Changeset 2499


Ignore:
Timestamp:
Jun 5, 2014, 3:42:33 PM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #595: Confirm alignment

Display PT_READS in the confirmation wizard.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/align_confirm.jsp

    r2420 r2499  
    135135  html += '<th>Library</th>';
    136136  html += '<th class="dottedleft">Plate</th>';
    137   html += '<th class="dottedleft" colspan="3">Reads</th>';
     137  html += '<th class="dottedleft" colspan="4">Reads</th>';
    138138  html += '<th class="dottedleft">Job</th>';
    139139  html += '<th class="dottedleft" colspan="4">Actions</th>';
     
    144144  html += '<th class="dottedleft"></th>';
    145145  html += '<th class="dottedleft">PF_READS</th>';
     146  html += '<th>PT_READS</th>';
    146147  html += '<th>PM_READS</th>';
    147148  html += '<th>ALIGNED_PAIRS</th>';
     
    167168    var merged = aligned.merged;
    168169    var pfReads = merged.PF_READS == null ? '-' : formatNumber(merged.PF_READS/1000000, null, 2)
     170    var ptReads = merged.PT_READS == null ? '-' : formatNumber(merged.PT_READS/1000000, null, 2)
    169171    var maskedReads = masked.PM_READS == null ? '-' : formatNumber(masked.PM_READS/1000000, null, 2)
    170172    var alignedReads = aligned.ALIGNED_PAIRS == null ? '-' : formatNumber(aligned.ALIGNED_PAIRS/1000000, null, 2);
    171173    var job = aligned.job;
    172174   
    173     html += '<tr class="highlight">';
    174     html += '<td class="prompt">'+lib.name+'</td>';
     175    html += '<tr class="highlight ' + (alignedNo % 4 < 2 ? 'evenrow' : 'oddrow') + '">';
     176    html += '<td class="prompt">'+aligned.name+'</td>';
    175177    html += '<td class="dottedleft">'+libPlate.name+'</td>';
    176178    html += '<td class="dottedleft">'+pfReads+'</td>';
     179    html += '<td>'+ptReads+' ('+Math.round(100*ptReads/pfReads)+'%)</td>';
    177180    html += '<td>'+maskedReads+'</td>';
    178     html += '<td>'+alignedReads+'</td>';
     181    html += '<td>'+alignedReads+' ('+Math.round(100*alignedReads/pfReads)+'%)</td>';
    179182
    180183    html += '<td class="dottedleft">';
     
    334337}
    335338
     339.oddrow
     340{
     341  background-color: #F0F0F0;
     342}
     343
    336344#alignedSequencesTable
    337345{
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MaskAlignServlet.java

    r2460 r2499  
    207207          MergedSequences merged = masked.getMergedSequences(dc);
    208208          merged.loadAnnotations(dc, "PF_READS", Annotationtype.PF_READS, null);
     209          merged.loadAnnotations(dc, "PT_READS", Annotationtype.PT_READS, null);
    209210          aligned.setAnnotation("merged", merged.asJSONObject());
    210211         
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