Changeset 1386


Ignore:
Timestamp:
Jan 16, 2006, 2:35:16 PM (17 years ago)
Author:
fredrik
Message:

Majore revision of datamodel

Location:
trunk/src/org/proteios/core/element
Files:
10 added
2 deleted
14 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/org/proteios/core/element/CvLookup.java

    r787 r1386  
    3434  /**
    3535    Get a reference to the associated MzData element.
    36     @hibernate.many-to-one class="org.proteios.core.element.MzData" column="`MzData`"
     36    @hibernate.many-to-one class="org.proteios.core.element.MzData" column="`mzData`"
    3737   */
    3838  public MzData getMzData()

  • trunk/src/org/proteios/core/element/DBSearchParameters.java

    r969 r1386  
    4141{
    4242
    43   private Set fixed_modification_collection = new HashSet();
    44   private Set variable_modification_collection = new HashSet();
    4543  private Set taxonomical_filter_collection = new HashSet();
    4644  private Set enzyme_collection = new HashSet();
    … …  
    180178    this.db_search_param_collection = db_search_param_collection;
    181179  }
    182  
    183   /**
    184    * @hibernate.set
    185    *  inverse="true"
    186    *  lazy="true"
    187    * @hibernate.collection-one-to-many
    188    *  class="org.proteios.core.element.FixedModification"
    189    * @hibernate.collection-key
    190    *  column="`DBSearchParameters`"
    191    */
    192   public Set getFixedModificationCollection()
    193   {
    194     return fixed_modification_collection;
    195   }
    196   private void setFixedModificationCollection(Set fixed_modification_collection)
    197   {
    198     this.fixed_modification_collection = fixed_modification_collection;
    199   }
    200  
    201   /**
    202    * @hibernate.set
    203    *  inverse="true"
    204    *  lazy="true"
    205    * @hibernate.collection-one-to-many
    206    *  class="org.proteios.core.element.VariableModification"
    207    * @hibernate.collection-key
    208    *  column="`DBSearchParameters`"
    209    */
    210   public Set getVariableModificationCollection()
    211   {
    212     return variable_modification_collection;
    213   }
    214   private void setVariableModificationCollection(Set variable_modification_collection)
    215   {
    216     this.variable_modification_collection = variable_modification_collection;
    217   }
    218  
     180
    219181  /**
    220182   * @hibernate.property

  • trunk/src/org/proteios/core/element/GelItem.java

    r1343 r1386  
    7878        System.out.println("Ok to add PLGS project");
    7979        retval=true;
     80      }
     81    }
     82    else if (child instanceof MzData)
     83    {
     84      String target=((MzData) child).getTarget_id();
     85      String microplate=((MzData) child).getMPId();
     86      if (!this.getTarget_id().equals("") || !this.getMPId().equals(""))
     87      {
     88        // Either target or microplate should be set in the MzData, not both
     89        if (target.equals(""))
     90        {
     91          retval= (this.getMPLabel().equals(((MzData)child).getMPLabel()) && this.getMPId().equals(microplate));
     92        }
     93        if (MPId.equals(""))
     94        {
     95          retval= (this.getTarget_id().equals(((MzData)child).getTarget_position()) && this.getTarget_id().equals(target));
     96        }
     97      }
     98      else     
     99      {
     100         retval = (this.getTarget_id().equals(target) && this.getMPId().equals(microplate) && this.getMPLabel().equals(((MzData) child).getMPLabel()) && this.getTarget_position().equals(((MzData) child).getTarget_position()));
    80101      }
    81102    }
    … …  
    171192          }
    172193        }
    173         // If neither MP or target is given in the mzData or in in the Spot it
    174         // is ok to add
    175         else if (this.getMPId().equals(microplate) && this.getTarget_id().equals(target) && target.equals(""))
     194        // If all MP and target info is equal it is ok to add.
     195        // Even if empty string att all positions
     196        else if (this.getMPId().equals(microplate) && this.getTarget_id().equals(target) && (this.getMPLabel().equals(((MzData) child).getMPLabel())) && (this.getTarget_position().equals(((MzData) child).getTarget_position())))
    176197        {
    177198          okpos=true;
    … …  
    204225      }
    205226    }
     227    // Go down one step to add MzAnalysis
     228    else if (child instanceof MzAnalysis)
     229    {
     230      List child_elts = getChildren(this);
     231      for (int i = 0; i < child_elts.size(); ++i)
     232      {
     233        Object child_elt = child_elts.get(i);
     234        if (child_elt instanceof MzData)
     235        {
     236          retval = ((MzData) child_elt).addChildTree((MzData) child_elt,child);
     237        }
     238      }
     239    }
    206240    // Use normal addition for addition of other elements
    207241    else
    … …  
    209243      retval=super.addChildTree(parent,child);
    210244    }
    211 
    212245    return retval;   
    213246  }

