<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>
--- /dev/null
+import java.awt.Color;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ColourSchemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import java.util.Map;
+import jalview.datamodel.SequenceI;
+
+/*
+ * Example script that registers two new alignment colour schemes
+ */
+
+/*
+ * Class that defines a colour scheme where odd columns are red,
+ * even numbered columns are blue, and gaps are yellow
+ */
+class Stripy extends ResidueColourScheme {
+ Stripy() { }
+ String getSchemeName() { "stripy" }
+ Stripy getInstance(AnnotatedCollectionI coll, Map map) { new Stripy() }
+ Color findColour(char res, int col, SequenceI seq) {
+ // determine the colour
+ Color colour = findColour(res, col)
+ // let Jalview apply conservation or consensus shading
+ adjustColour(res, col, colour);
+ }
+ Color findColour(char res, int col) {
+ if (res == ' ' || res == '-' || res == '.')
+ {
+ Color.yellow
+ } else if (col % 2 == 0)
+ {
+ Color.blue
+ } else
+ {
+ Color.red
+ }
+ }
+}
+
+/*
+ * Class that defines a colour scheme graduated
+ * (approximately) by amino acid weight
+ */
+class ByWeight extends ResidueColourScheme {
+ int min = 75
+ int max = 204
+ ByWeight() { }
+ boolean isPeptideSpecific() {true}
+ String getSchemeName() { "By Weight" }
+ ByWeight getInstance(AnnotatedCollectionI coll, Map map) { new ByWeight() }
+ Color makeColour(int weight) {
+ int i = 255 * (weight - min) / (max - min);
+ new Color(i, 0, i);
+ }
+ Color findColour(char res, int col, SequenceI seq) {
+ // determine the colour
+ Color colour = findColour(res, col)
+ // let Jalview apply any conservation or consensus shading
+ adjustColour(res, col, colour);
+ }
+ Color findColour(char res, int col) {
+ switch (res) {
+ case ' ':
+ case '-':
+ case '.':
+ Color.white
+ break
+ case 'A':
+ makeColour(89)
+ break
+ case 'R':
+ makeColour(174)
+ break
+ case 'N':
+ case 'D':
+ case 'B':
+ case 'I':
+ case 'L':
+ makeColour(132)
+ break
+ case 'C':
+ makeColour(121)
+ break
+ case 'Q':
+ case 'E':
+ case 'Z':
+ case 'K':
+ case 'M':
+ makeColour(146)
+ break
+ case 'G':
+ makeColour(75)
+ break
+ case 'H':
+ makeColour(155)
+ break
+ case 'F':
+ makeColour(165)
+ break
+ case 'P':
+ makeColour(115)
+ break
+ case 'S':
+ makeColour(105)
+ break
+ case 'T':
+ makeColour(119)
+ break
+ case 'W':
+ makeColour(204)
+ break
+ case 'Y':
+ makeColour(181)
+ break
+ case 'V':
+ makeColour(117)
+ break
+ default:
+ makeColour(150)
+ }
+ }
+}
+
+ColourSchemes.instance.registerColourScheme(new Stripy())
+ColourSchemes.instance.registerColourScheme(new ByWeight())
is assigned a colour if the amino acid profile of the alignment at
that position meets some minimum criteria specific for the residue
type.</p>
- <p>The table below gives these criteria as clauses: {+X%,xx,y},
- where X is the minimum percentage presence for any of the xx (or y)
- residue types.</p>
+ <p>The table below gives these criteria as clauses: {>X%,xx,y},
+ where X is the threshold percentage presence for any of the xx (or y)
+ residue types.
+ <br>For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).</p>
<div align="center">
<p> </p>
<table border="1">
<tr>
<td><table border="1">
<tr>
+ <th>Category</th>
+ <th>Colour</th>
<th>Residue at position</th>
- <th>Applied Colour</th>
- <th>{ Threshhold, Residue group }</th>
+ <th>{ Threshold, Residue group }</th>
</tr>
<tr>
+ <td rowspan="2">Hydrophobic</td>
+ <td rowspan="2" bgcolor="#80a0f0">BLUE</td>
<td>A,I,L,M,F,W,V</td>
- <td bgcolor="#80a0f0">BLUE</td>
- <td>{+60%, WLVIMAFCHP}</td>
+ <td>{>60%, WLVIMAFCHP}</td>
</tr>
<tr>
- <td>R,K</td>
+ <td>C</td>
+ <td>{>60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>Positive charge</td>
<td bgcolor="#f01505">RED</td>
- <td>{+60%,KR},{+80%, K,R,Q}</td>
+ <td>K,R</td>
+ <td>{>60%,KR},{>80%, K,R,Q}</td>
</tr>
<tr>
- <td>N</td>
- <td bgcolor="#15c015">GREEN</td>
- <td>{+50%, N}, {+85%, N,Y}</td>
+ <td rowspan="2">Negative charge</td>
+ <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
+ <td>E</td>
+ <td>{>60%,KR},{>50%,QE},{>85%,E,Q,D}</td>
</tr>
<tr>
- <td>C</td>
- <td bgcolor="#80a0f0">BLUE</td>
- <td>{+60%, WLVIMAFCHP}</td>
+ <td>D</td>
+ <td>{>60%,KR}, {>85%, K,R,Q}, {>50%,ED}</td>
</tr>
<tr>
- <td>C</td>
- <td bgcolor="#f08080">PINK</td>
- <td>{100%, C}</td>
+ <td rowspan="3">Polar</td>
+ <td rowspan="3" bgcolor="#15c015">GREEN</td>
+ <td>N</td>
+ <td>{>50%, N}, {>85%, N,Y}</td>
</tr>
<tr>
<td>Q</td>
- <td bgcolor="#15c015">GREEN</td>
- <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
+ <td>{>60%,KR},{>50%,QE},{>85%,Q,E,K,R}</td>
</tr>
<tr>
- <td>E</td>
- <td bgcolor="#c048c0">MAGENTA</td>
- <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
+ <td>S,T</td>
+ <td>{>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}</td>
</tr>
<tr>
- <td>D</td>
- <td bgcolor="#c048c0">MAGENTA</td>
- <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
+ <td>Cysteines</td>
+ <td bgcolor="#f08080">PINK</td>
+ <td>C</td>
+ <td>{100%, C}</td>
</tr>
<tr>
- <td>G</td>
+ <td>Glycines</td>
<td bgcolor="#f09048">ORANGE</td>
- <td>{+0%, G}</td>
+ <td>G</td>
+ <td>{>0%, G}</td>
</tr>
<tr>
- <td>H,Y</td>
- <td bgcolor="#15a4a4">CYAN</td>
- <td>{+60%, WLVIMAFCHP}, {+85%,
- W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
+ <td>Prolines</td>
+ <td bgcolor="#c0c000">YELLOW</td>
+ <td>P</td>
+ <td>{>0%, P}</td>
</tr>
<tr>
- <td>P</td>
- <td bgcolor="#c0c000">YELLOW</td>
- <td>{+0%, P}</td>
+ <td>Aromatic</td>
+ <td bgcolor="#15a4a4">CYAN</td>
+ <td>H,Y</td>
+ <td>{>60%, WLVIMAFCHP}, {>85%,
+ W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
</tr>
<tr>
- <td>S,T</td>
- <td bgcolor="#15c015">GREEN</td>
- <td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td>
+ <td>Unconserved</td>
+ <td>WHITE</td>
+ <td>any / gap</td>
+ <td>If none of the above criteria are met</td>
</tr>
</table></td>
</tr>
1QCF ----------6878742356789999999999889
cons 00100000006877641356789999999999889
</pre>
-
+<table border="1">
+<tr><th>Score</th><th>0</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th></tr>
+<tr>
+<td>RGB colour</td>
+<td bgcolor="#6666FF">102, 102, 255</td>
+<td bgcolor="#00FF00">0, 255, 0</td>
+<td bgcolor="#66FF00">102, 255, 0</td>
+<td bgcolor="#CCFF00">204, 255, 0</td>
+<td bgcolor="#FFFF00">255, 255, 0</td>
+<td bgcolor="#FFCC00">255, 204, 0</td>
+<td bgcolor="#FF9900">255, 153, 0</td>
+<td bgcolor="#FF6600">255, 102, 0</td>
+<td bgcolor="#FF3300">255, 51, 0</td>
+<td bgcolor="#FF2000">255, 34, 0</td></tr>
+</table>
</body>
</html>
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.style = Style:
label.calculating = Calculating....
label.modify_conservation_visibility = Modify conservation visibility
-label.colour_residues_above_occurence = Colour residues above % occurrence
+label.colour_residues_above_occurrence = Colour residues above % occurrence
label.set_this_label_text = set this label text
label.sequences_from = Sequences from {0}
label.successfully_loaded_file = Successfully loaded file {0}
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 ";"
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
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}
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
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
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}
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
zbuffer.addItemListener(this);
charge.setLabel(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(this);
- hydro.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydro.setLabel(MessageManager
+ .getString("label.colourScheme_hydrophobic"));
hydro.addActionListener(this);
chain.setLabel(MessageManager.getString("action.by_chain"));
chain.addActionListener(this);
.setLabel(MessageManager.getString("label.all_chains_visible"));
allchains.addItemListener(this);
viewMenu.setLabel(MessageManager.getString("action.view"));
- zappo.setLabel(MessageManager.getString("label.zappo"));
+ zappo.setLabel(MessageManager.getString("label.colourScheme_zappo"));
zappo.addActionListener(this);
- taylor.setLabel(MessageManager.getString("label.taylor"));
+ taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
taylor.addActionListener(this);
- helix.setLabel(MessageManager.getString("label.helix_propensity"));
+ helix.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
helix.addActionListener(this);
- strand.setLabel(MessageManager.getString("label.strand_propensity"));
+ strand.setLabel(MessageManager
+ .getString("label.colourScheme_strand_propensity"));
strand.addActionListener(this);
- turn.setLabel(MessageManager.getString("label.turn_propensity"));
+ turn.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
turn.addActionListener(this);
- buried.setLabel(MessageManager.getString("label.buried_index"));
+ buried.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
buried.addActionListener(this);
user.setLabel(MessageManager.getString("action.user_defined"));
user.addActionListener(this);
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package MCview;
-
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.OOMWarning;
-import jalview.gui.UserDefinedColours;
-import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.PrintWriter;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
-
-public class PDBViewer extends JInternalFrame implements Runnable
-{
-
- /**
- * The associated sequence in an alignment
- */
- PDBCanvas pdbcanvas;
-
- PDBEntry pdbentry;
-
- SequenceI[] seq;
-
- String[] chains;
-
- AlignmentPanel ap;
-
- DataSourceType protocol;
-
- String tmpPDBFile;
-
- public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, DataSourceType protocol)
- {
- this.pdbentry = pdbentry;
- this.seq = seq;
- this.chains = chains;
- this.ap = ap;
- this.protocol = protocol;
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- StringBuffer title = new StringBuffer(seq[0].getName() + ":"
- + pdbentry.getFile());
-
- pdbcanvas = new PDBCanvas();
-
- setContentPane(pdbcanvas);
-
- if (pdbentry.getFile() != null)
- {
- try
- {
- tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
- DataSourceType.FILE);
-
- pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
-
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
- }
- else
- {
- Thread worker = new Thread(this);
- worker.start();
- }
-
- String method = (String) pdbentry.getProperty("method");
- if (method != null)
- {
- title.append(" Method: ");
- title.append(method);
- }
- String ch = (String) pdbentry.getProperty("chains");
- if (ch != null)
- {
- title.append(" Chain:");
- title.append(ch);
- }
- Desktop.addInternalFrame(this, title.toString(), 400, 400);
- }
-
- @Override
- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
- .getAbsolutePath());
-
- if (pdbentry.getFile() != null)
- {
- pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
- }
- } catch (Exception ex)
- {
- pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- this.addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- pdbcanvas.keyPressed(evt);
- }
- });
-
- this.setJMenuBar(jMenuBar1);
- fileMenu.setText(MessageManager.getString("action.file"));
- coloursMenu.setText(MessageManager.getString("label.colours"));
- saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
- saveMenu.setText(MessageManager.getString("action.save_as"));
- png.setText("PNG");
- png.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- png_actionPerformed(e);
- }
- });
- eps.setText("EPS");
- eps.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- eps_actionPerformed(e);
- }
- });
- mapping.setText(MessageManager.getString("label.view_mapping"));
- mapping.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- mapping_actionPerformed(e);
- }
- });
- wire.setText(MessageManager.getString("label.wireframe"));
- wire.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- wire_actionPerformed(e);
- }
- });
- depth.setSelected(true);
- depth.setText(MessageManager.getString("label.depthcue"));
- depth.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- depth_actionPerformed(e);
- }
- });
- zbuffer.setSelected(true);
- zbuffer.setText(MessageManager.getString("label.z_buffering"));
- zbuffer.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zbuffer_actionPerformed(e);
- }
- });
- charge.setText(MessageManager.getString("label.charge_cysteine"));
- charge.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- charge_actionPerformed(e);
- }
- });
- chain.setText(MessageManager.getString("action.by_chain"));
- chain.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- chain_actionPerformed(e);
- }
- });
- seqButton.setSelected(true);
- seqButton.setText(MessageManager.getString("action.by_sequence"));
- seqButton.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- seqButton_actionPerformed(e);
- }
- });
- allchains.setSelected(true);
- allchains.setText(MessageManager.getString("label.show_all_chains"));
- allchains.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- allchains_itemStateChanged(e);
- }
- });
- zappo.setText(MessageManager.getString("label.zappo"));
- zappo.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappo_actionPerformed(e);
- }
- });
- taylor.setText(MessageManager.getString("label.taylor"));
- taylor.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylor_actionPerformed(e);
- }
- });
- hydro.setText(MessageManager.getString("label.hydrophobicity"));
- hydro.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydro_actionPerformed(e);
- }
- });
- helix.setText(MessageManager.getString("label.helix_propensity"));
- helix.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helix_actionPerformed(e);
- }
- });
- strand.setText(MessageManager.getString("label.strand_propensity"));
- strand.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strand_actionPerformed(e);
- }
- });
- turn.setText(MessageManager.getString("label.turn_propensity"));
- turn.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turn_actionPerformed(e);
- }
- });
- buried.setText(MessageManager.getString("label.buried_index"));
- buried.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buried_actionPerformed(e);
- }
- });
- user.setText(MessageManager.getString("action.user_defined"));
- user.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- user_actionPerformed(e);
- }
- });
- viewMenu.setText(MessageManager.getString("action.view"));
- background
- .setText(MessageManager.getString("action.background_colour"));
- background.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- background_actionPerformed(e);
- }
- });
- savePDB.setText(MessageManager.getString("label.pdb_file"));
- savePDB.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- savePDB_actionPerformed(e);
- }
- });
- jMenuBar1.add(fileMenu);
- jMenuBar1.add(coloursMenu);
- jMenuBar1.add(viewMenu);
- fileMenu.add(saveMenu);
- fileMenu.add(mapping);
- saveMenu.add(savePDB);
- saveMenu.add(png);
- saveMenu.add(eps);
- coloursMenu.add(seqButton);
- coloursMenu.add(chain);
- coloursMenu.add(charge);
- coloursMenu.add(zappo);
- coloursMenu.add(taylor);
- coloursMenu.add(hydro);
- coloursMenu.add(helix);
- coloursMenu.add(strand);
- coloursMenu.add(turn);
- coloursMenu.add(buried);
- coloursMenu.add(user);
- coloursMenu.add(background);
- ButtonGroup bg = new ButtonGroup();
- bg.add(seqButton);
- bg.add(chain);
- bg.add(charge);
- bg.add(zappo);
- bg.add(taylor);
- bg.add(hydro);
- bg.add(helix);
- bg.add(strand);
- bg.add(turn);
- bg.add(buried);
- bg.add(user);
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- coloursMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- coloursMenu.add(radioItem);
- bg.add(radioItem);
- }
- }
-
- viewMenu.add(wire);
- viewMenu.add(depth);
- viewMenu.add(zbuffer);
- viewMenu.add(allchains);
- }
-
- JMenuBar jMenuBar1 = new JMenuBar();
-
- JMenu fileMenu = new JMenu();
-
- JMenu coloursMenu = new JMenu();
-
- JMenu saveMenu = new JMenu();
-
- JMenuItem png = new JMenuItem();
-
- JMenuItem eps = new JMenuItem();
-
- JMenuItem mapping = new JMenuItem();
-
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem user = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
-
- JMenu viewMenu = new JMenu();
-
- JMenuItem background = new JMenuItem();
-
- JMenuItem savePDB = new JMenuItem();
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
- }
-
- void makePDBImage(jalview.util.ImageMaker.TYPE type)
- {
- int width = pdbcanvas.getWidth();
- int height = pdbcanvas.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
-
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
-
- if (im.getGraphics() != null)
- {
- pdbcanvas.drawAll(im.getGraphics(), width, height);
- im.writeImage();
- }
- }
-
- public void charge_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChargeColours();
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void hydro_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void chain_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChainColours();
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void zbuffer_actionPerformed(ActionEvent e)
- {
- pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void molecule_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void depth_actionPerformed(ActionEvent e)
- {
- pdbcanvas.depthcue = !pdbcanvas.depthcue;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void wire_actionPerformed(ActionEvent e)
- {
- pdbcanvas.wire = !pdbcanvas.wire;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void seqButton_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = true;
- pdbcanvas.updateSeqColours();
- }
-
- public void mapping_actionPerformed(ActionEvent e)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.setText(pdbcanvas.mappingDetails.toString());
- Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Opening sequence to structure mapping report", oom);
- cap.dispose();
- }
- }
-
- public void allchains_itemStateChanged(ItemEvent e)
- {
- pdbcanvas.setAllchainsVisible(allchains.getState());
- }
-
- public void zappo_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new ZappoColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void taylor_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TaylorColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void helix_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HelixColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void strand_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new StrandColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void turn_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TurnColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void buried_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new BuriedColourScheme());
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- public void user_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
- {
- // new UserDefinedColours(pdbcanvas, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- pdbcanvas.pdb.setColours(udc);
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
- }
-
- public void background_actionPerformed(ActionEvent e)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"),
- pdbcanvas.backgroundColour);
-
- if (col != null)
- {
- pdbcanvas.backgroundColour = col;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
- }
-
- public void savePDB_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- in.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-}
import java.util.Map.Entry;
import java.util.NoSuchElementException;
import java.util.Set;
+import java.util.SortedMap;
import java.util.TreeMap;
/**
* @param unmapped
* @return
*/
- static Map<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
+ static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
{
/*
* {unalignedSequence, characterPerSequence} at that position.
* TreeMap keeps the entries in ascending column order.
*/
- Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
/*
* record any sequences that have no mapping so can't be realigned
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
* or not conserved (-1)
* Using TreeMap means properties are displayed in alphabetical order
*/
- Map<String, Integer> resultHash = new TreeMap<String, Integer>();
+ SortedMap<String, Integer> resultHash = new TreeMap<String, Integer>();
SymbolCounts symbolCounts = values.getSymbolCounts();
char[] symbols = symbolCounts.symbols;
int[] counts = symbolCounts.values;
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 MenuItem userDefinedColour = new MenuItem();
+ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
- protected MenuItem PIDColour = new MenuItem();
+ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
- MenuItem noColourmenuItem = new MenuItem();
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
+
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
+
+ protected MenuItem userDefinedColour = new MenuItem();
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
MenuItem modifyPID = new MenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
MenuItem modifyConservation = new MenuItem();
+ MenuItem noColourmenuItem = new MenuItem();
+
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
MenuItem createGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
if (sg.cs != null)
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
+ conservationColour.setState(sg.cs.conservationApplied());
modifyPID.setEnabled(abovePIDColour.getState());
- conservationMenuItem.setState(sg.cs.conservationApplied());
- modifyConservation.setEnabled(conservationMenuItem.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
}
}
+ 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)
{
Object source = evt.getSource();
- if (source == abovePIDColour)
- {
- abovePIDColour_itemStateChanged();
- }
- else if (source == conservationMenuItem)
- {
- conservationMenuItem_itemStateChanged();
- }
- else if (source == showColourText)
- {
- showColourText_itemStateChanged();
- }
- else if (source == showText)
+ if (source == noColour)
{
- showText_itemStateChanged();
+ noColourmenuItem_actionPerformed();
}
- else if (source == showBoxes)
+ else if (source == clustalColour)
{
- showBoxes_itemStateChanged();
+ clustalColour_actionPerformed();
}
- 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 == userDefinedColour)
+ else if (source == purinePyrimidineColour)
{
- userDefinedColour_actionPerformed();
+ purinePyrimidineColour_actionPerformed();
}
- else if (source == PIDColour)
+ else if (source == abovePIDColour)
{
- PIDColour_actionPerformed();
+ abovePIDColour_itemStateChanged();
}
- else if (source == BLOSUM62Colour)
+ else if (source == conservationColour)
{
- BLOSUM62Colour_actionPerformed();
+ conservationMenuItem_itemStateChanged();
}
- else if (source == noColourmenuItem)
+ else if (source == showColourText)
{
- noColourmenuItem_actionPerformed();
+ showColourText_itemStateChanged();
+ }
+ else if (source == showText)
+ {
+ showText_itemStateChanged();
+ }
+ else if (source == showBoxes)
+ {
+ 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 == modifyConservation)
{
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
- if (pdbs != null&& !pdbs.isEmpty())
+ if (pdbs != null && !pdbs.isEmpty())
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, DataSourceType.URL);
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
else
{
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
- modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_threshold"));
- modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_threshold"));
- modifyPID.setEnabled(abovePIDColour.getState());
- modifyConservation.setEnabled(conservationMenuItem.getState());
- modifyConservation.addActionListener(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(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
+ colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
colourMenu.add(modifyPID);
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- 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.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.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
+ 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
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
+ 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.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
+ 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.percentage_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("label.conservation"));
+
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
+ conservationColour.setLabel(MessageManager
+ .getString("action.by_conservation"));
+ conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(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
SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
- modifyConservation.setEnabled(conservationMenuItem.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
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)
{
.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"));
if (colour != null)
{
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- colour);
+ globalColourScheme = ColourSchemeProperty.getColourScheme(
+ alignment, colour);
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
if (applet.getParameter("userDefinedColour") != null)
{
- ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
- .getParameter("userDefinedColour"));
+ globalColourScheme = new UserColourScheme(
+ applet.getParameter("userDefinedColour"));
}
}
initAutoAnnotation();
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
import jalview.io.DataSourceType;
+import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
+ MenuItem zappo = new MenuItem(
+ MessageManager.getString("label.colourScheme_zappo"));
- MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
+ MenuItem taylor = new MenuItem(
+ MessageManager.getString("label.colourScheme_taylor"));
MenuItem hydro = new MenuItem(
- MessageManager.getString("label.hydrophobicity"));
+ MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.helix_propensity"));
+ MessageManager.getString("label.colourScheme_helix_propensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.strand_propensity"));
+ MessageManager.getString("label.colourScheme_strand_propensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.turn_propensity"));
+ MessageManager.getString("label.colourScheme_turn_propensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.buried_index"));
+ MessageManager.getString("label.colourScheme_buried_index"));
MenuItem purinepyrimidine = new MenuItem(
- MessageManager.getString("label.purine_pyrimidine"));
+ MessageManager.getString("label.colourScheme_purine/pyrimidine"));
MenuItem user = new MenuItem(
MessageManager.getString("label.user_defined_colours"));
public void updateTitleAndMenus()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ if (jmb.hasFileLoadingError())
{
repaint();
return;
import jalview.datamodel.SequenceI;
import jalview.io.FeaturesFile;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- Color generatedColour = UserColourScheme
+ Color generatedColour = ColorUtils
.createColourFromName(name.getText());
col = new FeatureColour(generatedColour);
}
SliderPanel pid = null;
if (PIDSlider == null)
{
- pid = new SliderPanel(ap, 50, false, cs);
+ pid = new SliderPanel(ap, cs.getThreshold(), false, cs);
PIDSlider = new Frame();
PIDSlider.add(pid);
}
}
+ /**
+ * Hides the PID slider panel if it is shown
+ */
public static void hidePIDSlider()
{
- PIDSlider.setVisible(false);
+ if (PIDSlider != null)
+ {
+ PIDSlider.setVisible(false);
+ }
PIDSlider = null;
}
+ /**
+ * Hides the Conservation slider panel if it is shown
+ */
public static void hideConservationSlider()
{
- conservationSlider.setVisible(false);
+ if (conservationSlider != null)
+ {
+ conservationSlider.setVisible(false);
+ }
conservationSlider = null;
}
public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
}
else
{
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg,
+ ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
if (cs != null)
package jalview.bin;
import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
import jalview.structure.StructureImportSettings;
+import jalview.util.ColorUtils;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.ws.sifts.SiftsSettings;
import java.util.Enumeration;
import java.util.Locale;
import java.util.Properties;
+import java.util.StringTokenizer;
import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
+ jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
{
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)
- {
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
- + property);
- col = null;
- }
+ log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
}
return (col == null) ? defcolour : col;
}
Cache.applicationProperties.setProperty(propName, value);
}
}
+
+ /**
+ * Loads in user colour schemes from files.
