<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>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>
</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>
<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"/>
<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" />
<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>
<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>
<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>
* 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
</p>
The function available from the
<strong>Web Service→Secondary Structure
- Prediction→JNet Secondary Structure Prediction</strong> menu does two
+ Prediction→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
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>
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.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}
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.CollectionColourScheme;
+import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.JalviewColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
MenuItem editGroupName = new MenuItem();
- protected MenuItem clustalColour = new MenuItem();
+ CheckboxMenuItem noColour = new CheckboxMenuItem();
- protected MenuItem zappoColour = new MenuItem();
+ protected CheckboxMenuItem clustalColour = new CheckboxMenuItem();
- protected MenuItem taylorColour = new MenuItem();
+ protected CheckboxMenuItem zappoColour = new CheckboxMenuItem();
- protected MenuItem hydrophobicityColour = new MenuItem();
+ protected CheckboxMenuItem taylorColour = new CheckboxMenuItem();
- protected MenuItem helixColour = new MenuItem();
+ protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem();
- protected MenuItem strandColour = new MenuItem();
+ protected CheckboxMenuItem helixColour = new CheckboxMenuItem();
- protected MenuItem turnColour = new MenuItem();
+ protected CheckboxMenuItem strandColour = new CheckboxMenuItem();
- protected MenuItem buriedColour = new MenuItem();
+ protected CheckboxMenuItem turnColour = new CheckboxMenuItem();
- protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
- protected MenuItem userDefinedColour = new MenuItem();
+ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
- protected MenuItem PIDColour = new MenuItem();
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
- MenuItem noColourmenuItem = new MenuItem();
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ protected MenuItem userDefinedColour = new MenuItem();
+
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
final AlignmentPanel ap;
MenuItem createGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
-
- MenuItem purinePyrimidineMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
{
menu1.setLabel(MessageManager.getString("action.edit_group"));
groupMenu.remove(createGroupMenuItem);
+ if (sg.cs != null)
+ {
+ abovePIDColour.setState(sg.cs.getThreshold() > 0);
+ conservationColour.setState(sg.cs.conservationApplied());
+ }
}
-
+ setSelectedColour(sg.cs);
}
else
{
}
/**
+ * Select the menu item (if any) matching the current colour scheme. This
+ * works by matching the menu item name (not display text) to the canonical
+ * name of the colour scheme.
+ *
+ * @param cs
+ */
+ protected void setSelectedColour(CollectionColourSchemeI cs)
+ {
+ if (cs == null || cs.getColourScheme() == null)
+ {
+ noColour.setState(true);
+ }
+ else
+ {
+ String name = cs.getColourScheme().getSchemeName();
+ for (int i = 0; i < colourMenu.getItemCount(); i++)
+ {
+ MenuItem item = colourMenu.getItem(i);
+ if (item instanceof CheckboxMenuItem)
+ {
+ if (name.equals(item.getName()))
+ {
+ ((CheckboxMenuItem) item).setState(true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
*
* @param seq
linkMenu.add(item);
}
+ /**
+ * Actions on selecting / unselecting a checkbox menu item
+ */
@Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == abovePIDColour)
- {
- abovePIDColour_itemStateChanged();
- }
- else if (evt.getSource() == showColourText)
- {
- showColourText_itemStateChanged();
- }
- else if (evt.getSource() == showText)
+ Object source = evt.getSource();
+ if (source == noColour)
{
- showText_itemStateChanged();
+ noColourmenuItem_actionPerformed();
}
- else if (evt.getSource() == showBoxes)
+ else if (source == clustalColour)
{
- showBoxes_itemStateChanged();
+ clustalColour_actionPerformed();
}
- else if (evt.getSource() == displayNonconserved)
+ else if (source == BLOSUM62Colour)
{
- this.showNonconserved_itemStateChanged();
+ BLOSUM62Colour_actionPerformed();
}
- }
-
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
- if (source == clustalColour)
+ else if (evt.getSource() == PIDColour)
{
- clustalColour_actionPerformed();
+ PIDColour_actionPerformed();
}
else if (source == zappoColour)
{
{
buriedColour_actionPerformed();
}
- else if (source == nucleotideMenuItem)
+ else if (source == nucleotideColour)
{
nucleotideMenuItem_actionPerformed();
}
- else if (source == purinePyrimidineMenuItem)
+ else if (source == purinePyrimidineColour)
{
purinePyrimidineColour_actionPerformed();
}
-
- else if (source == userDefinedColour)
+ else if (source == abovePIDColour)