  • trunk/src/org/proteios/core/element/MatchedMass.java

    r787 r1386  
    1919package org.proteios.core.element;
    2020
    21 import java.util.Set;
    22 import java.util.HashSet;
     21import java.util.SortedSet;
     22import java.util.TreeSet;
    2323
    2424import org.proteios.core.Element;
    … …  
    3535  private ProteinHit protein_hit;
    3636  private Double predicted_mass = new Double(0);
    37   private Set modification_collection = new HashSet();
     37  private SortedSet modification_collection = new TreeSet();
    3838 
    3939  public MatchedMass()
    … …  
    7171   *  inverse="true"
    7272   *  lazy="true"
     73   *  sort="natural"
    7374   * @hibernate.collection-one-to-many
    7475   *  class="org.proteios.core.element.Modification"
    … …  
    7677   *  column="`MatchedMass`"
    7778   */
    78   public Set getModificationCollection()
     79  public SortedSet getModificationCollection()
    7980  {
    8081    return modification_collection;
    8182  }
    82   private void setModificationCollection(Set modification_collection)
     83  private void setModificationCollection(SortedSet modification_collection)
    8384  {
    8485    this.modification_collection = modification_collection;

  • trunk/src/org/proteios/core/element/Modification.java

    r787 r1386  
    3636public class Modification
    3737  extends Element
     38  implements Comparable     
    3839{
    3940
    40   private Protein protein;
     41  private MzAnalysis mzAnalysis;
    4142  private MatchedMass matched_mass;
    4243  private PeptideHit peptide_hit;
    43   private String modification = "";
     44  private String name = "";
     45  private float monoIsotopicDeltaMass;
     46  private float averageDeltaMass;
     47  private float averageMass;
     48  private float monoIsotopicMass;
     49  private boolean variable;
     50  private String terminalSpecificity="";
     51  private String residueSpecificity="";
    4452
    4553  public Modification()
    4654  {
    47     super("modification", "modification");
    48   }
    49 
     55    super("Modification", "name");
     56  }
     57
     58  public int compareTo(Object o)
     59  {
     60    String name2 = ((Modification)o).getName();
     61    return name.compareTo(name2);
     62  }
     63 
    5064  /**
    5165  * We never allow anything to be added as a child to a modification.
    … …  
    6377  /**
    6478   * @hibernate.many-to-one
    65    *  class="org.proteios.core.element.Protein"
    66    *  column="`Protein`"
    67    */
    68   public Protein getProtein()
    69   {
    70     return protein;
    71   }
    72   private void setProtein(Protein protein)
    73   {
    74     this.protein = protein;
    75   }
    76 
    77   /**
    78    * @hibernate.many-to-one
    7979   *  class="org.proteios.core.element.MatchedMass"
    8080   *  column="`MatchedMass`"
    … …  
    104104
    105105  /**
    106    * @hibernate.property
    107    *  column="`modification`"
    108    */
    109   public String getModification()
    110   {
    111     return modification;
    112   }
    113   private void setModification(String modification)
    114   {
    115     this.modification = modification;
    116   }
     106   * @hibernate.many-to-one
     107   *  class="org.proteios.core.element.MzAnalysis"
     108   *  column="`MzAnalysis`"
     109   */
     110  public MzAnalysis getMzAnalysis()
     111  {
     112    return mzAnalysis;
     113  }
     114  private void setMzAnalysis(MzAnalysis mzAnalysis)
     115  {
     116    this.mzAnalysis = mzAnalysis;
     117  }
     118
     119  /**
     120   * @hibernate.property
     121   *  column="`name`"
     122   */
     123  public String getName()
     124  {
     125    return name;
     126  }
     127  private void setName(String name)
     128  {
     129    this.name = name;
     130  }
     131 
     132  /**
     133   * @hibernate.property
     134   *  column="`terminalSpecificity`"
     135   */
     136  public String getTerminalSpecificity()
     137  {
     138    return terminalSpecificity;
     139  }
     140  private void setTerminalSpecificity(String terminalSpecificity)
     141  {
     142    this.terminalSpecificity = terminalSpecificity;
     143  }
     144 
     145  /**
     146   * @hibernate.property
     147   *  column="`residueSpecificity`"
     148   */
     149  public String getResidueSpecificity()
     150  {
     151    return residueSpecificity;
     152  }
     153  private void setResidueSpecificity(String residueSpecificity)
     154  {
     155    this.residueSpecificity = residueSpecificity;
     156  }
     157 
     158  /**
     159   * @hibernate.property
     160   *  column="`variable`"
     161   */
     162  public boolean getVariable()
     163  {
     164    return variable;
     165  }
     166  private void setVariable(boolean variable)
     167  {
     168    this.variable = variable;
     169  }
     170 
     171  /**
     172   * @hibernate.property
     173   *  column="`averageDeltaMass`"
     174   */
     175  public float getAverageDeltaMass()
     176  {
     177    return averageDeltaMass;
     178  }
     179  private void setAverageDeltaMass(float averageDeltaMass)
     180  {
     181    this.averageDeltaMass = averageDeltaMass;
     182  }   
     183 
     184  /**
     185   * @hibernate.property
     186   *  column="`monoIsotopicDeltaMass`"
     187   */
     188  public float getMonoIsotopicDeltaMass()
     189  {
     190    return monoIsotopicDeltaMass;
     191  }
     192  private void setMonoIsotopicDeltaMass(float monoIsotopicDeltaMass)
     193  {
     194    this.monoIsotopicDeltaMass = monoIsotopicDeltaMass;
     195  }
     196 
     197  /**
     198   * @hibernate.property
     199   *  column="`averageMass`"
     200   */
     201  public float getAverageMass()
     202  {
     203    return averageMass;
     204  }
     205  private void setAverageMass(float averageMass)
     206  {
     207    this.averageMass = averageMass;
     208  }     
     209  /**
     210   * @hibernate.property
     211   *  column="`monoIsotopicMass`"
     212   */
     213  public float getMonoIsotopicMass()
     214  {
     215    return monoIsotopicMass;
     216  }
     217  private void setMonoIsotopicMass(float monoIsotopicMass)
     218  {
     219    this.monoIsotopicMass = monoIsotopicMass;
     220  }   
     221
    117222}

