*/
package jalview.ws.rest;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
{
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
- restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()),
+ restClient._input.getVisibleAlignment(
+ restClient.service.getGapCharacter()),
restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
{
int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
- .getVisibleContigAlignments(restClient.service
- .getGapCharacter());
+ .getVisibleContigAlignments(
+ restClient.service.getGapCharacter());
if (viscontigals != null && viscontigals.length > 0)
{
jobs = new RestJob[viscontigals.length];
{
if (input.getValue().validFor(rj))
{
- postentity.addPart(input.getKey(), input.getValue()
- .formatForInput(rj));
+ postentity.addPart(input.getKey(),
+ input.getValue().formatForInput(rj));
}
else
{
markAsFailed(rj, response);
completeStatus(rj, response, "" + getStage(stg)
+ "failed. Reason below:\n");
-
break;
default:
// Some other response. Probably need to pop up the content in a window.
rj.setSubmitted(true);
try
{
- completeStatus(
- rj,
- response,
- ""
- + getStage(stg)
- + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
- + request.getURI()
- + "\">"
- + request.getURI()
- + "</a><br/>Filtered response content below:<br/>");
+ completeStatus(rj, response, "" + getStage(stg)
+ + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
+ + request.getURI() + "\">" + request.getURI()
+ + "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
Cache.log.debug("IOException when consuming unhandled response",
*/
String f;
StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
- f = f.toLowerCase();
+ f = f.toLowerCase(Locale.ROOT);
int body = f.indexOf("<body");
if (body > -1)
{
} catch (Error ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
rj.error = true;
rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
- + rj.resSet.getUrl()
- + "\">"
- + rj.resSet.getUrl()
+ + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl()
+ "</a><br>";
}
}
/**
* alignment panels derived from each alignment set returned by service.
*/
- ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
+ ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<>();
/**
* list of instructions for how to process each distinct alignment set
* returned by the job set
*/
- ArrayList<AddDataTo> resultDest = new ArrayList<AddDataTo>();
+ ArrayList<AddDataTo> resultDest = new ArrayList<>();
/**
* when false, zeroth pane is panel derived from input deta.
*/
boolean vsepjobs = restClient.service.isVseparable();
// total number of distinct alignment sets generated by job set.
int numAlSets = 0, als = 0;
- List<AlignmentI> destAls = new ArrayList<AlignmentI>();
- List<jalview.datamodel.ColumnSelection> destColsel = new ArrayList<jalview.datamodel.ColumnSelection>();
- List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
+ List<AlignmentI> destAls = new ArrayList<>();
+ List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<>();
+ List<List<NewickFile>> trees = new ArrayList<>();
do
{
if (alset.trees != null)
{
- trees.add(new ArrayList<NewickFile>(alset.trees));
+ trees.add(new ArrayList<>(alset.trees));
}
else
{
*/
int vrestjob = 0;
// Destination alignments for all result data.
- ArrayList<SequenceGroup> visgrps = new ArrayList<SequenceGroup>();
- Hashtable<String, SequenceGroup> groupNames = new Hashtable<String, SequenceGroup>();
+ ArrayList<SequenceGroup> visgrps = new ArrayList<>();
+ Hashtable<String, SequenceGroup> groupNames = new Hashtable<>();
ArrayList<AlignmentAnnotation> visAlAn = null;
for (nvertsep = 0; nvertsep < nvertseps; nvertsep++)
{
RestJob rj = (RestJob) jobs[nrj];
int contigs[] = input.getVisibleContigs();
AlignmentI destAl = null;
- jalview.datamodel.ColumnSelection destCs = null;
+ jalview.datamodel.HiddenColumns destHCs = null;
// Resolve destAl for this data.
if (als == 0 && rj.isInputContextModified())
{
if (!restClient.isAlignmentModified() && merge)
{
destAl = restClient.av.getAlignment();
- destCs = restClient.av.getColumnSelection();
- resultDest
- .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
- : AddDataTo.currentView);
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
+ resultDest.add(restClient.isShowResultsInNewView()
+ ? AddDataTo.newView
+ : AddDataTo.currentView);
destPanels.add(restClient.recoverAlignPanelForView());
}
else
newAlignment = true;
// recreate the input alignment data
Object[] idat = input
- .getAlignmentAndColumnSelection(gapCharacter);
+ .getAlignmentAndHiddenColumns(gapCharacter);
destAl = new Alignment((SequenceI[]) idat[0]);
- destCs = (ColumnSelection) idat[1];
+ destHCs = (HiddenColumns) idat[1];
resultDest.add(AddDataTo.newAlignment);
// but do not add to the alignment panel list - since we need to
// create a whole new alignFrame set.
