X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=d72ea5fbb398a19db82a2b7ffe1ca5e42fe81b18;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=635f92b90fb7e62994a1b2be122e6baaa90ccb01;hpb=6940b5ac884139626e962201ae00c56c66d18039;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index 635f92b..d72ea5f 100644 --- a/src/jalview/ws/jws2/MsaWSThread.java +++ b/src/jalview/ws/jws2/MsaWSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -23,6 +23,7 @@ package jalview.ws.jws2; 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; @@ -30,6 +31,7 @@ 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; @@ -44,6 +46,8 @@ 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; @@ -121,7 +125,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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++) { @@ -160,8 +166,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI .extractGaps(jalview.util.Comparison.GapChars, seqs[i].getSequenceAsString()); } - emptySeqs.add(new String[] - { newname, empty }); + emptySeqs.add(new String[] { newname, empty }); } } return valid; @@ -232,7 +237,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI int ow = w, nw = w; for (i = 0, w = emptySeqs.size(); i < w; i++) { - String[] es = (String[]) emptySeqs.get(i); + String[] es = emptySeqs.get(i); if (es != null && es[1] != null) { int sw = es[1].length(); @@ -263,7 +268,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI } for (i = 0, w = emptySeqs.size(); i < w; i++) { - String[] es = (String[]) emptySeqs.get(i); + String[] es = emptySeqs.get(i); if (es[1] == null) { t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0], @@ -292,8 +297,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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; } @@ -447,7 +451,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI * @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) { @@ -485,7 +489,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI SequenceI[][] conmsa = _msa.getVisibleContigs('-'); if (conmsa != null) { - int njobs = conmsa.length; + int nvalid = 0, njobs = conmsa.length; jobs = new MsaWSJob[njobs]; for (int j = 0; j < njobs; j++) { @@ -497,6 +501,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI { jobs[j] = new MsaWSJob(0, conmsa[j]); } + if (((MsaWSJob) jobs[j]).hasValidInput()) + { + nvalid++; + } ((MsaWSJob) jobs[j]).preset = preset; ((MsaWSJob) jobs[j]).arguments = paramset; ((MsaWSJob) jobs[j]).alignmentProgram = wsname; @@ -507,9 +515,21 @@ class MsaWSThread extends AWS2Thread implements WSClientI } wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader); } + validInput = nvalid > 0; } } + boolean validInput = false; + + /** + * + * @return true if the thread will perform a calculation + */ + public boolean hasValidInput() + { + return validInput; + } + public boolean isCancellable() { return true; @@ -636,7 +656,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI // 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()) @@ -682,28 +704,39 @@ class MsaWSThread extends AWS2Thread implements WSClientI } 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) @@ -736,8 +769,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI // 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")); } } } @@ -745,7 +778,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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 @@ -877,10 +912,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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 alorders = new ArrayList(); SequenceI[][] results = new SequenceI[jobs.length][]; AlignmentOrder[] orders = new AlignmentOrder[jobs.length]; String lastProgram = null; @@ -892,7 +933,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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]; @@ -929,71 +970,134 @@ class MsaWSThread extends AWS2Thread implements WSClientI if (newFrame) { - AlignFrame af = new AlignFrame(al, columnselection, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + displayInNewFrame(al, alorders, columnselection); - // 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; + } + 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 + } + } - while (j < l) - { - if (((AlignmentOrder) alorders.get(i)) - .equals(((AlignmentOrder) alorders.get(j)))) - { - alorders.remove(j); - l--; - orderName += "," + j; - } - else - { - j++; - } - } + /** + * Display the alignment result in a new frame. + * + * @param al + * @param alorders + * @param columnselection + */ + protected void displayInNewFrame(AlignmentI al, + List alorders, ColumnSelection columnselection) + { + AlignFrame af = new AlignFrame(al, columnselection, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - 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)); - } - } + // initialise with same renderer settings as in parent alignframe. + af.getFeatureRenderer().transferSettings(this.featureSettings); + + 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); + 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 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 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)); + } } }