  • trunk/src/org/proteios/core/element/MzData.java

    r1131 r1386  
    2424import java.util.TreeSet;
    2525
     26import org.proteios.core.Element;
     27import org.proteios.core.CoreException;
     28
    2629/**
    2730 * @hibernate.class
    … …  
    3639  }
    3740
     41  /**
     42   * For addition of mzAnalysis we first check that the accession number is correct
     43   */
     44  public Element addChildTree(Object parent, Element child)
     45    throws CoreException
     46  {
     47    Element retval = null;
     48   
     49    // Only allow addition of mzAnalysis if the accession number is correct
     50
     51    if (child instanceof MzAnalysis)
     52    {
     53      if (((MzAnalysis) child).getInputAccessionNumber().equals(this.getAccessionNumber()))
     54      {
     55        retval=super.addChildTree(parent,child);
     56      }
     57    }
     58    else
     59    {
     60      retval= super.addChildTree(parent,child);
     61    }
     62    return retval;
     63  }
     64 
     65  /**
     66   * @hibernate.set
     67   *  inverse="true"
     68   *  lazy="true"
     69   *  sort="natural"
     70   * @hibernate.collection-one-to-many
     71   *  class="org.proteios.core.element.MzAnalysis"
     72   * @hibernate.collection-key
     73   *  column="`mzData`"
     74   */
     75  public SortedSet getMzAnalysisCollection()
     76  {
     77    return mzAnalysisCollection;
     78  }
     79  private void setMzAnalysisCollection(SortedSet mzc)
     80  {
     81    this.mzAnalysisCollection = mzc;
     82  }
    3883
    3984  /**
    … …  
    78123
    79124  /**
     125    @hibernate.set inverse="true" lazy="true"
     126    @hibernate.collection-one-to-many class="org.proteios.core.element.CvLookup"
     127    @hibernate.collection-key column="`mzData`"
     128  */
     129  public Set getCvLookupCollection()
     130  {
     131    return cv_lookups;
     132  }
     133  void setCvLookupCollection(Set cv_lookups)
     134  {
     135    this.cv_lookups = cv_lookups;
     136  }
     137
     138  /**
    80139  * @hibernate.property
    81140  * column="`version`"
    … …  
    104163  }
    105164
    106   /**
    107     @hibernate.set inverse="true" lazy="true"
    108     @hibernate.collection-one-to-many class="org.proteios.core.element.CvLookup"
    109     @hibernate.collection-key column="`MzData`"
    110   */
    111   public Set getCvLookupCollection()
    112   {
    113     return cv_lookups;
    114   }
    115   void setCvLookupCollection(Set cv_lookups)
    116   {
    117     this.cv_lookups = cv_lookups;
    118   }
    119 
    120165
    121166  /**
    … …  
    175220
    176221  private Set cv_lookups = new HashSet();
     222  private SortedSet mzAnalysisCollection = new TreeSet();
    177223  private SortedSet spectrumListCollection = new TreeSet();
    178224  private SortedSet descriptionCollection = new TreeSet();

  • trunk/src/org/proteios/core/element/Peak.java

    r1343 r1386  
    4343  private Set peakSpecificChromatogramIntegrationCollection;
    4444  private Set chromatogramPointCollection;
    45   private Set peakListCollection;
    4645
    4746  public Peak()
    … …  
    5049    peakSpecificChromatogramIntegrationCollection = new HashSet();
    5150    chromatogramPointCollection = new HashSet();
    52     peakListCollection = new HashSet();
    53    
     51 
    5452  }
    5553
    … …  
    5957    return mass.compareTo(mass2);
    6058  }
    61 
    62 
    63   /**
