label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
info.no_pdb_entry_found_for = No PDB entry found for {0}
exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
- exception.fts_rest_service_no_longer_available = {0} rest services no longer available!
- exception.resource_not_be_found = The requested resource could not be found
- exception.fts_server_error = There seems to be an error from the {0} server
exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
action.prev_page= <<
label.next_page_tooltip=Next Page
label.prev_page_tooltip=Previous Page
- exception.bad_request=Bad request. There is a problem with your input.
- exception.service_not_available=Service not available. The server is being updated, try again later.
status.launching_3d_structure_viewer = Launching 3D Structure viewer...
status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
label.create_image_of = Create {0} image of {1}
label.click_to_edit = Click to edit, right-click for menu
label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
+label.show_linked_features = Show {0} features
+label.on_top = on top
+label.include_linked_features = Include {0} features
+label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
label.show_selected_annotations=Mostrar anotaciones seleccionadas
status.colouring_chimera=Coloreando Chimera
label.configure_displayed_columns=Configurar Columnas Mostradas
- exception.resource_not_be_found=El recurso solicitado no se ha encontrado
label.aacon_calculations=cálculos AACon
label.pdb_web-service_error=Error de servicio web PDB
exception.unable_to_detect_internet_connection=Jalview no puede detectar una conexión a Internet
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
label.pdb_sequence_fetcher=Recuperador de secuencias PDB
- exception.fts_server_error=Parece que hay un error desde el servidor {0}
- exception.service_not_available=Servicio no disponible. El servidor se está actualizando, vuelva a intentarlo más tarde.
status.waiting_for_user_to_select_output_file=Esperando que el usuario seleccione el fichero {0}
action.prev_page=<<
status.cancelled_image_export_operation=Operación de exportación {0} cancelada
label.couldnt_run_groovy_script=No se ha podido ejecutar el script Groovy
- exception.bad_request=Solicitud incorrecta. Hay un problema con su entrada.
label.run_groovy=Ejecutar script Groovy desde la consola
action.next_page=>>
label.uniprot_sequence_fetcher=Recuperador de secuencias UniProt
label.sifts_mapping=Mapeado SIFTs
label.mapping_method=Método de mapeo de secuencia \u27F7 estructura
info.error_creating_file=Error al crear fichero {0}
- exception.fts_rest_service_no_longer_available= Servicios Rest {0} ya no están disponibles!
status.launching_3d_structure_viewer=Lanzando visualizador de estructura 3D...
status.obtaining_mapping_with_sifts=Obteniendo mapeo por SIFTS
status.fetching_3d_structures_for=Buscando la estructura 3D para {0}
label.create_image_of = Crear imagen {0} de {1}
label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú
label.by_annotation_tooltip = El color de anotación se configura desde el menú principal de colores
+label.show_linked_features = Características de {0}
+label.on_top = encima
+label.include_linked_features = Incluir características de {0}
+label.include_linked_tooltip = Incluir características de {0}<br>convertidas a coordenadas de secuencia local
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(source);
+ if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+ {
+ // override default featureColourScheme so products have Ensembl variant colours
+ featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(DBRefSource.ENSEMBL);
+ }
+
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
xrefs);
if (!dna)
.isShowSequenceFeatures();
newFrame.setShowSeqFeatures(showSequenceFeatures);
copyThis.setShowSeqFeatures(showSequenceFeatures);
- FeatureRenderer myFeatureStyling = alignFrame.alignPanel
+ FeatureRendererModel myFeatureStyling = alignFrame.alignPanel
.getSeqPanel().seqCanvas.getFeatureRenderer();
/*
* copy feature rendering settings to split frame
*/
- FeatureRenderer fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
+ FeatureRendererModel fr1 = newFrame.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
fr1.transferSettings(myFeatureStyling);
fr1.findAllFeatures(true);
- FeatureRenderer fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
+ FeatureRendererModel fr2 = copyThis.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
fr2.transferSettings(myFeatureStyling);
fr2.findAllFeatures(true);
/*
* apply 'database source' feature configuration
- * if any was found
+ * if any - first to the new splitframe view about to be displayed
*/
- // TODO is this the feature colouring for the original
- // alignment or the fetched xrefs? either could be Ensembl
+
newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+ /*
+ * and for JAL-3330 also to original alignFrame view(s)
+ * this currently trashes any original settings.
+ */
+ for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ origpanel.getAlignViewport()
+ .mergeFeaturesStyle(featureColourScheme);
+ }
+
SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
dna ? newFrame : copyThis);
+
newFrame.setVisible(true);
copyThis.setVisible(true);
String linkedTitle = MessageManager
AlignFrame af;
@BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
+ public static void setUpBeforeClass() throws Exception
+ {
+ setUpJvOptionPane();
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "-nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * configure (read-only) properties for test to ensure Consensus is computed for
+ * colour Above PID testing
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.TRUE.toString());
+ af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+ DataSourceType.FILE);
+
+ /*
+ * wait for Consensus thread to complete
+ */
+ synchronized (this)
+ {
+ while (af.getViewport().getConsensusSeq() == null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ }
+
+ public static void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
assertEquals(next[1], 8);
}
- @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" });
- }
-
- @AfterMethod(alwaysRun = true)
- public void tearDown()
- {
- Desktop.instance.closeAll_actionPerformed(null);
- }
-
- /**
- * configure (read-only) properties for test to ensure Consensus is computed
- * for colour Above PID testing
- */
- @BeforeMethod(alwaysRun = true)
- public void setUp()
- {
- Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.TRUE.toString());
- af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
- DataSourceType.FILE);
-
- /*
- * wait for Consensus thread to complete
- */
- synchronized (this)
- {
- while (af.getViewport().getConsensusSeq() == null)
- {
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
- }
- }
- }
-
/**
* Test that changing background (alignment) colour scheme
* <ul>
/*
* apply 30% Conservation to group
+ * (notice menu action applies to selection group even if mouse click
+ * is at a sequence not in the group)
*/
- PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
+ null);
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
sg.setStartRes(15);
sg.setEndRes(25);
av.setSelectionGroup(sg);
- PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
+ null);
popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
git://source.jalview.org / jalview.git / commitdiff