JNet Secondary Structure Prediction

From: Jim Procter Date: Wed, 14 Dec 2016 15:08:47 +0000 (+0000) Subject: Merge branch 'patch/JAL-2197_jpredforjnets' into releases/Release_2_10_1_Branch X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4f02a7cced11020e3fc0c1220c98c3183955ae5c;hp=260f6abfaaafac067d5bda703e5b21be480bcc8f;p=jalview.git Merge branch 'patch/JAL-2197_jpredforjnets' into releases/Release_2_10_1_Branch merge was missed for 2.10.1 release! --- diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html index 7b4daee..e9c22e5 100644 --- a/examples/appletDeployment.html +++ b/examples/appletDeployment.html @@ -195,7 +195,7 @@ 2.1

Jalview Applet can read and display JNet secondary structure annotation +
Jalview Applet can read and display JPred secondary structure annotation directly via the jnetfile parameter.
Param "UserDefinedColour" - specify your own colours for each residue using a semi colon diff --git a/examples/appletParameters.html b/examples/appletParameters.html index cc95ecb..277fd69 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -91,8 +91,9 @@ the applet can be interacted with via its jnetfile fileName Secondary structure predictions from a Jnet Concise - file will be added to the first sequence in the alignment. + href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred Concise + file will be added to the first sequence in the alignment.
+ jpredfile can be used interchangeably with this parameter. PDBfile(x) diff --git a/examples/applets.html b/examples/applets.html index d997f14..b789672 100644 --- a/examples/applets.html +++ b/examples/applets.html @@ -136,7 +136,7 @@ Try out JalviewLite by pressing one of the buttons below. Displays a Multiple Sequence Alignment - Based JNet Prediction for a Sequence + Based JPred Prediction for a Sequence
diff --git a/help/help.jhm b/help/help.jhm index e034fc2..f69ed00 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -33,7 +33,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 3a6b0b3..54abd53 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -70,7 +70,7 @@ - + diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html index a79541b..7c0e3dc 100644 --- a/help/html/calculations/referenceseq.html +++ b/help/html/calculations/referenceseq.html @@ -58,7 +58,7 @@
Defining a reference when importing annotation
Jalview automatically assigns a reference sequence when importing analysis results, such as those returned - from JPred4 . A reference + from JPred . A reference sequence can also be assigned via the SET_REF command in an alignment annotation file.

JPred Secondary Structure Prediction
Secondary structure prediction by network - consensus. See the Jpred3 + consensus. See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:

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.

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.

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 first + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index 33282e9..b71bc1a 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -68,22 +68,22 @@

JPred Secondary Structure Prediction
Secondary structure prediction by network consensus. - See the Jpred3 client + See the Jpred client entry for more information. The behaviour of this calculation depends on the current selection:

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.

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 detection + automatic JPred prediction server for homolog detection and prediction.

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 first + for a JPred prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html index 396a3a7..077ace6 100755 --- a/help/html/webServices/jnet.html +++ b/help/html/webServices/jnet.html @@ -20,10 +20,10 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -JNet Secondary Structure Prediction +JPred Secondary Structure Prediction - JNet Secondary Structure Prediction + JPred Secondary Structure Prediction
Secondary structure prediction methods attempts to infer the likely secondary structure for a protein based on its amino acid @@ -52,35 +52,35 @@
The function available from the Web Service→Secondary Structure - Prediction→JNet Secondary Structure Prediction menu does two + Prediction→JPred Secondary Structure Prediction menu does two different kinds of prediction, dependent upon the currently selected region:

If nothing is selected, and the displayed sequences appear - to be aligned, then a JNet prediction will be run for the first + 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.

If just one sequence (or a region on one sequence) has been - selected, it will be submitted to the automatic JNet prediction + selected, it will be submitted to the automatic JPred prediction server for homolog detection and prediction.

If a set of sequences are selected, and they appear to be - aligned, then the alignment will be used for a Jnet prediction on + aligned, then the alignment will be used for a JPred prediction on the first sequence selected in the set (that is, the one nearest the top of the alignment window).

