merge was missed for 30th November release.
<td>Main Jalview Applet Jar</td>
</tr>
<tr>
- <td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.2.14_2015.06.11.jar">JmolApplet-14.2.14_2015.06.11.jar</a> </td>
+ <td><a href="http://www.jalview.org/builds/develop/examples/JmolApplet-14.6.4_2016.10.26.jar">JmolApplet-14.6.4_2016.10.26.jar</a> </td>
<td>Jmol Applet Jar</td>
</tr>
<tr>
<p>To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.
<pre><code>
-<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox" />
<param name="file" value="plantfdx.fa" />
<param name="features" value="plantfdx.features" />
<tr>
<td><strong>2.1</strong></td>
<td><ul>
- <li>Jalview Applet can read and display JNet secondary structure annotation
+ <li>Jalview Applet can read and display JPred secondary structure annotation
directly via the <strong>jnetfile</strong> parameter. <br>
</li>
<li>Param "UserDefinedColour" - specify your own colours for each residue using a semi colon
<td width="10%" valign="center">
<applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="uniref50.fa"/>
<param name="treeFile" value="ferredoxin.nw"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="uniref50.fa"/>
<param name="features" value="exampleFeatures.txt"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="uniref50.fa"/>
<param name="showFullId" value="false"/>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="jpred_msa.fasta"/>
<param name="jnetfile" value="jpred_msa.seq.concise"/>
</applet>
</td>
<td valign="middle">Displays a Multiple Sequence Alignment
- Based JNet Prediction for a Sequence</td>
+ Based JPred Prediction for a Sequence</td>
</tr>
</table>
<p>
<tr>
<td width="10%" valign="center"><applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file" value="RF00031_folded.stk"/>
<param name="showFullId" value="false"/>
<td width="10%" valign="center">
<applet
code="jalview.bin.JalviewLite" width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
+ archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
<param name="permissions" value="sandbox"/>
<param name="file2" value="estrogenReceptorCdna_frag.fa"/>
<param name="file" value="estrogenReceptorProtein_frag.fa"/>
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html#Jalview.2.9"/>
+ <mapID target="release" url="html/releases.html#Jalview.2.10.1"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
<mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
<mapID target="msaservice" url="html/webServices/msaclient.html"/>
- <mapID target="jnet" url="html/webServices/jnet.html"/>
+ <mapID target="jpred" url="html/webServices/jnet.html"/>
<mapID target="shmrws" url="html/webServices/shmr.html"/>
<mapID target="newsreader" url="html/webServices/newsreader.html"/>
<mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Retrieval from ENSEMBL" target="ensemblfetch" />
- <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
- <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
<tocitem text="Latest Release Notes" target="release"/>
</tocitem>
<tocitem text="Sequence Alignment" target="msaservice" expand="false">
<tocitem text="Multiple Alignment Subjobs" target="msaservice" />
</tocitem>
- <tocitem text="Secondary Structure Prediction" target="jnet" />
+ <tocitem text="Secondary Structure Prediction" target="jpred" />
<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
<tocitem text="Protein Disorder Prediction" target="disorder" />
<tocitem text="Alignment Conservation Analysis" target="aacon" />
Columns by Annotation</a></strong> <br /> <em>Select or Hide
columns in the alignment according to secondary structure,
labels and values shown in alignment annotation rows. </em></li>
+ <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
+ the columns currently highlighted as a result of a find, mouse
+ over, or selection event from a linked structure viewer or other
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
<ul>
<li><strong>JPred Secondary Structure Prediction</strong><br>
<em>Secondary structure prediction by network
- consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
+ consensus. See the <a href="../webServices/jnet.html">Jpred</a>
client entry for more information. The behaviour of this
calculation depends on the current selection:
<ul>
<li>If nothing is selected, and the displayed
- sequences appear to be aligned, then a JNet prediction
+ sequences appear to be aligned, then a JPred prediction
will be run for the first sequence in the alignment,
using the current alignment. Otherwise the first
sequence will be submitted for prediction.</li>
<li>If just one sequence (or a region on one
sequence) has been selected, it will be submitted to
- the automatic JNet prediction server for homolog
+ the automatic JPred prediction server for homolog
detection and prediction.</li>
<li>If a set of sequences are selected, and they
appear to be aligned, then the alignment will be used
- for a Jnet prediction on the <strong>first</strong>
+ for a JPred prediction on the <strong>first</strong>
sequence in the set (that is, the one that appears
first in the alignment window).
</li>
action.colour = Colour
action.calculate = Calculate
action.select_all = Select all
+action.select_highlighted_columns = Select Highlighted Columns
+tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns
action.deselect_all = Deselect all
action.invert_selection = Invert selection
action.using_jmol = Using Jmol
label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
label.implementation_error = Implementation error:
-label.automatically_associate_pdb_files_with_sequences_same_name = Do you want to automatically associate the {0} PDB files with sequences in the alignment that have the same name?
-label.automatically_associate_pdb_files_by_name = Automatically Associate PDB files by name
+label.automatically_associate_structure_files_with_sequences_same_name = Do you want to automatically associate the {0} structure file(s) with sequences in the alignment that have the same name?
