<td>jnetfile</td>
<td>fileName</td>
<td>Secondary structure predictions from a <a
- href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise
- file will be added to the first sequence in the alignment.</td>
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred</a> Concise
+ file will be added to the first sequence in the alignment.<br/>
+ <em>jpredfile</em> can be used interchangeably with this parameter.</td>
</tr>
<tr>
<td>PDBfile(x)</td>
<td>defaultColour</td>
<td> <em>One of: </em><br>
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices</td>
<td>Default is no colour.</td>
</tr>
<tr>
action.remove = Remove
action.remove_redundancy = Remove Redundancy...
action.pairwise_alignment = Pairwise Alignment
-action.by_rna_helixes = By RNA Helices
action.user_defined = User Defined...
action.by_conservation = By Conservation
action.wrap = Wrap
label.score_model_enhconservation = Physicochemical property conservation
label.status_bar = Status bar
label.out_to_textbox = Output to Textbox
-label.clustalx = Clustalx
+# delete Clustal - use FileFormat name instead
label.clustal = Clustal
-label.zappo = Zappo
-label.taylor = Taylor
+# label.colourScheme_<schemeName> as in JalviewColourScheme
+label.colourScheme_clustal = Clustalx
+label.colourScheme_blosum62 = BLOSUM62 Score
+label.colourScheme_%_identity = Percentage Identity
+label.colourScheme_zappo = Zappo
+label.colourScheme_taylor = Taylor
+label.colourScheme_hydrophobic = Hydrophobicity
+label.colourScheme_helix_propensity = Helix Propensity
+label.colourScheme_strand_propensity = Strand Propensity
+label.colourScheme_turn_propensity = Turn Propensity
+label.colourScheme_buried_index = Buried Index
+label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
+label.colourScheme_nucleotide = Nucleotide
+label.colourScheme_t-coffee_scores = T-Coffee Scores
+label.colourScheme_rna_helices = By RNA Helices
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.pfam = PFAM
label.pileup = Pileup
label.pir = PIR
-label.hydrophobicity = Hydrophobicity
-label.helix_propensity = Helix Propensity
-label.strand_propensity = Strand Propensity
-label.turn_propensity = Turn Propensity
-label.buried_index = Buried Index
-label.purine_pyrimidine = Purine/Pyrimidine
-label.percentage_identity = Percentage Identity
-label.blosum62 = BLOSUM62
-label.blosum62_score = BLOSUM62 Score
-label.tcoffee_scores = T-Coffee Scores
-label.average_distance_bloslum62 = Average Distance Using BLOSUM62
+label.average_distance_blosum62 = Average Distance Using BLOSUM62
label.neighbour_blosum62 = Neighbour Joining Using BLOSUM62
label.show_annotations = Show annotations
label.hide_annotations = Hide annotations
label.add_reference_annotations = Add reference annotations
label.find_tip = Search alignment, selection or sequence ids for a subsequence (ignoring gaps).<br>Accepts regular expressions - search Help for 'regex' for details.
label.colour_text = Colour Text
-label.show_non_conversed = Show nonconserved
+label.show_non_conserved = Show nonconserved
label.overview_window = Overview Window
label.none = None
label.above_identity_threshold = Above Identity Threshold
label.structure = Structure
label.show_pdbstruct_dialog = 3D Structure Data...
label.view_rna_structure = VARNA 2D Structure
-label.clustalx_colours = Clustalx colours
-label.above_identity_percentage = Above % Identity
label.create_sequence_details_report_annotation_for = Annotation for {0}
label.sequence_details_for = Sequence Details for {0}
label.sequence_name = Sequence Name
label.points_for_params = Points for {0}
label.transformed_points_for_params = Transformed points for {0}
label.graduated_color_for_params = Graduated Feature Colour for {0}
-label.select_backgroud_colour = Select Background Colour
+label.select_background_colour = Select Background Colour
label.invalid_font = Invalid Font
label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment
label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment
label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment
- label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction
+ label.jnet_secondary_structure_prediction = JPred Secondary Structure Prediction
label.multiharmony = Multi-Harmony
label.unable_start_web_service_analysis = Unable to start web service analysis
label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.
