Changeset 6600


Ignore:
Timestamp:
06/29/10 14:48:04 (9 years ago)
Author:
melissa
Message:

Fixed and uncommented most of the AnnotationRef conversion logic (and a few other *Ref conversions). Arc, Filament, Laser, LightEmittingDiode, and ListAnnotation.AnnotationRef are still not converted.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/bio-formats/src/loci/formats/meta/MetadataConverter.java

    r6568 r6600  
    2121Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA 
    2222*/ 
    23  
    24 /*----------------------------------------------------------------------------- 
    25  * 
    26  * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 3, 2010 12:36:59 PM CDT 
    28  * 
    29  *----------------------------------------------------------------------------- 
    30  */ 
    3123 
    3224package loci.formats.meta; 
     
    8577    for (int datasetIndex=0; datasetIndex<datasetCount; datasetIndex++) { 
    8678    try { 
    87       //String datasetAnnotationRefValue = src.getDatasetAnnotationRef(datasetIndex, annotationRefIndex); 
    88       //if (datasetAnnotationRefValue != null) dest.setDatasetAnnotationRef(datasetAnnotationRefValue, datasetIndex, annotationRefIndex); 
     79      for (int annotationRefIndex=0; annotationRefIndex<src.getDatasetAnnotationRefCount(datasetIndex); annotationRefIndex++) 
     80      { 
     81        String datasetAnnotationRefValue = src.getDatasetAnnotationRef(datasetIndex, annotationRefIndex); 
     82        if (datasetAnnotationRefValue != null) dest.setDatasetAnnotationRef(datasetAnnotationRefValue, datasetIndex, annotationRefIndex); 
     83      }  
    8984    } catch (NullPointerException e) { } 
    9085    try { 
     
    109104    } catch (NullPointerException e) { } 
    110105    try { 
    111       //String datasetProjectRefValue = src.getDatasetProjectRef(datasetIndex, projectRefIndex); 
    112       //if (datasetProjectRefValue != null) dest.setDatasetProjectRef(datasetProjectRefValue, datasetIndex, projectRefIndex); 
    113     } catch (NullPointerException e) { } 
    114       try { 
    115       //int annotationRefCount = src.getAnnotationRefCount(datasetIndex); 
    116       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    117       //} 
    118       } catch (NullPointerException e) { } 
    119       try { 
    120106      int projectRefCount = src.getProjectRefCount(datasetIndex); 
    121       for (int projectRefIndex=0; projectRefIndex<projectRefCount; projectRefIndex++) { 
     107      for (int projectRefIndex=0; projectRefIndex<projectRefCount; projectRefIndex++) 
     108      { 
     109        String datasetProjectRefValue = src.getDatasetProjectRef(datasetIndex, projectRefIndex); 
     110        if (datasetProjectRefValue != null) dest.setDatasetProjectRef(datasetProjectRefValue, datasetIndex, projectRefIndex); 
     111      } 
     112    } catch (NullPointerException e) { } 
     113      try { 
     114      int annotationRefCount = src.getDatasetAnnotationRefCount(datasetIndex); 
     115      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     116        String annotationValue = src.getDatasetAnnotationRef(datasetIndex, annotationRefIndex); 
     117        if (annotationValue != null) dest.setDatasetAnnotationRef(annotationValue, datasetIndex, annotationRefIndex); 
    122118      } 
    123119      } catch (NullPointerException e) { } 
     
    172168      } catch (NullPointerException e) { } 
    173169      try { 
    174         //String microbeamManipulationROIRefValue = src.getMicrobeamManipulationROIRef(experimentIndex, microbeamManipulationIndex, roiRefIndex); 
    175         //if (microbeamManipulationROIRefValue != null) dest.setMicrobeamManipulationROIRef(microbeamManipulationROIRefValue, experimentIndex, microbeamManipulationIndex, roiRefIndex); 
     170        int roiRefCount = src.getMicrobeamManipulationROIRefCount(experimentIndex, microbeamManipulationIndex); 
     171        for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
     172          String microbeamManipulationROIRefValue = src.getMicrobeamManipulationROIRef(experimentIndex, microbeamManipulationIndex, roiRefIndex); 
     173          if (microbeamManipulationROIRefValue != null) dest.setMicrobeamManipulationROIRef(microbeamManipulationROIRefValue, experimentIndex, microbeamManipulationIndex, roiRefIndex); 
     174        } 
    176175      } catch (NullPointerException e) { } 
    177176      try { 
     
    180179      } catch (NullPointerException e) { } 
    181180        try { 
    182         /* 
    183         int lightSourceSettingsCount = src.getLightSourceSettingsCount(experimentIndex, microbeamManipulationIndex); 
     181        int lightSourceSettingsCount = src.getMicrobeamManipulationLightSourceSettingsCount(experimentIndex, microbeamManipulationIndex); 
    184182        for (int lightSourceSettingsIndex=0; lightSourceSettingsIndex<lightSourceSettingsCount; lightSourceSettingsIndex++) { 
    185183        try { 
     
    196194        } catch (NullPointerException e) { } 
    197195        } 
    198         */ 
    199         } catch (NullPointerException e) { } 
    200         try { 
    201         //int roiRefCount = src.getROIRefCount(experimentIndex, microbeamManipulationIndex); 
    202         //for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
    203         //} 
    204196        } catch (NullPointerException e) { } 
    205197      } 
     
    211203    for (int experimenterIndex=0; experimenterIndex<experimenterCount; experimenterIndex++) { 
    212204    try { 
    213       //String experimenterAnnotationRefValue = src.getExperimenterAnnotationRef(experimenterIndex, annotationRefIndex); 
    214       //if (experimenterAnnotationRefValue != null) dest.setExperimenterAnnotationRef(experimenterAnnotationRefValue, experimenterIndex, annotationRefIndex); 
     205      int annotationRefCount = src.getExperimenterAnnotationRefCount(experimenterIndex); 
     206      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     207      { 
     208        String experimenterAnnotationRefValue = src.getExperimenterAnnotationRef(experimenterIndex, annotationRefIndex); 
     209        if (experimenterAnnotationRefValue != null) dest.setExperimenterAnnotationRef(experimenterAnnotationRefValue, experimenterIndex, annotationRefIndex); 
     210      } 
    215211    } catch (NullPointerException e) { } 
    216212    try { 
     
