label.fetch_retrieve_from =Retrieve from {0}</html>
label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html>
label.feature_settings_click_drag = Drag up or down to change render order.<br/>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 = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html>
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.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
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}<br>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.<br/>Haga doble clic para seleccionar las columnas que contienen las características del alineamiento/selección actual.<br/>
+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.<br/>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<br><img src="{0}"/>Haga clic en el botón derecho para obtener información adicional.
label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve<br>
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.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
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+ import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
}
/**
- * 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;
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)
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (Cache.getDefault("HIDE_INTRONS", true))
{
- newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ newFrame.hideFeatureColumns(false, SequenceOntologyI.EXON);
}
String newtitle = String.format("%s %s %s",
dna ? MessageManager.getString("label.proteins")
/*
* 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
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
*/
package jalview.io.gff;
+import jalview.datamodel.ontology.OntologyBase;
+
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
* @author gmcarstairs
*
*/
-public class SequenceOntologyLite implements SequenceOntologyI
+public class SequenceOntologyLite extends OntologyBase
+ implements SequenceOntologyI
{
/*
* initial selection of types of interest when processing Ensembl features
{ "snRNA", "transcript" },
{ "miRNA", "transcript" },
{ "lincRNA", "transcript" },
+ { "lnc_RNA", "transcript" },
{ "rRNA", "transcript" },
{ "mRNA", "transcript" },
// there are many more sub-types of ncRNA...
{ "sequence_variant", "sequence_variant" },
{ "structural_variant", "sequence_variant" },
{ "feature_variant", "sequence_variant" },
+ { "upstream_gene_variant", "sequence_variant" },
{ "gene_variant", "sequence_variant" },
{ "transcript_variant", "sequence_variant" },
+ { "non_coding_transcript_variant", "sequence_variant" },
+ { "non_coding_transcript_exon_variant", "sequence_variant" },
// NB Ensembl uses NMD_transcript_variant as if a 'transcript'
// but we model it here correctly as per the SO
{ "NMD_transcript_variant", "sequence_variant" },
return termsNotFound;
}
}
+
+ @Override
+ public List<String> getRootParents(final String term)
+ {
+ /*
+ * check in cache first
+ */
+ if (rootParents.containsKey(term))
+ {
+ return rootParents.get(term);
+ }
+
+ List<String> top = new ArrayList<>();
+ List<String> query = new ArrayList<>();
+ query.add(term);
+
+ while (!query.isEmpty())
+ {
+ List<String> nextQuery = new ArrayList<>();
+ for (String q : query)
+ {
+ List<String> theParents = parents.get(q);
+ if (theParents != null)
+ {
+ if (theParents.size() == 1 && theParents.get(0).equals(q))
+ {
+ /*
+ * top-level term
+ */
+ if (!top.contains(q))
+ {
+ top.add(q);
+ }
+ }
+ else
+ {
+ for (String p : theParents)
+ {
+ if (!p.equals(q))
+ {
+ nextQuery.add(p);
+ }
+ }
+ }
+ }
+ }
+ query = nextQuery;
+ }
+
+ rootParents.put(term, top);
+
+ return top.isEmpty() ? null : top;
+ }
+
+ @Override
+ public List<String> getParents(String term)
+ {
+ List<String> result = parents.get(term);
+ return result == null ? new ArrayList<>() : result;
+ }
+
+ @Override
+ public boolean isValidTerm(String term)
+ {
+ return parents.containsKey(term);
+ }
}
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);
@Test(groups = "Functional")
public void testHideFeatureColumns()
{
- SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
- SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
- seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
- Float.NaN, null));
- seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
- Float.NaN, null));
+ SequenceI seq1 = new Sequence("Seq1/01-10", "A---BCDEFG-HIJ");
+ SequenceI seq2 = new Sequence("Seq2/11-20", "-AB-CDEF--GHIJ");
+ String METAL = "Metal";
+ String TURN = "Turn";
+ seq1.addSequenceFeature(
+ new SequenceFeature(METAL, "", 1, 5, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(METAL, "", 16, 20, 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature(TURN, "", 2, 4, Float.NaN, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature(TURN, "", 17, 19, Float.NaN, null));
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
al.getHeight());
/*
* hiding a feature not present does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("exon", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
- assertFalse(alignFrame.hideFeatureColumns("exon", false));
+ assertFalse(alignFrame.hideFeatureColumns(false, "exon"));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* hiding a feature in all columns does nothing
*/
- assertFalse(alignFrame.hideFeatureColumns("Metal", true));
+ assertFalse(alignFrame.hideFeatureColumns(true, METAL));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
/*
* threshold Metal to hide features where score < 5
- * seq1 feature in columns 1-5 is hidden
- * seq2 feature in columns 6-10 is shown
+ * seq1 feature in columns 1-8 is hidden
+ * seq2 feature in columns 8-14 is shown
+ * result: columns 8-14 are hidden
+ * note this includes gapped columns spanned by the feature
*/
FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
- alignFrame.getFeatureRenderer().setColour("Metal", fc);
- assertTrue(alignFrame.hideFeatureColumns("Metal", true));
+ alignFrame.getFeatureRenderer().setColour(METAL, fc);
+ assertTrue(alignFrame.hideFeatureColumns(true, METAL));
HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
assertEquals(hidden.getNumberOfRegions(), 1);
Iterator<int[]> regions = hidden.iterator();
- int[] next = regions.next();
- assertEquals(next[0], 5);
- assertEquals(next[1], 9);
+ assertEquals(regions.next(), new int[] { 7, 13 }); // base 0
+ assertFalse(regions.hasNext());
/*
* hide a feature present in some columns
- * sequence positions [2-4], [7-9] are column positions
- * [1-3], [6-8] base zero
+ * seq1 positions [2-4] are column positions [4-6] base zero
+ * seq2 positions [17-19] are column positions [10-12] base zero
*/
alignFrame.getViewport().showAllHiddenColumns();
- assertTrue(alignFrame.hideFeatureColumns("Turn", true));
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN));
regions = alignFrame.getViewport().getAlignment()
.getHiddenColumns().iterator();
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 2);
- next = regions.next();
- assertEquals(next[0], 1);
- assertEquals(next[1], 3);
- next = regions.next();
- assertEquals(next[0], 6);
- assertEquals(next[1], 8);
+ assertEquals(regions.next(), new int[] { 4, 6 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
+
+ /*
+ * hiding a contact feature should only hide start and end positions,
+ * not the intermediate columns
+ */
+ String DISULFIDE = "Disulfide Bond";
+ seq1.addSequenceFeature(
+ new SequenceFeature(DISULFIDE, "", 1, 5, 0f, null));
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 2);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 7, 7 });
+ assertFalse(regions.hasNext());
+
+ /*
+ * hide multiple feature types:
+ * TURN columns hides 4-6, 10-12
+ * DISULFIDE columns hides 0, 7
+ * combined is { 0-0, 4-7, 10-12 }
+ */
+ alignFrame.getViewport().showAllHiddenColumns();
+ assertTrue(alignFrame.hideFeatureColumns(true, TURN, DISULFIDE));
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 3);
+ assertEquals(regions.next(), new int[] { 0, 0 });
+ assertEquals(regions.next(), new int[] { 4, 7 });
+ assertEquals(regions.next(), new int[] { 10, 12 });
+ assertFalse(regions.hasNext());
}
- @BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
- {
- /*
- * use read-only test properties file
- */
- Jalview.main(
- new String[]
- { "-nonews", "-props", "test/jalview/io/testProps.jvprops" });
- }
-
- @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>
git://source.jalview.org / jalview.git / commitdiff