From: Jim Procter Date: Wed, 14 Dec 2016 15:08:14 +0000 (+0000) Subject: Merge branch 'patch/JAL-2197_jpredforjnets' into develop X-Git-Tag: Release_2_10_3b1~386 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cd4e2687751aab1c9c5974e6966e610a3332236b;hp=-c;p=jalview.git Merge branch 'patch/JAL-2197_jpredforjnets' into develop merge was missed for 2.10.1 release! --- cd4e2687751aab1c9c5974e6966e610a3332236b diff --combined examples/appletDeployment.html index 7b4daee,9438fa4..e9c22e5 --- a/examples/appletDeployment.html +++ b/examples/appletDeployment.html @@@ -33,7 -33,7 +33,7 @@@ Main Jalview Applet Jar - JmolApplet-14.2.14_2015.06.11.jar + JmolApplet-14.6.4_2016.10.26.jar Jmol Applet Jar @@@ -48,7 -48,7 +48,7 @@@
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.

 -<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" />
@@@ -195,7 -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 --combined examples/applets.html
index d997f14,e0695b9..b789672
--- a/examples/applets.html
+++ b/examples/applets.html
@@@ -41,7 -41,7 +41,7 @@@ Try out JalviewLite by pressing one of 
        
          
 +   	archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">  
  	
  	
  	
@@@ -64,7 -64,7 +64,7 @@@
      
        
 +   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  
  
  
@@@ -89,7 -89,7 +89,7 @@@
      
        
 +   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  
  
  
@@@ -116,7 -116,7 +116,7 @@@
      
        
 +   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  
  
  
@@@ -136,7 -136,7 +136,7 @@@
  
  						       
        Displays a Multiple Sequence Alignment
- 	Based JNet Prediction for a Sequence
+ 	Based JPred Prediction for a Sequence
      
    
    
@@@ -147,7 -147,7 +147,7 @@@
      
        
 +   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  
  
  
@@@ -171,7 -171,7 +171,7 @@@
        
  
 +   archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  
  
  
diff --combined help/help.jhm
index e034fc2,06c5817..f69ed00
--- a/help/help.jhm
+++ b/help/help.jhm
@@@ -22,7 -22,7 +22,7 @@@
     
     
     
 -   
 +   
     
     
     
@@@ -33,7 -33,7 +33,7 @@@
     
     
     
-    
+    
     
     
     
diff --combined help/helpTOC.xml
index 3a6b0b3,1248d36..54abd53
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@@ -23,6 -23,9 +23,6 @@@
  
  	
  			
 -				
 -				
 -				
  				
  		
  		
@@@ -70,7 -73,7 +70,7 @@@
  			
  				
  			
- 			
+ 			
  			
  			
  			
diff --combined help/html/menus/alignmentMenu.html
index 167cb25,b30fbab..51ad601
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@@ -278,12 -278,6 +278,12 @@@
                Columns by Annotation 
 Select or Hide
              columns in the alignment according to secondary structure,
              labels and values shown in alignment annotation rows. 
 +        Select Highlighted Columns 
 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. 
        
