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package jalview.ws.jws1; |
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import jalview.analysis.AlignSeq; |
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import jalview.bin.Console; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentOrder; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.Desktop; |
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import jalview.gui.WebserviceInfo; |
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import jalview.util.MessageManager; |
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import jalview.ws.AWsJob; |
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import jalview.ws.JobStateSummary; |
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import jalview.ws.WSClientI; |
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import java.util.Hashtable; |
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import java.util.Vector; |
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import vamsas.objects.simple.MsaResult; |
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| 0% |
Uncovered Elements: 229 (229) |
Complexity: 57 |
Complexity Density: 0.39 |
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class MsaWSThread extends JWS1Thread implements WSClientI |
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{ |
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boolean submitGaps = false; |
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boolean preserveOrder = true; |
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| 0% |
Uncovered Elements: 145 (145) |
Complexity: 41 |
Complexity Density: 0.49 |
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class MsaWSJob extends WSJob |
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{ |
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vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet(); |
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@param |
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@param |
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| |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
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public MsaWSJob(int jobNum, SequenceI[] inSeqs)... |
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{ |
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this.jobnum = jobNum; |
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if (!prepareInput(inSeqs, 2)) |
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{ |
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submitted = true; |
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subjobComplete = true; |
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result = new MsaResult(); |
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result.setFinished(true); |
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result.setStatus(MessageManager.getString("label.job_never_ran")); |
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} |
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} |
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Hashtable SeqNames = new Hashtable(); |
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Vector emptySeqs = new Vector(); |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 40 (40) |
Complexity: 11 |
Complexity Density: 0.5 |
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private boolean prepareInput(SequenceI[] seqs, int minlen)... |
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{ |
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int nseqs = 0; |
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if (minlen < 0) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.implementation_error_minlen_must_be_greater_zero")); |
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} |
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for (int i = 0; i < seqs.length; i++) |
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{ |
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if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1) |
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{ |
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nseqs++; |
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} |
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} |
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boolean valid = nseqs > 1; |
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vamsas.objects.simple.Sequence[] seqarray = (valid) |
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? new vamsas.objects.simple.Sequence[nseqs] |
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: null; |
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for (int i = 0, n = 0; i < seqs.length; i++) |
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{ |
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String newname = jalview.analysis.SeqsetUtils.unique_name(i); |
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SeqNames.put(newname, |
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jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i])); |
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if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1) |
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{ |
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seqarray[n] = new vamsas.objects.simple.Sequence(); |
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seqarray[n].setId(newname); |
