From: Jim Procter <jprocter@issues.jalview.org>
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=c075b7f23933cbb3c6b1dda53d249d8cbefbe0b6;p=jalview.git

Merge branch 'patch/JAL-2197_jpredforjnets' into develop
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 @@
 	<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 &quot;UserDefinedColour&quot; - 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 <em>via</em> its
             <td>jnetfile</td>
             <td>fileName</td>
             <td>Secondary structure predictions from a <a
-            href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise 
-              file will be added to the first sequence in the alignment.</td>
+            href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred</a> Concise 
+              file will be added to the first sequence in the alignment.<br/>
+              <em>jpredfile</em> can be used interchangeably with this parameter.</td>
           </tr>
           <tr> 
             <td>PDBfile(x)</td>
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.
 </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>
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 @@
    <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"/>
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 @@
 			<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" />
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 @@
     <li><strong>Defining a reference when importing
         annotation</strong><br />Jalview automatically assigns a reference
       sequence when importing analysis results, such as those returned
-      from <a href="../webServices/jnet.html">JPred4</a> . A reference
+      from <a href="../webServices/jnet.html">JPred</a> . A reference
       sequence can also be assigned via the <a
       href="../features/annotationsFormat.html#refsandviews">SET_REF</a>
       command in an alignment annotation file.</li>
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 167cb25..51ad601 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -638,22 +638,22 @@
         <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>
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 @@
       <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> client
+            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 detection
+                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>
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.
  -->
 <head>
-<title>JNet Secondary Structure Prediction</title>
+<title>JPred Secondary Structure Prediction</title>
 </head>
 <body>
-  <strong>JNet Secondary Structure Prediction</strong>
+  <strong>JPred Secondary Structure Prediction</strong>
   <p>
     Secondary structure prediction methods attempts to infer the likely
     secondary structure for a protein based on its amino acid
@@ -52,35 +52,35 @@
   </p>
   The function available from the
   <strong>Web Service&#8594;Secondary Structure
-    Prediction&#8594;JNet Secondary Structure Prediction</strong> menu does two
+    Prediction&#8594;JPred Secondary Structure Prediction</strong> menu does two
   different kinds of prediction, dependent upon the currently selected
   region:
   </p>
   <ul>
     <li>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.</li>
     <li>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.</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
+      aligned, then the alignment will be used for a JPred prediction on
       the <strong>first</strong> sequence selected in the set (that is,
       the one nearest the top of the alignment window).
     </li>
   </ul>
   <p>
-    <strong>Note</strong>: JNet secondary structure prediction is a
+    <strong>Note</strong>: 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
     <a href="../features/hiddenRegions.html">hiding columns</a>) 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).
   </p>
-  <p>The result of a JNet prediction for a sequence is a new
+  <p>The result of a JPred prediction for a sequence is a new
     annotated alignment window:</p>
   <img src="jnetprediction.gif">
   <p>The sequence for which the prediction was made is the first one
@@ -124,12 +124,12 @@
         significantly different primary predictions.</em></li>
   </ul>
   </p>
-  <em>JNet annotation created in Jalview 2.8.2 and later versions
+  <em>JPred annotation created in Jalview 2.8.2 and later versions
     can be displayed on other alignments via the <a
     href="../features/annotation.html#seqannots">Add reference
       annotation</a> Sequence ID popup menu option.
   </em>
-  <em>As of Jalview 2.6, the Jnet service accessed accessed via the
+  <em>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.</em>
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 f830fe6..175b171 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1480,10 +1480,13 @@ 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 9fd8a90..de011ea 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2255,6 +2255,11 @@ 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 7258f51..ba4054e 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -222,7 +222,7 @@ 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);
diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 2c05386..65847e6 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