    227223    } catch (NullPointerException e) { } 
    228224    try { 
    229       //String experimenterGroupRefValue = src.getExperimenterGroupRef(experimenterIndex, groupRefIndex); 
    230       //if (experimenterGroupRefValue != null) dest.setExperimenterGroupRef(experimenterGroupRefValue, experimenterIndex, groupRefIndex); 
     225      int groupRefCount = src.getExperimenterGroupRefCount(experimenterIndex); 
     226      for (int groupRefIndex=0; groupRefIndex<groupRefCount; groupRefIndex++) { 
     227        String experimenterGroupRefValue = src.getExperimenterGroupRef(experimenterIndex, groupRefIndex); 
     228        if (experimenterGroupRefValue != null) dest.setExperimenterGroupRef(experimenterGroupRefValue, experimenterIndex, groupRefIndex); 
     229      } 
    231230    } catch (NullPointerException e) { } 
    232231    try { 
     
    251250    } catch (NullPointerException e) { } 
    252251      try { 
    253       //int annotationRefCount = src.getAnnotationRefCount(experimenterIndex); 
    254       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    255       //} 
    256       } catch (NullPointerException e) { } 
    257       try { 
    258       //int groupRefCount = src.getGroupRefCount(experimenterIndex); 
    259       //for (int groupRefIndex=0; groupRefIndex<groupRefCount; groupRefIndex++) { 
    260       //} 
     252        int annotationRefCount = src.getExperimenterAnnotationRefCount(experimenterIndex); 
     253        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     254          String annotationRef = src.getExperimenterAnnotationRef(experimenterIndex, annotationRefIndex); 
     255          if (annotationRef != null) dest.setExperimenterAnnotationRef(annotationRef, experimenterIndex, annotationRefIndex); 
     256        } 
     257      } catch (NullPointerException e) { } 
     258      try { 
     259        int groupRefCount = src.getExperimenterGroupRefCount(experimenterIndex); 
     260        for (int groupRefIndex=0; groupRefIndex<groupRefCount; groupRefIndex++) 
     261        { 
     262          String groupRef = src.getExperimenterGroupRef(experimenterIndex, groupRefIndex); 
     263          if (groupRef != null) dest.setExperimenterGroupRef(groupRef, experimenterIndex, groupRefIndex); 
     264        } 
    261265      } catch (NullPointerException e) { } 
    262266    } 
     
    320324    } catch (NullPointerException e) { } 
    321325    try { 
    322       //String imageAnnotationRefValue = src.getImageAnnotationRef(imageIndex, annotationRefIndex); 
    323       //if (imageAnnotationRefValue != null) dest.setImageAnnotationRef(imageAnnotationRefValue, imageIndex, annotationRefIndex); 
    324     } catch (NullPointerException e) { } 
    325     try { 
    326       //String imageDatasetRefValue = src.getImageDatasetRef(imageIndex, datasetRefIndex); 
    327       //if (imageDatasetRefValue != null) dest.setImageDatasetRef(imageDatasetRefValue, imageIndex, datasetRefIndex); 
     326      int annotationRefCount = src.getImageAnnotationRefCount(imageIndex); 
     327      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     328      { 
     329      String imageAnnotationRefValue = src.getImageAnnotationRef(imageIndex, annotationRefIndex); 
     330      if (imageAnnotationRefValue != null) dest.setImageAnnotationRef(imageAnnotationRefValue, imageIndex, annotationRefIndex); 
     331      } 
     332    } catch (NullPointerException e) { } 
     333    try { 
     334      int datasetRefCount = src.getDatasetRefCount(imageIndex); 
     335      for (int datasetRefIndex=0; datasetRefIndex<datasetRefCount; datasetRefIndex++) 
     336      { 
     337        String imageDatasetRefValue = src.getImageDatasetRef(imageIndex, datasetRefIndex); 
     338        if (imageDatasetRefValue != null) dest.setImageDatasetRef(imageDatasetRefValue, imageIndex, datasetRefIndex); 
     339      } 
    328340    } catch (NullPointerException e) { } 
    329341    try { 
     
    352364    } catch (NullPointerException e) { } 
    353365    try { 
    354       //String imageMicrobeamManipulationRefValue = src.getImageMicrobeamManipulationRef(imageIndex, microbeamManipulationRefIndex); 
    355       //if (imageMicrobeamManipulationRefValue != null) dest.setImageMicrobeamManipulationRef(imageMicrobeamManipulationRefValue, imageIndex, microbeamManipulationRefIndex); 
     366      int microbeamManipulationRefCount = src.getMicrobeamManipulationRefCount(imageIndex); 
     367      for (int microbeamManipulationRefIndex=0; microbeamManipulationRefIndex<microbeamManipulationRefCount; microbeamManipulationRefIndex++) 
     368      { 
     369        String imageMicrobeamManipulationRefValue = src.getImageMicrobeamManipulationRef(imageIndex, microbeamManipulationRefIndex); 
     370        if (imageMicrobeamManipulationRefValue != null) dest.setImageMicrobeamManipulationRef(imageMicrobeamManipulationRefValue, imageIndex, microbeamManipulationRefIndex); 
     371      } 
    356372    } catch (NullPointerException e) { } 
    357373    try { 
     
    376392    } catch (NullPointerException e) { } 
    377393    try { 
    378       //String imageROIRefValue = src.getImageROIRef(imageIndex, roiRefIndex); 
    379       //if (imageROIRefValue != null) dest.setImageROIRef(imageROIRefValue, imageIndex, roiRefIndex); 
    380     } catch (NullPointerException e) { } 
    381       try { 
    382       //int annotationRefCount = src.getAnnotationRefCount(imageIndex); 
    383       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    384       //} 
    385       } catch (NullPointerException e) { } 
     394      int roiRefCount = src.getImageROIRefCount(imageIndex); 
     395      for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
     396        String imageROIRefValue = src.getImageROIRef(imageIndex, roiRefIndex); 
     397        if (imageROIRefValue != null) dest.setImageROIRef(imageROIRefValue, imageIndex, roiRefIndex); 
     398      } 
     399    } catch (NullPointerException e) { } 
    386400      try { 
    387401      int channelCount = src.getChannelCount(imageIndex); 
     
    392406      } catch (NullPointerException e) { } 
    393407      try { 
    394         //String channelAnnotationRefValue = src.getChannelAnnotationRef(imageIndex, channelIndex, annotationRefIndex); 
    395         //if (channelAnnotationRefValue != null) dest.setChannelAnnotationRef(channelAnnotationRefValue, imageIndex, channelIndex, annotationRefIndex); 
     408        int annotationRefCount = src.getChannelAnnotationRefCount(imageIndex, channelIndex); 
     409        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
     410          String channelAnnotationRefValue = src.getChannelAnnotationRef(imageIndex, channelIndex, annotationRefIndex); 
     411          if (channelAnnotationRefValue != null) dest.setChannelAnnotationRef(channelAnnotationRefValue, imageIndex, channelIndex, annotationRefIndex); 
     412        } 
    396413      } catch (NullPointerException e) { } 
    397414      try { 
     
