X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSeqSearchWSThread.java;h=0c345184516c82dcb37b2a3024d5d4dbeafd5ada;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=07686fe56aac85c4edf994d82e07a9bc6ed155e4;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java
index 07686fe..0c34518 100644
--- a/src/jalview/ws/SeqSearchWSThread.java
+++ b/src/jalview/ws/SeqSearchWSThread.java
@@ -1,667 +1,679 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.NewickFile;
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.SeqSearchResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class SeqSearchWSThread
-    extends WSThread implements WSClientI
-{
-  String dbs=null;
-  boolean profile=false;
-
-  class SeqSearchWSJob
-      extends WSThread.WSJob
-  {
-    // hold special input for this
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    /**
-     * MsaWSJob
-     *
-     * @param jobNum
-     *            int
-     * @param jobId
-     *            String
-     */
-    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
-    {
-      this.jobnum = jobNum;
-      if (!prepareInput(inSeqs, 2))
-      {
-        submitted = true;
-        subjobComplete = true;
-        result = new MsaResult();
-        result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
-      }
-
-    }
-
-    Hashtable SeqNames = new Hashtable();
-    Vector emptySeqs = new Vector();
-    /**
-     * prepare input sequences for service
-     * @param seqs jalview sequences to be prepared
-     * @param minlen minimum number of residues required for this MsaWS service
-     * @return true if seqs contains sequences to be submitted to service.
-     */
-    private boolean prepareInput(SequenceI[] seqs, int minlen)
-    {
-      int nseqs = 0;
-      if (minlen < 0)
-      {
-        throw new Error("Implementation error: minlen must be zero or more.");
-      }
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          nseqs++;
-        }
-      }
-      boolean valid = nseqs >= 1; // need at least one sequence for valid input TODO: generalise
-      vamsas.objects.simple.Sequence[] seqarray =
-          (valid)
-          ? new vamsas.objects.simple.Sequence[nseqs]
-          : null;
-      boolean submitGaps = (nseqs==1) ? false : true; // profile is submitted with gaps  
-      for (int i = 0, n = 0; i < seqs.length; i++)
-      {
-
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-        // for
-        // any
-        // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                     .SeqCharacterHash(seqs[i]));
-        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          seqarray[n] = new vamsas.objects.simple.Sequence();
-          seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
-                               : AlignSeq.extractGaps(
-                                   jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequenceAsString()));
-        }
-        else
-        {
-          String empty = null;
-          if (seqs[i].getEnd() >= seqs[i].getStart())
-          {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString()
-                : AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequenceAsString());
-          }
-          emptySeqs.add(new String[]
-                        {newname, empty});
-        }
-      }
-      if (submitGaps)
-      {
-        // almost certainly have to remove gapped columns here
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-      return valid;
-    }
-
-    /**
-     *
-     * @return true if getAlignment will return a valid alignment result.
-     */
-    public boolean hasResults()
-    {
-      if (subjobComplete && result != null && result.isFinished()
-          && ( (SeqSearchResult) result).getAlignment() != null &&
-          ( (SeqSearchResult) result).getAlignment().getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-
-    /**
-     * return sequence search results for display
-     * @return null or { Alignment(+features and annotation), NewickFile)}
-     */
-    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
-    {
-
-      if (result != null && result.isFinished())
-      {
-        SequenceI[] alseqs = null;
-        //char alseq_gapchar = '-';
-        //int alseq_l = 0;
-        if ( ( (SeqSearchResult) result).getAlignment() != null)
-        {
-          alseqs = getVamsasAlignment( ( (SeqSearchResult) result).getAlignment());
-          //alseq_gapchar = ( (SeqSearchResult) result).getAlignment().getGapchar().charAt(0);
-          //alseq_l = alseqs.length;
-        }
-        /**
-         * what has to be done. 1 - annotate returned alignment with annotation file and sequence features file, and associate any tree-nodes.
-         * 2. connect alignment back to any associated dataset: 2.a. deuniquify recovers sequence information - but additionally, 
-         * relocations must be made from the returned aligned sequence back to the dataset.