+ *
+ * @param files
+ * a '|'-delimited list of file paths
+ */
+ public static void initUserColourSchemes(String files)
+ {
+ if (files == null || files.length() == 0)
+ {
+ return;
+ }
+
+ // In case colours can't be loaded, we'll remove them
+ // from the default list here.
+ StringBuffer coloursFound = new StringBuffer();
+ StringTokenizer st = new StringTokenizer(files, "|");
+ while (st.hasMoreElements())
+ {
+ String file = st.nextToken();
+ try
+ {
+ UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+ if (ucs != null)
+ {
+ if (coloursFound.length() > 0)
+ {
+ coloursFound.append("|");
+ }
+ coloursFound.append(file);
+ ColourSchemes.getInstance().registerColourScheme(ucs);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User ColourFile\n" + ex);
+ }
+ }
+ if (!files.equals(coloursFound.toString()))
+ {
+ if (coloursFound.toString().length() > 1)
+ {
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString());
+ }
+ else
+ {
+ applicationProperties.remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ }
+ }
+ }
}
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
.getViewport().getAlignment(), data);
- if (cs == null)
- {
- UserColourScheme ucs = new UserColourScheme("white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
- else
+ if (cs != null)
{
System.out.println("CMD [-color " + data
+ "] executed successfully!");
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
{
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()
protected char gapCharacter = '-';
- protected int type = NUCLEOTIDE;
-
- public static final int PROTEIN = 0;
-
- public static final int NUCLEOTIDE = 1;
+ private boolean nucleotide = true;
public boolean hasRNAStructure = false;
hiddenSequences = new HiddenSequences(this);
codonFrameList = new ArrayList<AlignedCodonFrame>();
- if (Comparison.isNucleotide(seqs))
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
+ nucleotide = Comparison.isNucleotide(seqs);
sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
}
/**
- * Adds a sequence to the alignment. Recalculates maxLength and size.
+ * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+ * this currently does not recalculate whether or not the alignment is
+ * nucleotide, so mixed alignments may have undefined behaviour.
*
* @param snew
*/
}
@Override
- public void setNucleotide(boolean b)
- {
- if (b)
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
- }
-
- @Override
public boolean isNucleotide()
{
- if (type == NUCLEOTIDE)
- {
- return true;
- }
- else
- {
- return false;
- }
+ return nucleotide;
}
@Override
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
- assert (name != null);
if (annotations != null)
{
for (AlignmentAnnotation annot : getAlignmentAnnotation())
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a : getAlignmentAnnotation())
+ List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a.getCalcId()
- .equals(calcId)))
+ for (AlignmentAnnotation a : alignmentAnnotation)
{
- aa.add(a);
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a
+ .getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
}
}
return aa;
boolean hasRNAStructure();
/**
- * Set alignment to be a nucleotide sequence
- *
- */
- void setNucleotide(boolean b);
-
- /**
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
*/
AlignmentAnnotation[] getAlignmentAnnotation();
+ /**
+ * Returns a list of annotations matching the given calc id, or an empty list
+ * if calcId is null
+ *
+ * @param calcId
+ * @return
+ */
Iterable<AlignmentAnnotation> findAnnotation(String calcId);
Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ if (calcId == null)
+ {
+ return aa;
+ }
for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId() == calcId)
+ if (calcId.equals(a.getCalcId()))
{
aa.add(a);
}
*/
package jalview.ext.jmol;
-import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
Hashtable<String, String> chainFile;
- public String fileLoadingError;
-
/*
* the default or current model displayed if the model cannot be identified
* from the selection message
* @param _hiddenCols
* an array of corresponding hidden columns for each alignment
*/
+ @Override
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
}
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
{
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (!colourBySequence || !isLoadingFinished())
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
{
for (String cbyseq : cpdbbyseq.commands)
{
* @param alignment
* @return
*/
+ @Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
}
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
* instruct the Jalview binding to update the pdbentries vector if necessary
* prior to matching the jmol view's contents to the list of structure files
* Jalview knows about.
return null;
}
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
+
// ///////////////////////////////
// JmolStatusListener
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
command.append("select *;color white;");
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
- for (String res : residueSet)
+ for (String resName : residueSet)
{
- Color col = cs.findColour(res.charAt(0));
- command.append("select " + res + ";color[" + col.getRed() + ","
+ char res = resName.length() == 3 ? ResidueProperties
+ .getSingleCharacterCode(resName) : resName.charAt(0);
+ Color col = cs.findColour(res);
+ command.append("select " + resName + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
protected org.jmol.api.JmolAppConsoleInterface console = null;
+ @Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import java.util.TreeMap;
/**
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
ssm, files, sequence, sr, fr, alignment);
List<String> colourCommands = buildColourCommands(colourMap);
* @return
*/
protected static List<String> buildColourCommands(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap)
{
/*
* This version concatenates all commands into a single String (semi-colon
* Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
* </pre>
*/
- protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
+ protected static Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> buildColoursMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
Color lastColour = null;
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
* @param chain
*/
protected static void addColourRange(
- Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap,
Color colour, int model, int startPos, int endPos, String chain)
{
/*
* Get/initialize map of data for the colour
*/
- Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+ SortedMap<Integer, Map<String, List<int[]>>> colourData = colourMap
.get(colour);
if (colourData == null)
{
*/
private boolean loadingFinished = true;
- public String fileLoadingError;
-
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
}
/**
- * Construct a title string for the viewer window based on the data Jalview
- * knows about
- *
- * @param verbose
- * @return
- */
- public String getViewerTitle(boolean verbose)
- {
- return getViewerTitle("Chimera", verbose);
- }
-
- /**
* Tells Chimera to display only the specified chains
*
* @param toshow
releaseUIResources();
}
+ @Override
public void colourByChain()
{
colourBySequence = false;
* <li>all others - white</li>
* </ul>
*/
+ @Override
public void colourByCharge()
{
colourBySequence = false;
* @param _hiddenCols
* an array of corresponding hidden columns for each alignment
*/
+ @Override
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
String progressMsg);
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
{
- if (!colourBySequence || !loadingFinished)
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
- files, sr, fr, alignment))
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
{
for (String command : cpdbbyseq.commands)
{
* @param alignment
* @return
*/
+ @Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
// //////////////////////////
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
* instruct the Jalview binding to update the pdbentries vector if necessary
* prior to matching the viewer's contents to the list of structure files
* Jalview knows about.
*/
public abstract void refreshPdbEntries();
- private int getModelNum(String modelFileName)
- {
- String[] mfn = getPdbFile();
- if (mfn == null)
- {
- return -1;
- }
- for (int i = 0; i < mfn.length; i++)
- {
- if (mfn[i].equalsIgnoreCase(modelFileName))
- {
- return i;
- }
- }
- return -1;
- }
-
/**
* map between index of model filename returned from getPdbFile and the first
* index of models from this file in the viewer. Note - this is not trimmed -
}
/**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
- /**
* Construct and send a command to highlight zero, one or more atoms. We do
* this by sending an "rlabel" command to show the residue label at that
* position.
return loadNotifiesHandled;
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
colourBySequence = false;
List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
false);
- for (String res : residueSet)
+ for (String resName : residueSet)
{
- Color col = cs.findColour(res.charAt(0));
+ char res = resName.length() == 3 ? ResidueProperties
+ .getSingleCharacterCode(resName) : resName.charAt(0);
+ Color col = cs.findColour(res);
command.append("color " + col.getRed() / normalise + ","
+ col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
+ / normalise + " ::" + resName + ";");
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
* .html
* @param col
*/
+ @Override
public void setBackgroundColour(Color col)
{
viewerCommandHistory(false);
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
- BLOSUM62Colour.setEnabled(false);
+ // BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
// PIDColour.setEnabled(false);
sortPairwiseMenuItem_actionPerformed(null);
}
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+ buildColourMenu();
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide();
+ }
if (viewport.getWrapAlignment())
{
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
- *
- * @param nucleotide
*/
- public void setGUINucleotide(boolean nucleotide)
+ public void setGUINucleotide()
{
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
+
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- nucleotideColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- RNAInteractionColour.setEnabled(nucleotide);
+
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ ColourMenuHelper.setColourSelected(colourMenu,
+ av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
/*
- * public void covariationColour_actionPerformed(ActionEvent e) {
+ * public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
new AnnotationColumnChooser(viewport, alignPanel);
}
+ /**
+ * Action on the user checking or unchecking the option to apply the selected
+ * colour scheme to all groups. If unchecked, groups may have their own
+ * independent colour schemes.
+ *
+ */
@Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
}
/**
- * DOCUMENT ME!
+ * Action on user selecting a colour from the colour menu
*
- * @param e
- * DOCUMENT ME!
+ * @param name
+ * the name (not the menu item label!) of the colour scheme
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void changeColour_actionPerformed(String name)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel, null);
+ return;
+ }
+
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
+ changeColour(cs);
}
/**
- * DOCUMENT ME!
+ * Actions on setting or changing the alignment colour scheme
*
* @param cs
- * DOCUMENT ME!
*/
@Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
-
if (cs != null)
{
+ ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
// Make sure viewport is up to date w.r.t. any sliders
if (viewport.getAbovePIDThreshold())
{
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
}
viewport.setGlobalColourScheme(cs);
/**
* DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
@Override
protected void modifyPID_actionPerformed()
/**
* DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
@Override
protected void modifyConservation_actionPerformed()
* DOCUMENT ME!
*/
@Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
- {
- new UserDefinedColours(alignPanel, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
- }
- }
-
- public void updateUserColourMenu()
- {
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
}
}
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
-
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
+ buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
true,
(actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
}
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ /*
+ * select the default colour for the alignment (this may be
+ * overridden later)
+ */
+ boolean nucleotide = viewport.getAlignment().isNucleotide();
+ String defaultColourScheme = Cache.getDefault(
+ nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT,
+ ResidueColourScheme.NONE);
+
+ ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
+ }
}
class PrintThread extends Thread
}
if (propertyValue != null)
{
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ globalColourScheme = ColourSchemeProperty.getColourScheme(alignment,
propertyValue);
if (globalColourScheme instanceof UserColourScheme)
package jalview.gui;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
public class AppJmol extends StructureViewerBase
{
RenderPanel renderPanel;
- ViewSelectionMenu seqColourBy;
-
/**
*
* @param files
{
useAlignmentPanelForSuperposition(ap);
}
+ initMenus();
if (leaveColouringToJmol || !usetoColour)
{
jmb.setColourBySequence(false);
viewerColour.setSelected(false);
}
this.setBounds(bounds);
- initMenus();
setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
}
- private void initMenus()
+ @Override
+ protected void initMenus()
{
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new String[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ super.initMenus();
- }
+ viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
- });
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
IProgressIndicator progressBar = null;
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
- /**
- * Answers true if this viewer already involves the given PDB ID
- */
- @Override
- protected boolean hasPdbId(String pdbId)
- {
- return jmb.hasPdbId(pdbId);
- }
-
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- }
-
- @Override
public void eps_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
{
getSize(currentSize);
- if (jmb != null && jmb.fileLoadingError != null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.getChainNames());
-
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
- }
-
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return getAlignmentPanel();
- }
-
@Override
public AAStructureBindingModel getBinding()
{
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Jmol";
}
-
}
package jalview.gui;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
import jalview.io.StructureFile;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
import java.awt.event.ActionEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
-import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
-import javax.swing.JOptionPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
/**
* GUI elements for handling an external chimera display
/**
* Initialise menu options.
*/
- private void initMenus()
+ @Override
+ protected void initMenus()
{
+ super.initMenus();
+
viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+
viewerColour.setText(MessageManager
.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
.getString("label.let_chimera_manage_structure_colours"));
- helpItem.setText(MessageManager.getString("label.chimera_help"));
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- // save As not yet implemented
- savemenu.setVisible(false);
- ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the Chimera display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
+ helpItem.setText(MessageManager.getString("label.chimera_help"));
+ savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
-
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new Object[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
- }
- });
}
/**
}
}
- /**
- * Answers true if this viewer already involves the given PDB ID
- */
- @Override
- protected boolean hasPdbId(String pdbId)
- {
- return jmb.hasPdbId(pdbId);
- }
-
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
}
-
-
/**
* Create a new viewer from saved session state data including Chimera session
* file
{
jmb.setFinishedInit(false);
jalview.gui.Desktop.addInternalFrame(this,
- jmb.getViewerTitle("Chimera", true), getBounds().width,
+ jmb.getViewerTitle(getViewerName(), true), getBounds().width,
getBounds().height);
if (!jmb.launchChimera())
{
String prompt = MessageManager.formatMessage(
"label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle("Chimera", false) });
+ new Object[] { jmb.getViewerTitle(getViewerName(),
+ false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
try
{
int pos = filePDBpos.get(num).intValue();
- long startTime = startProgressBar("Chimera "
+ long startTime = startProgressBar(getViewerName() + " "
+ MessageManager.getString("status.opening_file_for")
+ " " + pe.getId());
jmb.openFile(pe);
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- e.printStackTrace();
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- }
-
- @Override
public void eps_actionPerformed(ActionEvent e)
{
throw new Error(
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
} catch (Exception ex)
{
}
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.getChainNames());
-
- this.setTitle(jmb.getViewerTitle("Chimera", true));
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
-
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
-
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
- }
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return getAlignmentPanel();
- }
-
@Override
public AAStructureBindingModel getBinding()
{
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Chimera";
}
}
--- /dev/null
+package jalview.gui;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JMenu;
+import javax.swing.JRadioButtonMenuItem;
+
+public class ColourMenuHelper
+{
+ public interface ColourChangeListener
+ {
+ void changeColour_actionPerformed(String name);
+ }
+
+ /**
+ * Adds items to the colour menu, as mutually exclusive members of a button
+ * group. The callback handler is responsible for the action on selecting any
+ * of these options. The callback method receives the name of the selected
+ * colour, or "None" or "User Defined". This method returns the ButtonGroup to
+ * which items were added.
+ * <ul>
+ * <li>None</li>
+ * <li>Clustal</li>
+ * <li>...other 'built-in' colours</li>
+ * <li>...any user-defined colours</li>
+ * <li>User Defined..</li>
+ * </ul>
+ *
+ * @param colourMenu
+ * the menu to attach items to
+ * @param client
+ * a callback to handle menu selection
+ * @param coll
+ * the data the menu is being built for
+ * @param simpleOnly
+ * if true, only simple per-residue colour schemes are included
+ */
+ public static ButtonGroup addMenuItems(final JMenu colourMenu,
+ final ColourChangeListener client, AnnotatedCollectionI coll,
+ boolean simpleOnly)
+ {
+ /*
+ * ButtonGroup groups those items whose
+ * selection is mutually exclusive
+ */
+ ButtonGroup colours = new ButtonGroup();
+
+ if (!simpleOnly)
+ {
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(
+ MessageManager.getString("label.none"));
+ noColourmenuItem.setName(ResidueColourScheme.NONE);
+ noColourmenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ client.changeColour_actionPerformed(ResidueColourScheme.NONE);
+ }
+ });
+ colourMenu.add(noColourmenuItem);
+ colours.add(noColourmenuItem);
+ }
+
+ /*
+ * scan registered colour schemes (built-in or user-defined
+ * and add them to the menu (in the order they were added)
+ */
+ Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes();
+ for (ColourSchemeI scheme : colourSchemes)
+ {
+ if (simpleOnly && !scheme.isSimple())
+ {
+ continue;
+ }
+
+ /*
+ * button text is i18n'd but the name is the canonical name of
+ * the colour scheme (inspected in setColourSelected())
+ */
+ final String name = scheme.getSchemeName();
+ String label = MessageManager.getStringOrReturn("label.colourScheme_"
+ + name.toLowerCase().replace(" ", "_"), name);
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
+ radioItem.setName(name);
+ radioItem.setEnabled(scheme.isApplicableTo(coll));
+ if (scheme instanceof UserColourScheme)
+ {
+ /*
+ * user-defined colour scheme loaded on startup or during the
+ * Jalview session; right-click on this offers the option to
+ * remove it as a colour choice
+ */
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ offerRemoval();
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ offerRemoval();
+ }
+ }
+
+ void offerRemoval()
+ {
+ ActionListener al = radioItem.getActionListeners()[0];
+ radioItem.removeActionListener(al);
+ int option = JvOptionPane.showInternalConfirmDialog(
+ Desktop.desktop, MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
+ {
+ ColourSchemes.getInstance().removeColourScheme(
+ radioItem.getName());
+ colourMenu.remove(radioItem);
+ updatePreferences();
+ }
+ else
+ {
+ radioItem.addActionListener(al);
+ }
+ }
+ });
+ }
+ radioItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ client.changeColour_actionPerformed(name);
+ }
+ });
+ colourMenu.add(radioItem);
+ colours.add(radioItem);
+ }
+
+ /*
+ * only add the option to load/configure a user-defined colour
+ * to the AlignFrame colour menu
+ */
+ if (client instanceof AlignFrame)
+ {
+ final String label = MessageManager.getString("action.user_defined");
+ JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(
+ label);
+ userDefinedColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED);
+ }
+ });
+ colourMenu.add(userDefinedColour);
+ colours.add(userDefinedColour);
+ }
+
+ return colours;
+ }
+
+ /**
+ * Marks as selected the colour menu item matching the given name, or the
+ * first item ('None') if no match is found
+ *
+ * @param colourMenu
+ * @param colourName
+ */
+ public static void setColourSelected(JMenu colourMenu, String colourName)
+ {
+ if (colourName == null)
+ {
+ return;
+ }
+
+ JRadioButtonMenuItem none = null;
+
+ /*
+ * select the radio button whose name matches the colour name
+ * (not the button text, as it may be internationalised)
+ */
+ for (Component menuItem : colourMenu.getMenuComponents())
+ {
+ if (menuItem instanceof JRadioButtonMenuItem)
+ {
+ String buttonName = ((JRadioButtonMenuItem) menuItem).getName();
+ if (colourName.equals(buttonName))
+ {
+ ((JRadioButtonMenuItem) menuItem).setSelected(true);
+ return;
+ }
+ if (ResidueColourScheme.NONE.equals(buttonName))
+ {
+ none = (JRadioButtonMenuItem) menuItem;
+ }
+ }
+ }
+ if (none != null)
+ {
+ none.setSelected(true);
+ }
+ }
+
+ /**
+ * Marks as selected the colour menu item matching the given colour scheme, or
+ * the first item ('None') if no match is found
+ *
+ * @param colourMenu
+ * @param cs
+ */
+ public static void setColourSelected(JMenu colourMenu, ColourSchemeI cs)
+ {
+ setColourSelected(colourMenu, cs == null ? ResidueColourScheme.NONE
+ : cs.getSchemeName());
+ }
+
+ /**
+ * Updates the USER_DEFINE_COLOURS preference to remove any de-registered
+ * colour scheme
+ */
+ static void updatePreferences()
+ {
+ StringBuilder coloursFound = new StringBuilder();
+ String[] files = Cache.getProperty("USER_DEFINED_COLOURS").split("\\|");
+
+ /*
+ * the property does not include the scheme name, it is in the file;
+ * so just load the colour schemes and discard any whose name is not
+ * registered
+ */
+ for (String file : files)
+ {
+ try
+ {
+ UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+ if (ucs != null
+ && ColourSchemes.getInstance().nameExists(ucs.getName()))
+ {
+ if (coloursFound.length() > 0)
+ {
+ coloursFound.append("|");
+ }
+ coloursFound.append(file);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User ColourFile\n" + ex);
+ }
+ }
+
+ if (coloursFound.toString().length() > 1)
+ {
+ Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+ }
+ else
+ {
+ Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+ }
+ }
+}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new FeatureColour(UserColourScheme
+ col = new FeatureColour(ColorUtils
.createColourFromName(name.getText()));
}
oldcol = fcol = col;
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(sg.cs.getSchemeName());
}
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(sg.cs.getSchemeName());
}
jGroup.setPidThreshold(sg.cs.getThreshold());
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
}
else
{
- cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+ cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
}
if (cs != null)
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
if (cs != null)
);
}
- if (viewAnnColour.getColourScheme().equals("None"))
+ if (viewAnnColour.getColourScheme().equals(
+ ResidueColourScheme.NONE))
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
+ ColourSchemeProperty.getColourScheme(al,
viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}
}
/*
- * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
* new AnnotationColourGradient(
* annAlignment.getAlignmentAnnotation()[i], new
* java.awt.Color(viewAnnColour. getMinColour()), new
}
else
{
- cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+ cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
}
if (cs != null)
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
if (cs != null)
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
}
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"),
+ MessageManager.getString("label.select_background_colour"),
rc.bgColour);
if (col != null)
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
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 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 abovePIDColour = new JCheckBoxMenuItem();
protected JMenuItem modifyPID = new JMenuItem();
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 : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
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)
{
sequenceSelectionDetails_actionPerformed();
}
});
- PIDColour.setFocusPainted(false);
+
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
outline_actionPerformed();
}
});
- nucleotideMenuItem
- .setText(MessageManager.getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_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();
- 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);
- }
- }
+ initColourMenu();
+ buildColourMenu();
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(modifyPID);
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
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 ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
-
- clustalColour.setText(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new 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)
{
- purinePyrimidineColour_actionPerformed();
+ textColour_actionPerformed();
}
});
- /*
- * covariationColour.addActionListener(new ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
abovePIDColour.setText(MessageManager
- .getString("label.above_identity_percentage"));
+ .getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
});
conservationMenuItem.setText(MessageManager
- .getString("label.conservation"));
+ .getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
{
@Override
});
}
+ /**
+ * 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)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
protected void modifyConservation_actionPerformed()
{
SequenceGroup sg = getGroup();
* 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();
// or we simply trust the user wants
// wysiwig behaviour
- FileFormatI fileFormat = FileFormats.getInstance().forName(
- e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
}
}
+ /**
+ * 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();
+ }
+
}
import jalview.io.JalviewFileView;
import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
/*
* Set Colours tab defaults
*/
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
{
- protColour.addItem(ColourSchemeProperty.getColourName(i));
- nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
}
- String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
return sp.getValue();
}
+ /**
+ * Hides the PID slider panel if it is shown
+ */
public static void hidePIDSlider()
{
- try
- {
- PIDSlider.setClosed(true);
- PIDSlider = null;
- } catch (PropertyVetoException ex)
+ if (PIDSlider != null)
{
+ try
+ {
+ PIDSlider.setClosed(true);
+ PIDSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
}
}
+ /**
+ * Hides the conservation slider panel if it is shown
+ */
public static void hideConservationSlider()
{
- try
- {
- conservationSlider.setClosed(true);
- conservationSlider = null;
- } catch (PropertyVetoException ex)
+ if (conservationSlider != null)
{
+ try
+ {
+ conservationSlider.setClosed(true);
+ conservationSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
}
}
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
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.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
* Base class with common functionality for JMol, Chimera or other structure
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ /*
+ * names for colour options (additional to Jalview colour schemes)
+ */
+ enum ViewerColour
+ {
+ BySequence, ByChain, ChargeCysteine, ByViewer
+ }
/**
* list of sequenceSet ids associated with the view
protected boolean allChainsSelected = false;
/**
+ * Default constructor
+ */
+ public StructureViewerBase()
+ {
+ super();
+ }
+ /**
*
* @param ap2
* @return true if this Jmol instance is linked with the given alignPanel
public abstract ViewerType getViewerType();
- protected abstract AAStructureBindingModel getBindingModel();
-
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
}
}
// otherwise, start adding the structure.
- getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry },
+ getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
new SequenceI[][] { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
return option;
}
- protected abstract boolean hasPdbId(String pdbId);
+ protected boolean hasPdbId(String pdbId)
+ {
+ return getBinding().hasPdbId(pdbId);
+ }
protected abstract List<StructureViewerBase> getViewersFor(
AlignmentPanel alp);
// JBPNOTE: this looks like a binding routine, rather than a gui routine
for (StructureViewerBase viewer : getViewersFor(null))
{
- AAStructureBindingModel bindingModel = viewer.getBindingModel();
+ AAStructureBindingModel bindingModel = viewer.getBinding();
for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
{
if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
abstract void showSelectedChains();
+ /**
+ * Action on selecting one of Jalview's registered colour schemes
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
+ colourSchemeName, al, null);
+ getBinding().setJalviewColourScheme(cs);
+ }
+
+ /**
+ * Builds the colour menu
+ */
+ protected void buildColourMenu()
+ {
+ colourMenu.removeAll();
+ AlignmentI al = getAlignmentPanel().av.getAlignment();
+
+ /*
+ * add colour by sequence, by chain, by charge and cysteine
+ */
+ colourMenu.add(seqColour);
+ colourMenu.add(chainColour);
+ colourMenu.add(chargeColour);
+ chargeColour.setEnabled(!al.isNucleotide());
+
+ /*
+ * add all 'simple' (per-residue) colour schemes registered to Jalview
+ */
+ ButtonGroup itemGroup = ColourMenuHelper.addMenuItems(colourMenu, this,
+ al, true);
+
+ /*
+ * add 'colour by viewer' (menu item text is set in subclasses)
+ */
+ viewerColour.setSelected(false);
+ viewerColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewerColour_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(viewerColour);
+
+ /*
+ * add 'set background colour'
+ */
+ JMenuItem backGround = new JMenuItem();
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
+ backGround.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ background_actionPerformed(actionEvent);
+ }
+ });
+ colourMenu.add(backGround);
+
+ /*
+ * add colour buttons to a group so their selection is
+ * mutually exclusive (background colour is a separate option)
+ */
+ itemGroup.add(seqColour);
+ itemGroup.add(chainColour);
+ itemGroup.add(chargeColour);
+ itemGroup.add(viewerColour);
+ }
+
+ /**
+ * Construct menu items
+ */
+ protected void initMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+
+ seqColour = new JRadioButtonMenuItem();
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
+ seqColour.setName(ViewerColour.BySequence.name());
+ seqColour.setSelected(binding.isColourBySequence());
+ seqColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ seqColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chainColour = new JRadioButtonMenuItem();
+ chainColour.setText(MessageManager.getString("action.by_chain"));
+ chainColour.setName(ViewerColour.ByChain.name());
+ chainColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour_actionPerformed(actionEvent);
+ }
+ });
+
+ chargeColour = new JRadioButtonMenuItem();
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
+ chargeColour.setName(ViewerColour.ChargeCysteine.name());
+ chargeColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour_actionPerformed(actionEvent);
+ }
+ });
+
+ viewerColour = new JRadioButtonMenuItem();
+ // text is set in overrides of this method
+ viewerColour.setName(ViewerColour.ByViewer.name());
+ viewerColour.setSelected(!binding.isColourBySequence());
+
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the Chimera display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+
+ final ItemListener handler = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText(MessageManager.formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[] { String.valueOf(_alignwith.size()) }));
+ }
+ };
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
+ _alignwith, handler);
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+
+ buildColourMenu();
+ }
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs) {
+ getBinding().setJalviewColourScheme(cs);
+ }
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ protected void alignStructs_withAllAlignPanels()
+ {
+ if (getAlignmentPanel() == null)
+ {
+ return;
+ }
+
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(getAlignmentPanel());
+ }
+
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ getBinding().superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+ }
+ }
+ @Override
+ public void background_actionPerformed(ActionEvent actionEvent)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
+ null);
+ if (col != null)
+ {
+ getBinding().setBackgroundColour(col);
+ }
+ }
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ getBinding().setColourBySequence(false);
+ }
+ }
+ @Override
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour.setSelected(true);
+ getBinding().colourByChain();
+ }
+ @Override
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour.setSelected(true);
+ getBinding().colourByCharge();
+ }
+ @Override
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+ AAStructureBindingModel binding = getBinding();
+ binding.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (binding.isColourBySequence())
+ {
+ if (!binding.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ binding.colourBySequence(ap);
+ }
+ }
+ }
+ @Override
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ BufferedReader in = null;
+ try
+ {
+ // TODO: cope with multiple PDB files in view
+ in = new BufferedReader(
+ new FileReader(getBinding().getPdbFile()[0]));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+ }
+ @Override
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.appendText(getBinding().printMappings());
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
+ }
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ }
+
+ protected abstract String getViewerName();
+ public void updateTitleAndMenus()
+ {
+ AAStructureBindingModel binding = getBinding();
+ if (binding.hasFileLoadingError())
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(binding.getChainNames());
+
+ this.setTitle(binding.getViewerTitle(getViewerName(), true));
+ if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1)
+ {
+ viewerActionMenu.setVisible(true);
+ }
+ if (!binding.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
}
}
else
{
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg,
+ ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
if (cs != null)
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GUserDefinedColours;
+import jalview.schemabinding.version2.Colour;
+import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.ColorUtils;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Font;
+import java.awt.Insets;
import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.File;
-import java.io.FileInputStream;
import java.io.FileOutputStream;
-import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
+import java.util.List;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
public class UserDefinedColours extends GUserDefinedColours implements
ChangeListener
{
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
+
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
+
private static final int MY_FRAME_HEIGHT = 420;
private static final int MY_FRAME_WIDTH = 810;
SequenceGroup seqGroup;
- ArrayList<JButton> selectedButtons;
+ List<JButton> selectedButtons;
ColourSchemeI oldColourScheme;
JInternalFrame frame;
- JalviewStructureDisplayI jmol;
+ JalviewStructureDisplayI structureViewer;
- ArrayList<JButton> upperCaseButtons;
+ List<JButton> upperCaseButtons;
- ArrayList<JButton> lowerCaseButtons;
+ List<JButton> lowerCaseButtons;
/**
* Creates a new UserDefinedColours object.
*
* @param ap
- * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
*/
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
{
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(oldColourScheme.getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
showFrame();
}
- public UserDefinedColours(JalviewStructureDisplayI jmol,
+ public UserDefinedColours(JalviewStructureDisplayI viewer,
ColourSchemeI oldcs)
{
super();
- this.jmol = jmol;
+ this.structureViewer = viewer;
colorChooser.getSelectionModel().addChangeListener(this);
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
}
resetButtonPanel(false);
}
}
- void resetButtonPanel(boolean caseSensitive)
+ /**
+ * Rebuilds the panel with coloured buttons for residues. If not case
+ * sensitive colours, show 3-letter amino acid code as button text. If case
+ * sensitive, just show the single letter code, in order to make space for the
+ * additional buttons.
+ *
+ * @param isCaseSensitive
+ */
+ void resetButtonPanel(boolean isCaseSensitive)
{
buttonPanel.removeAll();
upperCaseButtons = new ArrayList<JButton>();
}
- JButton button;
- String label;
for (int i = 0; i < 20; i++)
{
- if (caseSensitive)
- {
- label = ResidueProperties.aa[i];
- }
- else
- {
- label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
- .toString();
- }
-
- button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
- i);
-
+ String label = isCaseSensitive ? ResidueProperties.aa[i]
+ : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+ .toString();
+ JButton button = makeButton(label, ResidueProperties.aa[i],
+ upperCaseButtons, i);
buttonPanel.add(button);
}
buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
- if (!caseSensitive)
+ if (!isCaseSensitive)
{
gridLayout.setRows(6);
gridLayout.setColumns(4);
{
int row = i / cols + 1;
int index = (row * cols) + i;
- button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
}
- if (caseSensitive)
+ if (isCaseSensitive)
{
buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
// codes
if (this.frame != null)
{
- int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
: MY_FRAME_WIDTH;
this.frame.setSize(newWidth, this.frame.getHeight());
}
}
/**
- * DOCUMENT ME!
+ * A helper method to update or make a colour button, whose background colour
+ * is the associated colour, and text colour a darker shade of the same. If
+ * the button is already in the list, then its text and margins are updated,
+ * if not then it is created and added. This method supports toggling between
+ * case-sensitive and case-insensitive button panels. The case-sensitive
+ * version has abbreviated button text in order to fit in more buttons.
*
* @param label
- * DOCUMENT ME!
- * @param aa
- * DOCUMENT ME!
+ * @param residue
+ * @param the
+ * list of buttons
+ * @param buttonIndex
+ * the button's position in the list
*/
- JButton makeButton(String label, String aa,
- ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
+ JButton makeButton(String label, String residue,
+ List<JButton> buttons, int buttonIndex)
{
final JButton button;
Color col;
- if (buttonIndex < caseSensitiveButtons.size())
+ if (buttonIndex < buttons.size())
{
- button = caseSensitiveButtons.get(buttonIndex);
+ button = buttons.get(buttonIndex);
col = button.getBackground();
}
else
{
button = new JButton();
- button.addMouseListener(new java.awt.event.MouseAdapter()
+ button.addMouseListener(new MouseAdapter()
{
@Override
public void mouseClicked(MouseEvent e)
}
});
- caseSensitiveButtons.add(button);
+ buttons.add(button);
+ /*
+ * make initial button colour that of the current colour scheme,
+ * if it is a simple per-residue colouring, else white
+ */
col = Color.white;
- if (oldColourScheme != null)
+ if (oldColourScheme != null && oldColourScheme.isSimple())
{
- try
- {
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(residue.charAt(0));
}
}
if (caseSensitive.isSelected())
{
- button.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ button.setMargin(new Insets(2, 2, 2, 2));
}
else
{
- button.setMargin(new java.awt.Insets(2, 14, 2, 14));
+ button.setMargin(new Insets(2, 14, 2, 14));
}
button.setOpaque(true); // required for the next line to have effect
button.setBackground(col);
button.setText(label);
button.setForeground(ColorUtils.darkerThan(col));
- button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
+ button.setFont(VERDANA_BOLD_10);
return button;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * On 'OK', check that at least one colour has been assigned to a residue (and
+ * if not issue a warning), and apply the chosen colour scheme and close the
+ * panel.
*/
@Override
- protected void okButton_actionPerformed(ActionEvent e)
+ protected void okButton_actionPerformed()
{
if (isNoSelectionMade())
{
}
else
{
- applyButton_actionPerformed(null);
+ applyButton_actionPerformed();
try
{
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Applies the current colour scheme to the alignment, sequence group or
+ * structure view.
*/
@Override
- protected void applyButton_actionPerformed(ActionEvent e)
+ protected void applyButton_actionPerformed()
{
if (isNoSelectionMade())
{
}
UserColourScheme ucs = getSchemeFromButtons();
- ucs.setName(schemeName.getText());
if (seqGroup != null)
{
{
ap.alignFrame.changeColour(ucs);
}
- else if (jmol != null)
+ else if (structureViewer != null)
{
- jmol.setJalviewColourScheme(ucs);
+ structureViewer.setJalviewColourScheme(ucs);
}
}
}
UserColourScheme ucs = new UserColourScheme(newColours);
+ ucs.setName(schemeName.getText());
if (caseSensitive.isSelected())
{
lowerCaseButtons = new ArrayList<JButton>();
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "jc",
- "Jalview User Colours");
+ Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.load_colour_scheme"));
int value = chooser.showOpenDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice.getPath());
- if (defaultColours.indexOf(choice.getPath()) == -1)
- {
- defaultColours = defaultColours.concat("|")
- .concat(choice.getPath());
- }
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getName());
-
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
+ return;
+ }
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
+ UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
- for (int i = 0; i < upperCaseButtons.size(); i++)
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
}
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
}
+
+ addNewColourScheme(choice.getPath());
}
/**
- * DOCUMENT ME!
+ * Loads the user-defined colour scheme from the first file listed in property
+ * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
*
- * @return DOCUMENT ME!
+ * @return
*/
public static UserColourScheme loadDefaultColours()
{
UserColourScheme ret = null;
- String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+ String colours = Cache.getProperty(USER_DEFINED_COLOURS);
if (colours != null)
{
if (colours.indexOf("|") > -1)
{
colours = colours.substring(0, colours.indexOf("|"));
}
-
- ret = loadColours(colours);
+ ret = ColourSchemes.loadColourScheme(colours);
}
if (ret == null)
{
- Color[] newColours = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = Color.white;
- }
- ret = new UserColourScheme(newColours);
+ ret = new UserColourScheme("white");
}
return ret;
/**
* DOCUMENT ME!
*
- * @param file
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- static UserColourScheme loadColours(String file)
- {
- UserColourScheme ucs = null;
- Color[] newColours = null;
- try
- {
- InputStreamReader in = new InputStreamReader(
- new FileInputStream(file), "UTF-8");
-
- jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
- org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
- jucs);
- jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
- .unmarshal(in);
-
- newColours = new Color[24];
-
- Color[] lowerCase = null;
- boolean caseSensitive = false;
-
- String name;
- int index;
- for (int i = 0; i < jucs.getColourCount(); i++)
- {
- name = jucs.getColour(i).getName();
- if (ResidueProperties.aa3Hash.containsKey(name))
- {
- index = ResidueProperties.aa3Hash.get(name).intValue();
- }
- else
- {
- index = ResidueProperties.aaIndex[name.charAt(0)];
- }
- if (index == -1)
- {
- continue;
- }
-
- if (name.toLowerCase().equals(name))
- {
- if (lowerCase == null)
- {
- lowerCase = new Color[23];
- }
- caseSensitive = true;
- lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- }
- else
- {
- newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- }
- }
-
- if (newColours != null)
- {
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- if (caseSensitive)
- {
- ucs.setLowerCaseColours(lowerCase);
- }
- }
-
- } catch (Exception ex)
- {
- // Could be Archive Jalview format
- try
- {
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
- jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-
- jucs = jucs.unmarshal(in);
-
- newColours = new Color[jucs.getColourCount()];
-
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- }
- if (newColours != null)
- {
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- }
- } catch (Exception ex2)
- {
- ex2.printStackTrace();
- }
-
- if (newColours == null)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
-
- return ucs;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param e
* DOCUMENT ME!
*/
@Override
protected void savebutton_actionPerformed(ActionEvent e)
{
- if (schemeName.getText().trim().length() < 1)
+ String name = schemeName.getText().trim();
+ if (name.length() < 1)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.user_colour_scheme_must_have_name"),
return;
}
- if (userColourSchemes != null
- && userColourSchemes.containsKey(schemeName.getText()))
+ if (ColourSchemes.getInstance().nameExists(name))
{
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.colour_scheme_exists_overwrite", new Object[] {
- schemeName.getText(), schemeName.getText() }),
+ name, name }),
MessageManager.getString("label.duplicate_scheme_name"),
JvOptionPane.YES_NO_OPTION);
if (reply != JvOptionPane.YES_OPTION)
{
return;
}
-
- userColourSchemes.remove(schemeName.getText());
+ ColourSchemes.getInstance().removeColourScheme(name);
}
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "jc",
+ Cache.getProperty(LAST_DIRECTORY), "jc",
"Jalview User Colours");
- chooser.setFileView(new JalviewFileView());
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
chooser.setDialogTitle(MessageManager
.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice);
- if (defaultColours.indexOf(choice) == -1)
+ File file = chooser.getSelectedFile();
+ addNewColourScheme(file.getPath());
+ saveToFile(file);
+ }
+ }
+
+ /**
+ * Adds the current colour scheme to the Jalview properties file so it is
+ * loaded on next startup, and updates the Colour menu in the parent
+ * AlignFrame (if there is one). Note this action does not including applying
+ * the colour scheme.
+ *
+ * @param filePath
+ */
+ protected void addNewColourScheme(String filePath)
+ {
+ /*
+ * update the delimited list of user defined colour files in
+ * Jalview property USER_DEFINED_COLOURS
+ */
+ String defaultColours = Cache
+ .getDefault(USER_DEFINED_COLOURS, filePath);
+ if (defaultColours.indexOf(filePath) == -1)
+ {
+ if (defaultColours.length() > 0)
{
- if (defaultColours.length() > 0)
- {
- defaultColours = defaultColours.concat("|");
- }
- defaultColours = defaultColours.concat(choice);
+ defaultColours = defaultColours.concat("|");
}
+ defaultColours = defaultColours.concat(filePath);
+ }
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
- userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
-
- ap.alignFrame.updateUserColourMenu();
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
+ /*
+ * construct and register the colour scheme
+ */
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
- ucs.setSchemeName(schemeName.getText());
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
+ {
+ ap.alignFrame.buildColourMenu();
+ }
+ }
- for (int i = 0; i < buttonPanel.getComponentCount(); i++)
- {
- JButton button = (JButton) buttonPanel.getComponent(i);
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(button.getText());
- col.setRGB(jalview.util.Format.getHexString(button
- .getBackground()));
- ucs.addColour(col);
- }
+ /**
+ * Saves the colour scheme to file in XML format
+ *
+ * @param path
+ */
+ protected void saveToFile(File toFile)
+ {
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName(schemeName.getText());
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(toFile), "UTF-8"));
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
- ex.printStackTrace();
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.addColour(col);
}
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
/**
- * DOCUMENT ME!
+ * On cancel, restores the colour scheme before the dialogue was opened
*
* @param e
- * DOCUMENT ME!
*/
@Override
protected void cancelButton_actionPerformed(ActionEvent e)
{
seqGroup.cs = oldColourScheme;
}
- else if (ap != null)
+ else
{
- ap.av.setGlobalColourScheme(oldColourScheme);
+ ap.alignFrame.changeColour(oldColourScheme);
}
ap.paintAlignment(true);
}
- if (jmol != null)
+ if (structureViewer != null)
{
- jmol.setJalviewColourScheme(oldColourScheme);
+ structureViewer.setJalviewColourScheme(oldColourScheme);
}
try
}
}
- static Hashtable userColourSchemes;
-
- public static Hashtable getUserColourSchemes()
- {
- return userColourSchemes;
- }
-
- public static void initUserColourSchemes(String files)
- {
- userColourSchemes = new Hashtable();
-
- if (files == null || files.length() == 0)
- {
- return;
- }
-
- // In case colours can't be loaded, we'll remove them
- // from the default list here.
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(files, "|");
- while (st.hasMoreElements())
- {
- String file = st.nextToken();
- try
- {
- UserColourScheme ucs = loadColours(file);
- if (ucs != null)
- {
- if (coloursFound.length() > 0)
- {
- coloursFound.append("|");
- }
- coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
- }
- } catch (Exception ex)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
- if (!files.equals(coloursFound.toString()))
- {
- if (coloursFound.toString().length() > 1)
- {
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
- }
- else
- {
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
- }
- }
- }
-
- public static void removeColourFromDefaults(String target)
- {
- // The only way to find colours by name is to load them in
- // In case colours can't be loaded, we'll remove them
- // from the default list here.