-error.implementation_error_cannot_duplicate_colour_scheme = Serious implementation error: cannot duplicate colourscheme {0}
error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
exception.ssm_context_is_null = SSM context is null
error.idstring_seqstrings_only_one_per_sequence = idstrings and seqstrings contain one string each per sequence
error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported
error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!
error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0}
- error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented
+ error.multiple_jnet_subjob_merge_not_implemented = Multiple JPred subjob merging not yet implemented
label.job_never_ran = Job never ran - input returned to user.
error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more
error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
exception.bad_pattern_to_regex_perl_code = bad pattern to Regex.perlCode: {0}
exception.no_stub_implementation_for_interface = There is no stub implementation for the interface: {0}
exception.cannot_set_endpoint_address_unknown_port = Cannot set Endpoint Address for Unknown Port {0}
-exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Querying matching opening parenthesis for non-closing parenthesis character {0}
exception.mismatched_unseen_closing_char = Mismatched (unseen) closing character {0}
exception.mismatched_closing_char = Mismatched closing character {0}
exception.mismatched_opening_char = Mismatched opening character {0} at {1}
exception.application_test_npe = Application test: throwing an NullPointerException It should arrive at the console
exception.overwriting_vamsas_id_binding = Overwriting vamsas id binding
exception.overwriting_jalview_id_binding = Overwriting jalview id binding
-error.implementation_error_unknown_file_format_string = Implementation error: Unknown file format string
exception.failed_to_resolve_gzip_stream = Failed to resolve GZIP stream
exception.problem_opening_file_also_tried = Problem opening {0} (also tried {1}) : {2}
exception.problem_opening_file = Problem opening {0} : {1}
exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
exception.unknown_format_for_file = Unknown format {0} for file \: \n{1}
label.remove_gaps = Remove Gaps
- exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence!
+ exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JPred Query sequence!
exception.server_timeout_try_later = Server timed out - try again later\n
exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later.
exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0}
info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
info.no_jobs_ran = No jobs ran
info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}
- info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}
+ info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JPred job result data\!\n{2}
info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n
info.alignment_object_method_notes = \nAlignment Object Method Notes\n
info.server_exception = \n{0} Server exception\!\n{1}
action.export_hidden_sequences = Export Hidden Sequences
action.export_features = Export Features
label.export_settings = Export Settings
-label.save_as_biojs_html = Save as BioJs HTML
label.pdb_web-service_error = PDB Web-service Error
label.structure_chooser_manual_association = Structure Chooser - Manual association
label.structure_chooser_filter_time = Structure Chooser - Filter time ({0})
action.remove = Eliminar
action.remove_redundancy = Eliminar redundancia...
action.pairwise_alignment = Alineamiento de pares...
-action.by_rna_helixes = Por hélices de RNA
action.user_defined = Definido por el usuario...
action.by_conservation = Por conservación
action.wrap = Envolver
label.score_model_enhconservation = Conservación de las propiedades físico-químicas
label.status_bar = Barra de estado
label.out_to_textbox = Generar cuadro de texto
-label.clustalx = Clustalx
label.clustal = Clustal
-label.zappo = Zappo
-label.taylor = Taylor
+# label.colourScheme_<schemeName> as in JalviewColourScheme
+label.colourScheme_clustal = Clustalx
+label.colourScheme_blosum62 = Puntuación del BLOSUM62
+label.colourScheme_%_identity = Porcentaje de identidad
+label.colourScheme_zappo = Zappo
+label.colourScheme_taylor = Taylor
+label.colourScheme_hydrophobic = Hidrofobicidad
+label.colourScheme_helix_propensity = Tendencia de la hélice
+label.colourScheme_strand_propensity = Tendencia de la hebra
+label.colourScheme_turn_propensity = Tendencia de giro
+label.colourScheme_buried_index = Índice de encubrimiento
+label.colourScheme_purine/pyrimidine = Purina/Pirimidina
+label.colourScheme_nucleotide = Nucleótido
+label.colourScheme_t-coffee_scores = Puntuación del T-Coffee
+label.colourScheme_rna_helices = Por hélices de RNA
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.pfam = PFAM
label.pileup = Pileup
label.pir = PIR
-label.hydrophobicity = Hidrofobicidad
-label.helix_propensity = Tendencia de la hélice
-label.strand_propensity = Tendencia de la hebra
-label.turn_propensity = Tendencia de giro
-label.buried_index = Índice de encubrimiento
-label.purine_pyrimidine = Purina/Pirimidina
-label.percentage_identity = Porcentaje de identidad
