X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=d2c1b383d1dbf1373e14ddacbdac7add90fc76fd;hb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;hp=5e8cb98a351e656cdfb5f52794c3099b1d9d05d6;hpb=10b903bf6b22d53e8920091efb2145d6b6a677ba;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index 5e8cb98..d2c1b38 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,7 +20,33 @@ */ package jalview.ws.jws2; -import java.util.*; +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.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.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; @@ -28,17 +54,6 @@ import compbio.metadata.ChunkHolder; import compbio.metadata.JobStatus; import compbio.metadata.Preset; -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.util.MessageManager; -import jalview.ws.AWsJob; -import jalview.ws.WSClientI; -import jalview.ws.JobStateSummary; -import jalview.ws.jws2.dm.JabaWsParamSet; -import jalview.ws.params.WsParamSetI; - class MsaWSThread extends AWS2Thread implements WSClientI { boolean submitGaps = false; // pass sequences including gaps to alignment @@ -221,7 +236,7 @@ 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(); @@ -252,7 +267,7 @@ 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], @@ -436,7 +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) { @@ -474,7 +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++) { @@ -486,6 +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; @@ -496,9 +515,20 @@ 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; @@ -866,10 +896,16 @@ 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; @@ -881,7 +917,7 @@ 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]; @@ -918,71 +954,132 @@ 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)); + } } }