-
- userColourSchemes = new Hashtable();
-
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
-
- while (st.hasMoreElements())
- {
- String file = st.nextToken();
- try
- {
- UserColourScheme ucs = loadColours(file);
- if (ucs != null && !ucs.getName().equals(target))
- {
- if (coloursFound.length() > 0)
- {
- coloursFound.append("|");
- }
- coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
- }
- } catch (Exception ex)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
-
- if (coloursFound.toString().length() > 1)
- {
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
- }
- else
- {
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
- }
-
- }
-
@Override
public void caseSensitive_actionPerformed(ActionEvent e)
{
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.InputStreamReader;
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(sg.cs.toString());
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
Annotation parseAnnotation(String string, int graphStyle)
{
- boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
- // do the
- // glyph
- // test
- // if we
- // don't
- // want
- // secondary
- // structure
+ // don't do the glyph test if we don't want secondary structure
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
- java.awt.Color colour = null;
+ Color colour = null;
int i = string.indexOf("[");
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
- UserColourScheme ucs = new UserColourScheme();
-
- colour = ucs.getColourFromString(string.substring(i + 1, j));
+ colour = ColorUtils.parseColourString(string.substring(i + 1,
+ j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
void colourAnnotations(AlignmentI al, String label, String colour)
{
- UserColourScheme ucs = new UserColourScheme(colour);
+ Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
{
if (annotations[j] != null)
{
- annotations[j].colour = ucs.findColour('A');
+ annotations[j].colour = awtColour;
}
}
}
SequenceGroup groupRef)
{
String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- float value = new Float(st.nextToken()).floatValue();
+ AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+ String nextToken = st.nextToken();
+ float value = 0f;
+ try
+ {
+ value = Float.valueOf(nextToken);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ + "' invalid, setting to zero");
+ }
String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
+ Color colour = null;
if (st.hasMoreTokens())
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
+ colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
}
}
}
- if (annotation == null)
- {
- return;
- }
}
void addGroup(AlignmentI al, StringTokenizer st)
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs = ColourSchemeProperty.getColourScheme(al, value);
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
}
else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
import jalview.io.gff.GffHelperFactory;
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MapList;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
+import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
* Perhaps an old style groups file with no colours -
* synthesize a colour from the feature type
*/
- UserColourScheme ucs = new UserColourScheme(ft);
- featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
+ Color colour = ColorUtils.createColourFromName(ft);
+ featureColours.put(ft, new FeatureColour(colour));
}
SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
endPos, featureGroup);
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
{
// These color schemes require annotation, disable them if annotations
// are not exported
- if (globalColourScheme.equalsIgnoreCase("RNA Helices")
- || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+ if (globalColourScheme
+ .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
+ || globalColourScheme
+ .equalsIgnoreCase(JalviewColourScheme.TCoffee
+ .toString()))
{
- jsonAlignmentPojo.setGlobalColorScheme("None");
+ jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
}
}
{
SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
seqGrpPojo.setGroupName(seqGrp.getName());
- seqGrpPojo.setColourScheme(ColourSchemeProperty
- .getColourName(seqGrp.cs));
+ seqGrpPojo.setColourScheme(seqGrp.cs.getSchemeName());
seqGrpPojo.setColourText(seqGrp.getColourText());
seqGrpPojo.setDescription(seqGrp.getDescription());
seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
annotations[count] = new Annotation(displayChar, desc, ss, val);
if (annot.get("colour") != null)
{
- Color color = UserColourScheme.getColourFromString(annot.get(
+ Color color = ColorUtils.parseColourString(annot.get(
"colour").toString());
annotations[count].colour = color;
}
}
}
}
- globalColourScheme = ColourSchemeProperty.getColourName(viewport
- .getGlobalColourScheme());
+ globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
import java.util.regex.Pattern;
/**
- * A file parse for T-Coffee score ascii format. This file contains the
- * alignment consensus for each resude in any sequence.
+ * A file parser for T-Coffee score ascii format. This file contains the
+ * alignment consensus for each residue in any sequence.
* <p>
- * This file is procuded by <code>t_coffee</code> providing the option
+ * This file is produced by <code>t_coffee</code> providing the option
* <code>-output=score_ascii </code> to the program command line
*
* An example file is the following
*/
public class TCoffeeScoreFile extends AlignFile
{
- public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
- throws IOException
- {
- super(inFile, fileSourceType);
- }
+ /**
+ * TCOFFEE score colourscheme
+ */
+ static final Color[] colors = { new Color(102, 102, 255), // 0: lilac #6666FF
+ new Color(0, 255, 0), // 1: green #00FF00
+ new Color(102, 255, 0), // 2: lime green #66FF00
+ new Color(204, 255, 0), // 3: greeny yellow #CCFF00
+ new Color(255, 255, 0), // 4: yellow #FFFF00
+ new Color(255, 204, 0), // 5: orange #FFCC00
+ new Color(255, 153, 0), // 6: deep orange #FF9900
+ new Color(255, 102, 0), // 7: ochre #FF6600
+ new Color(255, 51, 0), // 8: red #FF3300
+ new Color(255, 34, 0) // 9: redder #FF2000
+ };
- public TCoffeeScoreFile(FileParse source) throws IOException
- {
- super(source);
- }
+ public final static String TCOFFEE_SCORE = "TCoffeeScore";
+
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
Header header;
Integer fWidth;
+ public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ throws IOException
+ {
+ super(inFile, fileSourceType);
+
+ }
+
+ public TCoffeeScoreFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* Parse the provided reader for the T-Coffee scores file format
*
}
}
- static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
- .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-
/**
* Read a scores block ihe provided stream.
*
}
/**
- * TCOFFEE score colourscheme
- */
- static final Color[] colors = { new Color(102, 102, 255), // #6666FF
- new Color(0, 255, 0), // #00FF00
- new Color(102, 255, 0), // #66FF00
- new Color(204, 255, 0), // #CCFF00
- new Color(255, 255, 0), // #FFFF00
- new Color(255, 204, 0), // #FFCC00
- new Color(255, 153, 0), // #FF9900
- new Color(255, 102, 0), // #FF6600
- new Color(255, 51, 0), // #FF3300
- new Color(255, 34, 0) // #FF2000
- };
-
- public final static String TCOFFEE_SCORE = "TCoffeeScore";
-
- /**
* generate annotation for this TCoffee score set on the given alignment
*
* @param al
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
-import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
-import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu colourMenu = new JMenu();
-
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
protected JMenu outputTextboxMenu = new JMenu();
- 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 JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
JMenu pasteMenu = new JMenu();
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JMenu colourMenu = new JMenu();
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem textColour;
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem;
- protected JMenuItem modifyConservation = new JMenuItem();
+ protected JMenuItem modifyConservation;
- protected JMenuItem modifyPID = new JMenuItem();
+ protected JCheckBoxMenuItem abovePIDThreshold;
+
+ protected JMenuItem modifyPID;
+
+ protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected ButtonGroup colours = new ButtonGroup();
-
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem showReverse = new JMenuItem();
protected JMenuItem runGroovy = new JMenuItem();
- protected JMenuItem rnahelicesColour = new JMenuItem();
-
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
System.err.println(e.toString());
}
- if (!jalview.util.Platform.isAMac())
+ if (!Platform.isAMac())
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
pasteMenu.setMnemonic('P');
reload.setMnemonic('R');
}
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- 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(nucleotideColour);
- colours.add(purinePyrimidineColour);
- // colours.add(covariationColour);
- colours.add(tcoffeeColour);
- colours.add(RNAInteractionColour);
- setColourSelected(jalview.bin.Cache.getDefault(
- Preferences.DEFAULT_COLOUR, "None"));
- }
-
- public void setColourSelected(String defaultColour)
- {
-
- if (defaultColour != null)
- {
- int index = ColourSchemeProperty
- .getColourIndexFromName(defaultColour);
-
- switch (index)
- {
- case ColourSchemeProperty.CLUSTAL:
- clustalColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.BLOSUM:
- BLOSUM62Colour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.PID:
- PIDColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.ZAPPO:
- zappoColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TAYLOR:
- taylorColour.setSelected(true);
- break;
-
- case ColourSchemeProperty.HYDROPHOBIC:
- hydrophobicityColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.HELIX:
- helixColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.STRAND:
- strandColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TURN:
- turnColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.BURIED:
- buriedColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.NUCLEOTIDE:
- nucleotideColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TCOFFEE:
- tcoffeeColour.setSelected(true);
- break;
-
- case ColourSchemeProperty.PURINEPYRIMIDINE:
- purinePyrimidineColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.RNAINTERACTION:
- RNAInteractionColour.setSelected(true);
-
- break;
- /*
- * case ColourSchemeProperty.COVARIATION:
- * covariationColour.setSelected(true);
- *
- * break;
- */
- case ColourSchemeProperty.USER_DEFINED:
- userDefinedColour.setSelected(true);
-
- break;
- case ColourSchemeProperty.NONE:
- default:
- noColourmenuItem.setSelected(true);
- break;
-
- }
- }
-
}
private void jbInit() throws Exception
{
+ initColourMenu();
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed(e);
}
};
+
+ // FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK, false);
}
});
showNonconservedMenuItem.setText(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem.addActionListener(new ActionListener()
{
statusBar.setText(MessageManager.getString("label.status_bar"));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
- clustalColour.setText(MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed(e);
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed(e);
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed(e);
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed(e);
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed(e);
- }
- });
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed(e);
- }
- });
- BLOSUM62Colour
- .setText(MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed(e);
- }
- });
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed(e);
- }
- });
-
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed(e);
- }
- });
- RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed(e);
- }
- });
- /*
- * covariationColour.setText("Covariation");
- * covariationColour.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
- * });
- */
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_bloslum62"));
+ MessageManager.getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
{
@Override
sortAnnotations_actionPerformed();
}
});
- colourTextMenuItem.setText(MessageManager
+ colourTextMenuItem = new JCheckBoxMenuItem(
+ MessageManager
.getString("label.colour_text"));
colourTextMenuItem.addActionListener(new ActionListener()
{
conservationMenuItem_actionPerformed();
}
});
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
abovePIDThreshold_actionPerformed();
}
});
+
showSeqFeatures.setText(MessageManager
.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
}
});
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed(e);
- }
- });
-
- tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false);
- tcoffeeColour.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tcoffeeColorScheme_actionPerformed(e);
- }
- });
-
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+ JMenuItem annotationColumn = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
- applyToAllGroups.setText(MessageManager
- .getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- applyToAllGroups_actionPerformed(e);
- }
- });
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
modifyConservation_actionPerformed();
}
});
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
}
});
- JMenuItem annotationColour = new JMenuItem(
- MessageManager.getString("action.by_annotation"));
- annotationColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotationColour_actionPerformed(e);
- }
- });
-
- JMenuItem annotationColumn = new JMenuItem(
- MessageManager.getString("action.select_by_annotation"));
- annotationColumn.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotationColumn_actionPerformed(e);
- }
- });
-
- rnahelicesColour.setText(MessageManager
- .getString("action.by_rna_helixes"));
- rnahelicesColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- rnahelicesColour_actionPerformed(e);
- }
- });
-
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
- JMenuItem textColour = new JMenuItem(
- MessageManager.getString("action.set_text_colour"));
- textColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed(e);
- }
- });
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign.setText(MessageManager
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
- colourMenu.add(applyToAllGroups);
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- 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(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- // colourMenu.add(RNAInteractionColour);
- // colourMenu.add(covariationColour);
- colourMenu.add(tcoffeeColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
// selectMenu.add(listenToViewSelections);
}
+ /**
+ * Constructs the entries on the Colour menu (but does not add them to the
+ * menu).
+ */
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed();
+ }
+ });
+
+ textColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.set_text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ });
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation = new JMenuItem(
+ MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+
+ annotationColour = new JMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed();
+ }
+ });
+ }
+
protected void selectHighlightedColumns_actionPerformed(
ActionEvent actionEvent)
{
{
}
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void PIDColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void RNAInteractionColour_actionPerformed(ActionEvent e)
- {
- }
-
- /*
- * protected void covariationColour_actionPerformed(ActionEvent e) { }
- */
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void conservationMenuItem_actionPerformed()
{
}
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
- {
- }
-
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
}
}
- /**
- * Template method to handle the 'Color T-Coffee scores' menu event.
- * <p>
- * Subclasses override this method to provide a custom action.
- *
- * @param event
- * The raised event
- */
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
- {
-
- }
-
protected void jpred_actionPerformed(ActionEvent e)
{
}
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
-
}
public void annotationColumn_actionPerformed(ActionEvent e)
{
-
- }
-
- public void rnahelicesColour_actionPerformed(ActionEvent e)
- {
-
}
public void associatedData_actionPerformed(ActionEvent e)
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
package jalview.jbgui;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import javax.swing.ButtonGroup;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JRadioButtonMenuItem;
public abstract class GStructureViewer extends JInternalFrame implements
- JalviewStructureDisplayI
+ JalviewStructureDisplayI, ColourChangeListener
{
// private AAStructureBindingModel bindingModel;
- protected JMenu savemenu = new JMenu();
+ protected JMenu savemenu;
- protected JMenu viewMenu = new JMenu();
+ protected JMenu viewMenu;
- protected JMenu chainMenu = new JMenu();
+ protected JMenu colourMenu;
- protected JMenu viewerActionMenu = new JMenu();
+ protected JMenu chainMenu;
- protected JMenuItem alignStructs = new JMenuItem();
+ protected JMenu viewerActionMenu;
- protected JMenuItem fitToWindow = new JMenuItem();
+ protected JMenuItem alignStructs;
- protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+ protected JMenuItem fitToWindow;
- protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem seqColour;
- protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem chainColour;
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem chargeColour;
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem viewerColour;
- protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
+ protected JMenuItem helpItem;
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JLabel statusBar;
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
-
- protected JMenuItem helpItem = new JMenuItem();
-
- protected JLabel statusBar = new JLabel();
-
- protected JPanel statusPanel = new JPanel();
+ protected JPanel statusPanel;
/**
* Constructor
JMenu fileMenu = new JMenu();
fileMenu.setText(MessageManager.getString("action.file"));
+ savemenu = new JMenu();
savemenu.setActionCommand(MessageManager.getString("action.save_image"));
savemenu.setText(MessageManager.getString("action.save_as"));
viewMapping_actionPerformed(actionEvent);
}
});
+
+ viewMenu = new JMenu();
viewMenu.setText(MessageManager.getString("action.view"));
+ chainMenu = new JMenu();
chainMenu.setText(MessageManager.getString("action.show_chain"));
+ fitToWindow = new JMenuItem();
fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
fitToWindow.addActionListener(new ActionListener()
{
}
});
- JMenu colourMenu = new JMenu();
- colourMenu.setText(MessageManager.getString("label.colours"));
-
- JMenuItem backGround = new JMenuItem();
- backGround
- .setText(MessageManager.getString("action.background_colour"));
- backGround.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- backGround_actionPerformed(actionEvent);
- }
- });
- seqColour.setSelected(false);
- seqColour.setText(MessageManager.getString("action.by_sequence"));
- seqColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- seqColour_actionPerformed(actionEvent);
- }
- });
- chainColour.setText(MessageManager.getString("action.by_chain"));
- chainColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- chainColour_actionPerformed(actionEvent);
- }
- });
- chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
- chargeColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- chargeColour_actionPerformed(actionEvent);
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- zappoColour_actionPerformed(actionEvent);
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- taylorColour_actionPerformed(actionEvent);
- }
- });
- hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
- hydroColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- hydroColour_actionPerformed(actionEvent);
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- strandColour_actionPerformed(actionEvent);
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- helixColour_actionPerformed(actionEvent);
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- turnColour_actionPerformed(actionEvent);
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- buriedColour_actionPerformed(actionEvent);
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- purinePyrimidineColour_actionPerformed(actionEvent);
- }
- });
-
- userColour.setText(MessageManager.getString("action.user_defined"));
- userColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- userColour_actionPerformed(actionEvent);
- }
- });
- viewerColour.setSelected(false);
- viewerColour
- .setText(MessageManager.getString("label.colour_with_jmol"));
- viewerColour.setToolTipText(MessageManager
- .getString("label.let_jmol_manage_structure_colours"));
- viewerColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- viewerColour_actionPerformed(actionEvent);
- }
- });
-
JMenu helpMenu = new JMenu();
helpMenu.setText(MessageManager.getString("action.help"));
+ helpItem = new JMenuItem();
helpItem.setText(MessageManager.getString("label.jmol_help"));
helpItem.addActionListener(new ActionListener()
{
showHelp_actionPerformed(actionEvent);
}
});
+ alignStructs = new JMenuItem();
alignStructs
.setText(MessageManager.getString("label.align_structures"));
alignStructs.addActionListener(new ActionListener()
alignStructs_actionPerformed(actionEvent);
}
});
- viewerActionMenu.setText(MessageManager.getString("label.jmol"));
- menuBar.add(fileMenu);
- menuBar.add(viewMenu);
- menuBar.add(colourMenu);
- menuBar.add(viewerActionMenu);
+
+ viewerActionMenu = new JMenu();
viewerActionMenu.setVisible(false);
- menuBar.add(helpMenu);
+ viewerActionMenu.add(alignStructs);
+ colourMenu = new JMenu();
+ colourMenu.setText(MessageManager.getString("label.colours"));
fileMenu.add(savemenu);
fileMenu.add(viewMapping);
savemenu.add(pdbFile);
savemenu.add(png);
savemenu.add(eps);
viewMenu.add(chainMenu);
-
- colourMenu.add(seqColour);
- colourMenu.add(chainColour);
- colourMenu.add(chargeColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydroColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(purinePyrimidineColour);
- colourMenu.add(userColour);
- colourMenu.add(viewerColour);
- colourMenu.add(backGround);
-
- ButtonGroup colourButtons = new ButtonGroup();
-
- colourButtons.add(seqColour);
- colourButtons.add(chainColour);
- colourButtons.add(chargeColour);
- colourButtons.add(zappoColour);
- colourButtons.add(taylorColour);
- colourButtons.add(hydroColour);
- colourButtons.add(helixColour);
- colourButtons.add(strandColour);
- colourButtons.add(turnColour);
- colourButtons.add(buriedColour);
- colourButtons.add(purinePyrimidineColour);
- colourButtons.add(userColour);
- colourButtons.add(viewerColour);
-
helpMenu.add(helpItem);
- viewerActionMenu.add(alignStructs);
+ menuBar.add(fileMenu);
+ menuBar.add(viewMenu);
+ menuBar.add(colourMenu);
+ menuBar.add(viewerActionMenu);
+ menuBar.add(helpMenu);
+
+ statusPanel = new JPanel();
statusPanel.setLayout(new GridLayout());
- this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
+ statusBar = new JLabel();
statusPanel.add(statusBar, null);
}
}
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed(ActionEvent actionEvent)
{
}
{
}
-
- // {
- // return bindingModel;
- // }
-
- // public void setBindingModel(AAStructureBindingModel bindingModel)
- // {
- // this.bindingModel = bindingModel;
- // }
-
}
okButton.setText(MessageManager.getString("action.ok"));
okButton.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- okButton_actionPerformed(e);
+ okButton_actionPerformed();
}
});
applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
applyButton.setText(MessageManager.getString("action.apply"));
- applyButton.addActionListener(new java.awt.event.ActionListener()
+ applyButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- applyButton_actionPerformed(e);
+ applyButton_actionPerformed();
}
});
loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
loadbutton.setText(MessageManager.getString("action.load_scheme"));
loadbutton.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
loadbutton_actionPerformed(e);
savebutton.setText(MessageManager.getString("action.save_scheme"));
savebutton.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
savebutton_actionPerformed(e);
cancelButton.setText(MessageManager.getString("action.cancel"));
cancelButton.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancelButton_actionPerformed(e);
caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
caseSensitive_actionPerformed(e);
.setText(MessageManager.getString("label.lower_case_colour"));
lcaseColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
lcaseColour_actionPerformed(e);
/**
* DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
*/
- protected void okButton_actionPerformed(ActionEvent e)
+ protected void okButton_actionPerformed()
{
}
/**
* DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
*/
- protected void applyButton_actionPerformed(ActionEvent e)
+ protected void applyButton_actionPerformed()
{
}
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
return Color.red;
{
seqAssociated = sassoc;
}
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
super();
}
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new Blosum62ColourScheme();
+ }
+
@Override
public Color findColour(char res, int j, SequenceI seq)
{
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Blosum62.toString();
+ }
+
+ @Override
+ public boolean isSimple()
{
- ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
- return newcs;
+ return false;
}
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color makeColour(float c)
{
return new Color(0, (float) (1.0 - c), c);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Buried.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new BuriedColourScheme();
+ }
}
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
private static final int SIXTY = 60;
- /*
- * Map from conventional colour names to Clustal version of the same
- */
- private static Map<Color, Color> colhash = new HashMap<Color, Color>();
+ enum ClustalColour
+ {
+ RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
+ ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
+ 0.0f);
+
+ final Color colour;
+
+ ClustalColour(float r, float g, float b)
+ {
+ colour = new Color(r, g, b);
+ }
+ }
+ private class ConsensusColour
+ {
+ Consensus[] cons;
+
+ Color c;
+
+ public ConsensusColour(ClustalColour col, Consensus[] conses)
+ {
+ this.cons = conses;
+ this.c = col.colour;
+ }
+ }
private int[][] cons2;
private boolean includeGaps = true;
- static
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public ClustalxColourScheme()
{
- colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
- colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
- colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
- colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
- colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
- colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
- colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
- colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
+
}
public ClustalxColourScheme(AnnotatedCollectionI alignment,
alignmentChanged(alignment, hiddenReps);
}
+ @Override
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
// includeGaps param.
- int start = 0;
-
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (int i = 0; i < maxWidth; i++)
- {
- cons2[i][j] = 0;
- }
- }
-
- int res;
- int i;
- int j = 0;
- char[] seq;
+ int res = 0;
for (SequenceI sq : seqs)
{
- seq = sq.getSequence();
+ char[] seq = sq.getSequence();
int end_j = seq.length - 1;
- for (i = start; i <= end_j; i++)
+ for (int i = 0; i <= end_j; i++)
{
if ((seq.length - 1) < i)
{
{
res = ResidueProperties.aaIndex[seq[i]];
}
-
cons2[i][res]++;
}
-
- j++;
}
this.size = seqs.size();
makeColours();
}
- public void makeColours()
+ void makeColours()
{
conses[0] = new Consensus("WLVIMAFCYHP", SIXTY);
conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
Consensus[] tmp8 = new Consensus[1];
tmp8[0] = conses[30]; // G
- colours[7] = new ConsensusColour(colhash.get(Color.ORANGE), tmp8);
+ colours[7] = new ConsensusColour(ClustalColour.ORANGE, tmp8);
Consensus[] tmp9 = new Consensus[1];
tmp9[0] = conses[31]; // P
- colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
+ colours[8] = new ConsensusColour(ClustalColour.YELLOW, tmp9);
Consensus[] tmp10 = new Consensus[1];
tmp10[0] = conses[27]; // C
- colours[9] = new ConsensusColour(colhash.get(Color.PINK), tmp8);
+ colours[9] = new ConsensusColour(ClustalColour.PINK, tmp8);
Consensus[] tmp1 = new Consensus[14];
tmp1[0] = conses[0]; // %
tmp1[11] = conses[25]; // Y
tmp1[12] = conses[18]; // P
tmp1[13] = conses[19]; // p
- colours[0] = new ConsensusColour(colhash.get(Color.BLUE), tmp1);
+ colours[0] = new ConsensusColour(ClustalColour.BLUE, tmp1);
- colours[10] = new ConsensusColour(colhash.get(Color.CYAN), tmp1);
+ colours[10] = new ConsensusColour(ClustalColour.CYAN, tmp1);
Consensus[] tmp2 = new Consensus[5];
tmp2[0] = conses[8]; // t
tmp2[2] = conses[22]; // T
tmp2[3] = conses[0]; // %
tmp2[4] = conses[1]; // #
- colours[1] = new ConsensusColour(colhash.get(Color.GREEN), tmp2);
+ colours[1] = new ConsensusColour(ClustalColour.GREEN, tmp2);
Consensus[] tmp3 = new Consensus[3];
tmp3[0] = conses[17]; // N
tmp3[1] = conses[29]; // D
tmp3[2] = conses[5]; // n
- colours[2] = new ConsensusColour(colhash.get(Color.GREEN), tmp3);
+ colours[2] = new ConsensusColour(ClustalColour.GREEN, tmp3);
Consensus[] tmp4 = new Consensus[6];
tmp4[0] = conses[6]; // q = QE
tmp4[3] = conses[3]; // +
tmp4[4] = conses[28]; // K
tmp4[5] = conses[20]; // R
- colours[3] = new ConsensusColour(colhash.get(Color.GREEN), tmp4);
+ colours[3] = new ConsensusColour(ClustalColour.GREEN, tmp4);
Consensus[] tmp5 = new Consensus[4];
tmp5[0] = conses[3]; // +
tmp5[1] = conses[28]; // K
tmp5[2] = conses[20]; // R
tmp5[3] = conses[19]; // Q
- colours[4] = new ConsensusColour(colhash.get(Color.RED), tmp5);
+ colours[4] = new ConsensusColour(ClustalColour.RED, tmp5);
Consensus[] tmp6 = new Consensus[6];
tmp6[0] = conses[3]; // -
tmp6[3] = conses[6]; // QE
tmp6[4] = conses[19]; // Q
tmp6[5] = conses[2]; // DE
- colours[5] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp6);
+ colours[5] = new ConsensusColour(ClustalColour.MAGENTA, tmp6);
Consensus[] tmp7 = new Consensus[5];
tmp7[0] = conses[3]; // -
tmp7[2] = conses[10]; // E
tmp7[3] = conses[17]; // N
tmp7[4] = conses[2]; // DE
- colours[6] = new ConsensusColour(colhash.get(Color.MAGENTA), tmp7);
+ colours[6] = new ConsensusColour(ClustalColour.MAGENTA, tmp7);
// Now attach the ConsensusColours to the residue letters
residueColour = new ConsensusColour[20];
return currentColour;
}
- for (int k = 0; k < residueColour[i].conses.length; k++)
+ for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (residueColour[i].conses[k].isConserved(cons2, j, size,
+ if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
currentColour = residueColour[i].c;
if (i == 4)
{
+ /*
+ * override to colour C pink if 100% conserved
+ */
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = colhash.get(Color.PINK);
+ currentColour = ClustalColour.PINK.colour;
}
}
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
css.includeGaps = includeGaps;
return css;
}
-}
-class ConsensusColour
-{
- Consensus[] conses;
-
- Color c;
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
- public ConsensusColour(Color c, Consensus[] conses)
+ @Override
+ public String getSchemeName()
{
- this.conses = conses;
+ return JalviewColourScheme.Clustal.toString();
+ }
- // this.list = list;
- this.c = c;
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
}
*/
package jalview.schemes;
+import jalview.analysis.Conservation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
public interface ColourSchemeI
{
/**
+ * Returns the colour for the given character. For use when the colour depends
+ * only on the symbol.