-label.blosum62 = BLOSUM62
-label.blosum62_score = Puntuación del BLOSUM62
-label.tcoffee_scores = Puntuación del T-Coffee
-label.average_distance_bloslum62 = Distancia Media Usando BLOSUM62
+label.average_distance_blosum62 = Distancia Media Usando BLOSUM62
label.neighbour_blosum62 = Neighbour Joining usando BLOSUM62
label.show_annotations = Mostrar anotaciones
label.colour_text = Color del texto
-label.show_non_conversed = Mostrar no conservadas
+label.show_non_conserved = Mostrar no conservadas
label.overview_window = Ventana resumen
label.none = Ninguno
label.above_identity_threshold = Por encima del umbral de identidad
label.enter_pdb_id = Introducir PDB Id
label.text_colour = Color del texto
label.structure = Estructura
-label.clustalx_colours = Colores de Clustalx
-label.above_identity_percentage = Sobre % identidad
label.create_sequence_details_report_annotation_for = Anotación para {0}
label.sequence_details_for = Detalles de la secuencia para {0}
label.sequence_name = Nombre de la secuencia
label.points_for_params = Puntos de {0}
label.transformed_points_for_params = Puntos transformados de {0}
label.graduated_color_for_params = Color graduado para la característica de {0}
-label.select_backgroud_colour = Seleccionar color de fondo
+label.select_background_colour = Seleccionar color de fondo
label.invalid_font = Fuente no válida
label.separate_multiple_accession_ids = Separar los accession id con un punto y coma ";"
label.replace_commas_semicolons = Cambiar comas por puntos y comas
label.muscle_multiple_protein_sequence_alignment = Alineamiento múltiple de secuencias de proteínas con Muscle
label.mafft_multiple_sequence_alignment = Alineamiento múltiple de secuencias con MAFFT
label.clustalw_multiple_sequence_alignment = Alineamiento múltiple de secuencias con ClustalW
- label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JNet
+ label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JPred
label.multiharmony = Multi-Harmony
label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis
label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview.
error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento
error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia
error.implementation_error_cannot_map_alignment_sequences = Error de implementación: no es posible maper un alineamiento de secuencias desde distintos conjuntos de datos en un único alineamiento en el documento VAMSAS.
-error.implementation_error_cannot_duplicate_colour_scheme = Error grave de implementación: no es posible duplicar el esquema cromático {0}
error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo
exception.ssm_context_is_null = El contexto SSM es nulo
error.idstring_seqstrings_only_one_per_sequence = idstrings y seqstrings contienen una cadena por cada secuencia
error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = ¡Error de implementación! Todavía no se soportan varios trabajos de predicción asociados a una única secuencia.
error.implementation_error_invalid_msa_index_for_job = ¡Error de implementación! Valor msaIndex no válido para JPredJob en el objeto de entrada MSA padre!
error.implementation_error_startjob_called = Error de implementación - StartJob(JpredJob) invocado en {0}
- error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JNet conjuntos.
+ error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JPred conjuntos.
label.job_never_ran = El trabajo nunca se ejecutó - entrada devuelta al usuario.
error.implementation_error_minlen_must_be_greater_zero = Error de implementación: minlen debe ser cero o más
error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0}
exception.bad_pattern_to_regex_perl_code = patrón erróneo en Regex.perlCode: {0}
exception.no_stub_implementation_for_interface = No existe una implementación del stub para la interfaz: {0}
exception.cannot_set_endpoint_address_unknown_port = No es posible estabelcer la dirección de punto final para el puerto desconocido {0}
-exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis = Consultando la coincidencia de apertura de paréntesis para paréntesis sin cerrar (?)
exception.mismatched_unseen_closing_char = Discordancia (no vista) en el carácter de cierre {0}
exception.mismatched_closing_char = Carácter de cierre discordante {0}
exception.mismatched_opening_char = Carácter de apertura discordante {0} en {1}
exception.application_test_npe = Prueba de aplicación: lanzando un NullPointerException que debe aparecer en la consola
exception.overwriting_vamsas_id_binding = Sobreescribiendo la asociación al VAMSAS id
exception.overwriting_jalview_id_binding = Sobreescribiendo la asociación al Jalview id
-error.implementation_error_unknown_file_format_string = Error de implementación: cadena de formato de fichero desconocido
exception.failed_to_resolve_gzip_stream = Fallo al resolver el flujo GZIP
exception.problem_opening_file_also_tried = Problema abriendo {0} (también se intentó {1}) : {2}
exception.problem_opening_file = Problema abriendo {0} : {1}
exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
exception.unknown_format_for_file = Formato desconocido {0} para el fichero \: \n{1}
label.remove_gaps = Eliminar huecos
- exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JNet Query!
+ exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JPred Query!
exception.server_timeout_try_later = Tiempo de conexi\u00F3n ha expirado - int\u00E9ntelo de nuevo m\u00E1s tarde\n
exception.web_service_returned_null_try_later= El servidor {0} ha devuelto un objeto nulo, por lo que probablemente no se haya podido contactar con él. Inténtelo de nuevo más tarde.
exception.cannot_contact_service_endpoint_at = No es posible contactar por el punto de acceso al servicio en {0}
info.job_couldnt_be_run_incorrect_param_setting = No es posible ejecutar el trabjao porque el servidor no soporta algunos de los par\u00E1metros.\n{0}\nPor favor, aseg\u00FArese de que ha usado los par\u00E1metros adecuados para este servicio\n
info.no_jobs_ran = No se ha ejecutado ningún trabajo
info.failed_to_submit_prediction = Error al enviar la predicci\u00F3n\:\n{0} {1}
- info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JNet no v\u00E1lidos\!\n{2}
+ info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JPred no v\u00E1lidos\!\n{2}
info.failed_to_submit_sequences_for_alignment = Error al enviar la secuencias para el alineamiento.\nLo m\u00E1s probable es que haya un problema en el servidor.\nSimplemente, cierre la ventana\n
info.alignment_object_method_notes = \nNotas sobre los m\u00E9todos del objeto alineamiento\n
info.server_exception = \n{0} Excepci\u00F3n del servidor\!\n{1}
info.select_filter_option=Escoger Opción de Filtro / Entrada Manual
info.invalid_msa_input_mininfo=Necesita por lo menos dos secuencias con al menos 3 residuos cada una, sin regiones ocultas entre ellas.
label.chimera_missing=Visualizador de estructura Chimera no encontrado.<br/>Por favor, introduzca la ruta de Chimera,<br/>o descargar e instalar la UCSF Chimera.
-label.save_as_biojs_html=Guardar como HTML BioJs
exception.fts_server_unreachable=Jalview no puede conectar con el servidor {0}. \nPor favor asegúrese de que está conectado a Internet y vuelva a intentarlo.
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
++import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
++import jalview.schemes.JalviewColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
MenuItem editGroupName = new MenuItem();
-- protected MenuItem clustalColour = new MenuItem();
++ CheckboxMenuItem noColour = new CheckboxMenuItem();
-- protected MenuItem zappoColour = new MenuItem();
++ protected CheckboxMenuItem clustalColour = new CheckboxMenuItem();
-- protected MenuItem taylorColour = new MenuItem();
++ protected CheckboxMenuItem zappoColour = new CheckboxMenuItem();
-- protected MenuItem hydrophobicityColour = new MenuItem();
++ protected CheckboxMenuItem taylorColour = new CheckboxMenuItem();
-- protected MenuItem helixColour = new MenuItem();
++ protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem();
-- protected MenuItem strandColour = new MenuItem();
++ protected CheckboxMenuItem helixColour = new CheckboxMenuItem();
-- protected MenuItem turnColour = new MenuItem();
++ protected CheckboxMenuItem strandColour = new CheckboxMenuItem();
-- protected MenuItem buriedColour = new MenuItem();
++ protected CheckboxMenuItem turnColour = new CheckboxMenuItem();
-- protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
++ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
-- protected MenuItem userDefinedColour = new MenuItem();
++ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
-- protected MenuItem PIDColour = new MenuItem();
++ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
-- protected MenuItem BLOSUM62Colour = new MenuItem();
++ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
-- MenuItem noColourmenuItem = new MenuItem();
++ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
-- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
++ protected MenuItem userDefinedColour = new MenuItem();
++
++ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
++
++ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
final AlignmentPanel ap;
MenuItem createGroupMenuItem = new MenuItem();
-- MenuItem nucleotideMenuItem = new MenuItem();
--
- MenuItem purinePyrimidineMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
{
menu1.setLabel(MessageManager.getString("action.edit_group"));
groupMenu.remove(createGroupMenuItem);
+ if (sg.cs != null)
+ {
+ abovePIDColour.setState(sg.cs.getThreshold() > 0);
- conservationMenuItem.setState(sg.cs.conservationApplied());
++ conservationColour.setState(sg.cs.conservationApplied());
+ }
}
-
++ setSelectedColour(sg.cs);
}
else
{
}
/**
++ * Select the menu item (if any) matching the current colour scheme. This
++ * works by matching the menu item name (not display text) to the canonical
++ * name of the colour scheme.