    64   * Is the Element given as parameter OK to add as a child to this one?
    65   * Peaks can have PeakList both as parent and children.
    66   * Regular procedure is for parent and child not to be of the same type.
    67   * Here we have to do an exact comparison - {@link Element#equalElement}.
    68   *
    69   * @param parent - the parent in the graph to add in - Not necessarily the XML
    70   * parent. Used classes are DataConnection and Element.
    71   * @param child - a candidate child in the graph - Not necessarily a child in
    72   * XML tree.
    73   * @return true if child is OK to add
    74   */
    75   public boolean isAddableChild(Object parent, Element child)
    76   {
    77     boolean retval = false;
    78 
    79     // Exact comparison, since PeakList can be both parent and child
    80     retval = !(parent instanceof Element && child.equalElement((Element) parent));
    81 
    82     // Defer graph cycles by not adding any children already in connection.
    83     if (retval && (dataConnection == child.getDataConnection()))
    84     {
    85       try
    86       {
    87         // Defer graph cycles by not adding if already held in data connection.
    88         List child_roots = dataConnection.getRootElements(child.getElementName());
    89         Element child_root = null;
    90         for (int i = 0; retval && i < child_roots.size(); ++i)
    91         {
    92           // Check until we possibly find child already in data connection.
    93           child_root = (Element) child_roots.get(i);
    94           retval = !(child.equalElement(child_root));
    95         }
    96       }
    97       catch (CoreException e)
    98       {
    99         // Don't bother - don't add.
    100         retval = false;
    101       }
    102     }
    103 
    104     return retval;
    105   }
    106 
    107 
    108   /**
    109   * Get children as seen from parent. This is regular procedure, except
    110   * PeakList can be both child and parent.
    111   *
    112   * @param parent - indication of where we are viewing from in our graph.
    113   * @return a List of child elements.
    114   */
    115   public List getChildren(Object parent)
    116     throws CoreException
    117   {
    118     List children = null;
    119 
    120     // Make sure we do not readd our parent as child.
    121     if (parent == peakList)
    122     {
    123       // Fetch ALL children.
    124       children = super.getChildren(null);
    125       // Remove our parent from the children's list.
    126       children.remove(peakList);
    127     }
    128     else
    129     {
    130       // Regular procedure.
    131       children = super.getChildren(parent);
    132     }
    133 
    134     return children;
    135   }
    136      
    13759
    13860  /**
    … …  
    15072  }
    15173 
    152   /**
    153    * This method links to the MSMS PeakLists derived from this Peak.
    154    *
    155    * @hibernate.set inverse="true" lazy="true"
    156    * @hibernate.collection-one-to-many class="org.proteios.core.element.PeakList"
    157    * @hibernate.collection-key column="`peak`"
    158    */
    159   public Set getPeakListCollection()
    160   {
    161     return peakListCollection;
    162   }
    163  
    164   void setPeakListCollection(Set peakListCollection)
    165   {
    166     this.peakListCollection = peakListCollection;
    167   }
    168 
    16974  /**
    17075   * @hibernate.property