    464481      } catch (NullPointerException e) { } 
    465482        try { 
    466         //int annotationRefCount = src.getAnnotationRefCount(imageIndex, channelIndex); 
    467         //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    468         //} 
    469         } catch (NullPointerException e) { } 
    470         try { 
    471483          Binning detectorSettingsBinningValue = src.getDetectorSettingsBinning(imageIndex, channelIndex); 
    472484          if (detectorSettingsBinningValue != null) dest.setDetectorSettingsBinning(detectorSettingsBinningValue, imageIndex, channelIndex); 
     
    497509        } catch (NullPointerException e) { } 
    498510        try { 
    499           //String lightPathEmissionFilterRefValue = src.getLightPathEmissionFilterRef(imageIndex, channelIndex, emissionFilterRefIndex); 
    500           //if (lightPathEmissionFilterRefValue != null) dest.setLightPathEmissionFilterRef(lightPathEmissionFilterRefValue, imageIndex, channelIndex, emissionFilterRefIndex); 
    501         } catch (NullPointerException e) { } 
    502         try { 
    503           //String lightPathExcitationFilterRefValue = src.getLightPathExcitationFilterRef(imageIndex, channelIndex, excitationFilterRefIndex); 
    504           //if (lightPathExcitationFilterRefValue != null) dest.setLightPathExcitationFilterRef(lightPathExcitationFilterRefValue, imageIndex, channelIndex, excitationFilterRefIndex); 
    505         } catch (NullPointerException e) { } 
    506         try { 
    507         //int emissionFilterRefCount = src.getEmissionFilterRefCount(imageIndex, channelIndex); 
    508         //for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) { 
    509         //} 
    510         } catch (NullPointerException e) { } 
    511         try { 
    512         //int excitationFilterRefCount = src.getExcitationFilterRefCount(imageIndex, channelIndex); 
    513         //for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) { 
    514         //} 
     511          int emissionFilterRefCount = src.getLightPathEmissionFilterRefCount(imageIndex, channelIndex); 
     512          for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) 
     513          { 
     514            String lightPathEmissionFilterRefValue = src.getLightPathEmissionFilterRef(imageIndex, channelIndex, emissionFilterRefIndex); 
     515            if (lightPathEmissionFilterRefValue != null) dest.setLightPathEmissionFilterRef(lightPathEmissionFilterRefValue, imageIndex, channelIndex, emissionFilterRefIndex); 
     516          } 
     517        } catch (NullPointerException e) { } 
     518        try { 
     519          int excitationFilterRefCount = src.getLightPathExcitationFilterRefCount(imageIndex, channelIndex); 
     520          for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) 
     521          { 
     522            String lightPathExcitationFilterRefValue = src.getLightPathExcitationFilterRef(imageIndex, channelIndex, excitationFilterRefIndex); 
     523            if (lightPathExcitationFilterRefValue != null) dest.setLightPathExcitationFilterRef(lightPathExcitationFilterRefValue, imageIndex, channelIndex, excitationFilterRefIndex); 
     524          } 
    515525        } catch (NullPointerException e) { } 
    516526      } 
     
    543553      } catch (NullPointerException e) { } 
    544554      try { 
    545         //String pixelsAnnotationRefValue = src.getPixelsAnnotationRef(imageIndex, annotationRefIndex); 
    546         //if (pixelsAnnotationRefValue != null) dest.setPixelsAnnotationRef(pixelsAnnotationRefValue, imageIndex, annotationRefIndex); 
     555        int annotationRefCount = src.getPixelsAnnotationRefCount(imageIndex); 
     556        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     557        { 
     558          String pixelsAnnotationRefValue = src.getPixelsAnnotationRef(imageIndex, annotationRefIndex); 
     559          if (pixelsAnnotationRefValue != null) dest.setPixelsAnnotationRef(pixelsAnnotationRefValue, imageIndex, annotationRefIndex); 
     560        } 
    547561      } catch (NullPointerException e) { } 
    548562      try { 
     
    595609      } catch (NullPointerException e) { } 
    596610      try { 
    597       //int annotationRefCount = src.getAnnotationRefCount(imageIndex); 
    598       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    599       //} 
    600       } catch (NullPointerException e) { } 
    601       try { 
    602611      int binDataCount = src.getPixelsBinDataCount(imageIndex); 
    603612      for (int binDataIndex=0; binDataIndex<binDataCount; binDataIndex++) { 
     
    612621      for (int planeIndex=0; planeIndex<planeCount; planeIndex++) { 
    613622      try { 
    614         //String planeAnnotationRefValue = src.getPlaneAnnotationRef(imageIndex, planeIndex, annotationRefIndex); 
    615         //if (planeAnnotationRefValue != null) dest.setPlaneAnnotationRef(planeAnnotationRefValue, imageIndex, planeIndex, annotationRefIndex); 
     623        int planeAnnotationRefCount = src.getPlaneAnnotationRefCount(imageIndex, planeIndex); 
     624        for (int annotationRefIndex=0; annotationRefIndex<planeAnnotationRefCount; annotationRefIndex++) 
     625        { 
     626          String planeAnnotationRefValue = src.getPlaneAnnotationRef(imageIndex, planeIndex, annotationRefIndex); 
     627          if (planeAnnotationRefValue != null) dest.setPlaneAnnotationRef(planeAnnotationRefValue, imageIndex, planeIndex, annotationRefIndex); 
     628        } 
    616629      } catch (NullPointerException e) { } 
    617630      try { 
     
    651664        if (planeTheZValue != null) dest.setPlaneTheZ(planeTheZValue, imageIndex, planeIndex); 
    652665      } catch (NullPointerException e) { } 
    653         try { 
    654         //int annotationRefCount = src.getAnnotationRefCount(imageIndex, planeIndex); 
    655         //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    656         //} 
    657         } catch (NullPointerException e) { } 
    658       } 
    659       } catch (NullPointerException e) { } 
    660       try { 
    661       //int roiRefCount = src.getROIRefCount(imageIndex); 
    662       //for (int roiRefIndex=0; roiRefIndex<roiRefCount; roiRefIndex++) { 
    663       //} 
     666      } 
    664667      } catch (NullPointerException e) { } 
    665668      try { 
     