*
* @param c
- * @return the colour for the given character
+ * @return
*/
- public Color findColour(char c);
+ Color findColour(char c);
/**
+ * Returns the possibly context dependent colour for the given symbol at the
+ * aligned position in the given sequence. For example, the colour may depend
+ * on the symbol's relationship to the consensus residue for the column.
*
- * @param c
- * - sequence symbol or gap
- * @param j
- * - position in seq
+ * @param symbol
+ * @param position
* @param seq
- * - sequence being coloured
- * @return context dependent colour for the given symbol at the position in
- * the given sequence
+ * @return
*/
- public Color findColour(char c, int j, SequenceI seq);
+ Color findColour(char symbol, int position, SequenceI seq);
/**
- * assign the given consensus profile for the colourscheme
+ * Assigns the given consensus profile for the colourscheme
*/
- public void setConsensus(ProfilesI hconsensus);
+ void setConsensus(ProfilesI hconsensus);
/**
- * assign the given conservation to the colourscheme
+ * Assigns the given conservation to the colourscheme
*
* @param c
*/
- public void setConservation(jalview.analysis.Conservation c);
+ void setConservation(Conservation c);
/**
- * enable or disable conservation shading for this colourscheme
+ * Enable or disable conservation shading for this colourscheme
*
* @param conservationApplied
*/
- public void setConservationApplied(boolean conservationApplied);
+ void setConservationApplied(boolean conservationApplied);
/**
+ * Answers true if conservation shading is enabled for this colourscheme
*
- * @return true if conservation shading is enabled for this colourscheme
+ * @return
*/
- public boolean conservationApplied();
+ boolean conservationApplied();
/**
- * set scale factor for bleaching of colour in unconserved regions
+ * Sets the scale factor for bleaching of colour in unconserved regions
*
* @param i
*/
- public void setConservationInc(int i);
+ void setConservationInc(int i);
/**
+ * Returns the scale factor for bleaching colour in unconserved regions
*
- * @return scale factor for bleaching colour in unconserved regions
+ * @return
*/
- public int getConservationInc();
+ int getConservationInc();
/**
+ * Returns the percentage identity threshold for applying colourscheme
*
- * @return percentage identity threshold for applying colourscheme
+ * @return
*/
- public int getThreshold();
+ int getThreshold();
/**
- * set percentage identity threshold and type of %age identity calculation for
- * shading
+ * Sets the percentage identity threshold and type of %age identity
+ * calculation for shading
*
- * @param ct
+ * @param pct
* 0..100 percentage identity for applying this colourscheme
* @param ignoreGaps
* when true, calculate PID without including gapped positions
*/
- public void setThreshold(int ct, boolean ignoreGaps);
+ void setThreshold(int pct, boolean ignoreGaps);
/**
- * recalculate dependent data using the given sequence collection, taking
+ * Recalculate dependent data using the given sequence collection, taking
* account of hidden rows
*
* @param alignment
* @param hiddenReps
*/
- public void alignmentChanged(AnnotatedCollectionI alignment,
+ void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
- * create a new instance of the colourscheme configured to colour the given
- * connection
+ * Creates and returns a new instance of the colourscheme configured to colour
+ * the given collection. Note that even simple colour schemes should return a
+ * new instance for each call to this method, as different instances may have
+ * differing shading by consensus or percentage identity applied.
*
* @param sg
* @param hiddenRepSequences
- * @return copy of current scheme with any inherited settings transfered
+ * @return copy of current scheme with any inherited settings transferred
*/
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+ /**
+ * Answers true if the colour scheme is suitable for the given data, else
+ * false. For example, some colour schemes are specific to either peptide or
+ * nucleotide, or only apply if certain kinds of annotation are present.
+ *
+ * @param ac
+ * @return
+ */
+ // TODO can make this method static in Java 8
+ boolean isApplicableTo(AnnotatedCollectionI ac);
+
+ /**
+ * Answers the 'official' name of the colour scheme (as used, for example, as
+ * a Jalview startup parameter)
+ *
+ * @return
+ */
+ String getSchemeName();
+
+ /**
+ * Answers true if the colour scheme depends only on the sequence symbol, and
+ * not on other information such as alignment consensus or annotation. (Note
+ * that simple colour schemes may have a fading by percentage identity or
+ * conservation overlaid.) Simple colour schemes can be propagated to
+ * structure viewers.
+ *
+ * @return
+ */
+ boolean isSimple();
}
package jalview.schemes;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
import java.awt.Color;
*/
public class ColourSchemeProperty
{
- /** Undefined Colourscheme Index */
- public static final int UNDEFINED = -1;
-
- /** for schemes defined on the fly */
- public static final int USER_DEFINED = 0;
-
- /** No Colourscheme Index */
- public static final int NONE = 1;
-
- /** DOCUMENT ME!! */
- public static final int CLUSTAL = 2;
-
- /** DOCUMENT ME!! */
- public static final int BLOSUM = 3;
-
- /** DOCUMENT ME!! */
- public static final int PID = 4;
-
- /** DOCUMENT ME!! */
- public static final int ZAPPO = 5;
-
- /** DOCUMENT ME!! */
- public static final int TAYLOR = 6;
-
- /** DOCUMENT ME!! */
- public static final int HYDROPHOBIC = 7;
-
- /** DOCUMENT ME!! */
- public static final int HELIX = 8;
-
- /** DOCUMENT ME!! */
- public static final int STRAND = 9;
-
- /** DOCUMENT ME!! */
- public static final int TURN = 10;
-
- /** DOCUMENT ME!! */
- public static final int BURIED = 11;
-
- /** DOCUMENT ME!! */
- public static final int NUCLEOTIDE = 12;
/**
- * purine/pyrimidine
- */
- public static final int PURINEPYRIMIDINE = 13;
-
- public static final int COVARIATION = 14;
-
- public static final int TCOFFEE = 15;
-
- public static final int RNAHELIX = 16;
-
- public static final int RNAINTERACTION = 17;
-
- /**
- * index of first colourscheme (includes 'None')
- */
- public static final int FIRST_COLOUR = NONE;
-
- public static final int LAST_COLOUR = RNAINTERACTION;
-
- /**
- * DOCUMENT ME!
+ * Returns a colour scheme for the given name, with which the given data may
+ * be coloured. The name is not case-sensitive, and may be one of
+ * <ul>
+ * <li>Clustal</li>
+ * <li>Blosum62</li>
+ * <li>% Identity</li>
+ * <li>Hydrophobic</li>
+ * <li>Zappo</li>
+ * <li>Taylor</li>
+ * <li>Helix Propensity</li>
+ * <li>Strand Propensity</li>
+ * <li>Turn Propensity</li>
+ * <li>Buried Index</li>
+ * <li>Nucleotide</li>
+ * <li>Purine/Pyrimidine</li>
+ * <li>T-Coffee Scores</li>
+ * <li>RNA Helices</li>
+ * <li>User Defined</li>
+ * <li>an AWT colour name e.g. red</li>
+ * <li>an AWT hex rgb colour e.g. ff2288</li>
+ * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+ * </ul>
+ * If none of these formats is matched, the string is converted to a colour
+ * using a hashing algorithm. For name "None", returns null.
*
+ * @param forData
* @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return
*/
- public static int getColourIndexFromName(String name)
+ public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+ String name)
{
- int ret = UNDEFINED;
-
- if (name.equalsIgnoreCase("Clustal"))
- {
- ret = CLUSTAL;
- }
- else if (name.equalsIgnoreCase("Blosum62"))
+ if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
{
- ret = BLOSUM;
- }
- else if (name.equalsIgnoreCase("% Identity"))
- {
- ret = PID;
- }
- else if (name.equalsIgnoreCase("Zappo"))
- {
- ret = ZAPPO;
- }
- else if (name.equalsIgnoreCase("Taylor"))
- {
- ret = TAYLOR;
- }
- else if (name.equalsIgnoreCase("Hydrophobic"))
- {
- ret = HYDROPHOBIC;
- }
- else if (name.equalsIgnoreCase("Helix Propensity"))
- {
- ret = HELIX;
- }
- else if (name.equalsIgnoreCase("Strand Propensity"))
- {
- ret = STRAND;
- }
- else if (name.equalsIgnoreCase("Turn Propensity"))
- {
- ret = TURN;
- }
- else if (name.equalsIgnoreCase("Buried Index"))
- {
- ret = BURIED;
- }
- else if (name.equalsIgnoreCase("Nucleotide"))
- {
- ret = NUCLEOTIDE;
- }
- else if (name.equalsIgnoreCase("T-Coffee Scores"))
- {
- ret = TCOFFEE;
- }
+ return null;
- else if (name.equalsIgnoreCase("User Defined"))
- {
- ret = USER_DEFINED;
- }
- else if (name.equalsIgnoreCase("None"))
- {
- ret = NONE;
- }
- else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
- {
- ret = PURINEPYRIMIDINE;
- }
- else if (name.equalsIgnoreCase("RNA Interaction type"))
- {
- ret = RNAINTERACTION;
}
- else if (name.equalsIgnoreCase("RNA Helices"))
- {
- ret = RNAHELIX;
- }
- // else if (name.equalsIgnoreCase("Covariation"))
- // {
- // ret = COVARIATION;
- // }
-
- return ret;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cs
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String getColourName(ColourSchemeI cs)
- {
-
- int index = NONE;
- if (cs instanceof ClustalxColourScheme)
- {
- index = CLUSTAL;
- }
- else if (cs instanceof Blosum62ColourScheme)
- {
- index = BLOSUM;
- }
- else if (cs instanceof PIDColourScheme)
- {
- index = PID;
- }
- else if (cs instanceof ZappoColourScheme)
- {
- index = ZAPPO;
- }
- else if (cs instanceof TaylorColourScheme)
- {
- index = TAYLOR;
- }
- else if (cs instanceof HydrophobicColourScheme)
- {
- index = HYDROPHOBIC;
- }
- else if (cs instanceof HelixColourScheme)
- {
- index = HELIX;
- }
- else if (cs instanceof StrandColourScheme)
- {
- index = STRAND;
- }
- else if (cs instanceof TurnColourScheme)
- {
- index = TURN;
- }
- else if (cs instanceof BuriedColourScheme)
- {
- index = BURIED;
- }
- else if (cs instanceof NucleotideColourScheme)
- {
- index = NUCLEOTIDE;
- }
- else if (cs instanceof PurinePyrimidineColourScheme)
- {
- index = PURINEPYRIMIDINE;
- }
- else if (cs instanceof TCoffeeColourScheme)
- {
- index = TCOFFEE;
- }
- else if (cs instanceof RNAHelicesColour)
- {
- index = RNAHELIX;
- }
/*
- * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+ * if this is the name of a registered colour scheme, just
+ * create a new instance of it
*/
- else if (cs instanceof UserColourScheme)
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(
+ name, forData, null);
+ if (scheme != null)
{
- if ((((UserColourScheme) cs).getName() != null)
- && (((UserColourScheme) cs).getName().length() > 0))
- {
- return ((UserColourScheme) cs).getName();
- }
- // get default colourscheme name
- index = USER_DEFINED;
+ return scheme;
}
- return getColourName(index);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param index
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String getColourName(int index)
- {
- String ret = null;
-
- switch (index)
- {
- case CLUSTAL:
- ret = "Clustal";
-
- break;
-
- case BLOSUM:
- ret = "Blosum62";
-
- break;
-
- case PID:
- ret = "% Identity";
-
- break;
-
- case ZAPPO:
- ret = "Zappo";
-
- break;
-
- case TAYLOR:
- ret = "Taylor";
- break;
-
- case HYDROPHOBIC:
- ret = "Hydrophobic";
-
- break;
-
- case HELIX:
- ret = "Helix Propensity";
-
- break;
-
- case STRAND:
- ret = "Strand Propensity";
-
- break;
-
- case TURN:
- ret = "Turn Propensity";
-
- break;
-
- case BURIED:
- ret = "Buried Index";
-
- break;
-
- case NUCLEOTIDE:
- ret = "Nucleotide";
-
- break;
-
- case PURINEPYRIMIDINE:
- ret = "Purine/Pyrimidine";
-
- break;
-
- case TCOFFEE:
- ret = "T-Coffee Scores";
-
- break;
-
- case RNAINTERACTION:
- ret = "RNA Interaction type";
-
- break;
- case RNAHELIX:
- ret = "RNA Helices";
-
- break;
/*
- * case COVARIATION: ret = "Covariation";
- *
- * break;
+ * try to parse the string as a residues colour scheme
+ * e.g. A=red;T,G=blue etc
+ * else parse the name as a colour specification
+ * e.g. "red" or "ff00ed",
+ * or failing that hash the name to a colour
*/
- case USER_DEFINED:
- ret = "User Defined";
-
- break;
-
- default:
- ret = "None";
-
- break;
- }
-
- return ret;
- }
-
- /**
- * retrieve or create colourscheme associated with name
- *
- * @param seqs
- * sequences to colour
- * @param width
- * range of sequences to colour
- * @param name
- * colourscheme name, applet colour parameter specification, or
- * string to parse as colour for new coloursheme
- * @return Valid Colourscheme
- */
- public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
- String name)
- {
- int colindex = getColourIndexFromName(name);
- if (colindex == UNDEFINED)
- {
- if (name.indexOf('=') == -1)
- {
- // try to build a colour from the string directly
- try
- {
- return new UserColourScheme(name);
- } catch (Exception e)
- {
- // System.err.println("Ignoring unknown colourscheme name");
- }
- }
- else
- {
- // try to parse the string as a residue colourscheme
- try
- {
- // fix the launchApp user defined coloursheme transfer bug
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(name);
-
- } catch (Exception e)
- {
- // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
- }
- }
- }
- return getColour(alignment, getColourIndexFromName(name));
- }
-
- /**
- * Construct an instance of ColourSchemeI corresponding to the given
- * colourscheme index
- *
- * @param seqs
- * sequences to be coloured by colourscheme
- * @param width
- * geometry of alignment
- * @param index
- * colourscheme number
- *
- * @return null or an instance of the colourscheme configured to colour given
- * sequence set
- */
- public static ColourSchemeI getColour(
- jalview.datamodel.AnnotatedCollectionI coll, int index)
- {
- // TODO 3.0 2.8 refactor signature to take an alignmentI like container so
- // colourschemes based on annotation can be initialised
- ColourSchemeI cs = null;
-
- switch (index)
- {
- case CLUSTAL:
- cs = new ClustalxColourScheme(coll, null);
-
- break;
-
- case BLOSUM:
- cs = new Blosum62ColourScheme();
-
- break;
-
- case PID:
- cs = new PIDColourScheme();
-
- break;
-
- case ZAPPO:
- cs = new ZappoColourScheme();
-
- break;
-
- case TAYLOR:
- cs = new TaylorColourScheme();
- break;
-
- case HYDROPHOBIC:
- cs = new HydrophobicColourScheme();
-
- break;
-
- case HELIX:
- cs = new HelixColourScheme();
-
- break;
-
- case STRAND:
- cs = new StrandColourScheme();
-
- break;
-
- case TURN:
- cs = new TurnColourScheme();
-
- break;
-
- case BURIED:
- cs = new BuriedColourScheme();
-
- break;
-
- case NUCLEOTIDE:
- cs = new NucleotideColourScheme();
-
- break;
-
- case PURINEPYRIMIDINE:
- cs = new PurinePyrimidineColourScheme();
-
- break;
-
- case TCOFFEE:
- cs = new TCoffeeColourScheme(coll);
- break;
-
- case RNAHELIX:
- cs = new RNAHelicesColour(coll);
- break;
-
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
- // break;
-
- case USER_DEFINED:
- Color[] col = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- col[i] = Color.white;
- }
- cs = new UserColourScheme(col);
- break;
-
- default:
- break;
- }
-
- return cs;
- }
-
- public static Color getAWTColorFromName(String name)
- {
- Color col = null;
- name = name.toLowerCase();
- if (name.equals("black"))
- {
- col = Color.black;
- }
- else if (name.equals("blue"))
- {
- col = Color.blue;
- }
- else if (name.equals("cyan"))
- {
- col = Color.cyan;
- }
- else if (name.equals("darkGray"))
- {
- col = Color.darkGray;
- }
- else if (name.equals("gray"))
- {
- col = Color.gray;
- }
- else if (name.equals("green"))
- {
- col = Color.green;
- }
- else if (name.equals("lightGray"))
- {
- col = Color.lightGray;
- }
- else if (name.equals("magenta"))
- {
- col = Color.magenta;
- }
- else if (name.equals("orange"))
- {
- col = Color.orange;
- }
- else if (name.equals("pink"))
- {
- col = Color.pink;
- }
- else if (name.equals("red"))
- {
- col = Color.red;
- }
- else if (name.equals("white"))
- {
- col = Color.white;
- }
- else if (name.equals("yellow"))
- {
- col = Color.yellow;
- }
-
- return col;
+ UserColourScheme ucs = new UserColourScheme(name);
+ return ucs;
}
public static Color rnaHelices[] = null;
// Generate random colors and store
for (; j <= n; j++)
{
- rnaHelices[j] = jalview.util.ColorUtils
- .generateRandomColor(Color.white);
+ rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
}
}
/**
- * delete the existing cached RNA helces colours
+ * delete the existing cached RNA helices colours
*/
public static void resetRnaHelicesShading()
{
rnaHelices = null;
}
+ /**
+ * Returns the name of the colour scheme (or "None" if it is null)
+ *
+ * @param cs
+ * @return
+ */
+ public static String getColourName(ColourSchemeI cs)
+ {
+ return cs == null ? ResidueColourScheme.NONE : cs
+ .getSchemeName();
+ }
+
}
--- /dev/null
+package jalview.schemes;
+
+import jalview.binding.JalviewUserColours;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+public class ColourSchemes
+{
+ /*
+ * singleton instance of this class
+ */
+ private static ColourSchemes instance = new ColourSchemes();
+
+ /*
+ * a map from scheme name to an instance of it
+ */
+ private Map<String, ColourSchemeI> schemes;
+
+ /**
+ * Returns the singleton instance of this class
+ *
+ * @return
+ */
+ public static ColourSchemes getInstance()
+ {
+ return instance;
+ }
+
+ private ColourSchemes()
+ {
+ loadColourSchemes();
+ }
+
+ /**
+ * Loads an instance of each standard or user-defined colour scheme
+ *
+ * @return
+ */
+ void loadColourSchemes()
+ {
+ /*
+ * store in an order-preserving map, so items can be added to menus
+ * in the order in which they are 'discovered'
+ */
+ schemes = new LinkedHashMap<String, ColourSchemeI>();
+
+ for (JalviewColourScheme cs : JalviewColourScheme.values())
+ {
+ try
+ {
+ registerColourScheme(cs.getSchemeClass().newInstance());
+ } catch (InstantiationException | IllegalAccessException e)
+ {
+ System.err.println("Error instantiating colour scheme for "
+ + cs.toString() + " " + e.getMessage());
+ }
+ }
+ }
+
+ /**
+ * Registers a colour scheme
+ *
+ * @param cs
+ */
+ public void registerColourScheme(ColourSchemeI cs)
+ {
+ String name = cs.getSchemeName();
+ if (name == null)
+ {
+ System.err.println("ColourScheme name may not be null");
+ return;
+ }
+
+ /*
+ * name is lower-case for non-case-sensitive lookup
+ * (name in the colour keeps its true case)
+ */
+ String lower = name.toLowerCase();
+ if (schemes.containsKey(lower))
+ {
+ System.err
+ .println("Warning: overwriting colour scheme named " + name);
+ }
+ schemes.put(lower, cs);
+ }
+
+ /**
+ * Removes a colour scheme by name
+ *
+ * @param name
+ */
+ public void removeColourScheme(String name)
+ {
+ schemes.remove(name);
+ }
+
+ /**
+ * Returns an instance of the colour scheme with which the given view may be
+ * coloured
+ *
+ * @param name
+ * name of the colour scheme
+ * @param forData
+ * the data to be coloured
+ * @param optional
+ * map from hidden representative sequences to the sequences they
+ * represent
+ * @return
+ */
+ public ColourSchemeI getColourScheme(String name,
+ AnnotatedCollectionI forData,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ if (name == null)
+ {
+ return null;
+ }
+ ColourSchemeI cs = schemes.get(name.toLowerCase());
+ return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+ }
+
+ /**
+ * Returns an instance of the colour scheme with which the given view may be
+ * coloured
+ *
+ * @param name
+ * name of the colour scheme
+ * @param forData
+ * the data to be coloured
+ * @return
+ */
+ public ColourSchemeI getColourScheme(String name,
+ AnnotatedCollectionI forData)
+ {
+ return getColourScheme(name, forData, null);
+ }
+
+ /**
+ * Returns an iterable set of the colour schemes, in the order in which they
+ * were added
+ *
+ * @return
+ */
+ public Iterable<ColourSchemeI> getColourSchemes()
+ {
+ return schemes.values();
+ }
+
+ /**
+ * Answers true if there is a scheme with the given name, else false. The test
+ * is not case-sensitive.
