) {
+ if ( is_aa ) {
+ e.setMolecularSequence( BasicSequence.createAaSequence( e.getAccession(), sq_buffer.toString() ) );
+ }
+ else {
+ e.setMolecularSequence( BasicSequence.createDnaSequence( e.getAccession(), sq_buffer.toString() ) );
+ }
}
return e;
}
<name>bc seq</name>
<domain_architecture length="124">
<domain from="120" to="130" confidence="0.9" id=""> A </domain>
- <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
+ <domain from="21" to="44" confidence="0" id="pfam"> B </domain>
<domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
- <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
+ <domain id="123" from="34" to="43" confidence="1.3e-34"> D </domain>
</domain_architecture>
</sequence>
<date>
git://source.jalview.org / jalview.git / commitdiff