      View
        
@@@ -638,22 -632,22 +638,22 @@@
          
            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 --combined resources/lang/Messages.properties
index 6360dc7,fc35351..d418c76
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -125,8 -125,6 +125,8 @@@ action.change_font_tree_panel = Change 
  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
@@@ -384,8 -382,8 +384,8 @@@ label.select_at_least_three_bases_in_at
  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 = Do you want to ignore the {0} files whose names did not match any sequence IDs ?
  label.ignore_unmatched_dropped_files = Ignore unmatched dropped files?
  label.view_name_original = Original
@@@ -789,10 -787,8 +789,10 @@@ label.hide_columns_containing = Hide co
  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 $SEQUENCE_ID=//=$
 -label.use_sequence_id_2 = \nto embed sequence id in URL
 +label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=//=$
 +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
@@@ -835,7 -831,7 +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 -965,7 +969,7 @@@ error.cannot_have_zero_length_vector_re
  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 -1073,7 +1077,7 @@@ exception.unexpected_handling_rnaml_tra
  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 -1095,7 +1099,7 @@@ info.job_couldnt_be_run_exceeded_hard_l
  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}
@@@ -1146,7 -1142,7 +1146,7 @@@ warn.user_defined_width_requirements = 
  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 $SEQUENCE_ID=//=$
 +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)
@@@ -1270,8 -1266,3 +1270,8 @@@ status.exporting_alignment_as_x_file = 
  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
diff --combined resources/lang/Messages_es.properties
index e5b5e27,bf8e2fb..8cdcd52
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@@ -122,8 -122,6 +122,8 @@@ action.change_font_tree_panel = Cambia
  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
@@@ -353,8 -351,8 +353,8 @@@ label.select_at_least_three_bases_in_at
  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 ignorar 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
@@@ -722,10 -720,8 +722,10 @@@ label.select_columns_containing = Selec
  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 $SEQUENCE_ID=//=$
 -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 $DB_ACCESSION=//=$
 +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
@@@ -768,7 -764,7 +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 -898,7 +902,7 @@@ error.cannot_have_zero_length_vector_re
  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 -1006,7 +1010,7 @@@ exception.unexpected_handling_rnaml_tra
  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 -1027,7 +1031,7 @@@ info.job_couldnt_be_run_exceeded_hard_l
  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}
@@@ -1072,7 -1068,7 +1072,7 @@@ warn.user_defined_width_requirements = 
  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 $SEQUENCE_ID=//=$
 +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?
@@@ -1271,8 -1267,3 +1271,8 @@@ status.exporting_alignment_as_x_file = 
  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
diff --combined src/jalview/appletgui/AlignFrame.java
index f830fe6,af91399..175b171
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -49,9 -49,7 +49,9 @@@ import jalview.datamodel.SequenceGroup
  import jalview.datamodel.SequenceI;
  import jalview.io.AnnotationFile;
  import jalview.io.AppletFormatAdapter;
 +import jalview.io.DataSourceType;
  import jalview.io.FeaturesFile;
 +import jalview.io.FileFormat;
  import jalview.io.TCoffeeScoreFile;
  import jalview.schemes.Blosum62ColourScheme;
  import jalview.schemes.BuriedColourScheme;
@@@ -347,7 -345,7 +347,7 @@@ public class AlignFrame extends Embmenu
     *          is protocol for accessing data referred to by file
     */
  
 -  public boolean parseFeaturesFile(String file, String type)
 +  public boolean parseFeaturesFile(String file, DataSourceType type)
    {
      return parseFeaturesFile(file, type, true);
    }
@@@ -357,14 -355,14 +357,14 @@@
     * 
     * @param file
     *          file URL, content, or other resolvable path
 -   * @param type
 +   * @param sourceType
     *          is protocol for accessing data referred to by file
     * @param autoenabledisplay
     *          when true, display features flag will be automatically enabled if
     *          features are loaded
     * @return true if data parsed as a features file
     */
 -  public boolean parseFeaturesFile(String file, String type,
 +  public boolean parseFeaturesFile(String file, DataSourceType sourceType,
            boolean autoenabledisplay)
    {
      boolean featuresFile = false;
@@@ -374,7 -372,7 +374,7 @@@
                .getFeatureRenderer().getFeatureColours();
        boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
                "relaxedidmatch", false);
 -      featuresFile = new FeaturesFile(file, type).parse(
 +      featuresFile = new FeaturesFile(file, sourceType).parse(
                viewport.getAlignment(), colours, true, relaxedIdMatching);
      } catch (Exception ex)
      {
@@@ -1358,13 -1356,13 +1358,13 @@@
      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
      Frame frame = new Frame();
      frame.add(cap);
 -    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
 +    JalviewLite.addFrame(frame, MessageManager.formatMessage(
              "label.alignment_output_command",
              new Object[] { e.getActionCommand() }), 600, 500);
  
 -    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
 +    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
      cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
 -            e.getActionCommand(), viewport.getAlignment(),
 +            fileFormat, viewport.getAlignment(),
              viewport.getShowJVSuffix()));
    }
  