+ *
+ * @param name
+ * @return
+ */
+ public boolean nameExists(String name)
+ {
+ if (name == null)
+ {
+ return false;
+ }
+ name = name.toLowerCase();
+ for (ColourSchemeI scheme : getColourSchemes())
+ {
+ if (name.equals(scheme.getSchemeName().toLowerCase()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Loads a user defined colour scheme from file. The file should contain a
+ * definition of residue colours in XML format as defined in
+ * JalviewUserColours.xsd.
+ *
+ * @param filePath
+ *
+ * @return
+ */
+ public static UserColourScheme loadColourScheme(String filePath)
+ {
+ UserColourScheme ucs = null;
+ Color[] newColours = null;
+ File file = new File(filePath);
+ try
+ {
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
+
+ jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
+
+ org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
+ jucs);
+ jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
+ .unmarshal(in);
+
+ /*
+ * non-case-sensitive colours are for 20 amino acid codes,
+ * B, Z, X and Gap
+ * optionally, lower-case alternatives for all except Gap
+ */
+ newColours = new Color[24];
+ Color[] lowerCase = new Color[23];
+ boolean caseSensitive = false;
+
+ String name;
+ int index;
+ for (int i = 0; i < jucs.getColourCount(); i++)
+ {
+ name = jucs.getColour(i).getName();
+ if (ResidueProperties.aa3Hash.containsKey(name))
+ {
+ index = ResidueProperties.aa3Hash.get(name).intValue();
+ }
+ else
+ {
+ index = ResidueProperties.aaIndex[name.charAt(0)];
+ }
+ if (index == -1)
+ {
+ continue;
+ }
+
+ Color color = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
+ if (name.toLowerCase().equals(name))
+ {
+ caseSensitive = true;
+ lowerCase[index] = color;
+ }
+ else
+ {
+ newColours[index] = color;
+ }
+ }
+
+ /*
+ * instantiate the colour scheme
+ */
+ ucs = new UserColourScheme(newColours);
+ ucs.setName(jucs.getSchemeName());
+ if (caseSensitive)
+ {
+ ucs.setLowerCaseColours(lowerCase);
+ }
+ } catch (Exception ex)
+ {
+ // Could be old Jalview Archive format
+ try
+ {
+ InputStreamReader in = new InputStreamReader(new FileInputStream(
+ file), "UTF-8");
+
+ jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
+
+ jucs = JalviewUserColours.unmarshal(in);
+
+ newColours = new Color[jucs.getColourCount()];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
+ }
+ ucs = new UserColourScheme(newColours);
+ ucs.setName(jucs.getSchemeName());
+ } catch (Exception ex2)
+ {
+ ex2.printStackTrace();
+ }
+
+ if (newColours == null)
+ {
+ System.out.println("Error loading User ColourFile\n" + ex);
+ }
+ }
+
+ return ucs;
+ }
+}
package jalview.schemes;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.util.Hashtable;
+import java.util.Map;
/**
* Became RNAHelicesColour.java. Placeholder for true covariation color scheme
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Hashtable helixcolorhash = new Hashtable();
+ public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
- public Hashtable positionsToHelix = new Hashtable();
+ public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
int numHelix = 0;
public AlignmentAnnotation annotation;
/**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
+ }
+
+ /**
* Creates a new CovariationColourScheme object.
*/
public CovariationColourScheme(AlignmentAnnotation annotation)
for (int j = 0; j <= numHelix; j++)
{
- helixcolorhash.put(Integer.toString(j),
- jalview.util.ColorUtils.generateRandomColor(Color.white));
+ helixcolorhash.put(String.valueOf(j),
+ ColorUtils.generateRandomColor(Color.white));
}
}
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
// System.out.println("called"); log.debug
Color currentColour = Color.white;
String currentHelix = null;
// System.out.println(c + " " + j);
- currentHelix = (String) positionsToHelix.get(j);
+ currentHelix = positionsToHelix.get(j);
// System.out.println(positionsToHelix.get(j));
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = helixcolorhash.get(currentHelix);
}
// System.out.println(c + " " + j + " helix " + currentHelix + " " +
return currentColour;
}
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Covariation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import java.awt.Color;
/*
* only a simple colour specification - parse it
*/
- Color colour = UserColourScheme.getColourFromString(descriptor);
+ Color colour = ColorUtils.parseColourString(descriptor);
if (colour == null)
{
throw new IllegalArgumentException("Invalid colour descriptor: "
FeatureColour featureColour;
try
{
- featureColour = new FeatureColour(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min, max);
+ Color minColour = ColorUtils.parseColourString(mincol);
+ Color maxColour = ColorUtils.parseColourString(maxcol);
+ featureColour = new FeatureColour(minColour, maxColour, min, max);
featureColour.setColourByLabel(labelColour);
featureColour.setAutoScaled(autoScaled);
// add in any additional parameters
*/
public FeatureColour(Color low, Color high, float min, float max)
{
+ if (low == null)
+ {
+ low = Color.white;
+ }
+ if (high == null)
+ {
+ high = Color.black;
+ }
graduatedColour = true;
colour = null;
minColour = low;
{
if (isColourByLabel())
{
- return UserColourScheme
+ return ColorUtils
.createColourFromName(feature.getDescription());
}
package jalview.schemes;
import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
/**
* Colourscheme that takes its colours from some other colourscheme
}
}
+ @Override
+ public String getSchemeName()
+ {
+ return "Follower";
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new FollowerColourScheme();
+ }
+
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
public class HelixColourScheme extends ScoreColourScheme
{
ResidueProperties.helixmin, ResidueProperties.helixmax);
}
+ @Override
public Color makeColour(float c)
{
return new Color(c, (float) 1.0 - c, c);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Helix.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new HelixColourScheme();
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color makeColour(float c)
{
return new Color(c, (float) 0.0, (float) 1.0 - c);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Hydrophobic.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new HydrophobicColourScheme();
+ }
}
--- /dev/null
+package jalview.schemes;
+
+
+/**
+ * An enum with the colour schemes supported by Jalview.
+ */
+public enum JalviewColourScheme
+{
+ /*
+ * the order of declaration is the default order in which
+ * items are added to Colour menus
+ */
+ Clustal("Clustal", ClustalxColourScheme.class), Blosum62("Blosum62",
+ Blosum62ColourScheme.class), PID("% Identity",
+ PIDColourScheme.class), Zappo("Zappo", ZappoColourScheme.class),
+ Taylor("Taylor", TaylorColourScheme.class), Hydrophobic("Hydrophobic",
+ HydrophobicColourScheme.class), Helix("Helix Propensity",
+ HelixColourScheme.class), Strand("Strand Propensity",
+ StrandColourScheme.class), Turn("Turn Propensity",
+ TurnColourScheme.class), Buried("Buried Index",
+ BuriedColourScheme.class), Nucleotide("Nucleotide",
+ NucleotideColourScheme.class), PurinePyrimidine(
+ "Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
+ RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee(
+ "T-Coffee Scores", TCoffeeColourScheme.class);
+ // RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
+
+ private String name;
+
+ private Class<? extends ColourSchemeI> myClass;
+
+ /**
+ * Constructor given the name of the colour scheme (as used in Jalview
+ * parameters). Note this is not necessarily the same as the 'display name'
+ * used in menu options (as this may be language-dependent).
+ *
+ * @param s
+ */
+ JalviewColourScheme(String s, Class<? extends ColourSchemeI> cl)
+ {
+ name = s;
+ myClass = cl;
+ }
+
+ /**
+ * Returns the class of the colour scheme
+ *
+ * @return
+ */
+ public Class<? extends ColourSchemeI> getSchemeClass()
+ {
+ return myClass;
+ }
+
+ /**
+ * Returns the 'official' name of this colour scheme. This is the name that
+ * identifies the colour scheme as a start-up parameter for the Jalview
+ * application or applet. Note that it may not be the name shown in menu
+ * options, as these may be internationalised.
+ */
+ @Override
+ public String toString()
+ {
+ return name;
+ }
+}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
return currentColour;
}
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Nucleotide.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new NucleotideColourScheme();
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfileI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
+import java.util.Map;
public class PIDColourScheme extends ResidueColourScheme
{
return currentColour;
}
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PID.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new PIDColourScheme();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
/**
* Class is based off of NucleotideColourScheme
* @return Color from purinepyrimidineIndex in
* jalview.schemes.ResidueProperties
*/
+ @Override
public Color findColour(char c)
{
return colors[ResidueProperties.purinepyrimidineIndex[c]];
return currentColour;
}
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PurinePyrimidine.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new PurinePyrimidineColourScheme();
+ }
}
package jalview.schemes;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public AlignmentAnnotation annotation;
/**
+ * Default constructor (required for ColourSchemes cache)
+ */
+ public RNAHelicesColour()
+ {
+
+ }
+
+ /**
* Creates a new RNAHelicesColour object.
*/
public RNAHelicesColour(AlignmentAnnotation annotation)
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- return new RNAHelicesColour(this);
+ return new RNAHelicesColour(sg);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ /**
+ * Answers true if the data has RNA secondary structure annotation
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ if (ac instanceof AlignmentI && ((AlignmentI) ac).hasRNAStructure())
+ {
+ return true;
+ }
+
+ /*
+ * not currently supporting this option for group annotation / colouring
+ */
+ return false;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.RNAHelices.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
-}
\ No newline at end of file
+}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
-import java.awt.event.ActionEvent;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
/**
* change colors based on covariation.
*
* @author Lauren Michelle Lui
- *
+ * @deprecated this seems to be unfinished - just use RNAHelicesColour
*/
+@Deprecated
public class RNAHelicesColourChooser
{
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
+ Map<SequenceGroup, ColourSchemeI> oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.getAlignment().getGroups())
{
if (sg.cs != null)
this.av = av;
this.ap = ap;
- if (oldcs instanceof RNAHelicesColour)
- {
- RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
- }
-
adjusting = true;
- Vector list = new Vector();
+ Vector<String> list = new Vector<String>();
int index = 1;
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns != null)
}
adjusting = false;
-
changeColour();
-
}
void changeColour()
{
return;
}
- RNAHelicesColour rhc = null;
-
- rhc = new RNAHelicesColour(av.getAlignment());
+ RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
ap.paintAlignment(true);
}
-
- void reset()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
- {
- for (SequenceGroup sg : ap.getAlignment().getGroups())
- {
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
- }
- }
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.Map;
public class RNAInteractionColourScheme extends ResidueColourScheme
{
super();
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public Color findColour(char c)
{
- // System.out.println("called"); log.debug
+ // FIXME this is just a copy of NucleotideColourScheme
return colors[ResidueProperties.nucleotideIndex[c]];
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public Color findColour(char c, int j, SequenceI seq)
{
+ // FIXME this is just a copy of NucleotideColourScheme
Color currentColour;
if ((threshold == 0) || aboveThreshold(c, j))
{
return currentColour;
}
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "RNA Interaction type";
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new RNAInteractionColourScheme();
+ }
}
package jalview.schemes;
import jalview.analysis.Conservation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfileI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
-import jalview.util.MessageManager;
import java.awt.Color;
import java.util.Map;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Base class for residue-based colour schemes
*/
-public class ResidueColourScheme implements ColourSchemeI
+public abstract class ResidueColourScheme implements ColourSchemeI
{
+ public static final String NONE = "None";
+
+ public static final String USER_DEFINED = "User Defined";
+
+ /*
+ * lookup up by character value e.g. 'G' to the colors array index
+ * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
+ */
final int[] symbolIndex;
boolean conservationColouring = false;
+ /*
+ * colour for residue characters as indexed by symbolIndex
+ */
Color[] colors = null;
int threshold = 0;
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
+ Color colour = Color.white;
- if (colors != null && symbolIndex != null && (threshold == 0)
- || aboveThreshold(c, j))
+ if (colors != null && symbolIndex != null)
{
- currentColour = colors[symbolIndex[c]];
+ colour = colors[symbolIndex[c]];
}
- else
+ colour = adjustColour(c, j, colour);
+
+ return colour;
+ }
+
+ /**
+ * Adjusts colour by applying thresholding or conservation shading, if in
+ * force. That is
+ * <ul>
+ * <li>if there is a threshold set for colouring, and the residue doesn't
+ * match the consensus (or a joint consensus) residue, or the consensus score
+ * is not above the threshold, then the colour is set to white</li>
+ * <li>if conservation colouring is selected, the colour is faded by an amount
+ * depending on the conservation score for the column, and the conservation
+ * colour threshold</li>
+ * </ul>
+ *
+ * @param symbol
+ * @param column
+ * @param colour
+ * @return
+ */
+ protected Color adjustColour(char symbol, int column, Color colour)
+ {
+ if (!aboveThreshold(symbol, column))
{
- currentColour = Color.white;
+ colour = Color.white;
}
if (conservationColouring)
{
- currentColour = applyConservation(currentColour, j);
+ colour = applyConservation(colour, column);
}
-
- return currentColour;
+ return colour;
}
/**
*/
public boolean aboveThreshold(char residue, int column)
{
+ if (threshold == 0)
+ {
+ return true;
+ }
if ('a' <= residue && residue <= 'z')
{
// TO UPPERCASE !!!
{
}
+ /**
+ * Answers false if the colour scheme is nucleotide or peptide specific, and
+ * the data does not match, else true. Override to modify or extend this test
+ * as required.
+ */
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
{
- try
+ if (!isPeptideSpecific() && !isNucleotideSpecific())
{
- return getClass().newInstance();
- } catch (Exception q)
+ return true;
+ }
+
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = false;
+ if (ac instanceof AlignmentI)
{
- throw new Error(MessageManager.formatMessage(
- "error.implementation_error_cannot_duplicate_colour_scheme",
- new String[] { getClass().getName() }), q);
+ nucleotide = ((AlignmentI) ac).isNucleotide();
}
+ else
+ {
+ AnnotatedCollectionI context = ac.getContext();
+ if (context instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) context).isNucleotide();
+ }
+ else
+ {
+ // not sure what's going on, play safe
+ return true;
+ }
+ }
+
+ /*
+ * does data type match colour scheme type?
+ */
+ return (nucleotide && isNucleotideSpecific())
+ || (!nucleotide && isPeptideSpecific());
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for peptide data
+ *
+ * @return
+ */
+ public boolean isPeptideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for nucleotide data
+ *
+ * @return
+ */
+ public boolean isNucleotideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Default method returns true. Override this to return false in colour
+ * schemes that are not determined solely by the sequence symbol.
+ */
+ @Override
+ public boolean isSimple()
+ {
+ return true;
}
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
{
return new Color(c, (float) 0.0, (float) 1.0 - c);
}
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Score";
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new ScoreColourScheme(symbolIndex, scores, min, max);
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color makeColour(float c)
{
return new Color(c, c, (float) 1.0 - c);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Strand.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new StrandColourScheme();
+ }
}
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
+import java.util.List;
import java.util.Map;
/**
*/
public class TCoffeeColourScheme extends ResidueColourScheme
{
+ IdentityHashMap<SequenceI, Color[]> seqMap;
- static final Color[] colors = { new Color(102, 102, 255), // #6666FF
- new Color(0, 255, 0), // #00FF00
- new Color(102, 255, 0), // #66FF00
- new Color(204, 255, 0), // #CCFF00
- new Color(255, 255, 0), // #FFFF00
- new Color(255, 204, 0), // #FFCC00
- new Color(255, 153, 0), // #FF9900
- new Color(255, 102, 0), // #FF6600
- new Color(255, 51, 0), // #FF3300
- new Color(255, 34, 0) // #FF2000
- };
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public TCoffeeColourScheme()
+ {
- IdentityHashMap<SequenceI, Color[]> seqMap;
+ }
/**
* the color scheme needs to look at the alignment to get and cache T-COFFEE
alignmentChanged(alignment, null);
}
+ /**
+ * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
+ * annotation colour for each column position. The colours are fixed for
+ * scores 0-9 and are set when annotation is parsed.
+ *
+ * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
+ */
@Override
public void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
// assume only one set of TCOFFEE scores - but could have more than one
// potentially.
- ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color[] cols;
-
- if (seqMap == null || (cols = seqMap.get(seq)) == null)
+ if (seqMap == null)
+ {
+ return Color.WHITE;
+ }
+ Color[] cols = seqMap.get(seq);
+ if (cols == null)
{
// see above TODO about computing a colour for each residue in each
// column: cc = _rcols[i][indexFor[c]];
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
return new TCoffeeColourScheme(sg);
}
+
+ /**
+ * Answers true if the data has TCoffee score annotation
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac : ac
+ .getContext();
+ if (alcontext == null)
+ {
+ return false;
+ }
+ Iterable<AlignmentAnnotation> anns = alcontext
+ .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
+ return anns.iterator().hasNext();
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.TCoffee.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
public class TaylorColourScheme extends ResidueColourScheme
{
public TaylorColourScheme()
{
super(ResidueProperties.aaIndex, ResidueProperties.taylor, 0);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Taylor.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new TaylorColourScheme();
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public Color makeColour(float c)
{
return new Color(c, 1 - c, 1 - c);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Turn.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new TurnColourScheme();
+ }
}
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.StringUtils;
import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.StringTokenizer;
public class UserColourScheme extends ResidueColourScheme
{
+ /*
+ * lookup (by symbol index) of lower case colours (if configured)
+ */
Color[] lowerCaseColours;
protected String schemeName;
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- UserColourScheme usc = new UserColourScheme(colors);
- if (lowerCaseColours != null)
+ return new UserColourScheme(this);
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @return
+ */
+ protected UserColourScheme(UserColourScheme from)
+ {
+ this(from.colors);
+ schemeName = from.schemeName;
+ if (from.lowerCaseColours != null)
{
- usc.schemeName = new String(schemeName);
- usc.lowerCaseColours = new Color[lowerCaseColours.length];
- System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
- lowerCaseColours.length);
+ lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
+ from.lowerCaseColours.length);
}
- return usc;
}
+ /**
+ * Constructor for an animino acid colour scheme. The colour specification may
+ * be one of
+ * <ul>
+ * <li>an AWT colour name e.g. red</li>
+ * <li>an AWT hex rgb colour e.g. ff2288</li>
+ * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+ * </ul>
+ *
+ * @param colour
+ */
public UserColourScheme(String colour)
{
super(ResidueProperties.aaIndex);
- Color col = getColourFromString(colour);
+
+ if (colour.contains("="))
+ {
+ /*
+ * a list of colours per residue(s)
+ */
+ parseAppletParameter(colour);
+ return;
+ }
+
+ Color col = ColorUtils.parseColourString(colour);
if (col == null)
{
System.out.println("Making colour from name: " + colour);
- col = createColourFromName(colour);
+ col = ColorUtils.createColourFromName(colour);
}
- colors = new Color[24];
- for (int i = 0; i < 24; i++)
+ setAll(col);
+ schemeName = colour;
+ }
+
+ /**
+ * Sets all symbols to the specified colour
+ *
+ * @param col
+ */
+ protected void setAll(Color col)
+ {
+ if (symbolIndex == null)
+ {
+ return;
+ }
+ int max = 0;
+ for (int index : symbolIndex)
+ {
+ max = Math.max(max, index);
+ }
+ colors = new Color[max + 1];
+ for (int i = 0; i <= max; i++)
{
colors[i] = col;
}
- schemeName = colour;
}
public Color[] getColours()
return schemeName;
}
- public static Color getColourFromString(String colour)
- {
- if (colour == null)
- {
- return null;
- }
- colour = colour.trim();
-
- Color col = null;
- try
- {
- int value = Integer.parseInt(colour, 16);
- col = new Color(value);
- } catch (NumberFormatException ex)
- {
- }
-
- if (col == null)
- {
- col = ColourSchemeProperty.getAWTColorFromName(colour);
- }
-
- if (col == null)
- {
- try
- {
- java.util.StringTokenizer st = new java.util.StringTokenizer(
- colour, ",");
- int r = Integer.parseInt(st.nextToken());
- int g = Integer.parseInt(st.nextToken());
- int b = Integer.parseInt(st.nextToken());
- col = new Color(r, g, b);
- } catch (Exception ex)
- {
- }
- }
-
- return col;
-
- }
-
- public static Color createColourFromName(String name)
+ /**
+ * Parse and save residue colours specified as (for example)
+ *
+ * <pre>
+ * D,E=red; K,R,H=0022FF; c=100,50,75
+ * </pre>
+ *
+ * This should be a semi-colon separated list of colours, which may be defined
+ * by colour name, hex value or comma-separated RGB triple. Each colour is
+ * defined for a comma-separated list of amino acid single letter codes. (Note
+ * that this also allows a colour scheme to be defined for ACGT, but not for
+ * U.)
+ *
+ * @param paramValue
+ */
+ void parseAppletParameter(String paramValue)
{
- int r, g, b;
-
- int lsize = name.length();
- int start = 0, end = lsize / 3;
-
- int rgbOffset = Math.abs(name.hashCode() % 10) * 15;
-
- r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
- start = end;
- end += lsize / 3;
- if (end > lsize)
- {
- end = lsize;
- }
+ setAll(Color.white);
- g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
-
- b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
-
- Color color = new Color(r, g, b);
-
- return color;
- }
-
- public void parseAppletParameter(String paramValue)
- {
- // TODO: need a function to generate appletParameter colour string from a
- // UCS
StringTokenizer st = new StringTokenizer(paramValue, ";");
StringTokenizer st2;
String token = null, colour, residues;
st2 = new StringTokenizer(residues, " ,");
while (st2.hasMoreTokens())
{
- token = st2.nextToken();
+ String residue = st2.nextToken();
- if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+ int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
+ if (colIndex == -1)
{
continue;
}
- int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
-
- if (token.equalsIgnoreCase("lowerCase"))
+ if (residue.equalsIgnoreCase("lowerCase"))
{
if (lowerCaseColours == null)
{
- lowerCaseColours = new Color[23];
+ lowerCaseColours = new Color[colors.length];
}
- for (int i = 0; i < 23; i++)
+ for (int i = 0; i < lowerCaseColours.length; i++)
{
if (lowerCaseColours[i] == null)
{
- lowerCaseColours[i] = getColourFromString(colour);
+ lowerCaseColours[i] = ColorUtils.parseColourString(colour);
}
}
continue;
}
- if (token.equals(token.toLowerCase()))
+ if (residue.equals(residue.toLowerCase()))
{
if (lowerCaseColours == null)
{
- lowerCaseColours = new Color[23];
+ lowerCaseColours = new Color[colors.length];
}
- lowerCaseColours[colIndex] = getColourFromString(colour);
+ lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
}
else
{
- colors[colIndex] = getColourFromString(colour);
+ colors[colIndex] = ColorUtils.parseColourString(colour);
}
}
}
lowerCaseColours = lcolours;
}
+ /**
+ * Returns the colour for the given residue character. If the residue is
+ * lower-case, and there is a specific colour defined for lower case, that
+ * colour is returned, else the colour for the upper case residue.