    926929      } catch (NullPointerException e) { } 
    927930      try { 
    928         //String filterSetEmissionFilterRefValue = src.getFilterSetEmissionFilterRef(instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
    929         //if (filterSetEmissionFilterRefValue != null) dest.setFilterSetEmissionFilterRef(filterSetEmissionFilterRefValue, instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
    930       } catch (NullPointerException e) { } 
    931       try { 
    932         //String filterSetExcitationFilterRefValue = src.getFilterSetExcitationFilterRef(instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
    933         //if (filterSetExcitationFilterRefValue != null) dest.setFilterSetExcitationFilterRef(filterSetExcitationFilterRefValue, instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
     931        int emissionFilterRefCount = src.getFilterSetEmissionFilterRefCount(instrumentIndex, filterSetIndex); 
     932        for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) 
     933        { 
     934          String filterSetEmissionFilterRefValue = src.getFilterSetEmissionFilterRef(instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
     935          if (filterSetEmissionFilterRefValue != null) dest.setFilterSetEmissionFilterRef(filterSetEmissionFilterRefValue, instrumentIndex, filterSetIndex, emissionFilterRefIndex); 
     936        } 
     937      } catch (NullPointerException e) { } 
     938      try { 
     939        int excitationFilterRefCount = src.getFilterSetExcitationFilterRefCount(instrumentIndex, filterSetIndex); 
     940        for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) 
     941        { 
     942          String filterSetExcitationFilterRefValue = src.getFilterSetExcitationFilterRef(instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
     943          if (filterSetExcitationFilterRefValue != null) dest.setFilterSetExcitationFilterRef(filterSetExcitationFilterRefValue, instrumentIndex, filterSetIndex, excitationFilterRefIndex); 
     944        } 
    934945      } catch (NullPointerException e) { } 
    935946      try { 
     
    953964        if (filterSetSerialNumberValue != null) dest.setFilterSetSerialNumber(filterSetSerialNumberValue, instrumentIndex, filterSetIndex); 
    954965      } catch (NullPointerException e) { } 
    955         try { 
    956         //int emissionFilterRefCount = src.getEmissionFilterRefCount(instrumentIndex, filterSetIndex); 
    957         //for (int emissionFilterRefIndex=0; emissionFilterRefIndex<emissionFilterRefCount; emissionFilterRefIndex++) { 
    958         //} 
    959         } catch (NullPointerException e) { } 
    960         try { 
    961         //int excitationFilterRefCount = src.getExcitationFilterRefCount(instrumentIndex, filterSetIndex); 
    962         //for (int excitationFilterRefIndex=0; excitationFilterRefIndex<excitationFilterRefCount; excitationFilterRefIndex++) { 
    963         //} 
    964         } catch (NullPointerException e) { } 
    965966      } 
    966967      } catch (NullPointerException e) { } 
     
    11991200    for (int listAnnotationIndex=0; listAnnotationIndex<listAnnotationCount; listAnnotationIndex++) { 
    12001201    try { 
    1201       //String listAnnotationAnnotationRefValue = src.getListAnnotationAnnotationRef(listAnnotationIndex, annotationRefIndex); 
    1202       //if (listAnnotationAnnotationRefValue != null) dest.setListAnnotationAnnotationRef(listAnnotationAnnotationRefValue, listAnnotationIndex, annotationRefIndex); 
     1202      //int annotationRefCount = src.getListAnnotationAnnotationRefCount(listAnnotationIndex); 
     1203      //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1204      //{ 
     1205      //  String listAnnotationAnnotationRefValue = src.getListAnnotationAnnotationRef(listAnnotationIndex, annotationRefIndex); 
     1206      //  if (listAnnotationAnnotationRefValue != null) dest.setListAnnotationAnnotationRef(listAnnotationAnnotationRefValue, listAnnotationIndex, annotationRefIndex); 
     1207      //} 
    12031208    } catch (NullPointerException e) { } 
    12041209    try { 
     
    12101215      if (listAnnotationNamespaceValue != null) dest.setListAnnotationNamespace(listAnnotationNamespaceValue, listAnnotationIndex); 
    12111216    } catch (NullPointerException e) { } 
    1212       try { 
    1213       //int annotationRefCount = src.getAnnotationRefCount(listAnnotationIndex); 
    1214       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1215       //} 
    1216       } catch (NullPointerException e) { } 
    12171217    } 
    12181218    } catch (NullPointerException e) { } 
     
    12381238    for (int plateIndex=0; plateIndex<plateCount; plateIndex++) { 
    12391239    try { 
    1240       //String plateAnnotationRefValue = src.getPlateAnnotationRef(plateIndex, annotationRefIndex); 
    1241       //if (plateAnnotationRefValue != null) dest.setPlateAnnotationRef(plateAnnotationRefValue, plateIndex, annotationRefIndex); 
     1240      int annotationRefCount = src.getPlateAnnotationRefCount(plateIndex); 
     1241      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1242      { 
     1243        String plateAnnotationRefValue = src.getPlateAnnotationRef(plateIndex, annotationRefIndex); 
     1244        if (plateAnnotationRefValue != null) dest.setPlateAnnotationRef(plateAnnotationRefValue, plateIndex, annotationRefIndex); 
     1245      } 
    12421246    } catch (NullPointerException e) { } 
    12431247    try { 
     
    12741278    } catch (NullPointerException e) { } 
    12751279    try { 
    1276       //String plateScreenRefValue = src.getPlateScreenRef(plateIndex, screenRefIndex); 
    1277       //if (plateScreenRefValue != null) dest.setPlateScreenRef(plateScreenRefValue, plateIndex, screenRefIndex); 
     1280      int screenRefCount = src.getScreenRefCount(plateIndex); 
     1281      for (int screenRefIndex=0; screenRefIndex<screenRefCount; screenRefIndex++) 
     1282      { 
     1283        String plateScreenRefValue = src.getPlateScreenRef(plateIndex, screenRefIndex); 
     1284        if (plateScreenRefValue != null) dest.setPlateScreenRef(plateScreenRefValue, plateIndex, screenRefIndex); 
     1285      } 
    12781286    } catch (NullPointerException e) { } 
    12791287    try { 
     
    12901298    } catch (NullPointerException e) { } 
    12911299      try { 
    1292       //int annotationRefCount = src.getAnnotationRefCount(plateIndex); 
    1293       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1294       //} 
    1295       } catch (NullPointerException e) { } 
    1296       try { 
    12971300      int plateAcquisitionCount = src.getPlateAcquisitionCount(plateIndex); 
    12981301      for (int plateAcquisitionIndex=0; plateAcquisitionIndex<plateAcquisitionCount; plateAcquisitionIndex++) { 
    12991302      try { 
    1300         //String plateAcquisitionAnnotationRefValue = src.getPlateAcquisitionAnnotationRef(plateIndex, plateAcquisitionIndex, annotationRefIndex); 
    1301         //if (plateAcquisitionAnnotationRefValue != null) dest.setPlateAcquisitionAnnotationRef(plateAcquisitionAnnotationRefValue, plateIndex, plateAcquisitionIndex, annotationRefIndex); 
     1303        int annotationRefCount = src.getPlateAcquisitionAnnotationRefCount(plateIndex, plateAcquisitionIndex); 
     1304        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1305        { 
     1306          String plateAcquisitionAnnotationRefValue = src.getPlateAcquisitionAnnotationRef(plateIndex, plateAcquisitionIndex, annotationRefIndex); 
     1307          if (plateAcquisitionAnnotationRefValue != null) dest.setPlateAcquisitionAnnotationRef(plateAcquisitionAnnotationRefValue, plateIndex, plateAcquisitionIndex, annotationRefIndex); 
     1308        } 
    13021309      } catch (NullPointerException e) { } 
    13031310      try { 
     