++ *
++ * @param cs
++ */
++ protected void setSelectedColour(ColourSchemeI cs)
++ {
++ if (cs == null)
++ {
++ noColour.setState(true);
++ }
++ else
++ {
++ for (int i = 0; i < colourMenu.getItemCount(); i++)
++ {
++ MenuItem item = colourMenu.getItem(i);
++ if (item instanceof CheckboxMenuItem)
++ {
++ if (cs.getSchemeName().equals(item.getName()))
++ {
++ ((CheckboxMenuItem) item).setState(true);
++ }
++ }
++ }
++ }
++ }
++
++ /**
* Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
*
* @param seq
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- Map<String, String> tipEntries = new TreeMap<String, String>();
+ SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences,
linkMenu.add(item);
}
++ /**
++ * Actions on selecting / unselecting a checkbox menu item
++ */
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == abovePIDColour)
- {
- abovePIDColour_itemStateChanged();
- }
- else if (evt.getSource() == showColourText)
- {
- showColourText_itemStateChanged();
- }
- else if (evt.getSource() == showText)
+ Object source = evt.getSource();
- if (source == abovePIDColour)
- {
- abovePIDColour_itemStateChanged();
- }
- else if (source == conservationMenuItem)
++ if (source == noColour)
{
- showText_itemStateChanged();
- conservationMenuItem_itemStateChanged();
- }
- else if (source == showColourText)
- {
- showColourText_itemStateChanged();
- }
- else if (source == showText)
- {
- showText_itemStateChanged();
++ noColourmenuItem_actionPerformed();
}
- else if (evt.getSource() == showBoxes)
- else if (source == showBoxes)
++ else if (source == clustalColour)
{
-- showBoxes_itemStateChanged();
++ clustalColour_actionPerformed();
}
- else if (evt.getSource() == displayNonconserved)
- else if (source == displayNonconserved)
++ else if (source == BLOSUM62Colour)
{
-- this.showNonconserved_itemStateChanged();
++ BLOSUM62Colour_actionPerformed();
}
-- }
--
-- @Override
-- public void actionPerformed(ActionEvent evt)
-- {
-- Object source = evt.getSource();
-- if (source == clustalColour)
++ else if (source == PIDColour)
{
-- clustalColour_actionPerformed();
++ PIDColour_actionPerformed();
}
else if (source == zappoColour)
{
{
buriedColour_actionPerformed();
}
-- else if (source == nucleotideMenuItem)
++ else if (source == nucleotideColour)
{
nucleotideMenuItem_actionPerformed();
}
- else if (source == purinePyrimidineMenuItem)
-
- else if (source == userDefinedColour)
++ else if (source == purinePyrimidineColour)
{
- userDefinedColour_actionPerformed();
+ purinePyrimidineColour_actionPerformed();
}
-
- else if (source == userDefinedColour)
- else if (source == PIDColour)
++ else if (source == abovePIDColour)
{
- userDefinedColour_actionPerformed();
- PIDColour_actionPerformed();
++ abovePIDColour_itemStateChanged();
}
- else if (source == PIDColour)
- else if (source == BLOSUM62Colour)
++ else if (source == conservationColour)
{
- PIDColour_actionPerformed();
- BLOSUM62Colour_actionPerformed();
++ conservationMenuItem_itemStateChanged();
}
- else if (source == BLOSUM62Colour)
- else if (source == noColourmenuItem)
++ else if (source == showColourText)
{
- BLOSUM62Colour_actionPerformed();
- noColourmenuItem_actionPerformed();
++ showColourText_itemStateChanged();
+ }
- else if (source == noColourmenuItem)
++ else if (source == showText)
+ {
- noColourmenuItem_actionPerformed();
++ showText_itemStateChanged();
+ }
- else if (source == conservationMenuItem)
++ else if (source == showBoxes)
+ {
- conservationMenuItem_itemStateChanged();
++ showBoxes_itemStateChanged();
++ }
++ else if (source == displayNonconserved)
++ {
++ this.showNonconserved_itemStateChanged();
++ }
++ }
++
++ /**
++ * Actions on clicking a menu item
++ */
++ @Override
++ public void actionPerformed(ActionEvent evt)
++ {
++ Object source = evt.getSource();
++ if (source == userDefinedColour)
++ {
++ userDefinedColour_actionPerformed();
}
else if (source == unGroupMenuItem)
{
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
showText.setLabel(MessageManager.getString("action.text"));
groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
-- colourMenu.add(noColourmenuItem);
++ colourMenu.add(noColour);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
-- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(purinePyrimidineMenuItem);
++ colourMenu.add(nucleotideColour);
++ colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
-- colourMenu.add(conservationMenuItem);
++ colourMenu.add(conservationColour);
-- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
-- noColourmenuItem.addActionListener(this);
++ noColour.setLabel(MessageManager.getString("label.none"));
++ noColour.addItemListener(this);
++ /*
++ * setName allows setSelectedColour to do its thing
++ */
clustalColour.setLabel(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(this);
+ .getString("label.colourScheme_clustal"));