{
- userDefinedColour_actionPerformed();
+ abovePIDColour_itemStateChanged();
}
- else if (source == PIDColour)
+ else if (source == conservationColour)
{
- PIDColour_actionPerformed();
+ conservationMenuItem_itemStateChanged();
}
- else if (source == BLOSUM62Colour)
+ else if (source == showColourText)
{
- BLOSUM62Colour_actionPerformed();
+ showColourText_itemStateChanged();
}
- else if (source == noColourmenuItem)
+ else if (source == showText)
{
- noColourmenuItem_actionPerformed();
+ showText_itemStateChanged();
}
- else if (source == conservationMenuItem)
+ else if (source == showBoxes)
{
- conservationMenuItem_itemStateChanged();
+ showBoxes_itemStateChanged();
+ }
+ else if (source == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
+ }
+
+ /**
+ * Actions on clicking a menu item
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+ if (source == userDefinedColour)
+ {
+ userDefinedColour_actionPerformed();
}
else if (source == unGroupMenuItem)
{
groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
- colourMenu.add(noColourmenuItem);
+ colourMenu.add(noColour);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(purinePyrimidineMenuItem);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
+ colourMenu.add(conservationColour);
- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(this);
+ noColour.setLabel(MessageManager.getString("label.none"));
+ noColour.addItemListener(this);
+ /*
+ * setName allows setSelectedColour to do its thing
+ */
clustalColour.setLabel(MessageManager
.getString("label.colourScheme_clustal"));
- clustalColour.addActionListener(this);
+ clustalColour.setName(JalviewColourScheme.Clustal.toString());
+ clustalColour.addItemListener(this);
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
+ BLOSUM62Colour.addItemListener(this);
+ PIDColour.setLabel(MessageManager
+ .getString("label.colourScheme_%_identity"));
+ PIDColour.setName(JalviewColourScheme.PID.toString());
+ PIDColour.addItemListener(this);
zappoColour.setLabel(MessageManager
.getString("label.colourScheme_zappo"));
- zappoColour.addActionListener(this);
+ zappoColour.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
taylorColour.setLabel(MessageManager
.getString("label.colourScheme_taylor"));
- taylorColour.addActionListener(this);
+ taylorColour.setName(JalviewColourScheme.Taylor.toString());
+ taylorColour.addItemListener(this);
hydrophobicityColour.setLabel(MessageManager
.getString("label.colourScheme_hydrophobic"));
- hydrophobicityColour.addActionListener(this);
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
helixColour.setLabel(MessageManager
.getString("label.colourScheme_helix_propensity"));
- helixColour.addActionListener(this);
+ helixColour.setName(JalviewColourScheme.Helix.toString());
+ helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
.getString("label.colourScheme_strand_propensity"));
- strandColour.addActionListener(this);
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
turnColour.setLabel(MessageManager
.getString("label.colourScheme_turn_propensity"));
- turnColour.addActionListener(this);
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
buriedColour.setLabel(MessageManager
.getString("label.colourScheme_buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_threshold"));
+ buriedColour.setName(JalviewColourScheme.Buried.toString());
+ buriedColour.addItemListener(this);
+ nucleotideColour.setLabel(MessageManager
+ .getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
+ nucleotideColour.addItemListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.colourScheme_purine/pyrimidine"));
+ purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
+ .toString());
+ purinePyrimidineColour.addItemListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager
- .getString("label.colourScheme_%_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager
- .getString("label.colourScheme_blosum62"));
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("label.conservation"));
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.colourScheme_nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- purinePyrimidineMenuItem.setLabel(MessageManager
- .getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
+
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
+ conservationColour.setLabel(MessageManager
+ .getString("label.conservation"));
+ conservationColour.addItemListener(this);
editMenu.add(copy);
copy.addActionListener(this);
return;
}
- if (conservationMenuItem.getState())
+ if (conservationColour.getState())
{
- Conservation conservation = Conservation.calculateConservation("Group", sg
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg
.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
.getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
false);
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)
{
boolean result = false;
String param = applet.getParameter("jnetfile");
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = applet.getParameter("jpredfile");
+ }
if (param != null)
{
try
ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
- if (sg.cs != null && sg.cs.conservationApplied())