-         */
-        // construct annotated alignment as it would be done by the jalview applet
-        jalview.datamodel.Alignment al = new Alignment(alseqs);
-        // al.setDataset(dataset);
-        // make dataset
-        String inFile=null;
-        try {
-          inFile = ((SeqSearchResult) result).getAnnotation();
-          if (inFile!=null && inFile.length()>0)
-          {
-            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, jalview.io.AppletFormatAdapter.PASTE);
-          }
-          }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the annotation file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        try {
-          inFile = ((SeqSearchResult) result).getFeatures();
-          if (inFile!=null && inFile.length()>0)
-          {
-            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            ff.parse(al, featureColours, false);
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the Features file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        jalview.io.NewickFile nf=null;
-        try {
-          inFile = ((SeqSearchResult) result).getNewickTree();
-          if (inFile!=null && inFile.length()>0)
-          {
-            nf = new jalview.io.NewickFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            if (!nf.isValid()) {
-              nf.close();
-              nf = null;
-            }
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the treeFile associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        /* TODO: housekeeping w.r.t. recovery of dataset and annotation references for input sequences, and then dataset sequence creation for new sequences retrieved from service
-         * // finally, attempt to de-uniquify to recover input sequence identity, and try to map back onto dataset
-        Note: this
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
-        will NOT WORK - the returned alignment may contain multiple versions of the input sequence, each being a subsequence of the original.
-        deuniquify also removes existing annotation and features added in the previous step...
-        al.setDataset(dataset);
-        // add in new sequences retrieved from sequence search which are not already in dataset.
-        // trigger a 'fetchDBids' to annotate sequences with database ids...
-        */
-
-        return new Object[]
-            {
-            al, nf};
-      }
-      return null;
-    }
-
-    /**
-     * mark subjob as cancelled and set result object appropriatly
-     */
-    void cancel()
-    {
-      cancelled = true;
-      subjobComplete = true;
-      result = null;
-    }
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    boolean hasValidInput()
-    {
-      if (seqs.getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  String alTitle; // name which will be used to form new alignment window.
-  Alignment dataset; // dataset to which the new alignment will be
-
-  // associated.
-
-  ext.vamsas.SeqSearchI server = null;
-
-  private String dbArg;
-  /**
-   * set basic options for this (group) of Msa jobs
-   *
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              AlignmentView alview,
-              String wsname, String db)
-  {
-    super(alFrame, wsinfo, alview, wsname, wsUrl);
-    this.server = server;
-    this.dbArg = db;
-  }
-
-  /**
-   * create one or more Msa jobs to align visible seuqences in _msa
-   *
-   * @param title
-   *            String
-   * @param _msa
-   *            AlignmentView
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   * @param seqset
-   *            Alignment
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              String wsname, String title, AlignmentView _msa, String db, Alignment seqset)
-  {
-    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
-    OutputHeader = wsInfo.getProgressText();
-    alTitle = title;
-    dataset = seqset;
-
-    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
-    if (conmsa != null)
-    {
-      int njobs = conmsa.length;
-      jobs = new SeqSearchWSJob[njobs];
-      for (int j = 0; j < njobs; j++)
-      {
-        if (j != 0)
-        {
-          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
-        }
-        else
-        {
-          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
-        }
-        if (njobs > 0)
-        {
-          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
-        }
-        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-      }
-    }
-  }
-
-  public boolean isCancellable()
-  {
-    return true;
-  }
-
-  public void cancelJob()
-  {
-    if (!jobComplete && jobs != null)
-    {
-      boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++)
-      {
-        if (jobs[job].submitted && !jobs[job].subjobComplete)
-        {
-          String cancelledMessage = "";
-          try
-          {
-            vamsas.objects.simple.WsJobId cancelledJob = server
-                .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2)
-            {
-              // CANCELLED_JOB
-              cancelledMessage = "Job cancelled.";
-              ( (SeqSearchWSJob) jobs[job]).cancel();
-              wsInfo.setStatus(jobs[job].jobnum,
-                               WebserviceInfo.STATE_CANCELLED_OK);
-            }
-            else if (cancelledJob.getStatus() == 3)
-            {
-              // VALID UNSTOPPABLE JOB
-              cancelledMessage +=
-                  "Server cannot cancel this job. just close the window.\n";
-              cancelled = false;
-              // wsInfo.setStatus(jobs[job].jobnum,
-              //                 WebserviceInfo.STATE_RUNNING);
-            }
-
-            if (cancelledJob.getJobId() != null)
-            {
-              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
-            }
-
-            cancelledMessage += "\n";
-          }
-          catch (Exception exc)
-          {
-            cancelledMessage +=
-                ("\nProblems cancelling the job : Exception received...\n"
-                 + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
-                           exc);
-          }
-          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-                                 + cancelledMessage + "\n");
-        }
-      }
-      if (cancelled)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-        jobComplete = true;
-      }
-      this.interrupt(); // kick thread to update job states.
