Changeset 4146


Ignore:
Timestamp:
07/01/08 09:20:32 (12 years ago)
Author:
melissa
Message:

Fixed SPW bug - Well is now properly represented as a child of Plate.

Location:
trunk/loci/formats
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/auto/entities.txt

    r4117 r4146  
    11741174#description = TODO 
    11751175 
    1176 #[Plate Well] 
    1177 #type = Integer 
    1178 #description = TODO 
    1179  
    11801176[Plate Name] 
    11811177type = String 
     
    12631259path = - 
    12641260 
    1265 #[Screen Reagent] 
    1266 #type = String 
    1267 #description = TODO 
    1268  
    12691261#[Screen PlateRef] 
    12701262#type = String 
    12711263#description = TODO 
    1272  
    1273 #[Screen ScreenAcquisition] 
    12741264 
    12751265[Screen ID] 
     
    13491339[Well] 
    13501340countable = true 
    1351 path = Well+ 
     1341path = Plate+/Well+ 
    13521342description = describes a Well (part of a plate) 
    13531343 
     
    13551345path = - 
    13561346 
    1357 #[Well WellSample] 
    1358 #type = String 
    1359 #description = TODO 
    1360  
    13611347#[Well ReagentRef] 
    13621348#type = String 
     
    13931379[WellSample] 
    13941380countable = true 
    1395 path = Well+/WellSample+ 
     1381path = Plate+/Well+/WellSample+ 
    13961382description = individual image within a Well 
    13971383 
  • trunk/loci/formats/in/FlexReader.java

    r4114 r4146  
    475475        addMeta("Well" + ndx + " Row", attributes.getValue("Row")); 
    476476        addMeta("Well" + ndx + " Col", attributes.getValue("Col")); 
    477         store.setWellRow(new Integer(attributes.getValue("Row")), ndx); 
    478         store.setWellColumn(new Integer(attributes.getValue("Col")), ndx); 
     477        store.setWellRow(new Integer(attributes.getValue("Row")), 0,ndx); 
     478        store.setWellColumn(new Integer(attributes.getValue("Col")), 0, ndx); 
    479479      } 
    480480      else if (qName.equals("Status")) { 
  • trunk/loci/formats/in/InCellReader.java

    r4086 r4146  
    221221    private int nextExWave = 0; 
    222222    private MetadataStore store; 
     223    private int nextPlate = 0; 
    223224 
    224225    public InCellHandler(MetadataStore store) { 
     
    285286      } 
    286287      else if (qName.equals("Plate")) { 
    287         store.setPlateName(attributes.getValue("name"), 0); 
     288        store.setPlateName(attributes.getValue("name"), nextPlate); 
    288289        int rows = Integer.parseInt(attributes.getValue("rows")); 
    289290        int cols = Integer.parseInt(attributes.getValue("columns")); 
     
    291292        for (int r=0; r<rows; r++) { 
    292293          for (int c=0; c<cols; c++) { 
    293             store.setWellRow(new Integer(r), r*cols + c); 
    294             store.setWellColumn(new Integer(c), r*cols + c); 
     294            store.setWellRow(new Integer(r), nextPlate, r*cols + c); 
     295            store.setWellColumn(new Integer(c), nextPlate, r*cols + c); 
    295296          } 
    296297        } 
     298        nextPlate++; 
    297299      } 
    298300    } 
  • trunk/loci/formats/meta/AggregateMetadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    328328  } 
    329329 
    330   /* @see MetadataRetrieve#getWellCount() */ 
    331   public int getWellCount() { 
    332     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    333       Object o = iter.next(); 
    334       if (o instanceof MetadataRetrieve) { 
    335         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    336         int result = retrieve.getWellCount(); 
     330  /* @see MetadataRetrieve#getWellCount(int) */ 
     331  public int getWellCount(int plateIndex) { 
     332    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     333      Object o = iter.next(); 
     334      if (o instanceof MetadataRetrieve) { 
     335        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     336        int result = retrieve.getWellCount(plateIndex); 
    337337        if (result >= 0) return result; 
    338338      } 
     
    341341  } 
    342342 
    343   /* @see MetadataRetrieve#getWellSampleCount(int) */ 
    344   public int getWellSampleCount(int wellIndex) { 
    345     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    346       Object o = iter.next(); 
    347       if (o instanceof MetadataRetrieve) { 
    348         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    349         int result = retrieve.getWellSampleCount(wellIndex); 
     343  /* @see MetadataRetrieve#getWellSampleCount(int, int) */ 
     344  public int getWellSampleCount(int plateIndex, int wellIndex) { 
     345    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     346      Object o = iter.next(); 
     347      if (o instanceof MetadataRetrieve) { 
     348        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     349        int result = retrieve.getWellSampleCount(plateIndex, wellIndex); 
    350350        if (result >= 0) return result; 
    351351      } 
     