    13261333      } catch (NullPointerException e) { } 
    13271334      try { 
    1328         //String plateAcquisitionWellSampleRefValue = src.getPlateAcquisitionWellSampleRef(plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
    1329         //if (plateAcquisitionWellSampleRefValue != null) dest.setPlateAcquisitionWellSampleRef(plateAcquisitionWellSampleRefValue, plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
    1330       } catch (NullPointerException e) { } 
    1331         try { 
    1332         //int annotationRefCount = src.getAnnotationRefCount(plateIndex, plateAcquisitionIndex); 
    1333         //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1334         //} 
    1335         } catch (NullPointerException e) { } 
    1336         try { 
    13371335        int wellSampleRefCount = src.getWellSampleRefCount(plateIndex, plateAcquisitionIndex); 
    1338         for (int wellSampleRefIndex=0; wellSampleRefIndex<wellSampleRefCount; wellSampleRefIndex++) { 
     1336        for (int wellSampleRefIndex=0; wellSampleRefIndex<wellSampleRefCount; wellSampleRefIndex++) 
     1337        { 
     1338          String plateAcquisitionWellSampleRefValue = src.getPlateAcquisitionWellSampleRef(plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
     1339          if (plateAcquisitionWellSampleRefValue != null) dest.setPlateAcquisitionWellSampleRef(plateAcquisitionWellSampleRefValue, plateIndex, plateAcquisitionIndex, wellSampleRefIndex); 
    13391340        } 
    1340         } catch (NullPointerException e) { } 
    1341       } 
    1342       } catch (NullPointerException e) { } 
    1343       try { 
    1344       int screenRefCount = src.getScreenRefCount(plateIndex); 
    1345       for (int screenRefIndex=0; screenRefIndex<screenRefCount; screenRefIndex++) { 
     1341      } catch (NullPointerException e) { } 
    13461342      } 
    13471343      } catch (NullPointerException e) { } 
     
    13501346      for (int wellIndex=0; wellIndex<wellCount; wellIndex++) { 
    13511347      try { 
    1352         //String wellAnnotationRefValue = src.getWellAnnotationRef(plateIndex, wellIndex, annotationRefIndex); 
    1353         //if (wellAnnotationRefValue != null) dest.setWellAnnotationRef(wellAnnotationRefValue, plateIndex, wellIndex, annotationRefIndex); 
     1348        int annotationRefCount = src.getWellAnnotationRefCount(plateIndex, wellIndex); 
     1349        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1350        { 
     1351          String wellAnnotationRefValue = src.getWellAnnotationRef(plateIndex, wellIndex, annotationRefIndex); 
     1352          if (wellAnnotationRefValue != null) dest.setWellAnnotationRef(wellAnnotationRefValue, plateIndex, wellIndex, annotationRefIndex); 
     1353        } 
    13541354      } catch (NullPointerException e) { } 
    13551355      try { 
     
    13861386      } catch (NullPointerException e) { } 
    13871387        try { 
    1388         //int annotationRefCount = src.getAnnotationRefCount(plateIndex, wellIndex); 
    1389         //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1390         //} 
    1391         } catch (NullPointerException e) { } 
    1392         try { 
    13931388        int wellSampleCount = src.getWellSampleCount(plateIndex, wellIndex); 
    13941389        for (int wellSampleIndex=0; wellSampleIndex<wellSampleCount; wellSampleIndex++) { 
    13951390        try { 
    1396           //String wellSampleAnnotationRefValue = src.getWellSampleAnnotationRef(plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
    1397           //if (wellSampleAnnotationRefValue != null) dest.setWellSampleAnnotationRef(wellSampleAnnotationRefValue, plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
     1391          int annotationRefCount = src.getWellSampleAnnotationRefCount(plateIndex, wellIndex, wellSampleIndex); 
     1392          for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1393          { 
     1394            String wellSampleAnnotationRefValue = src.getWellSampleAnnotationRef(plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
     1395            if (wellSampleAnnotationRefValue != null) dest.setWellSampleAnnotationRef(wellSampleAnnotationRefValue, plateIndex, wellIndex, wellSampleIndex, annotationRefIndex); 
     1396          } 
    13981397        } catch (NullPointerException e) { } 
    13991398        try { 
     
    14211420          if (wellSampleTimepointValue != null) dest.setWellSampleTimepoint(wellSampleTimepointValue, plateIndex, wellIndex, wellSampleIndex); 
    14221421        } catch (NullPointerException e) { } 
    1423           try { 
    1424           //int annotationRefCount = src.getAnnotationRefCount(plateIndex, wellIndex, wellSampleIndex); 
    1425           //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1426           //} 
    1427           } catch (NullPointerException e) { } 
    14281422        } 
    14291423        } catch (NullPointerException e) { } 
     
    14361430    for (int projectIndex=0; projectIndex<projectCount; projectIndex++) { 
    14371431    try { 
    1438       //String projectAnnotationRefValue = src.getProjectAnnotationRef(projectIndex, annotationRefIndex); 
    1439       //if (projectAnnotationRefValue != null) dest.setProjectAnnotationRef(projectAnnotationRefValue, projectIndex, annotationRefIndex); 
     1432      int annotationRefCount = src.getProjectAnnotationRefCount(projectIndex); 
     1433      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1434      { 
     1435        String projectAnnotationRefValue = src.getProjectAnnotationRef(projectIndex, annotationRefIndex); 
     1436        if (projectAnnotationRefValue != null) dest.setProjectAnnotationRef(projectAnnotationRefValue, projectIndex, annotationRefIndex); 
     1437      } 
    14401438    } catch (NullPointerException e) { } 
    14411439    try { 
     
    14591457      if (projectNameValue != null) dest.setProjectName(projectNameValue, projectIndex); 
    14601458    } catch (NullPointerException e) { } 
    1461       try { 
    1462       //int annotationRefCount = src.getAnnotationRefCount(projectIndex); 
    1463       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1464       //} 
    1465       } catch (NullPointerException e) { } 
    14661459    } 
    14671460    } catch (NullPointerException e) { } 
     