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seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString() |
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: AlignSeq.extractGaps(jalview.util.Comparison.GapChars, |
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seqs[i].getSequenceAsString())); |
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} |
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else |
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{ |
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String empty = null; |
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if (seqs[i].getEnd() >= seqs[i].getStart()) |
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{ |
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empty = (submitGaps) ? seqs[i].getSequenceAsString() |
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: AlignSeq.extractGaps(jalview.util.Comparison.GapChars, |
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seqs[i].getSequenceAsString()); |
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} |
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emptySeqs.add(new String[] { newname, empty }); |
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} |
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} |
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this.seqs = new vamsas.objects.simple.SequenceSet(); |
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this.seqs.setSeqs(seqarray); |
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return valid; |
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} |
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@return |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 6 |
Complexity Density: 2 |
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@Override... |
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public boolean hasResults() |
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{ |
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if (subjobComplete && result != null && result.isFinished() |
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&& ((MsaResult) result).getMsa() != null |
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&& ((MsaResult) result).getMsa().getSeqs() != null) |
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{ |
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return true; |
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} |
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return false; |
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} |
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| 0% |
Uncovered Elements: 77 (77) |
Complexity: 19 |
Complexity Density: 0.42 |
|
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public Object[] getAlignment()... |
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{ |
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if (result != null && result.isFinished()) |
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{ |
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SequenceI[] alseqs = null; |
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char alseq_gapchar = '-'; |
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int alseq_l = 0; |
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if (((MsaResult) result).getMsa() != null) |
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{ |
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alseqs = getVamsasAlignment(((MsaResult) result).getMsa()); |
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alseq_gapchar = ((MsaResult) result).getMsa().getGapchar() |
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.charAt(0); |
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alseq_l = alseqs.length; |
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} |
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if (emptySeqs.size() > 0) |
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{ |
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SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()]; |
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int i, w = 0; |
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if (alseq_l > 0) |
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{ |
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for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++) |
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{ |
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0 |
if (w < alseqs[i].getLength()) |
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{ |
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w = alseqs[i].getLength(); |
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} |
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t_alseqs[i] = alseqs[i]; |
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alseqs[i] = null; |
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} |
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} |
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int ow = w, nw = w; |
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for (i = 0, w = emptySeqs.size(); i < w; i++) |
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{ |
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String[] es = (String[]) emptySeqs.get(i); |
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if (es != null && es[1] != null) |
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{ |
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int sw = es[1].length(); |
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if (nw < sw) |