- clustalColour.addActionListener(this);
++ clustalColour.setName(JalviewColourScheme.Clustal.toString());
++ clustalColour.addItemListener(this);
++ BLOSUM62Colour.setLabel(MessageManager
++ .getString("label.colourScheme_blosum62"));
++ BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
++ BLOSUM62Colour.addItemListener(this);
++ PIDColour.setLabel(MessageManager
++ .getString("label.colourScheme_%_identity"));
++ PIDColour.setName(JalviewColourScheme.PID.toString());
++ PIDColour.addItemListener(this);
+ zappoColour.setLabel(MessageManager
+ .getString("label.colourScheme_zappo"));
- zappoColour.addActionListener(this);
++ zappoColour.setName(JalviewColourScheme.Zappo.toString());
++ zappoColour.addItemListener(this);
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
- taylorColour.addActionListener(this);
++ taylorColour.setName(JalviewColourScheme.Taylor.toString());
++ taylorColour.addItemListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
+ .getString("label.colourScheme_hydrophobic"));
- hydrophobicityColour.addActionListener(this);
++ hydrophobicityColour
++ .setName(JalviewColourScheme.Hydrophobic.toString());
++ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
- helixColour.addActionListener(this);
++ helixColour.setName(JalviewColourScheme.Helix.toString());
++ helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_percentage"));
+ .getString("label.colourScheme_strand_propensity"));
- strandColour.addActionListener(this);
++ strandColour.setName(JalviewColourScheme.Strand.toString());
++ strandColour.addItemListener(this);
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
- turnColour.addActionListener(this);
++ turnColour.setName(JalviewColourScheme.Turn.toString());
++ turnColour.addItemListener(this);
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_threshold"));
++ buriedColour.setName(JalviewColourScheme.Buried.toString());
++ buriedColour.addItemListener(this);
++ nucleotideColour.setLabel(MessageManager
++ .getString("label.colourScheme_nucleotide"));
++ nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
++ nucleotideColour.addItemListener(this);
++ purinePyrimidineColour.setLabel(MessageManager
++ .getString("label.colourScheme_purine/pyrimidine"));
++ purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
++ .toString());
++ purinePyrimidineColour.addItemListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
-- PIDColour.setLabel(MessageManager
- .getString("label.colourScheme_%_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager
- .getString("label.colourScheme_blosum62"));
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("label.conservation"));
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.colourScheme_nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- purinePyrimidineMenuItem.setLabel(MessageManager
- .getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- .getString("label.percentage_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
++
++ abovePIDColour.setLabel(MessageManager
++ .getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
++ conservationColour.setLabel(MessageManager
+ .getString("label.conservation"));
++ conservationColour.addItemListener(this);
editMenu.add(copy);
copy.addActionListener(this);
refresh();
}
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
protected void abovePIDColour_itemStateChanged()
{
SequenceGroup sg = getGroup();
return;
}
-- if (conservationMenuItem.getState())
++ if (conservationColour.getState())
{
sg.cs.setConservation(Conservation.calculateConservation("Group", sg
.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColour;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
{
RNAHelixColour.setEnabled(false);
purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
}
// Some JVMS send keyevents to Top frame or lowest panel,
// Havent worked out why yet. So add to both this frame and seqCanvas for
// }
else if (source == RNAHelixColour)
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ changeColour(new RNAHelicesColour(viewport.getAlignment()));
+ // new RNAHelicesColourChooser(viewport, alignPanel);
}
else if (source == modifyPID)
{
url.append(appendProtocol(viewport.applet.getParameter("annotations")));
}
- if (viewport.applet.getParameter("jnetfile") != null)
+ if (viewport.applet.getParameter("jnetfile") != null
+ || viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+ .getParameter("jnetfile") : viewport.applet
+ .getParameter("jpredfile")));
}
if (viewport.applet.getParameter("defaultColour") != null)
.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconservedMenuItem.addItemListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+ clustalColour.setLabel(MessageManager
+ .getString("label.colourScheme_clustal"));
clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.setLabel(MessageManager
+ .getString("label.colourScheme_zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