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ if ('a' <= c && c <= 'z' && lowerCaseColours != null)
+ {
+ Color colour = lowerCaseColours[symbolIndex[c]];
+ if (colour != null)
+ {
+ return colour;
+ }
+ }
+ return super.findColour(c);
+ }
+
+ /**
+ * Answers the customised name of the colour scheme, if it has one, else
+ * "User Defined"
+ */
+ @Override
+ public String getSchemeName()
+ {
+ if (schemeName != null && schemeName.length() > 0)
+ {
+ return schemeName;
+ }
+ return "User Defined";
+ }
+
+ /**
+ * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd
+ *
+ * @return
+ */
+ public String toAppletParameter()
+ {
+ /*
+ * step 1: build a map from colours to the symbol(s) that have the colour
+ */
+ Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+
+ for (char symbol = 'A'; symbol <= 'Z'; symbol++)
+ {
+ String residue = String.valueOf(symbol);
+ int index = symbolIndex[symbol];
+ Color c = colors[index];
+ if (c != null && !c.equals(Color.white))
+ {
+ if (colours.get(c) == null)
+ {
+ colours.put(c, new ArrayList<String>());
+ }
+ colours.get(c).add(residue);
+ }
+ if (lowerCaseColours != null)
+ {
+ c = lowerCaseColours[index];
+ if (c != null && !c.equals(Color.white))
+ {
+ residue = residue.toLowerCase();
+ if (colours.get(c) == null)
+ {
+ colours.put(c, new ArrayList<String>());
+ }
+ colours.get(c).add(residue);
+ }
+ }
+ }
+
+ /*
+ * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
+ */
+ List<String> residueColours = new ArrayList<String>();
+ for (Entry<Color, List<String>> cols : colours.entrySet())
+ {
+ boolean first = true;
+ StringBuilder sb = new StringBuilder();
+ for (String residue : cols.getValue())
+ {
+ if (!first)
+ {
+ sb.append(",");
+ }
+ sb.append(residue);
+ first = false;
+ }
+ sb.append("=");
+ /*
+ * get color as hex value, dropping the alpha (ff) part
+ */
+ String hexString = Integer.toHexString(cols.getKey().getRGB())
+ .substring(2);
+ sb.append(hexString);
+ residueColours.add(sb.toString());
+ }
+
+ /*
+ * sort and output
+ */
+ Collections.sort(residueColours);
+ return StringUtils.listToDelimitedString(residueColours, ";");
+ }
}
*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
/**
* DOCUMENT ME!
*
{
super(ResidueProperties.aaIndex, ResidueProperties.zappo, 0);
}
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Zappo.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new ZappoColourScheme();
+ }
}
*/
package jalview.structures.models;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
*/
protected String[] modelFileNames = null;
+ public String fileLoadingError;
+
/**
* Data bean class to simplify parameterisation in superposeStructures
*/
{
return null;
}
+
+ public abstract void setJalviewColourScheme(ColourSchemeI cs);
+
+ public abstract void superposeStructures(AlignmentI[] als, int[] alm,
+ ColumnSelection[] alc);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment);
+
+ /**
+ * returns the current featureRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+
+ protected abstract void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands);
+
+ public abstract void colourByChain();
+
+ public abstract void colourByCharge();
+
+ /**
+ * colour any structures associated with sequences in the given alignment
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+ * if colourBySequence is enabled.
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv)
+ {
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (!colourBySequence || !isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ FeatureRenderer fr = null;
+ if (showFeatures)
+ {
+ fr = getFeatureRenderer(alignmentv);
+ }
+ AlignmentI alignment = alignmentv.getAlignment();
+
+ StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, sr, fr, alignment);
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
}
return new Color(red, green, blue);
}
}
+
+ /**
+ * Parses a string into a Color, where the accepted formats are
+ * <ul>
+ * <li>an AWT colour name e.g. white</li>
+ * <li>a hex colour value (without prefix) e.g. ff0000</li>
+ * <li>an rgb triple e.g. 100,50,150</li>
+ * </ul>
+ *
+ * @param colour
+ * @return the parsed colour, or null if parsing fails
+ */
+ public static Color parseColourString(String colour)
+ {
+ if (colour == null)
+ {
+ return null;
+ }
+ colour = colour.trim();
+
+ Color col = null;
+ try
+ {
+ int value = Integer.parseInt(colour, 16);
+ col = new Color(value);
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ if (col == null)
+ {
+ col = ColorUtils.getAWTColorFromName(colour);
+ }
+
+ if (col == null)
+ {
+ try
+ {
+ String[] tokens = colour.split(",");
+ if (tokens.length == 3)
+ {
+ int r = Integer.parseInt(tokens[0].trim());
+ int g = Integer.parseInt(tokens[1].trim());
+ int b = Integer.parseInt(tokens[2].trim());
+ col = new Color(r, g, b);
+ }
+ } catch (Exception ex)
+ {
+ // non-numeric token or out of 0-255 range
+ }
+ }
+
+ return col;
+ }
+
+ /**
+ * Constructs a colour from a text string. The hashcode of the whole string is
+ * scaled to the range 0-135. This is added to RGB values made from the
+ * hashcode of each third of the string, and scaled to the range 20-229.
+ *
+ * @param name
+ * @return
+ */
+ public static Color createColourFromName(String name)
+ {
+ if (name == null)
+ {
+ return Color.white;
+ }
+ int lsize = name.length();
+ int start = 0;
+ int end = lsize / 3;
+
+ int rgbOffset = Math.abs(name.hashCode() % 10) * 15; // 0-135
+
+ /*
+ * red: first third
+ */
+ int r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+ start = end;
+ end += lsize / 3;
+ if (end > lsize)
+ {
+ end = lsize;
+ }
+
+ /*
+ * green: second third
+ */
+ int g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+
+ /*
+ * blue: third third
+ */
+ int b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
+
+ Color color = new Color(r, g, b);
+
+ return color;
+ }
+
+ /**
+ * Returns the Color constant for a given colour name e.g. "pink", or null if
+ * the name is not recognised
+ *
+ * @param name
+ * @return
+ */
+ public static Color getAWTColorFromName(String name)
+ {
+ if (name == null)
+ {
+ return null;
+ }
+ Color col = null;
+ name = name.toLowerCase();
+
+ // or make a static map; or use reflection on the field name
+ switch (name)
+ {
+ case "black":
+ col = Color.black;
+ break;
+ case "blue":
+ col = Color.blue;
+ break;
+ case "cyan":
+ col = Color.cyan;
+ break;
+ case "darkgray":
+ col = Color.darkGray;
+ break;
+ case "gray":
+ col = Color.gray;
+ break;
+ case "green":
+ col = Color.green;
+ break;
+ case "lightgray":
+ col = Color.lightGray;
+ break;
+ case "magenta":
+ col = Color.magenta;
+ break;
+ case "orange":
+ col = Color.orange;
+ break;
+ case "pink":
+ col = Color.pink;
+ break;
+ case "red":
+ col = Color.red;
+ break;
+ case "white":
+ col = Color.white;
+ break;
+ case "yellow":
+ col = Color.yellow;
+ break;
+ }
+
+ return col;
+ }
}
public ParseHtmlBodyAndLinks(String description, boolean removeHTML,
String newline)
{
- StringBuilder sb = new StringBuilder(description.length());
if (description == null || description.length() == 0)
{
htmlContent = false;
return;
}
+ StringBuilder sb = new StringBuilder(description.length());
if (description.toUpperCase().indexOf("<HTML>") == -1)
{
htmlContent = false;
sg.cs = null;
continue;
}
- sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.cs = cs.getInstance(sg, getHiddenRepSequences());
sg.setConsPercGaps(ConsPercGaps);
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.beans.PropertyChangeListener;
FeatureColourI fc = featureColours.get(featureType);
if (fc == null)
{
- Color col = UserColourScheme.createColourFromName(featureType);
+ Color col = ColorUtils.createColourFromName(featureType);
fc = new FeatureColour(col);
featureColours.put(featureType, fc);
}
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
annot.description += "<br/>" + threshNote;
}
annot.description += "</html>";
- Color col = UserColourScheme.createColourFromName(typeName
+ Color col = ColorUtils.createColourFromName(typeName
+ scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
{
AlignmentAnnotation ann = iter.next();
assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
assertFalse(iter.hasNext());
+
+ // invalid id
+ anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+ assertFalse(iter.hasNext());
+ anns = al.findAnnotation(null);
+ assertFalse(iter.hasNext());
}
@Test(groups = { "Functional" })
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(groups = { "Functional" })
public void testAddColourRange()
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A");
ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A");
ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B");
public void testBuildColourCommands()
{
- Map<Color, Map<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
+ Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
public void testSetGlobalColourScheme()
{
/*
- * test for JAL-2283 don't inadvertently turn on colour by conservation
+ * test for JAL-2283: don't inadvertently turn on colour by conservation
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) showOptions[1]).getOrientation());
assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
assertEquals(2, showOptions.length); // includes 'All' and separator
assertEquals(4, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) showOptions[1]).getOrientation());
- assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
assertEquals(4, showOptions.length); // includes 'All' and separator
assertEquals(2, hideOptions.length);
- assertEquals("All", ((JMenuItem) showOptions[0]).getText());
+ String all = MessageManager.getString("label.all");
+ assertEquals(all, ((JMenuItem) showOptions[0]).getText());
assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) showOptions[1]).getOrientation());
assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());
- assertEquals("All", ((JMenuItem) hideOptions[0]).getText());
+ assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
assertEquals(JSeparator.HORIZONTAL,
((JSeparator) hideOptions[1]).getOrientation());
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.RNAHelicesColour;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.viewmodel.AlignmentViewport;
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @Override
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
- af.rnahelicesColour_actionPerformed(null);
- assertTrue(
- "Couldn't apply RNA helices colourscheme",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
+ .toString());
+ assertTrue("Couldn't apply RNA helices colourscheme", af.getViewport()
+ .getGlobalColourScheme() instanceof RNAHelicesColour);
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
+ olddsann + ")");
assertTrue(
"RNA helices colourscheme was not applied on import.",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour);
}
@Test(groups = { "Functional" })
assertSame("Didn't set T-coffee colourscheme", af.getViewport()
.getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
assertNotNull("Recognise T-Coffee score from string",
- ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(), ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())));
+ ColourSchemeProperty.getColourScheme(af.getViewport()
+ .getAlignment(), af.getViewport()
+ .getGlobalColourScheme().getSchemeName()));
assertTrue("Failed to store as a project.",
af.saveAlignment(tfile, FileFormat.Jalview));
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ClustalxColourSchemeTest
+{
+ // @formatter:off
+ private static final String FASTA =
+ ">seq1\nAAANNNRQ\n" +
+ ">seq2\nAAANNNRQ\n" +
+ ">seq3\nAAANNNRQ\n" +
+ ">seq4\nAAANNNRQ\n" +
+ ">seq5\nAAANYYKQ\n" +
+ ">seq6\nAAANYYKQ\n" +
+ ">seq7\nAVKWYYKQ\n" +
+ ">seq8\nKKKWYYQQ\n" +
+ ">seq9\nKKKWWYQQ\n" +
+ ">seq0\nKKKWWWQW\n";
+ // @formatter:on
+
+ @Test(groups = "Functional")
+ public void testFindColour()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ ColourSchemeI cs = new ClustalxColourScheme(al, null);
+
+ /*
+ * column 1 is 70% A which is above Clustalx threshold of 60%
+ */
+ Color clustalBlue = new Color(0.5f, 0.7f, 0.9f);
+ assertEquals(cs.findColour('A', 0, al.getSequenceAt(0)), clustalBlue);
+
+ /*
+ * column 2 is 70% A or V which is above Clustalx threshold for group
+ */
+ assertEquals(cs.findColour('A', 0, al.getSequenceAt(1)), clustalBlue);
+
+ /*
+ * column 3 is 60% A which is not above Clustalx threshold
+ * the Ks in the other rows are not in the same Clustalx group
+ */
+ assertEquals(cs.findColour('A', 2, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 4 is 60% N which is above Clustalx threshold of 50%
+ */
+ Color clustalGreen = new Color(0.1f, 0.8f, 0.1f);
+ assertEquals(cs.findColour('N', 3, al.getSequenceAt(1)), clustalGreen);
+
+ /*
+ * column 5 is 40% N and 40% Y which fails to pass the threshold of
+ * 50% N or 85% either
+ */
+ assertEquals(cs.findColour('N', 4, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 6 is 40% N and 50% Y which fails to pass the threshold of
+ * 85% for either
+ */
+ assertEquals(cs.findColour('N', 5, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 7 is 40% R and 30% K which combine to make > 60%
+ */
+ Color clustalRed = new Color(0.9f, 0.2f, 0.1f);
+ assertEquals(cs.findColour('R', 6, al.getSequenceAt(1)), clustalRed);
+ assertEquals(cs.findColour('K', 6, al.getSequenceAt(7)), clustalRed);
+
+ /*
+ * column 8 is >85% Q which qualifies K and R to be red
+ */
+ assertEquals(cs.findColour('R', 7, al.getSequenceAt(1)), clustalRed);
+ assertEquals(cs.findColour('K', 7, al.getSequenceAt(1)), clustalRed);
+
+ // TODO more test cases; check if help documentation matches implementation
+ }
+
+ // @formatter:on
+
+ /**
+ * Test for colour calculation when the consensus percentage ignores gapped
+ * sequences
+ */
+ @Test(groups = "Functional")
+ public void testFindColour_ignoreGaps()
+ {
+ /*
+ * CCC
+ * CCC
+ * -CC
+ * first column is 66% C (blue) including gaps
+ * or 100% C ignoring gaps
+ */
+ String fasta = ">seq1\nCCC\n>seq2\nccc\n>seq3\n-CC\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
+
+ /*
+ * column 1 is 66% C which is above Clustalx threshold of 60%
+ */
+ Color clustalBlue = ClustalxColourScheme.ClustalColour.BLUE.colour;
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+
+ /*
+ * set directly to ignore gaps
+ */
+ cs.setIncludeGaps(false);
+ Color clustalPink = ClustalxColourScheme.ClustalColour.PINK.colour;
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+
+ /*
+ * set ignore gaps on the viewport...
+ */
+ cs.setIncludeGaps(true);
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+ af.getViewport().setIgnoreGapsConsensus(true, af.alignPanel);
+ // next test fails: colour scheme does not read ignore gaps flag from
+ // viewport
+ // assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+ }
+}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ColourSchemePropertyTest
+{
+ @Test(groups = "Functional")
+ public void testGetColourName()
+ {
+ SequenceI seq = new Sequence("Seq1", "abcd");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ ColourSchemeI cs = new ClustalxColourScheme(al, null);
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Clustal");
+ cs = new Blosum62ColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Blosum62");
+ cs = new PIDColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "% Identity");
+ cs = new HydrophobicColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Hydrophobic");
+ cs = new ZappoColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Zappo");
+ cs = new TaylorColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Taylor");
+ cs = new HelixColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs),
+ "Helix Propensity");
+ cs = new StrandColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs),
+ "Strand Propensity");
+ cs = new TurnColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Turn Propensity");
+ cs = new BuriedColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Buried Index");
+ cs = new NucleotideColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "Nucleotide");
+ cs = new PurinePyrimidineColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs),
+ "Purine/Pyrimidine");
+ cs = new TCoffeeColourScheme(al);
+ assertEquals(ColourSchemeProperty.getColourName(cs), "T-Coffee Scores");
+ cs = new RNAHelicesColour(al);
+ assertEquals(ColourSchemeProperty.getColourName(cs), "RNA Helices");
+ cs = new RNAInteractionColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs),
+ "RNA Interaction type");
+ cs = new UserColourScheme();
+ assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+
+ /*
+ * UserColourScheme may have a bespoke name
+ */
+ ((UserColourScheme) cs).setName("stripy");
+ assertEquals(ColourSchemeProperty.getColourName(cs), "stripy");
+ ((UserColourScheme) cs).setName("");
+ assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+ ((UserColourScheme) cs).setName(null);
+ assertEquals(ColourSchemeProperty.getColourName(cs), "User Defined");
+
+ assertEquals(ColourSchemeProperty.getColourName(null), "None");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourScheme()
+ {
+ SequenceI seq = new Sequence("Seq1", "abcd");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ // the strings here correspond to JalviewColourScheme.toString() values
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Clustal") instanceof ClustalxColourScheme);
+ // not case-sensitive
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "CLUSTAL") instanceof ClustalxColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "clustal") instanceof ClustalxColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Blosum62") instanceof Blosum62ColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "% Identity") instanceof PIDColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Zappo") instanceof ZappoColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Taylor") instanceof TaylorColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Hydrophobic") instanceof HydrophobicColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Helix Propensity") instanceof HelixColourScheme);
+ assertTrue(ColourSchemeProperty
+ .getColourScheme(al, "Strand Propensity") instanceof StrandColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Turn Propensity") instanceof TurnColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Buried Index") instanceof BuriedColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "Nucleotide") instanceof NucleotideColourScheme);
+ assertTrue(ColourSchemeProperty
+ .getColourScheme(al, "Purine/Pyrimidine") instanceof PurinePyrimidineColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores") instanceof TCoffeeColourScheme);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "RNA Helices") instanceof RNAHelicesColour);
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "User Defined") instanceof UserColourScheme);
+ // 'None' is a special value
+ assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
+ assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+ // default is to convert the name into a fixed colour
+ assertTrue(ColourSchemeProperty.getColourScheme(al, "elephants") instanceof UserColourScheme);
+
+ /*
+ * explicit aa colours
+ */
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(al,
+ "R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
+ assertEquals(cs.findColour('H'), Color.white);
+ assertEquals(cs.findColour('R'), Color.red);
+ assertEquals(cs.findColour('r'), Color.red);
+ assertEquals(cs.findColour('G'), Color.red);
+ assertEquals(cs.findColour('C'), Color.blue);
+ assertEquals(cs.findColour('c'), Color.green);
+ assertEquals(cs.findColour('Q'), new Color(10, 20, 30));
+ assertEquals(cs.findColour('S'), new Color(0x11ffdd));
+ assertEquals(cs.findColour('T'), new Color(0x11ffdd));
+ }
+}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme.ClustalColour;
+
+import java.awt.Color;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ColourSchemesTest
+{
+ /*
+ * a colour scheme that alternates Taylor and Zappo
+ * colouring by column
+ */
+ class Stripy extends ResidueColourScheme
+ {
+ private ColourSchemeI odd;
+
+ private ColourSchemeI even;
+
+ private Stripy()
+ {
+ }
+
+ /**
+ * constructor given colours for odd and even columns
+ *
+ * @param odd
+ * @param even
+ */
+ private Stripy(ColourSchemeI cs1, ColourSchemeI cs2)
+ {
+ odd = cs1;
+ even = cs2;
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ final ColourSchemeI cs1 = ColourSchemes.getInstance()
+ .getColourScheme(JalviewColourScheme.Taylor.toString(),
+ (AnnotatedCollectionI) null);
+ final ColourSchemeI cs2 = ColourSchemes.getInstance()
+ .getColourScheme(JalviewColourScheme.Zappo.toString(),
+ (AnnotatedCollectionI) null);
+ return new Stripy(cs1, cs2);
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (j % 2 == 1)
+ {
+ return odd.findColour(c, j, seq);
+ }
+ else
+ {
+ return even.findColour(c, j, seq);
+ }
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "stripy";
+ }
+ };
+
+ /*
+ * a colour scheme that is Clustal but using AWT colour equivalents
+ */
+ class MyClustal extends ResidueColourScheme
+ {
+ ColourSchemeI delegate;
+
+ private MyClustal()
+ {
+ }
+
+ private MyClustal(ColourSchemeI scheme)
+ {
+ delegate = scheme;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color col = delegate.findColour(c, j, seq);
+ Color result = col;
+ if (col.equals(ClustalColour.BLUE.colour))
+ {
+ result = Color.blue;
+ }
+ else if (col.equals(ClustalColour.CYAN.colour))
+ {
+ result = Color.cyan;
+ }
+ else if (col.equals(ClustalColour.GREEN.colour))
+ {
+ result = Color.green;
+ }
+ else if (col.equals(ClustalColour.MAGENTA.colour))
+ {
+ result = Color.magenta;
+ }
+ else if (col.equals(ClustalColour.ORANGE.colour))
+ {
+ result = Color.orange;
+ }
+ else if (col.equals(ClustalColour.PINK.colour))
+ {
+ result = Color.pink;
+ }
+ else if (col.equals(ClustalColour.RED.colour))
+ {
+ result = Color.red;
+ }
+ else if (col.equals(ClustalColour.YELLOW.colour))
+ {
+ result = Color.yellow;
+ }
+ return result;
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return new MyClustal(new ClustalxColourScheme().getInstance(sg,
+ hiddenRepSequences));
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "MyClustal";
+ }
+
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourSchemes()
+ {
+ /*
+ * this just verifies that built-in colour schemes are loaded into ColourSchemes
+ * in the order in which they are declared in the JalviewColourScheme enum
+ * (this also determines their order in Colour menus)
+ */
+ Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance().getColourSchemes().iterator();
+ JalviewColourScheme[] jalviewSchemes = JalviewColourScheme.values();
+ int i = 0;
+ while (schemes.hasNext() && i < jalviewSchemes.length)
+ {
+ assertTrue(schemes.next().getSchemeName()
+ .equals(jalviewSchemes[i].toString()));
+ i++;
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourScheme_forViewport()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nAGLRTWQU", DataSourceType.PASTE);
+ ColourSchemes cs = ColourSchemes.getInstance();
+
+ AlignViewport viewport = af.getViewport();
+ AlignmentI alignment = viewport.getAlignment();
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
+ alignment) instanceof Blosum62ColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Buried.toString(),
+ alignment) instanceof BuriedColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
+ alignment) instanceof ClustalxColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(),
+ alignment) instanceof HelixColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Hydrophobic.toString(), alignment) instanceof HydrophobicColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Nucleotide.toString(), alignment) instanceof NucleotideColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(),
+ alignment) instanceof PIDColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.PurinePyrimidine.toString(), alignment) instanceof PurinePyrimidineColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.RNAHelices.toString(), alignment) instanceof RNAHelicesColour);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Strand.toString(),
+ alignment) instanceof StrandColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Taylor.toString(),
+ alignment) instanceof TaylorColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
+ alignment) instanceof TCoffeeColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(),
+ alignment) instanceof TurnColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(),
+ alignment) instanceof ZappoColourScheme);
+ af.closeMenuItem_actionPerformed(true);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourScheme_forAnnotatedCollection()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nAGLRTWQU", DataSourceType.PASTE);
+ ColourSchemes cs = ColourSchemes.getInstance();
+
+ AnnotatedCollectionI al = af.getViewport().getAlignment();
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
+ al) instanceof Blosum62ColourScheme);
+ assertTrue(cs
+ .getColourScheme(JalviewColourScheme.Buried.toString(), al) instanceof BuriedColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
+ al) instanceof ClustalxColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(), al) instanceof HelixColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Hydrophobic.toString(), al) instanceof HydrophobicColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.Nucleotide.toString(), al) instanceof NucleotideColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(), al) instanceof PIDColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.PurinePyrimidine.toString(), al) instanceof PurinePyrimidineColourScheme);
+ assertTrue(cs.getColourScheme(
+ JalviewColourScheme.RNAHelices.toString(), al) instanceof RNAHelicesColour);
+ assertTrue(cs
+ .getColourScheme(JalviewColourScheme.Strand.toString(), al) instanceof StrandColourScheme);
+ assertTrue(cs
+ .getColourScheme(JalviewColourScheme.Taylor.toString(), al) instanceof TaylorColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
+ al) instanceof TCoffeeColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(), al) instanceof TurnColourScheme);
+ assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(), al) instanceof ZappoColourScheme);
+ af.closeMenuItem_actionPerformed(true);
+ }
+
+ @Test(groups = "Functional")
+ public void testRegisterColourScheme()
+ {
+ ColourSchemes.getInstance().registerColourScheme(new Stripy());
+ ColourSchemes.getInstance().registerColourScheme(new MyClustal());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ /*
+ * set a breakpoint here to see and play with the newly registered
+ * colour schemes in the AlignFrame colour menu
+ */
+ SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+ SequenceI seq = af.getViewport().getAlignment().findName("FER_CAPAA");
+
+ /*
+ * set and check Taylor colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString());
+ Color taylor1 = sr.getResidueBoxColour(seq, 88); // E 255,0,102
+ Color taylor2 = sr.getResidueBoxColour(seq, 89); // A 204,255,0
+ Color taylor3 = sr.getResidueBoxColour(seq, 90); // G 255,153,0
+ assertEquals(taylor1, new Color(255, 0, 102));
+ assertEquals(taylor2, new Color(204, 255, 0));
+ assertEquals(taylor3, new Color(255, 153, 0));
+
+ /*
+ * set and check Zappo colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString());
+ Color zappo1 = sr.getResidueBoxColour(seq, 88); // E red
+ Color zappo2 = sr.getResidueBoxColour(seq, 89); // A pink
+ Color zappo3 = sr.getResidueBoxColour(seq, 90); // G magenta
+ assertEquals(zappo1, Color.red);
+ assertEquals(zappo2, Color.pink);
+ assertEquals(zappo3, Color.magenta);
+
+ /*
+ * set 'stripy' colours - odd columns are Taylor and even are Zappo
+ */
+ af.changeColour_actionPerformed("stripy");
+ Color stripy1 = sr.getResidueBoxColour(seq, 88);
+ Color stripy2 = sr.getResidueBoxColour(seq, 89);
+ Color stripy3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(stripy1, zappo1);
+ assertEquals(stripy2, taylor2);
+ assertEquals(stripy3, zappo3);
+
+ /*
+ * set and check Clustal colours
+ */
+ af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString());
+ Color clustal1 = sr.getResidueBoxColour(seq, 88);
+ Color clustal2 = sr.getResidueBoxColour(seq, 89);
+ Color clustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(clustal1, ClustalColour.MAGENTA.colour);
+ assertEquals(clustal2, ClustalColour.BLUE.colour);
+ assertEquals(clustal3, ClustalColour.ORANGE.colour);
+
+ /*
+ * set 'MyClustal' colours - uses AWT colour equivalents
+ */
+ af.changeColour_actionPerformed("MyClustal");
+ Color myclustal1 = sr.getResidueBoxColour(seq, 88);
+ Color myclustal2 = sr.getResidueBoxColour(seq, 89);
+ Color myclustal3 = sr.getResidueBoxColour(seq, 90);
+ assertEquals(myclustal1, Color.MAGENTA);
+ assertEquals(myclustal2, Color.BLUE);
+ assertEquals(myclustal3, Color.ORANGE);
+ }
+
+ /**
+ * Tests for check if scheme name exists. Built-in scheme names are the
+ * toString() values of enum JalviewColourScheme.