    14701463    for (int roiIndex=0; roiIndex<roiCount; roiIndex++) { 
    14711464    try { 
    1472       //String roiAnnotationRefValue = src.getROIAnnotationRef(roiIndex, annotationRefIndex); 
    1473       //if (roiAnnotationRefValue != null) dest.setROIAnnotationRef(roiAnnotationRefValue, roiIndex, annotationRefIndex); 
     1465      int annotationRefCount = src.getROIAnnotationRefCount(roiIndex); 
     1466      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     1467      { 
     1468        String roiAnnotationRefValue = src.getROIAnnotationRef(roiIndex, annotationRefIndex); 
     1469        if (roiAnnotationRefValue != null) dest.setROIAnnotationRef(roiAnnotationRefValue, roiIndex, annotationRefIndex); 
     1470      } 
    14741471    } catch (NullPointerException e) { } 
    14751472    try { 
     
    14901487    } catch (NullPointerException e) { } 
    14911488      try { 
    1492       //int annotationRefCount = src.getAnnotationRefCount(roiIndex); 
    1493       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1494       //} 
    1495       } catch (NullPointerException e) { } 
    1496       try { 
    1497       /* 
    1498       int shapeCount = src.getShapeCount(roiIndex, shapeIndex); 
     1489      int shapeCount = src.getShapeCount(roiIndex); 
    14991490      for (int shapeIndex=0; shapeIndex<shapeCount; shapeIndex++) { 
    1500         try { 
    1501         int annotationRefCount = src.getAnnotationRefCount(roiIndex, shapeIndex); 
    1502         for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    1503         } 
    1504         } catch (NullPointerException e) { } 
    15051491        try { 
    15061492          String ellipseDescriptionValue = src.getEllipseDescription(roiIndex, shapeIndex); 
     
    15121498        } catch (NullPointerException e) { } 
    15131499        try { 
    1514           Integer ellipseFontSizeValue = src.getEllipseFontSize(roiIndex, shapeIndex); 
     1500          NonNegativeInteger ellipseFontSizeValue = src.getEllipseFontSize(roiIndex, shapeIndex); 
    15151501          if (ellipseFontSizeValue != null) dest.setEllipseFontSize(ellipseFontSizeValue, roiIndex, shapeIndex); 
    15161502        } catch (NullPointerException e) { } 
     
    15481534        } catch (NullPointerException e) { } 
    15491535        try { 
    1550           Integer ellipseTheCValue = src.getEllipseTheC(roiIndex, shapeIndex); 
     1536          NonNegativeInteger ellipseTheCValue = src.getEllipseTheC(roiIndex, shapeIndex); 
    15511537          if (ellipseTheCValue != null) dest.setEllipseTheC(ellipseTheCValue, roiIndex, shapeIndex); 
    15521538        } catch (NullPointerException e) { } 
    15531539        try { 
    1554           Integer ellipseTheTValue = src.getEllipseTheT(roiIndex, shapeIndex); 
     1540          NonNegativeInteger ellipseTheTValue = src.getEllipseTheT(roiIndex, shapeIndex); 
    15551541          if (ellipseTheTValue != null) dest.setEllipseTheT(ellipseTheTValue, roiIndex, shapeIndex); 
    15561542        } catch (NullPointerException e) { } 
    15571543        try { 
    1558           Integer ellipseTheZValue = src.getEllipseTheZ(roiIndex, shapeIndex); 
     1544          NonNegativeInteger ellipseTheZValue = src.getEllipseTheZ(roiIndex, shapeIndex); 
    15591545          if (ellipseTheZValue != null) dest.setEllipseTheZ(ellipseTheZValue, roiIndex, shapeIndex); 
    15601546        } catch (NullPointerException e) { } 
     
    15801566        } catch (NullPointerException e) { } 
    15811567        try { 
    1582           Integer lineFontSizeValue = src.getLineFontSize(roiIndex, shapeIndex); 
     1568          NonNegativeInteger lineFontSizeValue = src.getLineFontSize(roiIndex, shapeIndex); 
    15831569          if (lineFontSizeValue != null) dest.setLineFontSize(lineFontSizeValue, roiIndex, shapeIndex); 
    15841570        } catch (NullPointerException e) { } 
     
    16081594        } catch (NullPointerException e) { } 
    16091595        try { 
    1610           Integer lineTheCValue = src.getLineTheC(roiIndex, shapeIndex); 
     1596          NonNegativeInteger lineTheCValue = src.getLineTheC(roiIndex, shapeIndex); 
    16111597          if (lineTheCValue != null) dest.setLineTheC(lineTheCValue, roiIndex, shapeIndex); 
    16121598        } catch (NullPointerException e) { } 
    16131599        try { 
    1614           Integer lineTheTValue = src.getLineTheT(roiIndex, shapeIndex); 
     1600          NonNegativeInteger lineTheTValue = src.getLineTheT(roiIndex, shapeIndex); 
    16151601          if (lineTheTValue != null) dest.setLineTheT(lineTheTValue, roiIndex, shapeIndex); 
    16161602        } catch (NullPointerException e) { } 
    16171603        try { 
    1618           Integer lineTheZValue = src.getLineTheZ(roiIndex, shapeIndex); 
     1604          NonNegativeInteger lineTheZValue = src.getLineTheZ(roiIndex, shapeIndex); 
    16191605          if (lineTheZValue != null) dest.setLineTheZ(lineTheZValue, roiIndex, shapeIndex); 
    16201606        } catch (NullPointerException e) { } 
     
    16481634        } catch (NullPointerException e) { } 
    16491635        try { 
    1650           Integer maskFontSizeValue = src.getMaskFontSize(roiIndex, shapeIndex); 
     1636          NonNegativeInteger maskFontSizeValue = src.getMaskFontSize(roiIndex, shapeIndex); 
    16511637          if (maskFontSizeValue != null) dest.setMaskFontSize(maskFontSizeValue, roiIndex, shapeIndex); 
    16521638        } catch (NullPointerException e) { } 
     
    16761662        } catch (NullPointerException e) { } 
    16771663        try { 
    1678           Integer maskTheCValue = src.getMaskTheC(roiIndex, shapeIndex); 
     1664          NonNegativeInteger maskTheCValue = src.getMaskTheC(roiIndex, shapeIndex); 
    16791665          if (maskTheCValue != null) dest.setMaskTheC(maskTheCValue, roiIndex, shapeIndex); 
    16801666        } catch (NullPointerException e) { } 
    16811667        try { 
    1682           Integer maskTheTValue = src.getMaskTheT(roiIndex, shapeIndex); 
     1668          NonNegativeInteger maskTheTValue = src.getMaskTheT(roiIndex, shapeIndex); 
    16831669          if (maskTheTValue != null) dest.setMaskTheT(maskTheTValue, roiIndex, shapeIndex); 
    16841670        } catch (NullPointerException e) { } 
    16851671        try { 
    1686           Integer maskTheZValue = src.getMaskTheZ(roiIndex, shapeIndex); 
     1672          NonNegativeInteger maskTheZValue = src.getMaskTheZ(roiIndex, shapeIndex); 
    16871673          if (maskTheZValue != null) dest.setMaskTheZ(maskTheZValue, roiIndex, shapeIndex); 
    16881674        } catch (NullPointerException e) { } 
     
