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relaxed ID matching parameter JAL-753 and sortBy JAL-754
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
MsaWSClient.java
diff --git
a/src/jalview/ws/jws2/MsaWSClient.java
b/src/jalview/ws/jws2/MsaWSClient.java
index
2453ac0
..
8a352bf
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSClient.java
+++ b/
src/jalview/ws/jws2/MsaWSClient.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-50,7
+50,7
@@
public class MsaWSClient extends Jws2Client
AlignFrame alignFrame;
AlignFrame alignFrame;
- private Preset preset;
+ private WsParamSetI preset;
private List<Argument> paramset;
private List<Argument> paramset;
@@
-112,10
+112,11
@@
public class MsaWSClient extends Jws2Client
return;
}
server = sh.service;
return;
}
server = sh.service;
+ this.preset=preset;
if (preset != null)
{
if (preset != null)
{
- if (preset instanceof JabaPreset)
- {
+ if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
+ /*{
this.preset = ((JabaPreset) preset).p;
}
else if (preset instanceof JabaWsParamSet)
this.preset = ((JabaPreset) preset).p;
}
else if (preset instanceof JabaWsParamSet)
@@
-137,7
+138,7
@@
public class MsaWSClient extends Jws2Client
paramset = newargs;
}
else
paramset = newargs;
}
else
- {
+ {*/
throw new Error(
"Implementation error: Can only instantiate Jaba parameter sets.");
}
throw new Error(
"Implementation error: Can only instantiate Jaba parameter sets.");
}
@@
-167,7
+168,7
@@
public class MsaWSClient extends Jws2Client
}
else
{
}
else
{
- this.preset = ((JabaPreset) prset).p;
+ this.preset = prset; // ((JabaPreset) prset).p;
paramset = null; // no user supplied parameters.
}
}
paramset = null; // no user supplied parameters.
}
}
@@
-274,15
+275,19
@@
public class MsaWSClient extends Jws2Client
boolean hasparams = service.hasParameters();
do
{
boolean hasparams = service.hasParameters();
do
{
+ String action = "Align ";
if (submitGaps == true)
{
if (submitGaps == true)
{
- msawsmenu = new JMenu("profile " + svcname);
+ action = "Realign ";
+ msawsmenu = new JMenu("Realign with " + svcname);
+ msawsmenu
+ .setToolTipText("Align sequences to an existing alignment");
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
- JMenuItem method = new JMenuItem(calcName + "Defaults");
- method.setToolTipText("Align with default settings");
+ JMenuItem method = new JMenuItem(calcName + "with Defaults");
+ method.setToolTipText(action + "with default settings");
method.addActionListener(new ActionListener()
{
method.addActionListener(new ActionListener()
{
@@
-298,8
+303,9
@@
public class MsaWSClient extends Jws2Client
msawsmenu.add(method);
if (hasparams)
{
msawsmenu.add(method);
if (hasparams)
{
- // only add these menu options if the service has user-modifiable arguments
- method = new JMenuItem(calcName + "Edit and run ...");
+ // only add these menu options if the service has user-modifiable
+ // arguments
+ method = new JMenuItem("Edit settings and run ...");
method.setToolTipText("View and change the parameters before alignment.");
method.addActionListener(new ActionListener()
method.setToolTipText("View and change the parameters before alignment.");
method.addActionListener(new ActionListener()
@@
-317,7
+323,7
@@
public class MsaWSClient extends Jws2Client
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(calcName + "Presets");
+ JMenu presetlist = new JMenu("Run "+calcName + "with preset");
for (final WsParamSetI preset : presets)
{
for (final WsParamSetI preset : presets)
{