  • trunk/src/org/proteios/core/element/PeakList.java

    r1355 r1386  
    4343
    4444  private SortedSet peakCollection;
    45   private Set peakListCollection;
    46   private PeakList peakList;
    4745  private Set deNovoSequencingCollection;
    4846  private Set listProcessingCollection;
    4947  private Set dbSearchCollection;
    5048  private Set mSMSFractionCollection;
    51   // "Full list", "Edited list" or "MSMS Result"
    5249  private String list_type = "Edited list";
    5350  private String description = "";
    … …  
    5552  private Boolean protonated;
    5653
    57   // Keys used to connect information from
    58   // different files.
    59   private String target_id;
    60   private String target_position;
    6154 
    6255  public PeakList()
    … …  
    6457    super("PeakList", "description");
    6558    peakCollection = new TreeSet();
    66     peakListCollection = new HashSet();
    6759    deNovoSequencingCollection = new HashSet();
    6860    listProcessingCollection = new HashSet();
    … …  
    7163  }
    7264
    73 
    74   /*
    75   * Special handling, since Peak can have PeakList both as parent and children.
    76   * Here we have to do an exact comparison - {@link Element#equalElement}.
    77   *
    78   * @param parent - the parent in the graph to add in - Not necessarily the XML
    79   * parent. Used classes are DataConnection and Element.
    80   * @param child - a candidate child in the graph - Not necessarily a child in
    81   * XML tree.
    82   * @return true if child is OK to add
    83   */
    84   public boolean isAddableChild(Object parent, Element child)
    85   {
    86     boolean retval = false;
    87 
    88     // Exact comparison, since PeakList can be both parent and child
    89     retval = !((parent instanceof Element && child.equalElement((Element) parent)) || child.equalElement(this));
    90 
    91     // Defer graph cycles by not adding any non Peak children already in conn.
    92     if (retval && !(child instanceof Peak) && (dataConnection == child.getDataConnection()))
    93     {
    94       try
    95       {
    96         // Defer graph cycles by not adding if already held in data connection.
    97         List child_roots = dataConnection.getRootElements(child.getElementName());
    98         Element child_root = null;
    99         for (int i = 0; retval && i < child_roots.size(); ++i)
    100         {
    101           // Check until we possibly find child already in data connection.
    102           child_root = (Element) child_roots.get(i);
    103           retval = !(child.equalElement(child_root));
    104         }
    105       }
    106       catch (CoreException e)
    107       {
    108         // Don't bother - don't add.
    109         retval = false;
    110       }
    111     }
    112 
    113     return retval;
    114   }
    115 
    116 
    117   /**
    118   * Get children as seen from parent. This is regular procedure, except
    119   * Peak can be both child and parent.
    120   *
    121   * @param parent - indication of where we are viewing from in our graph.
    122   * @return a List of child elements.
    123   */
    124   public List getChildren(Object parent)
    125     throws CoreException
    126   {
    127     List children = null;
    128 
    129     // Make sure we do not readd our parent as child.
    130     if (parent == peak)
    131     {
    132       // Fetch ALL children.
    133       children = super.getChildren(null);
    134       // Remove our parent from the children's list.
    135       children.remove(peak);
    136     }
    137     // Make sure we dont read our parent peaklist as a child
    138     else if (parent == peakList)
    139     {
    140       children = super.getChildren(null);
    141       children.remove(peakList);
    142     }
    143     else
    144     {
    145       // Regular procedure.
    146       children = super.getChildren(parent);
    147     }
    148 
    149     return children;
    150   }
    151  
    15265  /**
    15366   * @hibernate.many-to-one
    15467   *  class="org.proteios.core.element.Spectrum"
    155    *  column="`spectrum`"
     68   *  column="`Spectrum`"
    15669   */
    15770  public Spectrum getSpectrum()
    … …  
    16275  {
    16376    this.spectrum = spectrum;
    164   }
    165 
    166   /**
    167    * Link to the parent peaklist this (processed) peaklist is derived from.
    168    * @hibernate.many-to-one
    169    *  class="org.proteios.core.element.PeakList"
    170    *  column="`peakList`"
    171    */
    172   public PeakList getPeakList()
    173   {
    174     return peakList;
    175   }
    176   void setPeakList(PeakList peakList)
    177   {
    178     this.peakList = peakList;
    179   }
    180  
    181   /**
    182    * Links to the peak this (MSMS) peaklist is derived from.
    183    * @hibernate.many-to-one
    184    *  class="org.proteios.core.element.Peak"
    185    *  column="`peak`"
    186    */
    187   public Peak getPeak()
    188   {
    189     return peak;
    190   }
    191   void setPeak(Peak peak)
    192   {
    193     this.peak = peak;
    194   }
    195 
    196  
    197   /**
    198    * @hibernate.set
    199    *  inverse="true"
    200    *  lazy="true"
    201    * @hibernate.collection-one-to-many
    202    *  class="org.proteios.core.element.PeakList"
    203    * @hibernate.collection-key
    204    *  column="`peakList`"
    205    */
    206   public Set getPeakListCollection()
    207   {
    208     return peakListCollection;
    209   }
    210  
    211   void setPeakListCollection(Set peakListCollection)
    212   {
    213     this.peakListCollection = peakListCollection;
    21477  }
    21578

  • trunk/src/org/proteios/core/element/PeptideHit.java

    r1203 r1386  
    2020
    2121
    22 import java.util.Set;
    23 import java.util.HashSet;
     22import java.util.SortedSet;
     23import java.util.TreeSet;
    2424import java.util.List;
    2525import java.util.ArrayList;
    … …  
    6969   *  inverse="true"
    7070   *  lazy="true"
     71   *  sort="natural"
    7172   * @hibernate.collection-one-to-many
    7273   *  class="org.proteios.core.element.Modification"
    … …  
    7475   *  column="`PeptideHit`"
    7576   */
    76   public Set getModificationCollection()
     77  public SortedSet getModificationCollection()
    7778  {
    7879    return modification_collection;
    7980  }
    80   private void setModificationCollection(Set modification_collection)
     81  private void setModificationCollection(SortedSet modification_collection)
    8182  {
    8283    this.modification_collection = modification_collection;
    … …  
    168169
    169170  private ProteinHit protein_hit;
    170   private Set modification_collection = new HashSet();
     171  private SortedSet modification_collection = new TreeSet();
    171172  private Double predicted_mass = new Double(0);
    172173  private Double score = new Double(0);

  • trunk/src/org/proteios/core/element/Protein.java

    r1357 r1386  
    202202   *  lazy="true"
    203203   * @hibernate.collection-one-to-many
    204    *  class="org.proteios.core.element.Modification"
    205    * @hibernate.collection-key
    206    *  column="`Protein`"
    207    */
    208   public Set getModificationCollection()
    209   {
    210     return modification_collection;
    211   }
    212   private void setModificationCollection(Set modification_collection)
    213   {
    214     this.modification_collection = modification_collection;
    215   }
    216  
    217   /**
    218    * @hibernate.set
    219    *  inverse="true"
    220    *  lazy="true"
    221    * @hibernate.collection-one-to-many
    222204   *  class="org.proteios.core.element.Synonym"
    223205   * @hibernate.collection-key
    … …  
    259241    URL retval = null;
    260242    String identifier = "";
    261     if ((lsid != null) && lsid.matches("urn:lsid:thep.lu.se:uniprot:.*"))
     243    if ((lsid != null) && lsid.matches("urn:lsid:bioinfo.thep.lu.se:uniprot:.*"))
    262244    {
    263245      identifier = lsid.split(":")[4];

  • trunk/src/org/proteios/core/element/ProteiosElementFactory.java

    r1340 r1386  
    126126      nameClassMap.put("MatchedMass", org.proteios.core.element.MatchedMass.class);
    127127      nameClassMap.put("comments", org.proteios.core.element.Comments.class);
    128       nameClassMap.put("fixedModification", org.proteios.core.element.FixedModification.class);
    129       nameClassMap.put("variableModification", org.proteios.core.element.VariableModification.class);
     128      nameClassMap.put("UserModification", org.proteios.core.element.UserModification.class);
     129      nameClassMap.put("StandardModification", org.proteios.core.element.StandardModification.class);
    130130      nameClassMap.put("DeNovoSequencing", org.proteios.core.element.DeNovoSequencing.class);
    131131      nameClassMap.put("DeNovoSequencingParam", org.proteios.core.element.DeNovoSequencingParam.class);
    … …  
    137137      nameClassMap.put("DBSearchParam", org.proteios.core.element.DBSearchParam.class);
    138138      nameClassMap.put("synonym", org.proteios.core.element.Synonym.class);
    139       nameClassMap.put("modification", org.proteios.core.element.Modification.class);
     139      nameClassMap.put("Modification", org.proteios.core.element.Modification.class);
    140140      nameClassMap.put("stain_detail", org.proteios.core.element.StainDetail.class);
    141141      nameClassMap.put("first_dim_detail", org.proteios.core.element.FirstDimDetail.class);
    … …  
    143143      nameClassMap.put("result_citation", org.proteios.core.element.ResultCitation.class);
    144144      nameClassMap.put("method_citation", org.proteios.core.element.MethodCitation.class);
     145      nameClassMap.put("MzAnalysis", org.proteios.core.element.MzAnalysis.class);
     146      nameClassMap.put("IdentificationParameter", org.proteios.core.element.IdentificationParameter.class);
     147      nameClassMap.put("DigestParameter", org.proteios.core.element.DigestParameter.class);
     148      nameClassMap.put("Result", org.proteios.core.element.Result.class);
     149      nameClassMap.put("ResultRef", org.proteios.core.element.ResultRef.class);
     150      nameClassMap.put("IdentificationHypothesis", org.proteios.core.element.IdentificationHypothesis.class);
     151      nameClassMap.put("HypothesisProperty", org.proteios.core.element.HypothesisProperty.class);
     152      nameClassMap.put("PolyPeptide", org.proteios.core.element.PolyPeptide.class);
     153      nameClassMap.put("MoleculeIdentifier", org.proteios.core.element.MoleculeIdentifier.class);
     154      nameClassMap.put("ParentMolecule", org.proteios.core.element.ParentMolecule.class);
    145155      // All class names retrievable on a list.
    146156      nameList.addAll(nameClassMap.keySet());

  • trunk/src/org/proteios/core/element/Spectrum.java

    r1343 r1386  
    219219   *  class="org.proteios.core.element.PeakList"
    220220   * @hibernate.collection-key
    221    *  column="`spectrum`"
     221   *  column="`Spectrum`"
    222222   */
    223223  public Set getPeakListCollection()
    … …  
    284284   *  class="org.proteios.core.element.SpectrumDesc"
    285285   * @hibernate.collection-key
    286    *  column="`spectrum`"
     286   *  column="`Spectrum`"
    287287   */
    288288  public SortedSet getSpectrumDescCollection()

  • trunk/src/org/proteios/core/element/SpectrumDesc.java

    r1115 r1386  
    5555
    5656  /**
    57     @hibernate.many-to-one class="org.proteios.core.element.Spectrum" column="`spectrum`"
     57    @hibernate.many-to-one class="org.proteios.core.element.Spectrum" column="`Spectrum`"
    5858   */
    5959  public Spectrum getSpectrum()

  • trunk/src/org/proteios/core/element/SpectrumList.java

    r1291 r1386  
    3333  public SpectrumList()
    3434  {
    35     super("spectrumList");
     35    super("spectrumList","count");
    3636  }
    3737
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