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{ |
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nw = sw; |
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} |
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} |
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} |
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StringBuffer insbuff = new StringBuffer(w); |
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for (i = 0; i < nw; i++) |
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{ |
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insbuff.append(alseq_gapchar); |
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} |
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if (ow < nw) |
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{ |
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for (i = 0; i < alseq_l; i++) |
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{ |
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int sw = t_alseqs[i].getLength(); |
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0 |
if (nw > sw) |
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{ |
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alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() |
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+ insbuff.substring(0, sw - nw)); |
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} |
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} |
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} |
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for (i = 0, w = emptySeqs.size(); i < w; i++) |
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{ |
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String[] es = (String[]) emptySeqs.get(i); |
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if (es[1] == null) |
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{ |
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t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0], |
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insbuff.toString(), 1, 0); |
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} |
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else |
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{ |
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if (es[1].length() < nw) |
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{ |
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t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence( |
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es[0], |
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es[1] + insbuff.substring(0, nw - es[1].length()), |
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1, 1 + es[1].length()); |
| 244 |
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} |
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else |
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{ |
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t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence( |
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es[0], es[1]); |
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} |
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} |
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} |
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0 |
alseqs = t_alseqs; |
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} |
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0 |
AlignmentOrder msaorder = new AlignmentOrder(alseqs); |
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|
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jalview.analysis.AlignmentSorter.recoverOrder(alseqs); |
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|
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jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs); |
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return new Object[] { alseqs, msaorder }; |
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} |
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return null; |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
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0 |
void cancel()... |
| 268 |
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{ |
| 269 |
0 |
cancelled = true; |
| 270 |
0 |
subjobComplete = true; |
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result = null; |
| 272 |
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} |
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| 274 |
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| 275 |
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| 276 |
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@return |
| 277 |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
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0 |
@Override... |
| 279 |
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public boolean hasValidInput() |
| 280 |
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{ |
| 281 |
0 |
if (seqs.getSeqs() != null) |
| 282 |
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{ |
| 283 |
0 |
return true; |
| 284 |
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} |
| 285 |
0 |
return false; |
| 286 |
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} |
| 287 |
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} |
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String alTitle; |
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AlignmentI dataset; |
| 292 |