taylorColour.addActionListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
+ .getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
+ .getString("label.colourScheme_strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
- .getString("label.purine_pyrimidine"));
+ .getString("label.colourScheme_purine/pyrimidine"));
purinePyrimidineColour.addActionListener(this);
// RNAInteractionColour.setLabel(MessageManager
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(MessageManager
- .getString("action.by_rna_helixes"));
+ .getString("label.colourScheme_rna_helices"));
RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(MessageManager
- .getString("label.percentage_identity"));
+ .getString("label.colourScheme_%_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(MessageManager
- .getString("label.blosum62_score"));
+ .getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour
- .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setLabel(MessageManager
+ .getString("label.colourScheme_t-coffee_scores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
abovePIDThreshold.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.setLabel(MessageManager
+ .getString("label.colourScheme_nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
.getString("label.modify_identity_threshold"));
.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_bloslum62"));
+ .getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem.setLabel(MessageManager
.getString("label.neighbour_blosum62"));
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
{
return defcolour;
}
- Color col = jalview.schemes.ColourSchemeProperty
- .getAWTColorFromName(colprop);
+ Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- try
- {
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
- } catch (Exception ex)
- {
- System.err.println("Couldn't parse '" + colprop
- + "' as a colour for " + colparam);
- col = null;
- }
+ System.err.println("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
}
return (col == null) ? defcolour : col;
-
}
public void openJalviewHelpUrl()
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
-import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.118 $
*/
-public class PopupMenu extends JPopupMenu
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
AlignmentPanel ap;
JMenuItem outline = new JMenuItem();
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
-
JMenu colourMenu = new JMenu();
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
this.ap = ap;
sequence = seq;
- ButtonGroup colours = new ButtonGroup();
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(purinePyrimidineColour);
- colours.add(RNAInteractionColour);
-
for (String ff : FileFormat.getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_structure_line",
new Object[] { aa.label }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_sequence_name",
new Object[] { seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem = new JMenuItem(
MessageManager.getString("action.hide_sequences"));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem = new JMenuItem(MessageManager.formatMessage(
"label.represent_group_with",
new Object[] { seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
- if (sg.cs instanceof ZappoColourScheme)
- {
- zappoColour.setSelected(true);
- }
- else if (sg.cs instanceof TaylorColourScheme)
- {
- taylorColour.setSelected(true);
- }
- else if (sg.cs instanceof PIDColourScheme)
- {
- PIDColour.setSelected(true);
- }
- else if (sg.cs instanceof Blosum62ColourScheme)
- {
- BLOSUM62Colour.setSelected(true);
- }
- else if (sg.cs instanceof UserColourScheme)
- {
- userDefinedColour.setSelected(true);
- }
- else if (sg.cs instanceof HydrophobicColourScheme)
- {
- hydrophobicityColour.setSelected(true);
- }
- else if (sg.cs instanceof HelixColourScheme)
- {
- helixColour.setSelected(true);
- }
- else if (sg.cs instanceof StrandColourScheme)
- {
- strandColour.setSelected(true);
- }
- else if (sg.cs instanceof TurnColourScheme)
- {
- turnColour.setSelected(true);
- }
- else if (sg.cs instanceof BuriedColourScheme)
- {
- buriedColour.setSelected(true);
- }
- else if (sg.cs instanceof ClustalxColourScheme)
- {
- clustalColour.setSelected(true);
- }
- else if (sg.cs instanceof PurinePyrimidineColourScheme)
- {
- purinePyrimidineColour.setSelected(true);
- }
-
- /*
- * else if (sg.cs instanceof CovariationColourScheme) {
- * covariationColour.setSelected(true); }
- */
- else
- {
- noColourmenuItem.setSelected(true);
- }
+ ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
- if (sg.cs != null && sg.cs.conservationApplied())
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
- conservationMenuItem.setSelected(true);
++ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
"label.open_url_param", new Object[] { url }));
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
