From: gmungoc Date: Thu, 6 Jun 2019 14:10:48 +0000 (+0100) Subject: Merge branch 'develop' into trialMerge X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91e47ada7d1216e06dfcf2c32c7d2be396654455;hp=-c;p=jalview.git Merge branch 'develop' into trialMerge --- 91e47ada7d1216e06dfcf2c32c7d2be396654455 diff --combined resources/lang/Messages.properties index f213e66,f095290..3daba03 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@@ -801,7 -801,6 +801,7 @@@ label.rest_client_submit = {0} using {1 label.fetch_retrieve_from =Retrieve from {0} label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}
First is :{2} label.feature_settings_click_drag = Drag up or down to change render order.
Double click to select columns containing feature. +label.feature_settings_select_columns = Double click to select columns containing feature label.transparency_tip = Adjust transparency to 'see through' feature colours. label.opt_and_params_further_details = see further details by right-clicking label.opt_and_params_show_brief_desc_image_link = Click to show brief description

Right click for further information. @@@ -1340,10 -1339,6 +1340,10 @@@ label.most_bound_molecules = Most Boun label.most_polymer_residues = Most Polymer Residues label.cached_structures = Cached Structures label.free_text_search = Free Text Search +label.summary_view = Summary View +label.group_by_so = Group features by Sequence Ontology +label.apply_to_subtypes = Apply to features and sub-types of +label.apply_also_to = Apply also to: label.backupfiles_confirm_delete = Confirm delete label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options) label.backupfiles_confirm_save_file = Confirm save file @@@ -1359,12 -1354,13 +1359,13 @@@ label.append_to_filename = Append to fi label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above. label.index_digits = Number of digits to use for the backup number (%n) label.summary_of_backups_scheme = Summary of backup scheme + label.scheme_examples = Scheme examples label.increment_index = Increase appended text numbers - newest file has largest number. label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1. label.keep_files = Deleting old backup files label.keep_all_backup_files = Do not delete old backup files label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files - label.autodelete_old_backup_files = Autodelete old backup files: + label.autodelete_old_backup_files = Auto-delete old backup files: label.always_ask = Always ask label.auto_delete = Automatically delete label.filename = filename @@@ -1374,10 -1370,18 +1375,18 @@@ label.configuration = Configuratio label.configure_feature_tooltip = Click to configure variable colour or filters label.schemes = Schemes label.customise = Customise + label.custom = Custom label.default = Default label.single_file = Single backup label.keep_all_versions = Keep all versions label.rolled_backups = Rolled backup files + label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme + label.custom_description = Your own saved scheme + label.default_description = Keep the last three versions of the file + label.single_file_description = Keep the last version of the file + label.keep_all_versions_description = Keep all previous versions of the file + label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest) + label.cancel_changes_description = Cancel changes made to your last saved Custom scheme label.previously_saved_scheme = Previously saved scheme label.no_backup_files = NO BACKUP FILES label.include_backup_files = Include backup files diff --combined resources/lang/Messages_es.properties index 3e4cf682,ec7eb5d..0ec2810 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@@ -726,8 -726,7 +726,8 @@@ label.services_at = Servicios en {0 label.rest_client_submit = {0} utilizando {1} label.fetch_retrieve_from =Recuperar de {0} label.fetch_retrieve_from_all_sources = Recuperar de todas las fuentes {0} en {1}
La primera es :{2} -label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.
Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.
+label.feature_settings_click_drag = Haga clic o arrastre los tipos de las características hacia arriba o hacia abajo para cambiar el orden de visualización.
Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual. +label.feature_settings_select_columns =Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual label.opt_and_params_further_details = ver los detalles adicionales haciendo clic en el botón derecho label.opt_and_params_show_brief_desc_image_link = Haga clic para ver una descripción breve

Haga clic en el botón derecho para obtener información adicional. label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve
@@@ -1341,10 -1340,6 +1341,10 @@@ label.most_bound_molecules = Más Molécu label.most_polymer_residues = Más Residuos de Polímeros label.cached_structures = Estructuras en Caché label.free_text_search = Búsqueda de texto libre +label.summary_view = Vista Resumida +label.group_by_so = Agrupar por términos de la Sequence Ontology +label.apply_to_subtypes = Aplicar también a características y subtipos de +label.apply_also_to = Aplicar también a: label.backupfiles_confirm_delete = Confirmar borrar label.backupfiles_confirm_delete_old_files = ¿Borrar los siguientes archivos? (ver la pestaña 'Copias' de la ventana de Preferencias para más opciones) label.backupfiles_confirm_save_file = Confirmar guardar archivo @@@ -1360,6 -1355,7 +1360,7 @@@ label.append_to_filename = Adjuntar tex label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba. label.index_digits = Número de dígitos a utilizar para el número de respaldo. label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad + label.scheme_examples = Ejemplos de esquema label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1 label.keep_files = Borrando los respaldos antiguos @@@ -1374,11 -1370,19 +1375,19 @@@ label.braced_newest = (mas nuevo label.configuration = Configuración label.configure_feature_tooltip = Haga clic para configurar el color o los filtros label.schemes = Esquemas - label.customise = Personalizado + label.customise = Personalizar + label.custom = Personal label.default = Defecto label.single_file = Solo uno respaldo label.keep_all_versions = Mantener todas las versiones label.rolled_backups = Ciclos respaldos + label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado + label.custom_description = Tu propio esquema guardado + label.default_description = Conserve las últimas tres versiones del archivo + label.single_file_description = Conserve la última versión del archivo + label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo + label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua) + label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado label.previously_saved_scheme = Esquema previamente guardado label.no_backup_files = NO ARCHIVOS DE RESPALDOS label.include_backup_files = Incluir archivos de respaldos diff --combined src/jalview/bin/Jalview.java index 5ac38e4,449c1fb..61f0f8a --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@@ -345,7 -345,7 +345,7 @@@ public class Jalvie * configure 'full' SO model if preferences say to, * else use the default (SO Lite) */ - if (Cache.getDefault("USE_FULL_SO", false)) + if (Cache.getDefault("USE_FULL_SO", true)) { SequenceOntologyFactory.setInstance(new SequenceOntology()); } @@@ -360,10 -360,12 +360,12 @@@ JalviewTaskbar.setTaskbar(this); } catch (Exception e) { - e.printStackTrace(); + System.out.println("Cannot set Taskbar"); + // e.printStackTrace(); } catch (Throwable t) { - t.printStackTrace(); + System.out.println("Cannot set Taskbar"); + // t.printStackTrace(); } desktop.setVisible(true); diff --combined src/jalview/gui/AlignFrame.java index 3754a74,f3a8ab5..7b02aad --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -1203,23 -1203,7 +1203,7 @@@ public class AlignFrame extends GAlignF PrintWriter out = new PrintWriter( new FileWriter(backupfiles.getTempFilePath())); - // TESTING code here - boolean TESTING = true; - if (TESTING) - { - out.print("; TESTSTART\n"); - int count = 20; - for (int i = 0; i < count; i++) - { - // Thread.sleep(1000); - out.println("; TEST: " + (count - 1 - i)); - } - } out.print(output); - if (TESTING) - { - out.print("; TESTEND\n"); - } out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( @@@ -5568,23 -5552,22 +5552,23 @@@ } /** - * Hides columns containing (or not containing) a specified feature, provided - * that would not leave all columns hidden + * Hides columns containing (or not containing) the specified feature(s), + * provided that would not leave all columns hidden * - * @param featureType * @param columnsContaining + * @param featureTypes + * * @return */ - public boolean hideFeatureColumns(String featureType, - boolean columnsContaining) + public boolean hideFeatureColumns(boolean columnsContaining, + String... featureTypes) { boolean notForHiding = avc.markColumnsContainingFeatures( - columnsContaining, false, false, featureType); + columnsContaining, false, false, featureTypes); if (notForHiding) { if (avc.markColumnsContainingFeatures(!columnsContaining, false, - false, featureType)) + false, featureTypes)) { getViewport().hideSelectedColumns(); return true; diff --combined src/jalview/gui/FeatureTypeSettings.java index 167869d,7456e18..50efffc --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@@ -22,6 -22,7 +22,7 @@@ package jalview.gui import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; + import jalview.bin.Cache; import jalview.datamodel.GraphLine; import jalview.datamodel.features.FeatureAttributes; import jalview.datamodel.features.FeatureAttributes.Datatype; @@@ -29,8 -30,6 +30,8 @@@ import jalview.datamodel.features.Featu import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.io.gff.SequenceOntologyI; import jalview.schemes.FeatureColour; import jalview.util.ColorUtils; import jalview.util.MessageManager; @@@ -51,12 -50,7 +52,12 @@@ import java.awt.event.MouseAdapter import java.awt.event.MouseEvent; import java.text.DecimalFormat; import java.util.ArrayList; +import java.util.Collections; +import java.util.Comparator; +import java.util.HashMap; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; import javax.swing.BorderFactory; import javax.swing.BoxLayout; @@@ -124,11 -118,10 +125,11 @@@ public class FeatureTypeSettings extend /* * the colour and filters to reset to on Cancel + * (including feature sub-types if modified) */ - private final FeatureColourI originalColour; + private Map originalColours; - private final FeatureMatcherSetI originalFilter; + private Map originalFilters; /* * set flag to true when setting values programmatically, @@@ -173,7 -166,7 +174,7 @@@ private JPanel maxColour = new JPanel(); - private JComboBox threshold = new JComboBox<>(); + private JComboBox