+ */
+ @Test(groups = "Functional")
+ public void testNameExists()
+ {
+ ColourSchemes cs = ColourSchemes.getInstance();
+ assertFalse(cs.nameExists(null));
+ assertFalse(cs.nameExists(""));
+ assertTrue(cs.nameExists("Clustal"));
+ assertTrue(cs.nameExists("CLUSTAL"));
+ assertFalse(cs.nameExists("CLUSTAL "));
+ assertTrue(cs.nameExists("% Identity"));
+ assertFalse(cs.nameExists("PID"));
+ }
+}
import jalview.datamodel.SequenceFeature;
import jalview.gui.JvOptionPane;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import java.awt.Color;
fc.setColourByLabel(true);
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
null);
- Color expected = UserColourScheme.createColourFromName("desc");
+ Color expected = ColorUtils.createColourFromName("desc");
assertEquals(expected, fc.getColor(sf));
}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class JalviewColourSchemeTest
+{
+ @Test(groups = "Functional")
+ public void testGetSchemeClass()
+ {
+ assertTrue(JalviewColourScheme.Clustal.getSchemeClass() == ClustalxColourScheme.class);
+ assertTrue(JalviewColourScheme.Blosum62.getSchemeClass() == Blosum62ColourScheme.class);
+ assertTrue(JalviewColourScheme.PID.getSchemeClass() == PIDColourScheme.class);
+ assertTrue(JalviewColourScheme.Hydrophobic.getSchemeClass() == HydrophobicColourScheme.class);
+ assertTrue(JalviewColourScheme.Zappo.getSchemeClass() == ZappoColourScheme.class);
+ assertTrue(JalviewColourScheme.Taylor.getSchemeClass() == TaylorColourScheme.class);
+ assertTrue(JalviewColourScheme.Helix.getSchemeClass() == HelixColourScheme.class);
+ assertTrue(JalviewColourScheme.Strand.getSchemeClass() == StrandColourScheme.class);
+ assertTrue(JalviewColourScheme.Turn.getSchemeClass() == TurnColourScheme.class);
+ assertTrue(JalviewColourScheme.Buried.getSchemeClass() == BuriedColourScheme.class);
+ assertTrue(JalviewColourScheme.Nucleotide.getSchemeClass() == NucleotideColourScheme.class);
+ assertTrue(JalviewColourScheme.PurinePyrimidine.getSchemeClass() == PurinePyrimidineColourScheme.class);
+ assertTrue(JalviewColourScheme.TCoffee.getSchemeClass() == TCoffeeColourScheme.class);
+ assertTrue(JalviewColourScheme.RNAHelices.getSchemeClass() == RNAHelicesColour.class);
+ }
+
+ @Test(groups = "Functional")
+ public void testToString()
+ {
+ assertEquals(JalviewColourScheme.Clustal.toString(), "Clustal");
+ assertEquals(JalviewColourScheme.Blosum62.toString(), "Blosum62");
+ assertEquals(JalviewColourScheme.PID.toString(), "% Identity");
+ assertEquals(JalviewColourScheme.Zappo.toString(), "Zappo");
+ assertEquals(JalviewColourScheme.Taylor.toString(), "Taylor");
+ assertEquals(JalviewColourScheme.Hydrophobic.toString(), "Hydrophobic");
+ assertEquals(JalviewColourScheme.Helix.toString(), "Helix Propensity");
+ assertEquals(JalviewColourScheme.Strand.toString(), "Strand Propensity");
+ assertEquals(JalviewColourScheme.Turn.toString(), "Turn Propensity");
+ assertEquals(JalviewColourScheme.Buried.toString(), "Buried Index");
+ assertEquals(JalviewColourScheme.Nucleotide.toString(), "Nucleotide");
+ assertEquals(JalviewColourScheme.PurinePyrimidine.toString(),
+ "Purine/Pyrimidine");
+ assertEquals(JalviewColourScheme.TCoffee.toString(), "T-Coffee Scores");
+ assertEquals(JalviewColourScheme.RNAHelices.toString(), "RNA Helices");
+ }
+}
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
import jalview.datamodel.Profiles;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import jalview.io.TCoffeeScoreFile;
import java.awt.Color;
public class ResidueColourSchemeTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+
+ }
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
profiles[1] = new Profile(4, 0, 4, "R");
profiles[2] = new Profile(4, 4, 0, "");
profiles[3] = new Profile(4, 1, 2, "T");
- ResidueColourScheme rcs = new ResidueColourScheme();
+ ResidueColourScheme rcs = new PIDColourScheme();
rcs.setConsensus(new Profiles(profiles));
/*
rcs.setThreshold(0, true);
assertTrue(rcs.aboveThreshold('a', 0));
assertTrue(rcs.aboveThreshold('S', 0));
- assertFalse(rcs.aboveThreshold('W', 0));
+ assertTrue(rcs.aboveThreshold('W', 0));
assertTrue(rcs.aboveThreshold('R', 1));
- assertFalse(rcs.aboveThreshold('W', 2));
+ assertTrue(rcs.aboveThreshold('W', 2));
assertTrue(rcs.aboveThreshold('t', 3));
- assertFalse(rcs.aboveThreshold('Q', 3));
+ assertTrue(rcs.aboveThreshold('Q', 3));
/*
* with threshold, include gaps
@Test(groups = "Functional")
public void testApplyConservation()
{
- ResidueColourScheme rcs = new ResidueColourScheme();
+ ResidueColourScheme rcs = new PIDColourScheme();
// no conservation present - no fading
assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
assertEquals(colour, rcs.applyConservation(colour, 11));
assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
}
+
+ @Test(groups = "Functional")
+ public void testIsApplicableTo()
+ {
+ SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+ SequenceI pep2 = new Sequence("pep2", "AILFQYG");
+ SequenceI dna1 = new Sequence("dna1", "ACTGAC");
+ SequenceI dna2 = new Sequence("dna2", "TCCAAG");
+ AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
+ AlignmentI nucleotide = new Alignment(new SequenceI[] { dna1, dna2 });
+
+ /*
+ * peptide-specific colour schemes
+ */
+ assertTrue(new ClustalxColourScheme(peptide, null)
+ .isApplicableTo(peptide));
+ assertFalse(new ClustalxColourScheme(nucleotide, null)
+ .isApplicableTo(nucleotide));
+ assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
+ assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
+ assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new HelixColourScheme().isApplicableTo(peptide));
+ assertFalse(new HelixColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new HydrophobicColourScheme().isApplicableTo(peptide));
+ assertFalse(new HydrophobicColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new StrandColourScheme().isApplicableTo(peptide));
+ assertFalse(new StrandColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new TaylorColourScheme().isApplicableTo(peptide));
+ assertFalse(new TaylorColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new TurnColourScheme().isApplicableTo(peptide));
+ assertFalse(new TurnColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
+ assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
+
+ /*
+ * nucleotide-specific colour schemes
+ */
+ assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
+ assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
+ assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
+ assertTrue(new PurinePyrimidineColourScheme()
+ .isApplicableTo(nucleotide));
+ assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
+ assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
+
+ /*
+ * indifferent
+ */
+ assertTrue(new UserColourScheme().isApplicableTo(peptide));
+ assertTrue(new UserColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+ .isApplicableTo(peptide));
+ assertTrue(new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+ .isApplicableTo(nucleotide));
+ ResidueColourScheme rcs = new PIDColourScheme();
+ assertTrue(rcs.isApplicableTo(peptide));
+ assertTrue(rcs.isApplicableTo(nucleotide));
+ assertTrue(new PIDColourScheme().isApplicableTo(peptide));
+ assertTrue(new PIDColourScheme().isApplicableTo(nucleotide));
+ assertTrue(new FollowerColourScheme().isApplicableTo(peptide));
+ assertTrue(new FollowerColourScheme().isApplicableTo(nucleotide));
+
+ /*
+ * TCoffee colour requires the presence of TCoffee score annotation
+ */
+ assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
+ assertFalse(new TCoffeeColourScheme(nucleotide)
+ .isApplicableTo(nucleotide));
+ AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
+ aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
+ peptide.addAnnotation(aa);
+ aa = new AlignmentAnnotation("T-COFFEE", "", null);
+ aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
+ nucleotide.addAnnotation(aa);
+ assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
+ assertTrue(new TCoffeeColourScheme(nucleotide)
+ .isApplicableTo(nucleotide));
+
+ /*
+ * RNAHelices requires the presence of rna secondary structure
+ */
+ assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
+ assertFalse(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+ // add secondary structure (small but perfectly formed)
+ Annotation[] ss = new Annotation[2];
+ ss[0] = new Annotation("", "", '{', 0f);
+ ss[1] = new Annotation("", "", '}', 0f);
+ nucleotide.addAnnotation(new AlignmentAnnotation("SS", "", ss));
+ assertTrue(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+ }
+
+ @Test(groups = "Functional")
+ public void testIsApplicableTo_dynamicColourScheme()
+ {
+ SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+ SequenceI pep2 = new Sequence("pep2", "AILFQYG");
+ AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
+
+ /*
+ * demonstrate that we can 'plug in' a colour scheme with specified
+ * criteria for applicability; here, that there are more than 2 sequences
+ */
+ ColourSchemeI cs = new UserColourScheme()
+ {
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ AlignmentI al = ac.getContext() == null ? (AlignmentI) ac
+ : (AlignmentI) ac.getContext();
+ return al.getSequences().size() > 2;
+ }
+ };
+ assertFalse(cs.isApplicableTo(peptide));
+ peptide.addSequence(pep1);
+ assertTrue(cs.isApplicableTo(peptide));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetName()
+ {
+ SequenceI pep1 = new Sequence("pep1", "APQTWLS");
+ AlignmentI peptide = new Alignment(new SequenceI[] { pep1 });
+
+ assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
+ assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
+ assertEquals("Helix Propensity", new HelixColourScheme().getSchemeName());
+ assertEquals("Hydrophobic", new HydrophobicColourScheme().getSchemeName());
+ assertEquals("Strand Propensity", new StrandColourScheme().getSchemeName());
+ assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
+ assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
+ assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
+ assertEquals("Nucleotide", new NucleotideColourScheme().getSchemeName());
+ assertEquals("Purine/Pyrimidine",
+ new PurinePyrimidineColourScheme().getSchemeName());
+ assertEquals("RNA Interaction type",
+ new RNAInteractionColourScheme().getSchemeName());
+ assertEquals("User Defined", new UserColourScheme().getSchemeName());
+ assertEquals("Score", new ScoreColourScheme(new int[] {},
+ new double[] {}, 0, 0d).getSchemeName());
+ assertEquals("% Identity", new PIDColourScheme().getSchemeName());
+ assertEquals("Follower", new FollowerColourScheme().getSchemeName());
+ assertEquals("T-Coffee Scores",
+ new TCoffeeColourScheme(peptide).getSchemeName());
+ assertEquals("RNA Helices",
+ new RNAHelicesColour(peptide).getSchemeName());
+ }
}
package jalview.schemes;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
import jalview.gui.JvOptionPane;
}
@Test(groups = "Functional")
- public void testGetColourFromString()
+ public void testParseAppletParameter()
{
- /*
- * by colour name - if known to AWT, and included in
- *
- * @see ColourSchemeProperty.getAWTColorFromName()
- */
- assertSame(Color.RED, UserColourScheme.getColourFromString("red"));
- assertSame(Color.RED, UserColourScheme.getColourFromString("Red"));
- assertSame(Color.RED, UserColourScheme.getColourFromString(" RED "));
+ UserColourScheme cs = new UserColourScheme("white");
+ cs.parseAppletParameter("D,E=red; K,R,H=0022FF; c=10 , 20,30");
+ assertEquals(Color.RED, cs.findColour('D'));
+ assertEquals(Color.RED, cs.findColour('d'));
+ assertEquals(Color.RED, cs.findColour('E'));
+ assertEquals(Color.RED, cs.findColour('e'));
+ Color c1 = new Color(0x0022ff);
+ assertEquals(c1, cs.findColour('K'));
+ assertEquals(c1, cs.findColour('R'));
+ assertEquals(c1, cs.findColour('h'));
+ Color c2 = new Color(10, 20, 30);
+ assertEquals(c2, cs.findColour('c'));
- /*
- * by RGB hex code
- */
- String hexColour = Integer.toHexString(Color.RED.getRGB() & 0xffffff);
- assertEquals(Color.RED, UserColourScheme.getColourFromString(hexColour));
- // 'hex' prefixes _not_ wanted here
- assertNull(UserColourScheme.getColourFromString("0x" + hexColour));
- assertNull(UserColourScheme.getColourFromString("#" + hexColour));
-
- /*
- * by RGB triplet
- */
- String rgb = String.format("%d,%d,%d", Color.red.getRed(),
- Color.red.getGreen(), Color.red.getBlue());
- assertEquals(Color.RED, UserColourScheme.getColourFromString(rgb));
+ cs = new UserColourScheme("white");
+ cs.parseAppletParameter("D,E=red; K,R,H=0022FF; c=10 , 20,30;t=orange;lowercase=blue;s=pink");
+ assertEquals(Color.RED, cs.findColour('D'));
+ assertEquals(Color.blue, cs.findColour('d'));
+ assertEquals(Color.RED, cs.findColour('E'));
+ assertEquals(Color.blue, cs.findColour('e'));
+ assertEquals(c1, cs.findColour('K'));
+ assertEquals(c1, cs.findColour('R'));
+ assertEquals(Color.blue, cs.findColour('h'));
+ assertEquals(c2, cs.findColour('c'));
+ // 'lowercase' sets all lower-case not already set to the given colour
+ assertEquals(Color.orange, cs.findColour('t'));
+ assertEquals(Color.blue, cs.findColour('k'));
+ assertEquals(Color.blue, cs.findColour('a'));
+ assertEquals(Color.pink, cs.findColour('s'));
+ }
- /*
- * odds and ends
- */
- assertNull(UserColourScheme.getColourFromString(null));
- assertNull(UserColourScheme.getColourFromString("rubbish"));
- assertEquals(Color.WHITE, UserColourScheme.getColourFromString("-1"));
- assertNull(UserColourScheme.getColourFromString(String
- .valueOf(Integer.MAX_VALUE)));
+ @Test(groups = "Functional")
+ public void testToAppletParameter()
+ {
+ UserColourScheme cs = new UserColourScheme(
+ "E,D=red; K,R,H=0022FF; c=10 , 20,30");
+ String param = cs.toAppletParameter();
+ assertEquals("D,E=ff0000;H,K,R=0022ff;c=0a141e", param);
}
}
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
+import java.awt.Color;
import java.util.Arrays;
import java.util.List;
{
return null;
}
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ }
+
+ @Override
+ public void superposeStructures(AlignmentI[] als, int[] alm,
+ ColumnSelection[] alc)
+ {
+ }
+
+ @Override
+ public void setBackgroundColour(Color col)
+ {
+ }
+
+ @Override
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
+ {
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ @Override
+ protected void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands)
+ {
+ }
+
+ @Override
+ public void colourByChain()
+ {
+ }
+
+ @Override
+ public void colourByCharge()
+ {
+ }
};
}
assertFalse(matched[4]); // superposable, but hidden, column
assertTrue(matched[5]);
}
+
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
+
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ {
+ return null;
+ }
}
assertEquals(new Color(46, 31, 16), // with rounding down
ColorUtils.bleachColour(colour, -0.7f));
}
+
+ @Test(groups = "Functional")
+ public void testParseColourString()
+ {
+ /*
+ * by colour name - if known to AWT, and included in
+ *
+ * @see ColourSchemeProperty.getAWTColorFromName()
+ */
+ assertSame(Color.RED, ColorUtils.parseColourString("red"));
+ assertSame(Color.RED, ColorUtils.parseColourString("Red"));
+ assertSame(Color.RED, ColorUtils.parseColourString(" RED "));
+
+ /*
+ * by RGB hex code
+ */
+ String hexColour = Integer.toHexString(Color.RED.getRGB() & 0xffffff);
+ assertEquals("ff0000", hexColour);
+ assertEquals(Color.RED, ColorUtils.parseColourString(hexColour));
+ // 'hex' prefixes _not_ wanted here
+ assertNull(ColorUtils.parseColourString("0x" + hexColour));
+ assertNull(ColorUtils.parseColourString("#" + hexColour));
+ // out of range, but Color constructor just or's the rgb value with 0
+ assertEquals(Color.black, ColorUtils.parseColourString("1000000"));
+
+ /*
+ * by RGB triplet
+ */
+ Color c = Color.pink;
+ String rgb = String.format("%d,%d,%d", c.getRed(), c.getGreen(),
+ c.getBlue());
+ assertEquals("255,175,175", rgb);
+ assertEquals(c, ColorUtils.parseColourString(rgb));
+ assertEquals(c, ColorUtils.parseColourString("255, 175 , 175"));
+
+ /*
+ * odds and ends
+ */
+ assertNull(ColorUtils.parseColourString(null));
+ assertNull(ColorUtils.parseColourString("rubbish"));
+ assertEquals(Color.WHITE, ColorUtils.parseColourString("-1"));
+ assertNull(ColorUtils.parseColourString(String
+ .valueOf(Integer.MAX_VALUE)));
+ assertNull(ColorUtils.parseColourString("100,200,300")); // out of range
+ assertNull(ColorUtils.parseColourString("100,200")); // too few
+ assertNull(ColorUtils.parseColourString("100,200,100,200")); // too many
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAWTColorFromName() {
+ assertEquals(Color.white, ColorUtils.getAWTColorFromName("white"));
+ assertEquals(Color.white, ColorUtils.getAWTColorFromName("White"));
+ assertEquals(Color.white, ColorUtils.getAWTColorFromName("WHITE"));
+ assertEquals(Color.pink, ColorUtils.getAWTColorFromName("pink"));
+ assertNull(ColorUtils.getAWTColorFromName("mauve")); // no such name
+ assertNull(ColorUtils.getAWTColorFromName(""));
+ assertNull(ColorUtils.getAWTColorFromName(null));
+ }
+
+ @Test(groups = "Functional")
+ public void testCreateColourFromName()
+ {
+ assertEquals(Color.white, ColorUtils.createColourFromName(null));
+ assertEquals(new Color(20, 20, 20), ColorUtils.createColourFromName(""));
+ assertEquals(new Color(123, 211, 122),
+ ColorUtils.createColourFromName("hello world"));
+ assertEquals(new Color(27, 147, 112),
+ ColorUtils.createColourFromName("HELLO WORLD"));
+ /*
+ * the algorithm makes the same values for r,g,b if
+ * the string consists of 3 repeating substrings
+ */
+ assertEquals(new Color(184, 184, 184),
+ ColorUtils.createColourFromName("HELLO HELLO HELLO "));
+ }
}
git://source.jalview.org / jalview.git / commitdiff