@@@ -1480,10 -1478,13 +1480,13 @@@
        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)
@@@ -3236,9 -3237,11 +3239,9 @@@
      inputText.addActionListener(this);
      Menu outputTextboxMenu = new Menu(
              MessageManager.getString("label.out_to_textbox"));
 -    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
 +    for (String ff : FileFormat.getWritableFormats(true))
      {
 -
 -      MenuItem item = new MenuItem(
 -              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 +      MenuItem item = new MenuItem(ff);
  
        item.addActionListener(new java.awt.event.ActionListener()
        {
@@@ -4016,8 -4019,7 +4019,8 @@@
        }
        // resolve data source
        // TODO: this code should be a refactored to an io package
 -      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
 +      DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
 +              pdbFile, FileFormat.PDB);
        if (protocol == null)
        {
          return false;
@@@ -4061,7 -4063,7 +4064,7 @@@
    }
  
    public void newStructureView(JalviewLite applet, PDBEntry pdb,
 -          SequenceI[] seqs, String[] chains, String protocol)
 +          SequenceI[] seqs, String[] chains, DataSourceType protocol)
    {
      // Scrub any null sequences from the array
      Object[] sqch = cleanSeqChainArrays(seqs, chains);
@@@ -4072,16 -4074,10 +4075,16 @@@
        System.err
                .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
      }
 -    if (protocol == null || protocol.trim().length() == 0
 -            || protocol.equals("null"))
 +    if (protocol == null)
      {
 -      protocol = (String) pdb.getProperty("protocol");
 +      String sourceType = (String) pdb.getProperty("protocol");
 +      try
 +      {
 +        protocol = DataSourceType.valueOf(sourceType);
 +      } catch (IllegalArgumentException e)
 +      {
 +        // ignore
 +      }
        if (protocol == null)
        {
          System.err.println("Couldn't work out protocol to open structure: "
@@@ -4104,11 -4100,12 +4107,11 @@@
      {
        // can only do alignments with Jmol
        // find the last jmol window assigned to this alignment
 -      jalview.appletgui.AppletJmol ajm = null, tajm;
 -      Vector jmols = applet
 -              .getAppletWindow(jalview.appletgui.AppletJmol.class);
 +      AppletJmol ajm = null, tajm;
 +      Vector jmols = applet.getAppletWindow(AppletJmol.class);
        for (int i = 0, iSize = jmols.size(); i < iSize; i++)
        {
 -        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
 +        tajm = (AppletJmol) jmols.elementAt(i);
          if (tajm.ap.alignFrame == this)
          {
            ajm = tajm;
@@@ -4127,7 -4124,7 +4130,7 @@@
      // otherwise, create a new window
      if (applet.jmolAvailable)
      {
 -      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
 +      new AppletJmol(pdb, seqs, chains, alignPanel,
                protocol);
        applet.lastFrameX += 40;
        applet.lastFrameY += 40;
diff --combined src/jalview/bin/JalviewLite.java
index 9fd8a90,a3b2b0b..de011ea
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@@ -37,9 -37,6 +37,9 @@@ import jalview.datamodel.SequenceGroup
  import jalview.datamodel.SequenceI;
  import jalview.io.AnnotationFile;
  import jalview.io.AppletFormatAdapter;
 +import jalview.io.DataSourceType;
 +import jalview.io.FileFormat;
 +import jalview.io.FileFormatI;
  import jalview.io.FileParse;
  import jalview.io.IdentifyFile;
  import jalview.io.JPredFile;
@@@ -66,7 -63,6 +66,7 @@@ import java.awt.event.ActionEvent
  import java.awt.event.WindowAdapter;
  import java.awt.event.WindowEvent;
  import java.io.BufferedReader;
 +import java.io.IOException;
  import java.io.InputStreamReader;
  import java.net.URL;
  import java.util.ArrayList;
@@@ -517,23 -513,21 +517,23 @@@ public class JalviewLite extends Apple
    {
      try
      {
 +      FileFormatI theFormat = FileFormat.valueOf(format);
        boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
        if (alf.viewport.getSelectionGroup() != null)
        {
          // JBPNote: getSelectionAsNewSequence behaviour has changed - this
          // method now returns a full copy of sequence data
          // TODO consider using getSequenceSelection instead here
 -        String reply = new AppletFormatAdapter().formatSequences(format,
 +        String reply = new AppletFormatAdapter().formatSequences(theFormat,
                  new Alignment(alf.viewport.getSelectionAsNewSequence()),
                  seqlimits);
          return reply;
        }
 -    } catch (Exception ex)
 +    } catch (IllegalArgumentException ex)
      {
        ex.printStackTrace();
 -      return "Error retrieving alignment in " + format + " format. ";
 +      return "Error retrieving alignment, possibly invalid format specifier: "
 +              + format;
      }
      return "";
    }
@@@ -715,15 -709,13 +715,15 @@@
      {
        boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
  