}
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
}
}
else
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log
- .warn("dealing with multiple alignment products returned by non-vertically separable service.");
+ Cache.log.warn(
+ "dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
// ready for extension
destAl = destAls.get(als);
- destCs = destColsel.get(als);
+ destHCs = destColsel.get(als);
}
else
{
newview = input.getUpdatedView(rseqs, orders, gapCharacter);
}
destAl = new Alignment((SequenceI[]) newview[0]);
- destCs = (ColumnSelection) newview[1];
+ destHCs = (HiddenColumns) newview[1];
newAlignment = true;
// TODO create alignment from result data with propagated
// references.
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
resultDest.add(AddDataTo.newAlignment);
throw new Error(
- MessageManager
- .getString("error.implementation_error")
+ MessageManager.getString("error.implementation_error")
+ "TODO: ");
}
}
}
else
{
- Cache.log
- .warn("Couldn't resolve original sequence for new sequence.");
+ Cache.log.warn(
+ "Couldn't resolve original sequence for new sequence.");
}
}
if (sg.hasSeqrep())
{
// adjust boundaries of recovered group w.r.t. new group being
// merged on to original alignment.
- int start = sg.getStartRes() + contigs[ncnt], end = sg
- .getEndRes() + contigs[ncnt];
+ int start = sg.getStartRes() + contigs[ncnt],
+ end = sg.getEndRes() + contigs[ncnt];
if (start < exsg.getStartRes())
{
exsg.setStartRes(start);
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log
- .error("Couldn't relocate group referemce for group "
+ Cache.log.error(
+ "Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
}
if (visAlAn == null)
{
- visAlAn = new ArrayList<AlignmentAnnotation>();
+ visAlAn = new ArrayList<>();
}
AlignmentAnnotation visan = null;
for (AlignmentAnnotation v : visAlAn)
visan.sequenceRef = sqass;
visAlAn.add(visan);
}
- if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
+ if (contigs[ncnt]
+ + alan[nrj][an].annotations.length > visan.annotations.length)
{
// increase width of annotation row
Annotation[] newannv = new Annotation[contigs[ncnt]
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log
- .error("Tree recovery from restjob not yet implemented.");
+ Cache.log.error(
+ "Tree recovery from restjob not yet implemented.");
}
}
}
for (AddDataTo action : resultDest)
{
AlignmentI destal;
- ColumnSelection destcs;
- String alTitle = MessageManager.formatMessage(
- "label.webservice_job_title_on", new String[] {
- restClient.service.details.Action,
- restClient.service.details.Name, restClient.viewTitle });
+ HiddenColumns destcs;
+ String alTitle = MessageManager
+ .formatMessage("label.webservice_job_title_on", new String[]
+ { restClient.service.details.getAction(),
+ restClient.service.details.getName(),
+ restClient.viewTitle });
switch (action)
{
case newAlignment:
destcs = destColsel.get(als);
destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- PaintRefresher.Refresh(destaf, destaf.getViewport()
- .getSequenceSetId());
+ PaintRefresher.Refresh(destaf,
+ destaf.getViewport().getSequenceSetId());
// todo transfer any feature settings and colouring
/*
* destaf.getFeatureRenderer().transferSettings(this.featureSettings);
{
if (start + width < end)
{
- blocks[c][s] = sequenceIs[s].getSubSequence(start, start
- + width);
+ blocks[c][s] = sequenceIs[s].getSubSequence(start,
+ start + width);
}
else
{
*/
public boolean isValid()
{
- ArrayList<String> _warnings = new ArrayList<String>();
+ ArrayList<String> _warnings = new ArrayList<>();
boolean validt = true;
if (jobs != null)
{
git://source.jalview.org / jalview.git / blobdiff