    17121698        } catch (NullPointerException e) { } 
    17131699        try { 
    1714           Integer pathFontSizeValue = src.getPathFontSize(roiIndex, shapeIndex); 
     1700          NonNegativeInteger pathFontSizeValue = src.getPathFontSize(roiIndex, shapeIndex); 
    17151701          if (pathFontSizeValue != null) dest.setPathFontSize(pathFontSizeValue, roiIndex, shapeIndex); 
    17161702        } catch (NullPointerException e) { } 
     
    17401726        } catch (NullPointerException e) { } 
    17411727        try { 
    1742           Integer pathTheCValue = src.getPathTheC(roiIndex, shapeIndex); 
     1728          NonNegativeInteger pathTheCValue = src.getPathTheC(roiIndex, shapeIndex); 
    17431729          if (pathTheCValue != null) dest.setPathTheC(pathTheCValue, roiIndex, shapeIndex); 
    17441730        } catch (NullPointerException e) { } 
    17451731        try { 
    1746           Integer pathTheTValue = src.getPathTheT(roiIndex, shapeIndex); 
     1732          NonNegativeInteger pathTheTValue = src.getPathTheT(roiIndex, shapeIndex); 
    17471733          if (pathTheTValue != null) dest.setPathTheT(pathTheTValue, roiIndex, shapeIndex); 
    17481734        } catch (NullPointerException e) { } 
    17491735        try { 
    1750           Integer pathTheZValue = src.getPathTheZ(roiIndex, shapeIndex); 
     1736          NonNegativeInteger pathTheZValue = src.getPathTheZ(roiIndex, shapeIndex); 
    17511737          if (pathTheZValue != null) dest.setPathTheZ(pathTheZValue, roiIndex, shapeIndex); 
    17521738        } catch (NullPointerException e) { } 
     
    17641750        } catch (NullPointerException e) { } 
    17651751        try { 
    1766           Integer pointFontSizeValue = src.getPointFontSize(roiIndex, shapeIndex); 
     1752          NonNegativeInteger pointFontSizeValue = src.getPointFontSize(roiIndex, shapeIndex); 
    17671753          if (pointFontSizeValue != null) dest.setPointFontSize(pointFontSizeValue, roiIndex, shapeIndex); 
    17681754        } catch (NullPointerException e) { } 
     
    17921778        } catch (NullPointerException e) { } 
    17931779        try { 
    1794           Integer pointTheCValue = src.getPointTheC(roiIndex, shapeIndex); 
     1780          NonNegativeInteger pointTheCValue = src.getPointTheC(roiIndex, shapeIndex); 
    17951781          if (pointTheCValue != null) dest.setPointTheC(pointTheCValue, roiIndex, shapeIndex); 
    17961782        } catch (NullPointerException e) { } 
    17971783        try { 
    1798           Integer pointTheTValue = src.getPointTheT(roiIndex, shapeIndex); 
     1784          NonNegativeInteger pointTheTValue = src.getPointTheT(roiIndex, shapeIndex); 
    17991785          if (pointTheTValue != null) dest.setPointTheT(pointTheTValue, roiIndex, shapeIndex); 
    18001786        } catch (NullPointerException e) { } 
    18011787        try { 
    1802           Integer pointTheZValue = src.getPointTheZ(roiIndex, shapeIndex); 
     1788          NonNegativeInteger pointTheZValue = src.getPointTheZ(roiIndex, shapeIndex); 
    18031789          if (pointTheZValue != null) dest.setPointTheZ(pointTheZValue, roiIndex, shapeIndex); 
    18041790        } catch (NullPointerException e) { } 
     
    18281814        } catch (NullPointerException e) { } 
    18291815        try { 
    1830           Integer polylineFontSizeValue = src.getPolylineFontSize(roiIndex, shapeIndex); 
     1816          NonNegativeInteger polylineFontSizeValue = src.getPolylineFontSize(roiIndex, shapeIndex); 
    18311817          if (polylineFontSizeValue != null) dest.setPolylineFontSize(polylineFontSizeValue, roiIndex, shapeIndex); 
    18321818        } catch (NullPointerException e) { } 
     
    18601846        } catch (NullPointerException e) { } 
    18611847        try { 
    1862           Integer polylineTheCValue = src.getPolylineTheC(roiIndex, shapeIndex); 
     1848          NonNegativeInteger polylineTheCValue = src.getPolylineTheC(roiIndex, shapeIndex); 
    18631849          if (polylineTheCValue != null) dest.setPolylineTheC(polylineTheCValue, roiIndex, shapeIndex); 
    18641850        } catch (NullPointerException e) { } 
    18651851        try { 
    1866           Integer polylineTheTValue = src.getPolylineTheT(roiIndex, shapeIndex); 
     1852          NonNegativeInteger polylineTheTValue = src.getPolylineTheT(roiIndex, shapeIndex); 
    18671853          if (polylineTheTValue != null) dest.setPolylineTheT(polylineTheTValue, roiIndex, shapeIndex); 
    18681854        } catch (NullPointerException e) { } 
    18691855        try { 
    1870           Integer polylineTheZValue = src.getPolylineTheZ(roiIndex, shapeIndex); 
     1856          NonNegativeInteger polylineTheZValue = src.getPolylineTheZ(roiIndex, shapeIndex); 
    18711857          if (polylineTheZValue != null) dest.setPolylineTheZ(polylineTheZValue, roiIndex, shapeIndex); 
    18721858        } catch (NullPointerException e) { } 
     
    18841870        } catch (NullPointerException e) { } 
    18851871        try { 
    1886           Integer rectangleFontSizeValue = src.getRectangleFontSize(roiIndex, shapeIndex); 
     1872          NonNegativeInteger rectangleFontSizeValue = src.getRectangleFontSize(roiIndex, shapeIndex); 
    18871873          if (rectangleFontSizeValue != null) dest.setRectangleFontSize(rectangleFontSizeValue, roiIndex, shapeIndex); 
    18881874        } catch (NullPointerException e) { } 
     