- groupName.addActionListener(new java.awt.event.ActionListener()
+ groupName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
sequenceMenu.setText(MessageManager.getString("label.sequence"));
sequenceName.setText(MessageManager
.getString("label.edit_name_description"));
- sequenceName.addActionListener(new java.awt.event.ActionListener()
+ sequenceName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
chooseAnnotations.setText(MessageManager
.getString("action.choose_annotations"));
- chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+ chooseAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
sequenceDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ sequenceDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
sequenceSelDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceSelDetails
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ unGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
createGroupMenuItem.setText(MessageManager
.getString("action.create_group"));
- createGroupMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
-
- outline.setText(MessageManager.getString("action.border_colour"));
- outline.addActionListener(new java.awt.event.ActionListener()
+ createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- outline_actionPerformed();
+ createGroupMenuItem_actionPerformed();
}
});
- nucleotideMenuItem
- .setText(MessageManager.getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(new ActionListener()
+
+ outline.setText(MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- nucleotideMenuItem_actionPerformed();
+ outline_actionPerformed();
}
});
- colourMenu.setText(MessageManager.getString("label.group_colour"));
showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
}
});
displayNonconserved.setText(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText(MessageManager.getString("label.text_colour"));
- textColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed();
- }
- });
jMenu1.setText(MessageManager.getString("label.group"));
pdbStructureDialog.setText(MessageManager
.getString("label.show_pdbstruct_dialog"));
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
- colourMenu.add(textColour);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide())
- {
- // JBPNote - commented since the colourscheme isn't functional
- colourMenu.add(purinePyrimidineColour);
- }
- colourMenu.add(userDefinedColour);
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
+ initColourMenu();
+ buildColourMenu();
- while (userColours.hasMoreElements())
- {
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- }
- }
-
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
+ }
- clustalColour.setText(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed();
+ textColour_actionPerformed();
}
});
abovePIDColour.setText(MessageManager
- .getString("label.above_identity_percentage"));
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+ .getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- PIDColour_actionPerformed();
+ conservationMenuItem_actionPerformed();
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ }
+
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
- /*
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
- conservationMenuItem.setText(MessageManager
- .getString("label.conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(abovePIDColour);
}
/**
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- Map<String, String> tipEntries = new TreeMap<String, String>();
+ SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences,
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void purinePyrimidineColour_actionPerformed()
- {
- getGroup().cs = new PurinePyrimidineColourScheme();
- refresh();
- }
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getSource().equals(userDefinedColour))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
- }
- refresh();
- }
-
- /**
* Open a panel where the user can choose which types of sequence annotation
* to show or hide.
*
* @param e
* DOCUMENT ME!
*/
- protected void PIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
protected void conservationMenuItem_actionPerformed()
{
SequenceGroup sg = getGroup();
}
}
+ /**
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ SequenceGroup sg = getGroup();
+ if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
+ {
+ /*
+ * open a panel to load or configure a user-defined colour scheme
+ */
+ new UserDefinedColours(ap, sg);
+ }
+ else
+ {
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ sg.cs = ColourSchemes.getInstance().getColourScheme(colourSchemeName,
+ sg, ap.av.getHiddenRepSequences());
+ if (sg.cs instanceof Blosum62ColourScheme
+ || sg.cs instanceof PIDColourScheme)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
+ }
+
+ refresh();
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff