final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(service.details.Action+" using "+service.details.Name);
+ submit.setToolTipText(service.details.Action + " using "
+ + service.details.Name);
submit.addActionListener(new ActionListener()
{
*/
protected boolean isAlignmentModified()
{
- if (undoredo == null || av==null || av.getAlignment()==null)
+ if (undoredo == null || av == null || av.getAlignment() == null)
{
- // always return modified if we don't have access to live GUI elements anymore.
+ // always return modified if we don't have access to live GUI elements
+ // anymore.
return true;
}
if (av.isUndoRedoHashModified(undoredo))
{
- // alignment has been modified in some way.
+ // alignment has been modified in some way.
return true;
}
- // TODO: look deeper into modification of selection state, etc that may affect RestJobThread.realiseResults(boolean merge);
+ // TODO: look deeper into modification of selection state, etc that may
+ // affect RestJobThread.realiseResults(boolean merge);
return false;
}
*/
boolean selExists = (av.getSelectionGroup() != null)
&& (av.getSelectionGroup().getSize() > 1);
- // TODO: JAL-715: refactor to alignViewport methods and revise to full focus+context+dataset input data staging model
+ // TODO: JAL-715: refactor to alignViewport methods and revise to full
+ // focus+context+dataset input data staging model
if (selExists)
{
if (service.partitiondata)
{
- if (av.getAlignment().getGroups()!=null && av.getAlignment().getGroups().size() > 0)
+ if (av.getAlignment().getGroups() != null
+ && av.getAlignment().getGroups().size() > 0)
{
// intersect groups with selected region
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- av.getSelectionGroup(),
- av.hasHiddenColumns(),
- true,
- true);
- viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
+ _input = new AlignmentView(av.getAlignment(),
+ av.getColumnSelection(), av.getSelectionGroup(),
+ av.hasHiddenColumns(), true, true);
+ viewTitle = "selected "
+ + (av.hasHiddenColumns() ? "visible" : "")
+ + " region of " + af.getTitle();
}
else
{
// use selected region to partition alignment
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- av.getSelectionGroup(),
- av.hasHiddenColumns(),
- false,
- true);
+ _input = new AlignmentView(av.getAlignment(),
+ av.getColumnSelection(), av.getSelectionGroup(),
+ av.hasHiddenColumns(), false, true);
}
- viewTitle = "select and unselected "+(av.hasHiddenColumns() ? "visible" : "") + " regions from "+af.getTitle();
+ viewTitle = "select and unselected "
+ + (av.hasHiddenColumns() ? "visible" : "")
+ + " regions from " + af.getTitle();
}
else
{
// just take selected region intersection
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- av.getSelectionGroup(),
- av.hasHiddenColumns(),
- true,
- true);
- viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle();
+ _input = new AlignmentView(av.getAlignment(),
+ av.getColumnSelection(), av.getSelectionGroup(),
+ av.hasHiddenColumns(), true, true);
+ viewTitle = "selected " + (av.hasHiddenColumns() ? "visible" : "")
+ + " region of " + af.getTitle();
}
- } else {
+ }
+ else
+ {
// standard alignment view without selection present
- _input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(),
- null,
- av.hasHiddenColumns(),
- false,
+ _input = new AlignmentView(av.getAlignment(),
+ av.getColumnSelection(), null, av.hasHiddenColumns(), false,
true);
- viewTitle = ""+(av.hasHiddenColumns() ? "visible region of " : "") + af.getTitle();
+ viewTitle = "" + (av.hasHiddenColumns() ? "visible region of " : "")
+ + af.getTitle();
}
-
+
RestJobThread jobsthread = new RestJobThread(this);
-
+
if (jobsthread.isValid())
{
setWebserviceInfo(false);
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane.showMessageDialog(Desktop.desktop,
- (jobsthread.hasWarnings() ? jobsthread.getWarnings() : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
- "Unable to start web service analysis", JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings()
+ : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."),
+ "Unable to start web service analysis",
+ JOptionPane.WARNING_MESSAGE);
}
}
String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
jalview.ws.rest.params.JobConstant toolp;
- //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- //iparams.put(toolp.token, toolp);
- //toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- //iparams.put(toolp.token, toolp);
- //toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- //iparams.put(toolp.token, toolp);
- //toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- //iparams.put(toolp.token, toolp);
- //toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- //iparams.put(toolp.token, toolp);
-
+ // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new
+ // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
+ // iparams.put(toolp.token, toolp);
+
jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter, so we always upload our files.
+ // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
+ // so we always upload our files.
aliinput.token = "ali_file";
- aliinput.writeAsFile=true;
+ aliinput.writeAsFile = true;
iparams.put(aliinput.token, aliinput);
jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
sgroups.setMinsize(2);
- sgroups.min=2;// need at least two group defined to make a partition
+ sgroups.min = 2;// need at least two group defined to make a partition
iparams.put("groups", sgroups);
sgroups.token = "groups";
sgroups.sep = " ";
public AlignmentPanel recoverAlignPanelForView()
{
- AlignmentPanel[] aps = Desktop.getAlignmentPanels(av.getSequenceSetId());
- for (AlignmentPanel alp:aps)
+ AlignmentPanel[] aps = Desktop
+ .getAlignmentPanels(av.getSequenceSetId());
+ for (AlignmentPanel alp : aps)
{
if (alp.av == av)
{
return true;
}
- protected static Vector<String> services=null;
- public static final String RSBS_SERVICES="RSBS_SERVICES";
+ protected static Vector<String> services = null;
+
+ public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
public static RestClient[] getRestClients()
{
- if (services==null)
+ if (services == null)
{
services = new Vector<String>();
- try {
- for (RestServiceDescription descr: RestServiceDescription.parseDescriptions(jalview.bin.Cache.getDefault(RSBS_SERVICES,makeShmmrRestClient().service.toString())))
+ try
{
- services.add(descr.toString());
- }
- }
- catch (Exception ex) {
- System.err.println("Serious - RSBS descriptions in user preferences are corrupt!");
+ for (RestServiceDescription descr : RestServiceDescription
+ .parseDescriptions(jalview.bin.Cache.getDefault(
+ RSBS_SERVICES,
+ makeShmmrRestClient().service.toString())))
+ {
+ services.add(descr.toString());
+ }
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Serious - RSBS descriptions in user preferences are corrupt!");
ex.printStackTrace();
}
-
+
}
RestClient[] lst = new RestClient[services.size()];
- int i=0;
- for (String svc:services) {
+ int i = 0;
+ for (String svc : services)
+ {
lst[i++] = new RestClient(new RestServiceDescription(svc));
}
return lst;
}
+
public static void main(String args[])
{
- try {
+ try
+ {
RestClient[] clients = getRestClients();
- System.out.println("Got "+clients.length+" clients.");
- int i=0;
- Vector<String> urls=new Vector<String>();
- for (RestClient cl:clients) {
- System.out.println(""+(++i)+": "+cl.service.toString());
+ System.out.println("Got " + clients.length + " clients.");
+ int i = 0;
+ Vector<String> urls = new Vector<String>();
+ for (RestClient cl : clients)
+ {
+ System.out.println("" + (++i) + ": " + cl.service.toString());
urls.add(cl.service.toString());
}
setRsbsServices(urls);
- if (clients.length!=getRestClients().length)
+ if (clients.length != getRestClients().length)
{
- System.err.println("Failed. Differing numbers of clients when stringified and parsed again.");
+ System.err
+ .println("Failed. Differing numbers of clients when stringified and parsed again.");
}
-
+
} catch (Throwable x)
{
System.err.println("Failed. Unexpected exception.");
x.printStackTrace();
}
}
+
public String getAction()
{
return service.details.Action;
public static Vector<String> getRsbsDescriptions()
{
Vector<String> rsbsDescrs = new Vector<String>();
- for (RestClient rsbs:getRestClients())
+ for (RestClient rsbs : getRestClients())
{
rsbsDescrs.add(rsbs.getRestDescription().toString());
}
public static void setRsbsServices(Vector<String> rsbsUrls)
{
- if (rsbsUrls!=null)
+ if (rsbsUrls != null)
{
// TODO: consider validating services ?
services = new Vector<String>(rsbsUrls);
StringBuffer sprop = new StringBuffer();
- for (String s:services)
+ for (String s : services)
{
sprop.append(s);
}
Cache.setProperty(RSBS_SERVICES, sprop.toString());
- }
+ }
else
{
Cache.removeProperty(RSBS_SERVICES);
git://source.jalview.org / jalview.git / blobdiff