    19161902        } catch (NullPointerException e) { } 
    19171903        try { 
    1918           Integer rectangleTheCValue = src.getRectangleTheC(roiIndex, shapeIndex); 
     1904          NonNegativeInteger rectangleTheCValue = src.getRectangleTheC(roiIndex, shapeIndex); 
    19191905          if (rectangleTheCValue != null) dest.setRectangleTheC(rectangleTheCValue, roiIndex, shapeIndex); 
    19201906        } catch (NullPointerException e) { } 
    19211907        try { 
    1922           Integer rectangleTheTValue = src.getRectangleTheT(roiIndex, shapeIndex); 
     1908          NonNegativeInteger rectangleTheTValue = src.getRectangleTheT(roiIndex, shapeIndex); 
    19231909          if (rectangleTheTValue != null) dest.setRectangleTheT(rectangleTheTValue, roiIndex, shapeIndex); 
    19241910        } catch (NullPointerException e) { } 
    19251911        try { 
    1926           Integer rectangleTheZValue = src.getRectangleTheZ(roiIndex, shapeIndex); 
     1912          NonNegativeInteger rectangleTheZValue = src.getRectangleTheZ(roiIndex, shapeIndex); 
    19271913          if (rectangleTheZValue != null) dest.setRectangleTheZ(rectangleTheZValue, roiIndex, shapeIndex); 
    19281914        } catch (NullPointerException e) { } 
     
    19521938        } catch (NullPointerException e) { } 
    19531939        try { 
    1954           Integer textFontSizeValue = src.getTextFontSize(roiIndex, shapeIndex); 
     1940          NonNegativeInteger textFontSizeValue = src.getTextFontSize(roiIndex, shapeIndex); 
    19551941          if (textFontSizeValue != null) dest.setTextFontSize(textFontSizeValue, roiIndex, shapeIndex); 
    19561942        } catch (NullPointerException e) { } 
     
    19801966        } catch (NullPointerException e) { } 
    19811967        try { 
    1982           Integer textTheCValue = src.getTextTheC(roiIndex, shapeIndex); 
     1968          NonNegativeInteger textTheCValue = src.getTextTheC(roiIndex, shapeIndex); 
    19831969          if (textTheCValue != null) dest.setTextTheC(textTheCValue, roiIndex, shapeIndex); 
    19841970        } catch (NullPointerException e) { } 
    19851971        try { 
    1986           Integer textTheTValue = src.getTextTheT(roiIndex, shapeIndex); 
     1972          NonNegativeInteger textTheTValue = src.getTextTheT(roiIndex, shapeIndex); 
    19871973          if (textTheTValue != null) dest.setTextTheT(textTheTValue, roiIndex, shapeIndex); 
    19881974        } catch (NullPointerException e) { } 
    19891975        try { 
    1990           Integer textTheZValue = src.getTextTheZ(roiIndex, shapeIndex); 
     1976          NonNegativeInteger textTheZValue = src.getTextTheZ(roiIndex, shapeIndex); 
    19911977          if (textTheZValue != null) dest.setTextTheZ(textTheZValue, roiIndex, shapeIndex); 
    19921978        } catch (NullPointerException e) { } 
     
    20081994        } catch (NullPointerException e) { } 
    20091995      } 
    2010       */ 
    20111996      } catch (NullPointerException e) { } 
    20121997    } 
     
    20162001    for (int screenIndex=0; screenIndex<screenCount; screenIndex++) { 
    20172002    try { 
    2018       //String screenAnnotationRefValue = src.getScreenAnnotationRef(screenIndex, annotationRefIndex); 
    2019       //if (screenAnnotationRefValue != null) dest.setScreenAnnotationRef(screenAnnotationRefValue, screenIndex, annotationRefIndex); 
     2003      int annotationRefCount = src.getScreenAnnotationRefCount(screenIndex); 
     2004      for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     2005      { 
     2006        String screenAnnotationRefValue = src.getScreenAnnotationRef(screenIndex, annotationRefIndex); 
     2007        if (screenAnnotationRefValue != null) dest.setScreenAnnotationRef(screenAnnotationRefValue, screenIndex, annotationRefIndex); 
     2008      } 
    20202009    } catch (NullPointerException e) { } 
    20212010    try { 
     
    20322021    } catch (NullPointerException e) { } 
    20332022    try { 
    2034       //String screenPlateRefValue = src.getScreenPlateRef(screenIndex, plateRefIndex); 
    2035       //if (screenPlateRefValue != null) dest.setScreenPlateRef(screenPlateRefValue, screenIndex, plateRefIndex); 
     2023      int plateRefCount = src.getPlateRefCount(screenIndex); 
     2024      for (int plateRefIndex=0; plateRefIndex<plateRefCount; plateRefIndex++) { 
     2025        String screenPlateRefValue = src.getScreenPlateRef(screenIndex, plateRefIndex); 
     2026        if (screenPlateRefValue != null) dest.setScreenPlateRef(screenPlateRefValue, screenIndex, plateRefIndex); 
     2027      } 
    20362028    } catch (NullPointerException e) { } 
    20372029    try { 
     
    20562048    } catch (NullPointerException e) { } 
    20572049      try { 
    2058       //int annotationRefCount = src.getAnnotationRefCount(screenIndex); 
    2059       //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    2060       //} 
    2061       } catch (NullPointerException e) { } 
    2062       try { 
    2063       int plateRefCount = src.getPlateRefCount(screenIndex); 
    2064       for (int plateRefIndex=0; plateRefIndex<plateRefCount; plateRefIndex++) { 
    2065       } 
    2066       } catch (NullPointerException e) { } 
    2067       try { 
    20682050      int reagentCount = src.getReagentCount(screenIndex); 
    20692051      for (int reagentIndex=0; reagentIndex<reagentCount; reagentIndex++) { 
    20702052      try { 
    2071         //String reagentAnnotationRefValue = src.getReagentAnnotationRef(screenIndex, reagentIndex, annotationRefIndex); 
    2072         //if (reagentAnnotationRefValue != null) dest.setReagentAnnotationRef(reagentAnnotationRefValue, screenIndex, reagentIndex, annotationRefIndex); 
     2053        int annotationRefCount = src.getReagentAnnotationRefCount(screenIndex, reagentIndex); 
     2054        for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) 
     2055        { 
     2056          String reagentAnnotationRefValue = src.getReagentAnnotationRef(screenIndex, reagentIndex, annotationRefIndex); 
     2057          if (reagentAnnotationRefValue != null) dest.setReagentAnnotationRef(reagentAnnotationRefValue, screenIndex, reagentIndex, annotationRefIndex); 
     2058        } 
    20732059      } catch (NullPointerException e) { } 
    20742060      try { 
     
    20882074        if (reagentReagentIdentifierValue != null) dest.setReagentReagentIdentifier(reagentReagentIdentifierValue, screenIndex, reagentIndex); 
    20892075      } catch (NullPointerException e) { } 
    2090         try { 
    2091         //int annotationRefCount = src.getAnnotationRefCount(screenIndex, reagentIndex); 
    2092         //for (int annotationRefIndex=0; annotationRefIndex<annotationRefCount; annotationRefIndex++) { 
    2093         //} 
    2094         } catch (NullPointerException e) { } 
    20952076      } 
    20962077      } catch (NullPointerException e) { } 
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