-    }
-    else
-    {
-      if (!jobComplete)
-      {
-        wsInfo
-            .setProgressText(OutputHeader
-                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-      }
-    }
-  }
-
-  void pollJob(WSJob job)
-      throws Exception
-  {
-    ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);
-  }
-
-  void StartJob(WSJob job)
-  {
-    if (! (job instanceof SeqSearchWSJob))
-    {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
-                      job.getClass());
-    }
-    SeqSearchWSJob j = (SeqSearchWSJob) job;
-    if (j.submitted)
-    {
-      if (Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
-      }
-      return;
-    }
-    if (j.seqs.getSeqs() == null)
-    {
-      // special case - selection consisted entirely of empty sequences...
-      j.submitted = true;
-      j.result = new MsaResult();
-      j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
-      ( (MsaResult) j.result).setMsa(null);
-    }
-    try
-    {
-      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs.getSeqs()[0], dbArg);
-
-      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-      {
-        j.jobId = jobsubmit.getJobId();
-        j.submitted = true;
-        j.subjobComplete = false;
-        // System.out.println(WsURL + " Job Id '" + jobId + "'");
-      }
-      else
-      {
-        if (jobsubmit == null)
-        {
-          throw new Exception(
-              "Server at "
-              + WsUrl
-              +
-              " returned null object, it probably cannot be contacted. Try again later ?");
-        }
-
-        throw new Exception(jobsubmit.getJobId());
-      }
-    }
-    catch (Exception e)
-    {
-      // TODO: JBPNote catch timeout or other fault types explicitly
-      // 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"
-                   + e.toString() + "\n");
-      j.allowedServerExceptions = 0;
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-          .appendProgressText(
-              j.jobnum,
-              "Failed to submit sequences for alignment.\n"
-              + "It is most likely that there is a problem with the server.\n"
-              + "Just close the window\n");
-
-      // e.printStackTrace(); // TODO: JBPNote DEBUG
-    }
-  }
-
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
-      vamsas.objects.simple.Alignment valign)
-  {
-    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
-        length];
-
-    for (int i = 0, j = seqs.length; i < j; i++)
-    {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
-                                              .getSeq());
-    }
-
-    return msa;
-  }
-
-  void parseResult()
-  {
-    int results = 0; // number of result sets received
-    JobStateSummary finalState = new JobStateSummary();
-    try
-    {
-      for (int j = 0; j < jobs.length; j++)
-      {
-        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-        {
-          results++;
-          vamsas.objects.simple.Alignment valign = ( (SeqSearchResult) jobs[j].result).
-              getAlignment();
-          if (valign != null)
-          {
-            wsInfo.appendProgressText(jobs[j].jobnum,
-                                      "\nAlignment Object Method Notes\n");
-            String[] lines = valign.getMethod();
-            for (int line = 0; line < lines.length; line++)
-            {
-              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
-            }
-            // 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);
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    if (results > 0)
-    {
-      wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
-      wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
-      wsInfo.setResultsReady();
-    }
-    else
-    {
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  void displayResults(boolean newFrame)
-  {
-    if (!newFrame)
-    {
-      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
-      return;
-    }
-    // each subjob is an independent alignment for the moment
-    //Alignment al[] = new Alignment[jobs.length];
-    //NewickFile nf[] = new NewickFile[jobs.length];
-    for (int j = 0; j < jobs.length; j++)
-    {
-      Hashtable featureColours = new Hashtable();
-      Alignment al=null;
-      NewickFile nf = null;
-      if (jobs[j].hasResults())
-      {
-        Object[] res = ( (SeqSearchWSJob) jobs[j]).getAlignment(dataset, featureColours);
-        if (res==null) { continue; };
-        al = (Alignment) res[0];
-        nf = (NewickFile) res[1];
-      }
-      else
-      {
-        al = null;
-        nf = null;
-        continue;
-      }
-    /*
-     * We can't map new alignment back with insertions from input's hidden regions until dataset mapping is sorted out...
-     * but basically it goes like this:
-     1. Merge each domain hit back onto the visible segments in the same way as a Jnet prediction is mapped back
-     
-     Object[] newview = input.getUpdatedView(results, orders, getGapChar());
-    // trash references to original result data
-    for (int j = 0; j < jobs.length; j++)
-    {
-      results[j] = null;
-      orders[j] = null;
-    }
-    SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
-    Alignment al = new Alignment(alignment);
-
-    if (dataset != null)
-    {
-      al.setDataset(dataset);
-    }
-
-    propagateDatasetMappings(al);
-    }
-    */
-      
-      AlignFrame af = new AlignFrame(al,//  columnselection,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-      if (nf!=null)
-      {
-        af.ShowNewickTree(nf, "Tree from "+this.alTitle);
-      }
-      // initialise with same renderer settings as in parent alignframe.
