/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.SplitFrame;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
-import java.util.Map;
import java.util.Vector;
+import javax.swing.JInternalFrame;
+
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
{
long lastChunk = 0;
- WsParamSetI preset = null;
-
- List<Argument> arguments = null;
-
/**
* input
*/
- ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+ ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
/**
* output
}
- Hashtable<String, Map> SeqNames = new Hashtable();
-
Vector<String[]> emptySeqs = new Vector();
/**
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
compbio.data.sequence.FastaSequence seq;
for (int i = 0, n = 0; i < seqs.length; i++)
{
-
String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
// for
// any
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
- emptySeqs.add(new String[]
- { newname, empty });
+ emptySeqs.add(new String[] { newname, empty });
}
}
return valid;
*
* @return true if getAlignment will return a valid alignment result.
*/
+ @Override
public boolean hasResults()
{
- if (subjobComplete
- && isFinished()
- && (alignment != null || (emptySeqs != null && emptySeqs
- .size() > 0)))
+ if (subjobComplete && isFinished() && (alignment != null
+ || (emptySeqs != null && emptySeqs.size() > 0)))
{
return true;
}
for (compbio.data.sequence.FastaSequence seq : alignment
.getSequences())
{
- alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
+ alseqs[alseq_l++] = new Sequence(seq.getId(),
+ seq.getSequence());
}
alseq_gapchar = alignment.getMetadata().getGapchar();
jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
// account for any missing sequences
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[]
- { alseqs, msaorder };
+ return new Object[] { alseqs, msaorder };
}
return null;
}
*
* @return boolean true if job can be submitted.
*/
+ @Override
public boolean hasValidInput()
{
// TODO: get attributes for this MsaWS instance to check if it can do two
public List<Argument> getJabaArguments()
{
- List<Argument> newargs = new ArrayList<Argument>();
+ List<Argument> newargs = new ArrayList<>();
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
}
if (arguments != null && arguments.size() > 0)
{
- newargs.addAll(arguments);
+ newargs.addAll(JabaParamStore.getJabafromJwsArgs(arguments));
}
return newargs;
}
+ "Preset: " + preset.getName());
if (preset instanceof JabaWsParamSet)
{
- for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+ for (Argument opt : getJabaArguments())
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
}
{
jobProgress.append("With custom parameters : \n");
// merge arguments with preset's own arguments.
- for (Argument opt : arguments)
+ for (Argument opt : getJabaArguments())
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
jobProgress.append("\nJob Output:\n");
String alTitle; // name which will be used to form new alignment window.
- Alignment dataset; // dataset to which the new alignment will be
+ AlignmentI dataset; // dataset to which the new alignment will be
// associated.
* @param presorder
* boolean
*/
- MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
+ private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, AlignmentView alview,
String wsname, boolean subgaps, boolean presorder)
{
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
+ MsaWSThread(MsaWS server2, WsParamSetI preset, List<ArgumentI> paramset,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
- Alignment seqset)
+ AlignmentI seqset)
{
this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
OutputHeader = wsInfo.getProgressText();
if (conmsa != null)
{
int nvalid = 0, njobs = conmsa.length;
- jobs = new MsaWSJob[njobs];
+ jobs = new AWsJob[njobs];
for (int j = 0; j < njobs; j++)
{
if (j != 0)
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
- if (((MsaWSJob) jobs[j]).hasValidInput())
+ if (jobs[j].hasValidInput())
{
nvalid++;
}
- ((MsaWSJob) jobs[j]).preset = preset;
- ((MsaWSJob) jobs[j]).arguments = paramset;
+ jobs[j].setPreset(preset);
+ jobs[j].setArguments(paramset);
((MsaWSJob) jobs[j]).alignmentProgram = wsname;
if (njobs > 0)
{
{
return validInput;
}
+
+ @Override
public boolean isCancellable()
{
return true;
}
+ @Override
public void cancelJob()
{
if (!jobComplete && jobs != null)
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
else
{
}
}
+ @Override
public void pollJob(AWsJob job) throws Exception
{
// TODO: investigate if we still need to cast here in J1.6
do
{
j.setLastChunk(lastchunk);
- ChunkHolder chunk = server
- .pullExecStatistics(j.getJobId(), lastchunk);
+ ChunkHolder chunk = server.pullExecStatistics(j.getJobId(),
+ lastchunk);
if (chunk != null)
{
changed |= chunk.getChunk().length() > 0;
return changed;
}
+ @Override
public void StartJob(AWsJob job)
{
Exception lex = null;
// boiler plate template
if (!(job instanceof MsaWSJob))
{
- throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Cache.log.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
}
else
{
- throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.web_service_returned_null_try_later",
+ new String[]
+ { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_server_doesnt_support_program",
+ new String[]
+ { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (compbio.metadata.LimitExceededException _lex)
{
lex = _lex;
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
+ { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (compbio.metadata.WrongParameterException _lex)
{
lex = _lex;
- wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
- wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_incorrect_param_setting",
+ new String[]
+ { _lex.getMessage() }));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
} catch (Exception e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
// TODO: JBPNote catch timeout or other fault types explicitly