- Note: JNet secondary structure prediction is a + Note: JPred secondary structure prediction is a 'non-column-separable' service - predictions are based on the sequence profile of contiguous stretches of amino-acid sequence. A prediction will only be made on the visible parts of a sequence (see hiding columns) as if it were a contiguous polypeptide chain. Prediction accuracy at the hidden column boundaries may therefore be less than indicated by - JNet's own reliability score (see below). + JPred's own reliability score (see below).
-
The result of a JNet prediction for a sequence is a new +
The result of a JPred prediction for a sequence is a new annotated alignment window:

The sequence for which the prediction was made is the first one @@ -124,12 +124,12 @@ significantly different primary predictions.

- JNet annotation created in Jalview 2.8.2 and later versions + JPred annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the Add reference annotation Sequence ID popup menu option. - As of Jalview 2.6, the Jnet service accessed accessed via the + As of Jalview 2.6, the JPred service accessed accessed via the 'Secondary structure prediction' submenu should be considered a legacy Jalview SOAP service, and will be replaced in the near future by a JPred4 Rest service. diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 6360dc7..d418c76 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -835,7 +835,7 @@ label.colour_by = Colour by... 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. @@ -969,7 +969,7 @@ error.cannot_have_zero_length_vector_replacement_strings = Cannot have zero leng 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} @@ -1077,7 +1077,7 @@ exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception w 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} @@ -1099,7 +1099,7 @@ info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it ex 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} diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index e5b5e27..8cdcd52 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -768,7 +768,7 @@ label.colour_by = Colorear por... 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. @@ -902,7 +902,7 @@ error.cannot_have_zero_length_vector_replacement_strings = No es posible tener u 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} @@ -1010,7 +1010,7 @@ exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada c 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} @@ -1031,7 +1031,7 @@ info.job_couldnt_be_run_exceeded_hard_limit = No es posible ejecutar el trabajo 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} diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 122afa8..af91399 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1478,10 +1478,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index b30ad41..a3b2b0b 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -2247,6 +2247,11 @@ public class JalviewLite extends Applet implements { boolean result = false; String param = applet.getParameter("jnetfile"); + if (param == null) + { + // jnet became jpred around 2016 + param = applet.getParameter("jpredfile"); + } if (param != null) { try diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 4643119..b30f6cb 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -223,7 +223,7 @@ public class Discoverer implements Runnable + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" + "\ndoi://10.1093/nar/gkv332", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JNet Secondary Structure Prediction") }; + "JPred Secondary Structure Prediction") }; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); @@ -383,11 +383,13 @@ public class Discoverer implements Runnable /** * creates a new thread to call discoverServices() */ + @Override public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { + @Override public void run() { discoverer.doDiscovery(); diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java index f13672b..b20a100 100644 --- a/src/jalview/ws/jws1/JPredClient.java +++ b/src/jalview/ws/jws1/JPredClient.java @@ -238,7 +238,7 @@ public class JPredClient extends WS1Client SequenceI seq = msf[0]; - String altitle = "JNet prediction on " + seq.getName() + String altitle = "JPred prediction on " + seq.getName() + " using alignment from " + title; wsInfo.setProgressText("Job details for MSA based prediction (" + title @@ -275,7 +275,7 @@ public class JPredClient extends WS1Client wsInfo.setProgressText("Job details for prediction on sequence :\n>" + seq.getName() + "\n" + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n"); - String altitle = "JNet prediction for sequence " + seq.getName() + String altitle = "JPred prediction for sequence " + seq.getName() + " from " + title; Hashtable SequenceInfo = jalview.analysis.SeqsetUtils @@ -345,6 +345,7 @@ public class JPredClient extends WS1Client return server; } + @Override public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, final AlignFrame af) { @@ -352,6 +353,7 @@ public class JPredClient extends WS1Client method.setToolTipText(sh.getEndpointURL()); method.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();