-      af.getFeatureRenderer().transferSettings(
-              this.featureSettings);
-      Desktop.addInternalFrame(af, alTitle,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-    }
-  }
-
-  public boolean canMergeResults()
-  {
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.NewickFile;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SeqSearchResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * 
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
+ * @author not attributable
+ * @version 1.0
+ */
+class SeqSearchWSThread extends WSThread implements WSClientI
+{
+  String dbs = null;
+
+  boolean profile = false;
+
+  class SeqSearchWSJob extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+
+    /**
+     * MsaWSJob
+     * 
+     * @param jobNum
+     *                int
+     * @param jobId
+     *                String
+     */
+    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+
+    Vector emptySeqs = new Vector();
+
+    /**
+     * prepare input sequences for service
+     * 
+     * @param seqs
+     *                jalview sequences to be prepared
+     * @param minlen
+     *                minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error(
+                "Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs >= 1; // need at least one sequence for valid input
+                                  // TODO: generalise
+      vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+              : null;
+      boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
+                                                        // with gaps
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
+                  : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          seqs[i].getSequenceAsString()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
+                    .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
+                            .getSequenceAsString());
+          }
+          emptySeqs.add(new String[]
+          { newname, empty });
+        }
+      }
+      if (submitGaps)
+      {
+        // almost certainly have to remove gapped columns here
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     * 
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete
+              && result != null
+              && result.isFinished()
+              && ((SeqSearchResult) result).getAlignment() != null
+              && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    /**
+     * return sequence search results for display
+     * 
+     * @return null or { Alignment(+features and annotation), NewickFile)}
+     */
+    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        // char alseq_gapchar = '-';
+        // int alseq_l = 0;
+        if (((SeqSearchResult) result).getAlignment() != null)
+        {
+          alseqs = getVamsasAlignment(((SeqSearchResult) result)
+                  .getAlignment());
+          // alseq_gapchar = ( (SeqSearchResult)
+          // result).getAlignment().getGapchar().charAt(0);
+          // alseq_l = alseqs.length;
+        }
+        /**
+         * what has to be done. 1 - annotate returned alignment with annotation
+         * file and sequence features file, and associate any tree-nodes. 2.
+         * connect alignment back to any associated dataset: 2.a. deuniquify
+         * recovers sequence information - but additionally, relocations must be
+         * made from the returned aligned sequence back to the dataset.
+         */
+        // construct annotated alignment as it would be done by the jalview
+        // applet
+        jalview.datamodel.Alignment al = new Alignment(alseqs);
+        // al.setDataset(dataset);
+        // make dataset
+        String inFile = null;
+        try
+        {
+          inFile = ((SeqSearchResult) result).getAnnotation();
+          if (inFile != null && inFile.length() > 0)
+          {
+            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
+                    jalview.io.AppletFormatAdapter.PASTE);
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the annotation file associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+
+        try
+        {
+          inFile = ((SeqSearchResult) result).getFeatures();
+          if (inFile != null && inFile.length() > 0)
+          {
+            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
+                    inFile, jalview.io.AppletFormatAdapter.PASTE);
+            ff.parse(al, featureColours, false);
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the Features file associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+        jalview.io.NewickFile nf = null;
+        try
+        {
+          inFile = ((SeqSearchResult) result).getNewickTree();
+          if (inFile != null && inFile.length() > 0)
+          {
+            nf = new jalview.io.NewickFile(inFile,
+                    jalview.io.AppletFormatAdapter.PASTE);
+            if (!nf.isValid())
+            {
+              nf.close();
+              nf = null;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err
+                  .println("Failed to parse the treeFile associated with the alignment.");
+          System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+
+        /*
+         * TODO: housekeeping w.r.t. recovery of dataset and annotation
+         * references for input sequences, and then dataset sequence creation
+         * for new sequences retrieved from service // finally, attempt to
+         * de-uniquify to recover input sequence identity, and try to map back
+         * onto dataset Note: this
+         * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
+         * NOT WORK - the returned alignment may contain multiple versions of
+         * the input sequence, each being a subsequence of the original.
+         * deuniquify also removes existing annotation and features added in the
+         * previous step... al.setDataset(dataset); // add in new sequences
+         * retrieved from sequence search which are not already in dataset. //
+         * trigger a 'fetchDBids' to annotate sequences with database ids...
+         */
+
+        return new Object[]
+        { al, nf };
+      }
+      return null;
+    }
+
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel()
+    {
+      cancelled = true;
+      subjobComplete = true;
+      result = null;
+    }
+
+    /**
+     * 
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  String alTitle; // name which will be used to form new alignment window.
