From 01695c742a6ff14ef4928fc305e6d2a30035f9ac Mon Sep 17 00:00:00 2001 From: darolmar Date: Sat, 27 Sep 2014 17:35:27 +0200 Subject: [PATCH] JAL-1355 --- resources/lang/Messages.properties | 24 ++++++++++++------------ src/jalview/datamodel/Alignment.java | 2 ++ 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 50086dc..cdbe0f3 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -365,7 +365,7 @@ label.enter_label = Enter label label.enter_label_for_the_structure = Enter a label for the structure? label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ? label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0} -label.add_pdbentry_to_view = Do you want to add {0} to the view called\n'{1}'\n +label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n label.align_to_existing_structure_view = Align to existing structure view label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually. label.couldnt_load_file = Couldn't load file @@ -378,7 +378,7 @@ label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remov label.public_das_source = Public DAS source - not editable label.input_alignment_from_url = Input Alignment From URL label.input_alignment = Input Alignment -label.couldnt_import_as_vamsas_session = Couldn't import '{0}' as a new vamsas session. +label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session. label.vamsas_document_import_failed = Vamsas Document Import Failed label.couldnt_locate = Couldn't locate {0} label.url_not_found = URL not found @@ -495,7 +495,7 @@ label.select_colour_maximum_value = Select Colour for Maximum Value label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment = Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment. label.open_url_param = Open URL {0} label.open_url_seqs_param = Open URL ({0}..) ({1} seqs) -label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence '{0}' +label.load_pdb_file_associate_with_sequence = Load a PDB file and associate it with sequence {0} label.reveal_hidden_columns = Reveal Hidden Columns with Right Mouse Button label.dark_colour = Dark Colour label.light_colour = Light Colour @@ -770,7 +770,7 @@ label.sequence_database_search = Sequence Database Search label.analysis = Analysis label.protein_disorder = Protein Disorder label.source_from_db_source = Sources from {0} -label.from_msname = from '{0}' +label.from_msname = from {0} label.superpose_with = Superpose with ... action.do = Do label.scale_label_to_column = Scale Label to Column @@ -873,13 +873,13 @@ error.empty_view_cannot_be_updated = empty view cannot be updated. error.mismatch_between_number_of_sequences_in_block = Mismatch between number of sequences in block {0} ({1}) and the original view ({2}) error.padding_not_yet_implemented = Padding not yet implemented error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view = Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks={0}) -error.unknown_seq_cigar_operation = Unknown SeqCigar operation '{0}' +error.unknown_seq_cigar_operation = Unknown SeqCigar operation {0} error.implementation_bug_parse_cigar_string = Implementation bug in parseCigarString error.implementation_error_invalid_operation_string = Implementation error. Invalid operation string. error.invalid_range_string = Invalid range string (must be zero or positive number) error.implementation_error_delete_range_out_of_bounds = Implementation Error: deleteRange out of bounds: start must be non-negative and less than end. error.implementation_error = Implementation error -error.implementation_error_unknown_operation = Implementation Error! Unknown operation '{0}' +error.implementation_error_unknown_operation = Implementation Error! Unknown operation {0} error.implementation_error_unexpected_null_from_get_sequence_and_deletions = Implementation Error - unexpected null from getSequenceAndDeletions error.implementation_error_set_seq_null = Implementation Error - _setSeq(null,...) error.implementation_error_s = Implementation Error: _s= {0} @@ -887,9 +887,9 @@ error.implementation_error_seqcigar_possible = SeqCigar: Possible implementation error.implmentation_bug_seq_null = Implementation Bug. Null seq error.implementation_bug_cigar_operation_list_range_list = Implementation Bug. Cigar Operation list!= range list error.not_yet_implemented_cigar_object_from_cigar_string = NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence. -error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation '{0}' '{1}' not one of '{2}', '{3}', or '{4}'. +error.implementation_bug_cigar_operation = Implementation Bug. Cigar Operation {0} {1} not one of {2}, {3}, or {4}. error.implementation_error_for_new_cigar = Implementation error for new Cigar(SequenceI) -error.implementation_error_cigar_seq_no_operations = Implementation error: {0}'th sequence Cigar has no operations. +error.implementation_error_cigar_seq_no_operations = Implementation error: {0}th sequence Cigar has no operations. error.implementation_error_jmol_getting_data = Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016 error.implementation_error_no_pdbentry_from_index = Implementation error - no corresponding pdbentry (for index {0}) to add sequences mappings to error.jmol_version_not_compatible_with_jalview_version = Jmol version {0} is not compatible with this version of Jalview. Report this problem at issues.jalview.org @@ -955,7 +955,7 @@ error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web ser error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets error.no_aacon_service_found = No AACon service found error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain! -error.couldnt_encode_as_utf8 = Couldn't encode '{0}' as UTF-8. +error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8. error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process error.dbrefsource_implementation_exception =DBRefSource Implementation Exception @@ -994,9 +994,9 @@ exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character exception.mismatched_closing_char = Mismatched closing character {0} exception.mismatched_opening_char = Mismatched opening character {0} at {1} exception.invalid_datasource_couldnt_obtain_reader = Invalid datasource. Could not obtain Reader -exception.index_value_not_in_range = {0}: Index value '{1}' not in range [0..{2}] +exception.index_value_not_in_range = {0}: Index value {1} not in range [0..{2}] exception.unterminated_cigar_string = Unterminated cigar string -exception.unexpected_operation_cigar_string_pos = Unexpected operation '{0}' in cigar string (position {1} in '{2}' +exception.unexpected_operation_cigar_string_pos = Unexpected operation {0} in cigar string (position {1} in {2} exception.couldnt_parse_responde_from_annotated3d_server = Couldn't parse response from Annotate3d server exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding @@ -1009,7 +1009,7 @@ exception.failed_to_read_data_from_source = Failed to read data from source: {0} exception.no_init_source_stream = Unitialised Source Stream exception.invalid_source_stream = Invalid Source Stream: {0} error.implementation_error_reset_called_for_invalid_source = Implementation Error: Reset called for invalid source. -exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ('{1}'\n{2})\ndiffer from number of prediction sites in prediction ({3}) +exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3}) label.mapped = mapped exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0} diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 98abfe2..5e75725 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -20,6 +20,8 @@ */ package jalview.datamodel; +import jalview.util.MessageManager; + import java.util.*; /** -- 1.7.10.2