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
+ "\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);
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
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
siftsDownloadDir.mkdirs();
}
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
}
outputStream.close();
inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+// System.out.println(">>> File downloaded : " + downloadedSiftsFile
+// + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
*/
package jalview.ws.sifts;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
import jalview.api.DBRefEntryI;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
}
@BeforeTest(alwaysRun = true)
- public void setUpSiftsClient() throws SiftsException
+ public void setUpSiftsClient() throws SiftsException, IOException
{
// read test props before manipulating config
Cache.loadProperties("test/jalview/io/testProps.jvprops");
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
- try
- {
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
- + testPDBId + ".pdb", DataSourceType.FILE);
- siftsClient = new SiftsClient(pdbFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
+ + testPDBId + ".pdb", DataSourceType.FILE);
+ siftsClient = new SiftsClient(pdbFile);
}
@AfterTest(alwaysRun = true)
siftsClient = null;
}
- @Test(groups = { "Functional" })
- public void getSIFTsFileTest() throws SiftsException
+ @Test(groups = { "Network" })
+ public void getSIFTsFileTest() throws SiftsException, IOException
{
File siftsFile;
- try
- {
- siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
- FileAssert.assertFile(siftsFile);
- // test for SIFTs file caching
- SiftsSettings.setCacheThresholdInDays("0");
- siftsFile = SiftsClient.getSiftsFile(testPDBId);
- FileAssert.assertFile(siftsFile);
- SiftsSettings.setCacheThresholdInDays("2");
- } catch (IOException e)
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t1 = siftsFile.lastModified();
+
+ // re-read file should be returned from cache
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t2 = siftsFile.lastModified();
+ assertEquals(t1, t2);
+
+ /*
+ * force fetch by having 0 expiry of cache
+ * also wait one second, because file timestamp does not
+ * give millisecond resolution :-(
+ */
+ synchronized (this)
{
- e.printStackTrace();
+ try
+ {
+ wait(1000);
+ } catch (InterruptedException e)
+ {
+ }
}
+ SiftsSettings.setCacheThresholdInDays("0");
+ siftsFile = SiftsClient.getSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t3 = siftsFile.lastModified();
+ assertTrue(t3 > t2, "file timestamp unchanged at " + t3);
+
+ SiftsSettings.setCacheThresholdInDays("2");
}
- @Test(groups = { "Functional" })
- public void downloadSiftsFileTest() throws SiftsException
+ @Test(groups = { "Network" })
+ public void downloadSiftsFileTest() throws SiftsException, IOException
{
// Assert that file isn't yet downloaded - if already downloaded, assert it
// is deleted
Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
File siftsFile;
- try
- {
- siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
- FileAssert.assertFile(siftsFile);
- SiftsClient.downloadSiftsFile(testPDBId);
- } catch (IOException e)
- {
- e.printStackTrace();
- }
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ SiftsClient.downloadSiftsFile(testPDBId);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getAllMappingAccessionTest()
{
Assert.assertNotNull(siftsClient);
Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getGreedyMappingTest()
{
Assert.assertNotNull(siftsClient);
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
private void getAtomIndexTest()
{
ArrayList<Atom> atoms = new ArrayList<Atom>();
}
@Test(
- groups = { "Functional" },
+ groups = { "Network" },
expectedExceptions = IllegalArgumentException.class)
private void getAtomIndexNullTest()
{
siftsClient.getAtomIndex(1, null);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
private void padWithGapsTest()
{
}
@Test(
- groups = { "Functional" },
+groups = { "Network" },
expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest1()
throws IllegalArgumentException, SiftsException
}
@Test(
- groups = { "Functional" },
+groups = { "Network" },
expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest2()
throws IllegalArgumentException, SiftsException
siftsClient.populateAtomPositions("A", null);
}
- @Test(groups = { "Functional" })
- public void getValidSourceDBRefTest()
+ @Test(groups = { "Network" })
+ public void getValidSourceDBRefTest() throws SiftsException
{
- try
- {
- DBRefEntryI actualValidSrcDBRef = siftsClient
- .getValidSourceDBRef(testSeq);
- DBRefEntryI expectedDBRef = new DBRefEntry();
- expectedDBRef.setSource(DBRefSource.UNIPROT);
- expectedDBRef.setAccessionId("P00221");
- expectedDBRef.setVersion("");
- Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
- } catch (Exception e)
- {
- }
+ DBRefEntryI actualValidSrcDBRef = siftsClient
+ .getValidSourceDBRef(testSeq);
+ DBRefEntryI expectedDBRef = new DBRefEntry();
+ expectedDBRef.setSource(DBRefSource.UNIPROT);
+ expectedDBRef.setAccessionId("P00221");
+ expectedDBRef.setVersion("");
+ Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
}
@Test(
- groups = { "Functional" },
+groups = { "Network" },
expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionTest() throws SiftsException
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
- try
- {
- siftsClient.getValidSourceDBRef(invalidTestSeq);
- } catch (SiftsException e)
- {
- throw new SiftsException(e.getMessage());
- }
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
}
@Test(
- groups = { "Functional" },
+groups = { "Network" },
expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionXTest() throws SiftsException
{
DBRefEntry invalidDBRef = new DBRefEntry();
invalidDBRef.setAccessionId("BLAR");
invalidTestSeq.addDBRef(invalidDBRef);
- try
- {
- siftsClient.getValidSourceDBRef(invalidTestSeq);
- } catch (SiftsException e)
- {
- throw new SiftsException(e.getMessage());
- }
-
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void isValidDBRefEntryTest()
{
DBRefEntryI validDBRef = new DBRefEntry();
Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
}
- @Test(groups = { "Functional" })
- public void getSiftsStructureMappingTest()
+ @Test(groups = { "Network" })
+ public void getSiftsStructureMappingTest() throws SiftsException
{
- try
- {
- Assert.assertTrue(SiftsSettings.isMapWithSifts());
- StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
- testSeq, testPDBId, "A");
- String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
- + "Method: SIFTS\n\n"
- + "P00221 : 51 - 147 Maps to \n"
- + "1A70|A : 1 - 97\n\n"
- + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
- + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
- + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
-
- + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
- + " |||||||||||||||||||||||||| |||||\n"
- + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
-
- "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
-
- Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
- expectedMappingOutput);
- Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
- } catch (SiftsException e)
- {
- e.printStackTrace();
- }
+ Assert.assertTrue(SiftsSettings.isMapWithSifts());
+ StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
+ testSeq, testPDBId, "A");
+ String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
+ + "Method: SIFTS\n\n"
+ + "P00221 : 51 - 147 Maps to \n"
+ + "1A70|A : 1 - 97\n\n"
+ + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
+ + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
+ + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
+
+ + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
+ + " |||||||||||||||||||||||||| |||||\n"
+ + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
+
+ "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
+
+ Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
+ expectedMappingOutput);
+ Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getEntityCountTest()
{
int actualEntityCount = siftsClient.getEntityCount();
Assert.assertEquals(actualEntityCount, 1);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getDbAccessionIdTest()
{
String actualDbAccId = siftsClient.getDbAccessionId();
Assert.assertEquals(actualDbAccId, "1a70");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getDbCoordSysTest()
{
String actualDbCoordSys = siftsClient.getDbCoordSys();
Assert.assertEquals(actualDbCoordSys, "PDBe");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getDbSourceTest()
{
String actualDbSource = siftsClient.getDbSource();
Assert.assertEquals(actualDbSource, "PDBe");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getDbVersionTest()
{
String actualDbVersion = siftsClient.getDbVersion();
Assert.assertEquals(actualDbVersion, "2.0");
}
- @Test(groups = { "Functional" })
- public void getEntityByMostOptimalMatchedIdTest1()
+ @Test(groups = { "Network" })
+ public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
+ SiftsException
{
SiftsClient siftsClientX = null;
PDBfile pdbFile;
- try
- {
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
- + ".pdb", DataSourceType.FILE);
- siftsClientX = new SiftsClient(pdbFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
+ + ".pdb", DataSourceType.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
Assert.assertEquals(entityA.getEntityId(), "A");
Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
}
- @Test(groups = { "Functional" })
- public void getEntityByMostOptimalMatchedIdTest2()
+ @Test(groups = { "Network" })
+ public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
+ SiftsException
{
// This test is for a SIFTS file in which entity A should map to chain P for
// the given PDB Id. All the other chains shouldn't be mapped as there are
// no SIFTS entity records for them.
SiftsClient siftsClientX = null;
PDBfile pdbFile;
- try
- {
- pdbFile = new PDBfile(false, false, false,
- "test/jalview/io/3ucu.cif", DataSourceType.FILE);
- siftsClientX = new SiftsClient(pdbFile);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif",
+ DataSourceType.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
git://source.jalview.org / jalview.git / commitdiff