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| 293 |
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| 294 |
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ext.vamsas.MuscleWS server = null; |
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@param |
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@param |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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0 |
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,... |
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WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, |
| 307 |
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AlignmentView alview, String wsname, boolean subgaps, |
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boolean presorder) |
| 309 |
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{ |
| 310 |
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super(alFrame, wsinfo, alview, wsname, wsUrl); |
| 311 |
0 |
this.server = server; |
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0 |
this.submitGaps = subgaps; |
| 313 |
0 |
this.preserveOrder = presorder; |
| 314 |
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} |
| 315 |
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| 317 |
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@param |
| 320 |
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| 321 |
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@param |
| 322 |
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| 323 |
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@param |
| 324 |
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| 325 |
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@param |
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| 327 |
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@param |
| 328 |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 5 |
Complexity Density: 0.33 |
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0 |
MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,... |
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WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, |
| 332 |
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String wsname, String title, AlignmentView _msa, boolean subgaps, |
| 333 |
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boolean presorder, AlignmentI seqset) |
| 334 |
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{ |
| 335 |
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this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder); |
| 336 |
0 |
OutputHeader = wsInfo.getProgressText(); |
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0 |
alTitle = title; |
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0 |
dataset = seqset; |
| 339 |
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|
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0 |
SequenceI[][] conmsa = _msa.getVisibleContigs('-'); |
| 341 |
0 |
if (conmsa != null) |
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{ |
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int njobs = conmsa.length; |
| 344 |
0 |
jobs = new MsaWSJob[njobs]; |
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0 |
for (int j = 0; j < njobs; j++) |
| 346 |
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{ |
| 347 |
0 |
if (j != 0) |
| 348 |
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{ |
| 349 |
0 |
jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]); |
| 350 |
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} |
| 351 |
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else |
| 352 |
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{ |
| 353 |
0 |
jobs[j] = new MsaWSJob(0, conmsa[j]); |
| 354 |
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} |
| 355 |
0 |
if (njobs > 0) |
| 356 |
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{ |
| 357 |
0 |
wsinfo.setProgressName("region " + jobs[j].getJobnum(), |
| 358 |
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jobs[j].getJobnum()); |
| 359 |
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} |
| 360 |
0 |
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader); |
| 361 |
|
} |
| 362 |
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} |
| 363 |
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} |
| 364 |
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|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 365 |
0 |
@Override... |
| 366 |
|
public boolean isCancellable() |
| 367 |
|
{ |
| 368 |
0 |
return true; |
| 369 |
|
} |
| 370 |
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|
| |
|
| 0% |
Uncovered Elements: 42 (42) |
Complexity: 12 |
Complexity Density: 0.46 |
|
| 371 |
0 |
@Override... |
| 372 |
|
public void cancelJob() |
| 373 |
|
{ |
| 374 |
0 |
if (!jobComplete && jobs != null) |
| 375 |
|
{ |
| 376 |
0 |
boolean cancelled = true; |
| 377 |
0 |
for (int job = 0; job < jobs.length; job++) |
| 378 |
|
{ |
| 379 |
0 |
if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete()) |
| 380 |
|
{ |
| 381 |
0 |
String cancelledMessage = ""; |
| 382 |
0 |
try |
| 383 |
|
{ |
| 384 |
0 |
vamsas.objects.simple.WsJobId cancelledJob = server |
| 385 |
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.cancel(jobs[job].getJobId()); |
| 386 |
0 |
if (cancelledJob.getStatus() == 2) |
| 387 |
|
{ |
| 388 |
|
|
| 389 |
0 |
cancelledMessage = "Job cancelled."; |
| 390 |
0 |
((MsaWSJob) jobs[job]).cancel(); |
| 391 |
0 |
wsInfo.setStatus(jobs[job].getJobnum(), |
| 392 |
|
WebserviceInfo.STATE_CANCELLED_OK); |