 -      String reply = new AppletFormatAdapter().formatSequences(format,
 +      FileFormatI theFormat = FileFormat.valueOf(format);
 +      String reply = new AppletFormatAdapter().formatSequences(theFormat,
                alf.viewport.getAlignment(), seqlimits);
        return reply;
 -    } catch (Exception ex)
 +    } catch (IllegalArgumentException ex)
      {
        ex.printStackTrace();
 -      return "Error retrieving alignment in " + format + " format. ";
 +      return "Error retrieving alignment, possibly invalid format specifier: "
 +              + format;
      }
    }
  
@@@ -749,14 -741,14 +749,14 @@@
    public void loadAnnotationFrom(AlignFrame alf, String annotation)
    {
      if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
 -            annotation, AppletFormatAdapter.PASTE))
 +            annotation, DataSourceType.PASTE))
      {
        alf.alignPanel.fontChanged();
        alf.alignPanel.setScrollValues(0, 0);
      }
      else
      {
 -      alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
 +      alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
      }
    }
  
@@@ -782,7 -774,7 +782,7 @@@
    public boolean loadFeaturesFrom(AlignFrame alf, String features,
            boolean autoenabledisplay)
    {
 -    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
 +    return alf.parseFeaturesFile(features, DataSourceType.PASTE,
              autoenabledisplay);
    }
  
@@@ -890,17 -882,17 +890,17 @@@
    {
      AlignmentI al = null;
  
 -    String format = new IdentifyFile().identify(text,
 -            AppletFormatAdapter.PASTE);
      try
      {
 -      al = new AppletFormatAdapter().readFile(text,
 -              AppletFormatAdapter.PASTE, format);
 +      FileFormatI format = new IdentifyFile().identify(text,
 +              DataSourceType.PASTE);
 +      al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
 +              format);
        if (al.getHeight() > 0)
        {
          return new AlignFrame(al, this, title, false);
        }
 -    } catch (java.io.IOException ex)
 +    } catch (IOException ex)
      {
        ex.printStackTrace();
      }
@@@ -1826,7 -1818,7 +1826,7 @@@
      /**
       * State variable: protocol for access to file source
       */
 -    String protocol;
 +    DataSourceType protocol;
  
      String _file; // alignment file or URL spec
  
@@@ -1856,7 -1848,7 +1856,7 @@@
         */
        if (path.startsWith("PASTE"))
        {
 -        protocol = AppletFormatAdapter.PASTE;
 +        protocol = DataSourceType.PASTE;
          return path.substring(5);
        }
  
@@@ -1865,7 -1857,7 +1865,7 @@@
         */
        if (path.indexOf("://") != -1)
        {
 -        protocol = AppletFormatAdapter.URL;
 +        protocol = DataSourceType.URL;
          return path;
        }
  
@@@ -1881,7 -1873,7 +1881,7 @@@
            System.err.println("Prepended document base '" + documentBase
                    + "' to make: '" + withDocBase + "'");
          }
 -        protocol = AppletFormatAdapter.URL;
 +        protocol = DataSourceType.URL;
          return withDocBase;
        }
  