+label.automatically_associate_structure_files_by_name = Automatically Associate Structure files by name
label.ignore_unmatched_dropped_files_info = <html>Do you want to <em>ignore</em> the {0} files whose names did not match any sequence IDs ?</html>
label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
label.view_name_original = Original
label.hide_columns_not_containing = Hide columns that do not contain
option.trim_retrieved_seqs = Trim retrieved sequences
label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
-label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = \nto embed sequence id in URL
+label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = to embed accession id in URL
+label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence id
+label.use_sequence_id_4 =
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
label.choose_jabaws_server = Choose a server for running this service
label.muscle_multiple_protein_sequence_alignment = Muscle Multiple Protein Sequence Alignment
label.mafft_multiple_sequence_alignment = MAFFT Multiple Sequence Alignment
label.clustalw_multiple_sequence_alignment = ClustalW Multiple Sequence Alignment
- label.jnet_secondary_structure_prediction = JNet Secondary Structure Prediction
+ label.jnet_secondary_structure_prediction = JPred Secondary Structure Prediction
label.multiharmony = Multi-Harmony
label.unable_start_web_service_analysis = Unable to start web service analysis
label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = Implementation Error! Multiple single sequence prediction jobs are not yet supported
error.implementation_error_invalid_msa_index_for_job =Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!
error.implementation_error_startjob_called = Implementation error - StartJob(JpredJob) called on {0}
- error.multiple_jnet_subjob_merge_not_implemented = Multiple JNet subjob merging not yet implemented
+ error.multiple_jnet_subjob_merge_not_implemented = Multiple JPred subjob merging not yet implemented
label.job_never_ran = Job never ran - input returned to user.
error.implementation_error_minlen_must_be_greater_zero = Implementation error: minlen must be zero or more
error.implementation_error_msawbjob_called = Implementation error - StartJob(MsaWSJob) called on a WSJobInstance {0}
exception.couldnt_recover_sequence_properties_for_alignment = Couldn't recover sequence properties for alignment
exception.unknown_format_for_file = Unknown format {0} for file \: \n{1}
label.remove_gaps = Remove Gaps
- exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JNet Query sequence!
+ exception.couldnt_recover_sequence_props_for_jnet_query = Couldn't recover sequence properties for JPred Query sequence!
exception.server_timeout_try_later = Server timed out - try again later\n
exception.web_service_returned_null_try_later= Server at {0} returned null object, it probably cannot be contacted. Try again later.
exception.cannot_contact_service_endpoint_at = Cannot contact service endpoint at {0}
info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
info.no_jobs_ran = No jobs ran
info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}
- info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}
+ info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JPred job result data\!\n{2}
info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n
info.alignment_object_method_notes = \nAlignment Object Method Notes\n
info.server_exception = \n{0} Server exception\!\n{1}
label.couldnt_create_sequence_fetcher = Couldn't create SequenceFetcher
warn.couldnt_create_sequence_fetcher_client = Could not create the sequence fetcher client. Check error logs for details.
warn.server_didnt_pass_validation = Service did not pass validation.\nCheck the Jalview Console for more details.
-warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$
+warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$, $DB_ACCESSION$, or a regex
warn.urls_not_contacted = URLs that could not be contacted
warn.urls_no_jaba = URLs without any JABA Services
info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)
label.column = Column
label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
label.operation_failed = Operation failed
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = Do not display this message again
+label.output_seq_details = Output Sequence Details to list all database references
action.colour = Color
action.calculate = Calcular
action.select_all = Seleccionar Todo
+action.select_highlighted_columns = Seleccionar columnas resaltadas
+tooltip.select_highlighted_columns = Presione B para marcar las columnas resaltadas, Ctrl (o Cmd)-B para cambiarlas, y Alt-B para marcar todas menos las columnas resaltadas
action.deselect_all = Deseleccionar Todo
action.invert_selection = Invertir selección
action.using_jmol = Usar Jmol
label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Desafortunadamente, algo fue mal a la hora de traducir tus secuencias.\nPor favor, revisa la consola Jalview java \ny presenta un informe de error que incluya el seguimiento.
label.implementation_error = Error de implementación:
-label.automatically_associate_pdb_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros PDB con las secuencias del alineamiento que tengan el mismo nombre?
-label.automatically_associate_pdb_files_by_name = Asociar los ficheros PDB por nombre automáticamente
+label.automatically_associate_structure_files_with_sequences_same_name = Quieres asociar automáticamente los {0} ficheros estructura con las secuencias del alineamiento que tengan el mismo nombre?
+label.automatically_associate_structure_files_by_name = Asociar los ficheros estructura por nombre automáticamente
label.ignore_unmatched_dropped_files_info = Quieres <em>ignorar</em> los {0} ficheros cuyos nombres no coincidan con ningún IDs de las secuencias ?
label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias?
label.enter_view_name = Introduzca un nombre para la vista
label.select_columns_not_containing = Seleccione las columnas que no contengan
option.trim_retrieved_seqs = Ajustar las secuencias recuperadas
label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes.
