action.by_conservation = By Conservation
action.wrap = Wrap
action.show_gaps = Show Gaps
-action.show_occupancy = Show Occupancy
action.show_hidden_markers = Show Hidden Markers
action.find = Find
action.undefine_groups = Undefine Groups
action.scale_right = Scale Right
action.by_tree_order = By Tree Order
action.sort = Sort
- action.calculate_tree = Calculate Tree
+ action.calculate_tree = Calculate Tree...
+ action.calculate_tree_pca = Calculate Tree or PCA...
action.help = Help
action.by_annotation = By Annotation...
action.invert_sequence_selection = Invert Sequence Selection
label.principal_component_analysis = Principal Component Analysis
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
+ label.choose_calculation = Choose Calculation
label.treecalc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
label.score_model_pid = % Identity
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
+ label.score_model_smithwatermanscore = Score between two sequences aligned with Smith-Waterman with default Peptide/Nucleotide matrix
+ label.score_model_sequencefeaturesimilarity = Distance measure of average number of features not shared at sequence positions
label.score_model_conservation = Physicochemical property conservation
label.score_model_enhconservation = Physicochemical property conservation
label.status_bar = Status bar
label.set_this_label_text = set this label text
label.sequences_from = Sequences from {0}
label.successfully_loaded_file = Successfully loaded file {0}
+ label.successfully_loaded_matrix = Successfully loaded score matrix {0}
label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format.
label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard.
label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment.
label.principal_component_analysis_must_take_least_four_input_sequences = Principal component analysis must take\nat least 4 input sequences.
label.sequence_selection_insufficient = Sequence selection insufficient
label.you_need_more_two_sequences_selected_build_tree = You need to have more than two sequences selected to build a tree!
+ label.you_need_more_than_n_sequences = You need to have more than {0} sequences
label.not_enough_sequences = Not enough sequences
label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.sequences_selection_not_aligned = Sequences in selection are not aligned
- label.sequences_must_be_aligned_before_creating_tree = The sequences must be aligned before creating a tree.\nTry using the Pad function in the edit menu,\n or one of the multiple sequence alignment web services.
- label.sequences_not_aligned = Sequences not aligned
label.problem_reading_tree_file = Problem reading tree file
label.possible_problem_with_tree_file = Possible problem with tree file
label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
label.show_labels = Show labels
action.background_colour = Background Colour...
label.associate_nodes_with = Associate Nodes With
- label.jalview_pca_calculation = Jalview PCA Calculation
label.link_name = Link Name
label.pdb_file = PDB file
label.colour_with_jmol = Colour with Jmol
label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}
label.error_whilst_loading_project_from = Error whilst loading project from {0}
label.couldnt_load_project = Couldn't load project
- label.pca_sequences_not_aligned = The sequences must be aligned before calculating PCA.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.invalid_name_preset_exists = Invalid name - preset already exists.
label.invalid_name = Invalid name
label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
label.save_as_html = Save as HTML
label.recently_opened = Recently Opened
label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0} jobs running.
+ label.tree = Tree
label.tree_from = Tree from {0}
label.webservice_job_title = {0} using {1}
label.select_visible_region_of = selected {0} region of {1}
label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
+label.quality_descr = Alignment Quality based on Blosum62 scores
+label.conservation_descr = Conservation of total alignment less than {0}% gaps
+label.consensus_descr = PID
+label.complement_consensus_descr = PID for cDNA
+label.strucconsensus_descr = PID for base pairs
+label.occupancy_descr = Number of aligned positions
action.scale_right = Escala derecha
action.by_tree_order = Por orden del árbol
action.sort = Ordenar
- action.calculate_tree = Calcular árbol
+ action.calculate_tree = Calcular árbol...
+ action.calculate_tree_pca = Calcular árbol o ACP...
action.help = Ayuda
action.by_annotation = Por anotación...
action.invert_sequence_selection = Invertir selección de secuencias
label.principal_component_analysis = Análisis del Componente Principal
label.average_distance_identity = Distancia Media Usando % de Identidad
label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad
+ label.choose_calculation = Elegir el cálculo
label.treecalc_title = {0} utilizando {1}
label.tree_calc_av = Distancia media
label.tree_calc_nj = Unir vecinos
label.score_model_pid = % Identidad
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
+ label.score_model_smithwatermanscore = Puntuación entre secuencias alineadas por Smith-Waterman con matriz por defecto proteica / nucleotídica
+ label.score_model_sequencefeaturesimilarity = Medida de distancia por cuenta promedia de características no compartidas at sequence positions
label.score_model_conservation = Conservación de las propiedades físico-químicas
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.occupancy = Ocupación
label.clustal = Clustal
# label.colourScheme_<schemeName> as in JalviewColourScheme
label.colourScheme_clustal = Clustalx
label.set_this_label_text = fijar como etiqueta
label.sequences_from = Secuencias de {0}
label.successfully_loaded_file = Fichero cargado exitosamente {0}
+ label.successfully_loaded_matrix = Matriz cargada exitosamente {0}
label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}.
label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles.
label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento.
label.not_enough_sequences = No suficientes secuencias
label.selected_region_to_tree_may_only_contain_residues_or_gaps = La regi\u00F3n seleccionada para construir un \u00E1rbol puede\ncontener s\u00F3lo residuos o espacios.\nPrueba usando la funci\u00F3n Pad en el men\u00FA de edici\u00F3n,\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
label.sequences_selection_not_aligned = Las secuencias seleccionadas no están alineadas
- label.sequences_must_be_aligned_before_creating_tree = Las secuencias deben estar alineadas antes de crear el \u00E1rbol.\nPrueba usando la funci\u00F3n Pad en el men\u00FA de editar,\n o uno de los m\u00FAltiples servicios web de alineamiento de secuencias.