| 393 |
|
} |
| 394 |
0 |
else if (cancelledJob.getStatus() == 3) |
| 395 |
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{ |
| 396 |
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|
| 397 |
0 |
cancelledMessage += "Server cannot cancel this job. just close the window.\n"; |
| 398 |
0 |
cancelled = false; |
| 399 |
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|
| 400 |
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|
| 401 |
|
} |
| 402 |
|
|
| 403 |
0 |
if (cancelledJob.getJobId() != null) |
| 404 |
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{ |
| 405 |
0 |
cancelledMessage += ("[" + cancelledJob.getJobId() + "]"); |
| 406 |
|
} |
| 407 |
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|
| 408 |
0 |
cancelledMessage += "\n"; |
| 409 |
|
} catch (Exception exc) |
| 410 |
|
{ |
| 411 |
0 |
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" |
| 412 |
|
+ exc + "\n"); |
| 413 |
0 |
Console.warn( |
| 414 |
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"Exception whilst cancelling " + jobs[job].getJobId(), |
| 415 |
|
exc); |
| 416 |
|
} |
| 417 |
0 |
wsInfo.setProgressText(jobs[job].getJobnum(), |
| 418 |
|
OutputHeader + cancelledMessage + "\n"); |
| 419 |
|
} |
| 420 |
|
} |
| 421 |
0 |
if (cancelled) |
| 422 |
|
{ |
| 423 |
0 |
wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK); |
| 424 |
0 |
jobComplete = true; |
| 425 |
|
} |
| 426 |
0 |
this.interrupt(); |
| 427 |
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} |
| 428 |
|
else |
| 429 |
|
{ |
| 430 |
0 |
if (!jobComplete) |
| 431 |
|
{ |
| 432 |
0 |
wsInfo.setProgressText(OutputHeader |
| 433 |
|
+ "Server cannot cancel this job because it has not been submitted properly. just close the window.\n"); |
| 434 |
|
} |
| 435 |
|
} |
| 436 |
|
} |
| 437 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 438 |
0 |
@Override... |
| 439 |
|
public void pollJob(AWsJob job) throws Exception |
| 440 |
|
{ |
| 441 |
0 |
((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId()); |
| 442 |
|
} |
| 443 |
|
|
| |
|
| 0% |
Uncovered Elements: 39 (39) |
Complexity: 9 |
Complexity Density: 0.33 |
|
| 444 |
0 |
@Override... |
| 445 |
|
public void StartJob(AWsJob job) |
| 446 |
|
{ |
| 447 |
0 |
if (!(job instanceof MsaWSJob)) |
| 448 |
|
{ |
| 449 |
0 |
throw new Error(MessageManager.formatMessage( |
| 450 |
|
"error.implementation_error_msawbjob_called", new String[] |
| 451 |
|
{ job.getClass().toString() })); |
| 452 |
|
} |
| 453 |
0 |
MsaWSJob j = (MsaWSJob) job; |
| 454 |
0 |
if (j.isSubmitted()) |
| 455 |
|
{ |
| 456 |
0 |
if (Console.isDebugEnabled()) |
| 457 |
|
{ |
| 458 |
0 |
Console.debug( |
| 459 |
|
"Tried to submit an already submitted job " + j.getJobId()); |
| 460 |
|
} |
| 461 |
0 |
return; |
| 462 |
|
} |
| 463 |
0 |
if (j.seqs.getSeqs() == null) |
| 464 |
|
{ |
| 465 |
|
|
| 466 |
0 |
j.setSubmitted(true); |
| 467 |
0 |
j.result = new MsaResult(); |
| 468 |
0 |
j.result.setFinished(true); |
| 469 |
0 |
j.result.setStatus( |
| 470 |
|
MessageManager.getString("label.empty_alignment_job")); |
| 471 |
0 |
((MsaResult) j.result).setMsa(null); |
| 472 |
|
} |
| 473 |
0 |
try |
| 474 |
|
{ |
| 475 |
0 |
vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs); |
| 476 |
|
|
| 477 |
0 |
if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) |
| 478 |
|
{ |
| 479 |
0 |
j.setJobId(jobsubmit.getJobId()); |
| 480 |
0 |
j.setSubmitted(true); |
| 481 |
0 |
j.setSubjobComplete(false); |
| 482 |
|
|
| 483 |
|
} |
| 484 |
|
else |
| 485 |
|
{ |
| 486 |
0 |
if (jobsubmit == null) |
| 487 |
|
{ |
| 488 |
0 |
throw new Exception(MessageManager.formatMessage( |
| 489 |
|
"exception.web_service_returned_null_try_later", |
| 490 |
|
new String[] |
| 491 |
|
{ WsUrl })); |
| 492 |
|
} |
| 493 |
|
|
| 494 |
0 |
throw new Exception(jobsubmit.getJobId()); |
| 495 |
|
} |
| 496 |
|
} catch (Exception e) |
| 497 |
|
{ |
| 498 |
|
|
| 499 |
|
|
| 500 |
0 |
jalview.bin.Console.errPrintln(WebServiceName |
| 501 |
|
+ "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" |
| 502 |
|
+ "When contacting Server:" + WsUrl + "\n" + e.toString() |
| 503 |
|
+ "\n"); |
| 504 |
0 |
j.setAllowedServerExceptions(0); |
| 505 |
0 |
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); |
| 506 |
0 |
wsInfo.setStatus(j.getJobnum(), |
| 507 |
|
WebserviceInfo.STATE_STOPPED_SERVERERROR); |
| 508 |
0 |
wsInfo.appendProgressText(j.getJobnum(), MessageManager |
| 509 |
|
.getString("info.failed_to_submit_sequences_for_alignment")); |
| 510 |
|
|
| 511 |
|
|
| 512 |
|
} |
| 513 |
|
} |
| 514 |
|
|
| |
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
| 515 |
0 |
private jalview.datamodel.Sequence[] getVamsasAlignment(... |
| 516 |
|
vamsas.objects.simple.Alignment valign) |
| 517 |
|
{ |
| 518 |
|
|
| 519 |
0 |
vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs(); |
| 520 |
0 |
jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length]; |
| 521 |
|
|
| 522 |
0 |
for (int i = 0, j = seqs.length; i < j; i++) |
| 523 |
|
{ |
| 524 |
0 |
msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), |
| 525 |
|
seqs[i].getSeq()); |
| 526 |
|
} |
| 527 |
|
|
| 528 |
0 |
return msa; |
| 529 |
|
} |
| 530 |
|
|
| |
|
| 0% |
Uncovered Elements: 30 (30) |
Complexity: 9 |
Complexity Density: 0.45 |
|
| 531 |
0 |
@Override... |
| 532 |
|
public void parseResult() |
| 533 |
|
{ |
| 534 |
0 |
int results = 0; |
| 535 |
0 |
JobStateSummary finalState = new JobStateSummary(); |
| 536 |
0 |
try |
| 537 |
|
{ |
| 538 |
0 |
for (int j = 0; j < jobs.length; j++) |
| 539 |
|
{ |
| 540 |
0 |
finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]); |
| 541 |
0 |
if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete() |
| 542 |
|
&& jobs[j].hasResults()) |
| 543 |
|
{ |
| 544 |
0 |
results++; |
| 545 |
|
|
| 546 |
|
|
| 547 |
|
|
| 548 |
|
|
| 549 |
|
|
| 550 |
|
|
| 551 |
|
|
| 552 |
0 |
vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result) |
| 553 |
|
.getMsa(); |
| 554 |
0 |
if (valign != null) |
| 555 |
|
{ |
| 556 |
0 |
wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager |
| 557 |
|
.getString("info.alignment_object_method_notes")); |
| 558 |
0 |
String[] lines = valign.getMethod(); |
| 559 |
0 |
for (int line = 0; line < lines.length; line++) |
| 560 |
|
{ |
| 561 |
0 |
wsInfo.appendProgressText(jobs[j].getJobnum(), |
| 562 |
|
lines[line] + "\n"); |
| 563 |
|
} |
| 564 |
|
|
| 565 |
|
|
| 566 |
|
|
| 567 |
|
|
| 568 |
|
} |
| 569 |
|
} |
| 570 |
|
} |
| 571 |
|
} catch (Exception ex) |
| 572 |
|
{ |
| 573 |
|
|
| 574 |
0 |
Console.error( |
| 575 |
|
"Unexpected exception when processing results for " + alTitle, |
| 576 |
|
ex); |
| 577 |
0 |
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); |
| 578 |
|
} |
| 579 |
0 |
if (results > 0) |
| 580 |
|
{ |
| 581 |
0 |
wsInfo.showResultsNewFrame |
| 582 |
|
.addActionListener(new java.awt.event.ActionListener() |
| 583 |
|
{ |
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 584 |
0 |
@Override... |
| 585 |
|
public void actionPerformed(java.awt.event.ActionEvent evt) |
| 586 |
|
{ |
| 587 |
0 |
displayResults(true); |
| 588 |
|
} |
| 589 |
|
}); |
| 590 |
0 |
wsInfo.mergeResults |
| 591 |
|
.addActionListener(new java.awt.event.ActionListener() |
| 592 |
|
{ |
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 593 |
0 |
@Override... |
| 594 |
|
public void actionPerformed(java.awt.event.ActionEvent evt) |
| 595 |
|
{ |
| 596 |
0 |
displayResults(false); |
| 597 |
|
} |
| 598 |
|
}); |
| 599 |
0 |
wsInfo.setResultsReady(); |
| 600 |
|
} |
| 601 |
|
else |
| 602 |
|
{ |
| 603 |
0 |
wsInfo.setFinishedNoResults(); |
| 604 |
|
} |
| 605 |
|
} |
| 606 |
|
|
| |
|
| 0% |
Uncovered Elements: 67 (67) |
Complexity: 14 |
Complexity Density: 0.33 |
|
| 607 |
0 |
void displayResults(boolean newFrame)... |
| 608 |
|
{ |
| 609 |
|
|
| 610 |
0 |
Vector alorders = new Vector(); |
| 611 |
0 |
SequenceI[][] results = new SequenceI[jobs.length][]; |
| 612 |
0 |
AlignmentOrder[] orders = new AlignmentOrder[jobs.length]; |
| 613 |
0 |
for (int j = 0; j < jobs.length; j++) |
| 614 |
|
{ |
| 615 |
0 |
if (jobs[j].hasResults()) |
| 616 |
|
{ |
| 617 |
0 |
Object[] res = ((MsaWSJob) jobs[j]).getAlignment(); |
| 618 |
0 |
alorders.add(res[1]); |
| 619 |
0 |
results[j] = (SequenceI[]) res[0]; |
| 620 |
0 |
orders[j] = (AlignmentOrder) res[1]; |
| 621 |
|
|
| 622 |
|
|
| 623 |
|
} |
| 624 |
|
else |
| 625 |
|
{ |
| 626 |
0 |
results[j] = null; |
| 627 |
|
} |
| 628 |
|
} |
| 629 |
0 |
Object[] newview = input.getUpdatedView(results, orders, getGapChar()); |
| 630 |
|
|
| 631 |
0 |
for (int j = 0; j < jobs.length; j++) |
| 632 |
|
{ |
| 633 |
0 |
results[j] = null; |
| 634 |
0 |
orders[j] = null; |
| 635 |
|
} |
| 636 |
0 |
SequenceI[] alignment = (SequenceI[]) newview[0]; |
| 637 |
0 |
HiddenColumns hidden = (HiddenColumns) newview[1]; |
| 638 |
0 |
Alignment al = new Alignment(alignment); |
| 639 |
|
|
| 640 |
|
|
| 641 |
0 |
if (dataset != null) |
| 642 |
|
{ |
| 643 |
0 |
al.setDataset(dataset); |
| 644 |
|
} |
| 645 |
|
|
| 646 |
0 |
propagateDatasetMappings(al); |
| 647 |
|
|
| 648 |
|
|
| 649 |
0 |
if (newFrame) |
| 650 |
|
{ |
| 651 |
0 |
AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH, |
| 652 |
|
AlignFrame.DEFAULT_HEIGHT); |
| 653 |
|
|
| 654 |
|
|
| 655 |
0 |
af.getFeatureRenderer().transferSettings(this.featureSettings); |
| 656 |
|
|
| 657 |
0 |
if (alorders.size() > 0) |
| 658 |
|
{ |
| 659 |
0 |
if (alorders.size() == 1) |
| 660 |
|
{ |
| 661 |
0 |
af.addSortByOrderMenuItem(WebServiceName + " Ordering", |
| 662 |
|
(AlignmentOrder) alorders.get(0)); |
| 663 |
|
} |
| 664 |
|
else |
| 665 |
|
{ |
| 666 |
|
|
| 667 |
0 |
Vector names = new Vector(); |
| 668 |
0 |
for (int i = 0, l = alorders.size(); i < l; i++) |
| 669 |
|
{ |
| 670 |
0 |
String orderName = new String(" Region " + i); |
| 671 |
0 |
int j = i + 1; |
| 672 |
|
|
| 673 |
0 |
while (j < l) |
| 674 |
|
{ |
| 675 |
0 |
if (((AlignmentOrder) alorders.get(i)) |
| 676 |
|
.equals((alorders.get(j)))) |
| 677 |
|
{ |
| 678 |
0 |
alorders.remove(j); |
| 679 |
0 |
l--; |
| 680 |
0 |
orderName += "," + j; |
| 681 |
|
} |
| 682 |
|
else |
| 683 |
|
{ |
| 684 |
0 |
j++; |
| 685 |
|
} |
| 686 |
|
} |
| 687 |
|
|
| 688 |
0 |
if (i == 0 && j == 1) |
| 689 |
|
{ |
| 690 |
0 |
names.add(new String("")); |
| 691 |
|
} |
| 692 |
|
else |
| 693 |
|
{ |
| 694 |
0 |
names.add(orderName); |
| 695 |
|
} |
| 696 |
|
} |
| 697 |
0 |
for (int i = 0, l = alorders.size(); i < l; i++) |
| 698 |
|
{ |
| 699 |
0 |
af.addSortByOrderMenuItem( |
| 700 |
|
WebServiceName + ((String) names.get(i)) + " Ordering", |
| 701 |
|
(AlignmentOrder) alorders.get(i)); |
| 702 |
|
} |
| 703 |
|
} |
| 704 |
|
} |
| 705 |
|
|
| 706 |
0 |
Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH, |
| 707 |
|
AlignFrame.DEFAULT_HEIGHT); |
| 708 |
|
|
| 709 |
|
} |
| 710 |
|
else |
| 711 |
|
{ |
| 712 |
0 |
jalview.bin.Console.outPrintln("MERGE WITH OLD FRAME"); |
| 713 |
|
|
| 714 |
|
|
| 715 |
|
|
| 716 |
|
} |
| 717 |
|
} |
| 718 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 719 |
0 |
@Override... |
| 720 |
|
public boolean canMergeResults() |
| 721 |
|
{ |
| 722 |
0 |
return false; |
| 723 |
|
} |
| 724 |
|
} |