-label.use_sequence_id_1 = Utilice $SEQUENCE_ID$ o $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = \nto para embeber el id de la secuencia en una URL
+label.use_sequence_id_1 = Utilice $DB_ACCESSION$ o $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = para embeber el ID de accesión en una URL
+label.use_sequence_id_3 = Utilice $SEQUENCE_ID$ de manera similar para embeber
+label.use_sequence_id_4 = el ID de la secuencia
label.ws_parameters_for = Parámetros para {0}
label.switch_server = Cambiar servidor
label.open_jabaws_web_page = Abra el página principal del servidor JABAWS en un navegador web
label.muscle_multiple_protein_sequence_alignment = Alineamiento múltiple de secuencias de proteínas con Muscle
label.mafft_multiple_sequence_alignment = Alineamiento múltiple de secuencias con MAFFT
label.clustalw_multiple_sequence_alignment = Alineamiento múltiple de secuencias con ClustalW
- label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JNet
+ label.jnet_secondary_structure_prediction = Predicción de la estructura secundaria con JPred
label.multiharmony = Multi-Harmony
label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis
label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview.
error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported = ¡Error de implementación! Todavía no se soportan varios trabajos de predicción asociados a una única secuencia.
error.implementation_error_invalid_msa_index_for_job = ¡Error de implementación! Valor msaIndex no válido para JPredJob en el objeto de entrada MSA padre!
error.implementation_error_startjob_called = Error de implementación - StartJob(JpredJob) invocado en {0}
- error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JNet conjuntos.
+ error.multiple_jnet_subjob_merge_not_implemented = Todavía no se han implementado varios subtrabajos JPred conjuntos.
label.job_never_ran = El trabajo nunca se ejecutó - entrada devuelta al usuario.
error.implementation_error_minlen_must_be_greater_zero = Error de implementación: minlen debe ser cero o más
error.implementation_error_msawbjob_called = Error de implementación - StartJob(MsaWSJob) invocado en un WSJobInstance {0}
exception.couldnt_recover_sequence_properties_for_alignment = No es posible recuperar las propiedades de la secuencia para el alineamiento
exception.unknown_format_for_file = Formato desconocido {0} para el fichero \: \n{1}
label.remove_gaps = Eliminar huecos
- exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JNet Query!
+ exception.couldnt_recover_sequence_props_for_jnet_query = No ha sido posible recuperar las propiedades de la secuencia para la secuencia JPred Query!
exception.server_timeout_try_later = Tiempo de conexi\u00F3n ha expirado - int\u00E9ntelo de nuevo m\u00E1s tarde\n
exception.web_service_returned_null_try_later= El servidor {0} ha devuelto un objeto nulo, por lo que probablemente no se haya podido contactar con él. Inténtelo de nuevo más tarde.
exception.cannot_contact_service_endpoint_at = No es posible contactar por el punto de acceso al servicio en {0}
info.job_couldnt_be_run_incorrect_param_setting = No es posible ejecutar el trabjao porque el servidor no soporta algunos de los par\u00E1metros.\n{0}\nPor favor, aseg\u00FArese de que ha usado los par\u00E1metros adecuados para este servicio\n
info.no_jobs_ran = No se ha ejecutado ningún trabajo
info.failed_to_submit_prediction = Error al enviar la predicci\u00F3n\:\n{0} {1}
- info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JNet no v\u00E1lidos\!\n{2}
+ info.invalid_jnet_job_result_data ={0}\n{1}\nResultados del trabajo JPred no v\u00E1lidos\!\n{2}
info.failed_to_submit_sequences_for_alignment = Error al enviar la secuencias para el alineamiento.\nLo m\u00E1s probable es que haya un problema en el servidor.\nSimplemente, cierre la ventana\n
info.alignment_object_method_notes = \nNotas sobre los m\u00E9todos del objeto alineamiento\n
info.server_exception = \n{0} Excepci\u00F3n del servidor\!\n{1}
label.couldnt_create_sequence_fetcher = No es posible crear SequenceFetcher
warn.couldnt_create_sequence_fetcher_client = No es posible crear el cliente de recuperador de secuencias. Comprueba el fichero de log para más detalles.
warn.server_didnt_pass_validation = El servicio no ha pasado la validaci\u00F3n.\nCompruebe la consola de Jalview para m\u00E1s detalles.
-warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$ o un regex $SEQUENCE_ID=/<regex>/=$
+warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$, $DB_ACCESSION$ o un regex
info.validate_jabaws_server = \u00BFValidar el servidor JabaWS?\n(Consulte la consola de salida para obtener los resultados)
label.test_server = ¿Probar servidor?
info.you_want_jalview_to_find_uniprot_accessions = \u00BFDesea que Jalview encuentre\nUniprot Accession ids para los nombres de secuencias dados?
label.column = Columna
label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
label.operation_failed = Operación fallada
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ no se utiliza más para accesiones DB
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Por favor, revise sus URLs en la pestaña 'Conexiones' de la ventana de Preferencias:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
+label.do_not_display_again = No mostrar este mensaje de nuevo
+label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
git://source.jalview.org / jalview.git / commitdiff