j.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(j.getJobnum(),
- MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString(
+ "info.failed_to_submit_sequences_for_alignment"));
}
}
}
+ @Override
public void parseResult()
{
long progbar = System.currentTimeMillis();
- wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
+ wsInfo.setProgressBar(
+ MessageManager.getString("status.collecting_job_results"),
+ progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
} catch (Exception e)
{
- Cache.log
- .warn("Exception when retrieving remaining Job progress data for job "
+ Cache.log.warn(
+ "Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
nexcept--;
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log
- .debug("Results not available for finished job - marking as broken job.",
- e);
- msjob.jobProgress
- .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ Cache.log.debug(
+ "Results not available for finished job - marking as broken job.",
+ e);
+ msjob.jobProgress.append(
+ "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
// wsInfo.appendProgressText(jobs[j].getJobnum(),
// "\nAlignment Object Method Notes\n");
// wsInfo.appendProgressText(jobs[j].getJobnum(),
- // "Calculated with "+alignment.getMetadata().getProgram().toString());
+ // "Calculated with
+ // "+alignment.getMetadata().getProgram().toString());
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
// when clicked, pop up their corresponding data
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + alTitle, ex);
+ Cache.log.error(
+ "Unexpected exception when processing results for " + alTitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
wsInfo.showResultsNewFrame
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(true);
wsInfo.mergeResults
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(java.awt.event.ActionEvent evt)
{
displayResults(false);
wsInfo.setProgressBar(null, progbar);
}
+ /**
+ * Display alignment results in a new frame (or - not currently supported -
+ * added to an existing alignment).
+ *
+ * @param newFrame
+ */
void displayResults(boolean newFrame)
{
// view input or result data for each block
- Vector alorders = new Vector();
+ List<AlignmentOrder> alorders = new ArrayList<>();
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
msjob = (MsaWSJob) jobs[j];
Object[] res = msjob.getAlignment();
lastProgram = msjob.getAlignmentProgram();
- alorders.add(res[1]);
+ alorders.add((AlignmentOrder) res[1]);
results[j] = (SequenceI[]) res[0];
orders[j] = (AlignmentOrder) res[1];
orders[j] = null;
}
SequenceI[] alignment = (SequenceI[]) newview[0];
- ColumnSelection columnselection = (ColumnSelection) newview[1];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
Alignment al = new Alignment(alignment);
// TODO: add 'provenance' property to alignment from the method notes
if (lastProgram != null)
if (newFrame)
{
- AlignFrame af = new AlignFrame(al, columnselection,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ displayInNewFrame(al, alorders, hidden);
+ }
+ else
+ {
+ // TODO 2.9.x feature
+ System.out.println("MERGE WITH OLD FRAME");
+ // TODO: modify alignment in original frame, replacing old for new
+ // alignment using the commands.EditCommand model to ensure the update can
+ // be undone
+ }
+ }
- // initialise with same renderer settings as in parent alignframe.
- af.getFeatureRenderer().transferSettings(this.featureSettings);
- // update orders
- if (alorders.size() > 0)
- {
- if (alorders.size() == 1)
- {
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- }
- else
- {
- // construct a non-redundant ordering set
- Vector names = new Vector();
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- String orderName = new String(" Region " + i);
- int j = i + 1;
+ /**
+ * Display the alignment result in a new frame.
+ *
+ * @param al
+ * @param alorders
+ * @param columnselection
+ */
+ protected void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, HiddenColumns hidden)
+ {
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- while (j < l)
- {
- if (((AlignmentOrder) alorders.get(i))
- .equals(((AlignmentOrder) alorders.get(j))))
- {
- alorders.remove(j);
- l--;
- orderName += "," + j;
- }
- else
- {
- j++;
- }
- }
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
- if (i == 0 && j == 1)
- {
- names.add(new String(""));
- }
- else
- {
- names.add(orderName);
- }
- }
- for (int i = 0, l = alorders.size(); i < l; i++)
- {
- af.addSortByOrderMenuItem(
- WebServiceName + ((String) names.get(i)) + " Ordering",
- (AlignmentOrder) alorders.get(i));
- }
- }
+ if (alorders.size() > 0)
+ {
+ addSortByMenuItems(af, alorders);
+ }
+
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = getRequestingAlignFrame();
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complement.getDataset());
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ af.setTitle(alTitle);
+ AlignFrame af2 = new AlignFrame(copyComplement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af2.setTitle(complementTitle);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(
+ al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
}
+ }
- Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+ /**
+ * Add sort order options to the AlignFrame menus.
+ *
+ * @param af
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame af,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+ alorders.get(0));
}
else
{
- System.out.println("MERGE WITH OLD FRAME");
- // TODO: modify alignment in original frame, replacing old for new
- // alignment using the commands.EditCommand model to ensure the update can
- // be undone
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem(
+ WebServiceName + (names.get(i)) + " Ordering",
+ alorders.get(i));
+ }
}
}
+ @Override
public boolean canMergeResults()
{
return false;
git://source.jalview.org / jalview.git / blobdiff