- label.sequences_not_aligned = Secuencias no alineadas
label.problem_reading_tree_file = Problema al leer el fichero del árbol
label.possible_problem_with_tree_file = Posible problema con el fichero del árbol
label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Por favor seleccionar al menos tres bases de al menos una secuencia para poder realizar la traducción de cDNA.
label.selection_output_command = Seleccionar salida - {0}
label.annotation_for_displayid = <p><h2>Anotación para {0} </h2></p><p>
label.pdb_sequence_mapping = PDB - Mapeado de secuencia
- label.pca_details = detalles de la PCA
+ label.pca_details = detalles de la ACP
label.redundancy_threshold_selection = Selección del umbral de redundancia
label.user_defined_colours = Colores definidos del usuario
label.jalviewLite_release = JalviewLite - versión {0}
label.no_features_added_to_this_alignment = No hay funciones asociadas a este alineamiento!!
label.features_can_be_added_from_searches_1 = (Las funciones pueden ser añadidas de búsquedas o
label.features_can_be_added_from_searches_2 = de ficheros de funciones Jalview / GFF)
- label.calculating_pca= Calculando PCA
+ label.calculating_pca= Calculando ACP
label.jalview_cannot_open_file = Jalview no puede abrir el fichero
label.jalview_applet = Aplicación Jalview
label.loading_data = Cargando datos
label.set_as_default = Establecer por defecto
label.show_labels = Mostrar etiquetas
label.associate_nodes_with = Asociar nodos con
label.link_name = Nombre del enalce
label.pdb_file = Fichero PDB
label.colour_with_jmol = Colorear con Jmol
- label.align_structures = Alinear estructuras
label.jmol = Jmol
label.sort_alignment_by_tree = Ordenar alineamiento por árbol
label.mark_unlinked_leaves = Marcar las hojas como no enlazadas
label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0}
label.error_whilst_loading_project_from = Error cargando el proyecto desde {0}
label.couldnt_load_project = No es posible cargar el proyecto
- label.pca_sequences_not_aligned = Las secuencias deben estar alineadas antes de calcular el PCA.\nPruebe a utilizar la funci\u00F3n de rellenar huecos en el men\u00FA Editar,\no cualquiera de los servicios web de alineamiento m\u00FAltiple.
label.invalid_name_preset_exists = Nombre no válido - esta preconfiguración ya existe.
label.invalid_name = Nombre no válido
label.set_proxy_settings = Por favor, configure su proxy en la pestaña 'Conexiones' de la ventana de Preferencia
label.save_as_html = Guardar como HTML
label.recently_opened = Abiertos recientemente
label.blasting_for_unidentified_sequence_jobs_running = Ejecutando BLAST de las secuencias no indentificadas - {0} trabajos en marcha.
+ label.tree = Árbol
label.tree_from = Árbol de {0}
label.webservice_job_title = {0} usando {1}
label.select_visible_region_of = seleccionada {0} región de {1}
label.updating_vamsas_session = Actualizando sesión VAMSAS
label.loading_file = Cargando fichero: {0}
label.edit_params = Editar {0}
+label.as_percentage = Como Porcentaje
error.not_implemented = No implementado
error.no_such_method_as_clone1_for = No existe ese método como un clone1 de {0}
error.null_from_clone1 = Nulo de clone1!
label.empty_alignment_job = Trabajo de alineamiento vacío
label.add_new_sbrs_service = Añadir un nuevo SBRS
label.edit_sbrs_entry = Editar entrada SBRS
- label.pca_recalculating = Recalculando PCA
- label.pca_calculating = Calculando PCA
+ label.pca_recalculating = Recalculando ACP
+ label.pca_calculating = Calculando ACP
label.select_foreground_colour = Escoger color del primer plano
label.select_colour_for_text = Seleccione el color del texto
label.adjunst_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano
label.alpha_helix=Hélice Alfa
label.chimera_help=Ayuda para Chimera
label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
- label.structure_viewer=Visualizador de estructura for defecto
+ label.structure_viewer=Visualizador de estructura por defecto
label.embbed_biojson=Incrustar BioJSON al exportar HTML
label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las características.
label.choose_annotations=Escoja anotaciones
*/
package jalview.gui;
+ import jalview.analysis.scoremodels.ScoreModels;
+ import jalview.analysis.scoremodels.SimilarityParams;
+ import jalview.api.analysis.ScoreModelI;
+ import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
- import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
- import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
PCAModel pcaModel;
+ private static final int MIN_WIDTH = 470;
+
+ private static final int MIN_HEIGHT = 250;
+
int top = 0;
/**
- * Creates a new PCAPanel object.
