Changeset 3835


Ignore:
Timestamp:
Sep 8, 2010, 11:28:25 AM (13 years ago)
Author:
Fredrik Levander
Message:

Fixes #703. Retrieving prot_empai and parsing it in hits import.

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • trunk/api/core/src/org/proteios/io/AHit.java

    r3207 r3835  
    6161  private String spectrumStringId;
    6262  private Float retentionTimeInMinutes;
     63  private Float quantity;
    6364
    6465
    … …  
    562563    this.spectrumStringId = spectrumStringId;
    563564  }
     565 
     566
     567  public void setQuantity(Float quantity)
     568  {
     569    this.quantity = quantity;
     570  }
    564571
    565572
    … …  
    584591    return null;
    585592  }
     593
     594
     595  @Override
     596  public Float getQuantity()
     597  {
     598    return quantity;
     599  }
    586600}

  • trunk/api/core/src/org/proteios/io/HitInterface.java

    r3207 r3835  
    104104  public abstract Boolean isProtein();
    105105
     106  public abstract Float getQuantity();
    106107
    107108  /**

  • trunk/api/core/src/org/proteios/io/MascotFileReader.java

    r3699 r3835  
    323323            {
    324324              currentProteinHit.setPi(Float.parseFloat(parser
     325                .getElementText()));
     326              continue;
     327            }
     328            if (tag.equals("prot_empai"))
     329            {
     330              currentProteinHit.setQuantity(Float.parseFloat(parser
    325331                .getElementText()));
    326332              continue;

  • trunk/plugin/src/org/proteios/plugins/MascotResultRetrievalPlugin.java

    r2957 r3835  
    454454    mascotResultExportArgHashtable.put("prot_len", "0");
    455455    mascotResultExportArgHashtable.put("prot_pi", "1");
     456    mascotResultExportArgHashtable.put("prot_empai", "1");
    456457    mascotResultExportArgHashtable.put("prot_tax_str", "0");
    457458    mascotResultExportArgHashtable.put("prot_tax_id", "0");

  • trunk/plugin/src/org/proteios/plugins/SearchMascotPlugin.java

    r3763 r3835  
    12031203    mascotResultExportArgHashtable.put("prot_len", "0");
    12041204    mascotResultExportArgHashtable.put("prot_pi", "1");
     1205    mascotResultExportArgHashtable.put("prot_empai", "1");
    12051206    mascotResultExportArgHashtable.put("prot_tax_str", "0");
    12061207    mascotResultExportArgHashtable.put("prot_tax_id", "0");

  • trunk/plugin/src/org/proteios/plugins/SearchResultsImporter.java

    r3507 r3835  
    256256            hit.setTotalIntensity(ahit.getTotalIntensity());
    257257            hit.setTotalPeaks(ahit.getTotalPeaks());
     258            hit.setPrecursorQuantity(ahit.getQuantity());
    258259            if (hit.isProtein().booleanValue())
    259260            {
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