+
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.SeqSearchI server = null;
+
+  private String dbArg;
+
+  /**
+   * set basic options for this (group) of Msa jobs
+   * 
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          AlignmentView alview, String wsname, String db)
+  {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
+    this.server = server;
+    this.dbArg = db;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   * 
+   * @param title
+   *                String
+   * @param _msa
+   *                AlignmentView
+   * @param subgaps
+   *                boolean
+   * @param presorder
+   *                boolean
+   * @param seqset
+   *                Alignment
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          String wsname, String title, AlignmentView _msa, String db,
+          Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new SeqSearchWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+        {
+          wsinfo
+                  .setProgressName("region " + jobs[j].jobnum,
+                          jobs[j].jobnum);
+        }
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                    .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ((SeqSearchWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                      WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              // WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          } catch (Exception exc)
+          {
+            cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+                    + exc + "\n");
+            Cache.log.warn(
+                    "Exception whilst cancelling " + jobs[job].jobId, exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                  + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+                .setProgressText(OutputHeader
+                        + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+
+  void pollJob(WSJob job) throws Exception
+  {
+    ((SeqSearchWSJob) job).result = server
+            .getResult(((SeqSearchWSJob) job).jobId);
+  }
+
+  void StartJob(WSJob job)
+  {
+    if (!(job instanceof SeqSearchWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
+              + job.getClass());
+    }
+    SeqSearchWSJob j = (SeqSearchWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job "
+                + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ((MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
+              .getSeqs()[0], dbArg);
+
+      if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+      }
+      else
+      {
+        if (jobsubmit == null)
+        {
+          throw new Exception(
+                  "Server at "
+                          + WsUrl
+                          + " returned null object, it probably cannot be contacted. Try again later ?");
+        }
+
+        throw new Exception(jobsubmit.getJobId());
+      }
+    } catch (Exception e)
+    {
+      // TODO: JBPNote catch timeout or other fault types explicitly
+      // 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"
+                      + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+              .appendProgressText(
+                      j.jobnum,
+                      "Failed to submit sequences for alignment.\n"
+                              + "It is most likely that there is a problem with the server.\n"
+                              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  private jalview.datamodel.Sequence[] getVamsasAlignment(
+          vamsas.objects.simple.Alignment valign)
+  {
+    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+    for (int i = 0, j = seqs.length; i < j; i++)
+    {
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+              .getSeq());
+    }
+
+    return msa;
+  }
+
+  void parseResult()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete
+                && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ((SeqSearchResult) jobs[j].result)
+                  .getAlignment();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                    "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
+            }
+            // 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);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(true);
+                }
+              });
+      wsInfo.mergeResults
+              .addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(java.awt.event.ActionEvent evt)
+                {
+                  displayResults(false);
+                }
+              });
+      wsInfo.setResultsReady();
+    }
+    else
+    {
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    if (!newFrame)
+    {
+      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+      return;
+    }
+    // each subjob is an independent alignment for the moment
+    // Alignment al[] = new Alignment[jobs.length];
+    // NewickFile nf[] = new NewickFile[jobs.length];
+    for (int j = 0; j < jobs.length; j++)
+    {
+      Hashtable featureColours = new Hashtable();
+      Alignment al = null;
+      NewickFile nf = null;
+      if (jobs[j].hasResults())
+      {
+        Object[] res = ((SeqSearchWSJob) jobs[j]).getAlignment(dataset,
+                featureColours);
+        if (res == null)
+        {
+          continue;
+        }
+        ;
+        al = (Alignment) res[0];
+        nf = (NewickFile) res[1];
+      }
+      else
+      {
+        al = null;
+        nf = null;
+        continue;
+      }
+      /*
+       * We can't map new alignment back with insertions from input's hidden
+       * regions until dataset mapping is sorted out... but basically it goes
+       * like this: 1. Merge each domain hit back onto the visible segments in
+       * the same way as a Jnet prediction is mapped back
+       * 
+       * Object[] newview = input.getUpdatedView(results, orders, getGapChar()); //
+       * trash references to original result data for (int j = 0; j <
+       * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]
+       * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =
+       * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);
+       * 
+       * if (dataset != null) { al.setDataset(dataset); }
+       * 
+       * propagateDatasetMappings(al); }
+       */
+
+      AlignFrame af = new AlignFrame(al,// columnselection,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      if (nf != null)
+      {
+        af.ShowNewickTree(nf, "Tree from " + this.alTitle);
+      }
+      // initialise with same renderer settings as in parent alignframe.
+      af.getFeatureRenderer().transferSettings(this.featureSettings);
+      Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}