+ * Creates a new PCAPanel object using default score model and parameters
*
- * @param av
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
+ * @param alignPanel
+ */
+ public PCAPanel(AlignmentPanel alignPanel)
+ {
+ this(alignPanel, ScoreModels.getInstance()
+ .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
+ .getName(), SimilarityParams.SeqSpace);
+ }
+
+ /**
+ * Constructor given sequence data, a similarity (or distance) score model
+ * name, and score calculation parameters
+ *
+ * @param alignPanel
+ * @param modelName
+ * @param params
*/
- public PCAPanel(AlignmentPanel ap)
+ public PCAPanel(AlignmentPanel alignPanel, String modelName,
+ SimilarityParamsI params)
{
super();
- this.av = ap.av;
- this.ap = ap;
+ this.av = alignPanel.av;
+ this.ap = alignPanel;
+ boolean nucleotide = av.getAlignment().isNucleotide();
progressBar = new ProgressBar(statusPanel, statusBar);
- boolean sameLength = true;
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ close_actionPerformed();
+ }
+ });
+
boolean selected = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 0;
AlignmentView seqstrings = av.getAlignmentView(selected);
- boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
if (!selected)
{
{
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- SeqCigar sq[] = seqstrings.getSequences();
- int length = sq[0].getWidth();
-
- for (int i = 0; i < seqs.length; i++)
- {
- if (sq[i].getWidth() != length)
- {
- sameLength = false;
- break;
- }
- }
- if (!sameLength)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent e)
- {
- close_actionPerformed();
- }
- });
-
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
+ modelName, ap);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params);
PaintRefresher.Register(this, av.getSequenceSetId());
- rc = new RotatableCanvas(ap);
+ rc = new RotatableCanvas(alignPanel);
this.getContentPane().add(rc, BorderLayout.CENTER);
Thread worker = new Thread(this);
worker.start();
pcaModel = null;
}
+ /**
+ * Repopulate the options and actions under the score model menu when it is
+ * selected. Options will depend on whether 'nucleotide' or 'peptide'
+ * modelling is selected (and also possibly on whether any additional score
+ * models have been added).
+ */
@Override
- protected void scoreMatrix_menuSelected()
+ protected void scoreModel_menuSelected()
{
- scoreMatrixMenu.removeAll();
- for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ scoreModelMenu.removeAll();
+ for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
{
- if (ResidueProperties.getScoreMatrix(sm) != null)
+ final String name = sm.getName();
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
+
+ /*
+ * if the score model doesn't provide a description, try to look one
+ * up in the text bundle, falling back on its name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
+ {
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ name);
+ }
+ jm.setToolTipText(tooltip);
+ jm.setSelected(pcaModel.getScoreModelName().equals(name));
+ if ((pcaModel.isNucleotide() && sm.isDNA())
+ || (!pcaModel.isNucleotide() && sm.isProtein()))
{
- // create an entry for this score matrix for use in PCA
- JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
- jm.setText(MessageManager.getStringOrReturn("label.score_model_",
- sm));
- jm.setSelected(pcaModel.getScore_matrix().equals(sm));
- if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
- .get(sm).isProtein())
- || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
- .get(sm).isDNA())
+ jm.addActionListener(new ActionListener()
{
- final PCAPanel us = this;
- jm.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!pcaModel.getScoreModelName().equals(name))
{
- if (!pcaModel.getScore_matrix().equals(sm))
- {
- pcaModel.setScore_matrix(sm);
- Thread worker = new Thread(us);
- worker.start();
- }
+ ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
+ name, ap);
+ pcaModel.setScoreModel(sm2);
+ Thread worker = new Thread(PCAPanel.this);
+ worker.start();
}
- });
- scoreMatrixMenu.add(jm);
- }
+ }
+ });
+ scoreModelMenu.add(jm);
}
}
}
// rc.invalidate();
nuclSetting.setSelected(pcaModel.isNucleotide());
protSetting.setSelected(!pcaModel.isNucleotide());
- jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
top = pcaModel.getTop();
} catch (OutOfMemoryError er)
addKeyListener(rc);
Desktop.addInternalFrame(this, MessageManager
.getString("label.principal_component_analysis"), 475, 450);
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
}
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- pcaModel.setScore_matrix("DNA");
+ pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
+ false));
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
- pcaModel.setScore_matrix("BLOSUM62");
+ pcaModel.setScoreModel(ScoreModels.getInstance()
+ .getDefaultModel(true));
Thread worker = new Thread(this);
worker.start();
}
}
- @Override
- protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
- {
- pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
- Thread worker = new Thread(this);
- worker.start();
- }
-
/**
* DOCUMENT ME!
*/
git://source.jalview.org / jalview.git / commitdiff