@@@ -1894,7 -1886,7 +1894,7 @@@
        if (!withCodeBase.equals(withDocBase)
                && HttpUtils.isValidUrl(withCodeBase))
        {
 -        protocol = AppletFormatAdapter.URL;
 +        protocol = DataSourceType.URL;
          if (debug)
          {
            System.err.println("Prepended codebase '" + codeBase
@@@ -1909,7 -1901,7 +1909,7 @@@
         */
        if (inArchive(path))
        {
 -        protocol = AppletFormatAdapter.CLASSLOADER;
 +        protocol = DataSourceType.CLASSLOADER;
        }
        return path;
      }
@@@ -2023,12 -2015,11 +2023,12 @@@
          return null;
        }
        String resolvedFile = resolveFileProtocol(fileParam);
        AlignmentI al = null;
        try
        {
 +        FileFormatI format = new IdentifyFile().identify(resolvedFile,
 +                protocol);
 +        dbgMsg("File identified as '" + format + "'");
          al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
                  format);
          if ((al != null) && (al.getHeight() > 0))
@@@ -2045,7 -2036,7 +2045,7 @@@
            // update the focus.
            currentAlignFrame = newAlignFrame;
  
 -          if (protocol == AppletFormatAdapter.PASTE)
 +          if (protocol == DataSourceType.PASTE)
            {
              newAlignFrame.setTitle(MessageManager.formatMessage(
                      "label.sequences_from", new Object[] { applet
@@@ -2216,7 -2207,8 +2216,7 @@@
              }
              else
              {
 -              pdbs.addElement(new Object[] { pdb, seqs, chains,
 -                  new String(protocol) });
 +              pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
              }
            }
          }
@@@ -2255,6 -2247,11 +2255,11 @@@
      {
        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 --combined src/jalview/ws/jws1/Discoverer.java
index 7258f51,b30f6cb..ba4054e
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@@ -20,13 -20,14 +20,13 @@@
   */
  package jalview.ws.jws1;
  
 +import jalview.gui.JvOptionPane;
  import jalview.util.MessageManager;
  
  import java.util.Hashtable;
  import java.util.StringTokenizer;
  import java.util.Vector;
  
 -import javax.swing.JOptionPane;
 -
  import ext.vamsas.IRegistry;
  import ext.vamsas.IRegistryServiceLocator;
  import ext.vamsas.RegistryServiceSoapBindingStub;
@@@ -222,7 -223,7 +222,7 @@@ public class Discoverer implements Runn
                              + "\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);
@@@ -254,11 -255,11 +254,11 @@@
        {
          if (jalview.gui.Desktop.desktop != null)
          {
 -          JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
 +          JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
                    MessageManager.getString("label.set_proxy_settings"),
                    MessageManager
                            .getString("label.proxy_authorization_failed"),
 -                  JOptionPane.WARNING_MESSAGE);
 +                  JvOptionPane.WARNING_MESSAGE);
          }
        }
        else
diff --combined src/jalview/ws/jws1/JPredClient.java
index 2c05386,b20a100..65847e6
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@@ -27,7 -27,6 +27,7 @@@ import jalview.datamodel.SeqCigar
  import jalview.datamodel.SequenceI;
  import jalview.gui.AlignFrame;
  import jalview.gui.Desktop;
 +import jalview.gui.JvOptionPane;
  import jalview.gui.WebserviceInfo;
  import jalview.util.MessageManager;
  
@@@ -37,6 -36,7 +37,6 @@@ import java.util.Hashtable
  
  import javax.swing.JMenu;
  import javax.swing.JMenuItem;
 -import javax.swing.JOptionPane;
  
  import ext.vamsas.Jpred;
  import ext.vamsas.JpredServiceLocator;
@@@ -238,7 -238,7 +238,7 @@@ public class JPredClient extends WS1Cli
  
      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 +275,7 @@@
      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
@@@ -323,7 -323,7 +323,7 @@@
  
      } catch (Exception ex)
      {
 -      JOptionPane
 +      JvOptionPane
                .showMessageDialog(
                        Desktop.desktop,
                        MessageManager
@@@ -332,7 -332,7 +332,7 @@@
                                        new String[] { WebServiceName, WsURL }),
                        MessageManager
                                .getString("label.internal_jalview_error"),
 -                      JOptionPane.WARNING_MESSAGE);
 +                      JvOptionPane.WARNING_MESSAGE);
        wsInfo.setProgressText(MessageManager
                .formatMessage(
                        "label.secondary_structure_prediction_service_couldnt_be_located",