    22532253  // - Well property retrieval - 
    22542254 
    2255   /* @see MetadataRetrieve#getWellColumn(int) */ 
    2256   public Integer getWellColumn(int wellIndex) { 
    2257     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2258       Object o = iter.next(); 
    2259       if (o instanceof MetadataRetrieve) { 
    2260         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2261         Integer result = retrieve.getWellColumn(wellIndex); 
    2262         if (result != null) return result; 
    2263       } 
    2264     } 
    2265     return null; 
    2266   } 
    2267  
    2268   /* @see MetadataRetrieve#getWellExternalDescription(int) */ 
    2269   public String getWellExternalDescription(int wellIndex) { 
    2270     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2271       Object o = iter.next(); 
    2272       if (o instanceof MetadataRetrieve) { 
    2273         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2274         String result = retrieve.getWellExternalDescription(wellIndex); 
    2275         if (result != null) return result; 
    2276       } 
    2277     } 
    2278     return null; 
    2279   } 
    2280  
    2281   /* @see MetadataRetrieve#getWellExternalIdentifier(int) */ 
    2282   public String getWellExternalIdentifier(int wellIndex) { 
    2283     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2284       Object o = iter.next(); 
    2285       if (o instanceof MetadataRetrieve) { 
    2286         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2287         String result = retrieve.getWellExternalIdentifier(wellIndex); 
    2288         if (result != null) return result; 
    2289       } 
    2290     } 
    2291     return null; 
    2292   } 
    2293  
    2294   /* @see MetadataRetrieve#getWellID(int) */ 
    2295   public String getWellID(int wellIndex) { 
    2296     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2297       Object o = iter.next(); 
    2298       if (o instanceof MetadataRetrieve) { 
    2299         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2300         String result = retrieve.getWellID(wellIndex); 
    2301         if (result != null) return result; 
    2302       } 
    2303     } 
    2304     return null; 
    2305   } 
    2306  
    2307   /* @see MetadataRetrieve#getWellRow(int) */ 
    2308   public Integer getWellRow(int wellIndex) { 
    2309     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2310       Object o = iter.next(); 
    2311       if (o instanceof MetadataRetrieve) { 
    2312         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2313         Integer result = retrieve.getWellRow(wellIndex); 
    2314         if (result != null) return result; 
    2315       } 
    2316     } 
    2317     return null; 
    2318   } 
    2319  
    2320   /* @see MetadataRetrieve#getWellType(int) */ 
    2321   public String getWellType(int wellIndex) { 
    2322     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2323       Object o = iter.next(); 
    2324       if (o instanceof MetadataRetrieve) { 
    2325         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2326         String result = retrieve.getWellType(wellIndex); 
     2255  /* @see MetadataRetrieve#getWellColumn(int, int) */ 
     2256  public Integer getWellColumn(int plateIndex, int wellIndex) { 
     2257    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2258      Object o = iter.next(); 
     2259      if (o instanceof MetadataRetrieve) { 
     2260        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2261        Integer result = retrieve.getWellColumn(plateIndex, wellIndex); 
     2262        if (result != null) return result; 
     2263      } 
     2264    } 
     2265    return null; 
     2266  } 
     2267 
     2268  /* @see MetadataRetrieve#getWellExternalDescription(int, int) */ 
     2269  public String getWellExternalDescription(int plateIndex, int wellIndex) { 
     2270    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2271      Object o = iter.next(); 
     2272      if (o instanceof MetadataRetrieve) { 
     2273        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2274        String result = retrieve.getWellExternalDescription(plateIndex, wellIndex); 
     2275        if (result != null) return result; 
     2276      } 
     2277    } 
     2278    return null; 
     2279  } 
     2280 
     2281  /* @see MetadataRetrieve#getWellExternalIdentifier(int, int) */ 
     2282  public String getWellExternalIdentifier(int plateIndex, int wellIndex) { 
     2283    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2284      Object o = iter.next(); 
     2285      if (o instanceof MetadataRetrieve) { 
     2286        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2287        String result = retrieve.getWellExternalIdentifier(plateIndex, wellIndex); 
     2288        if (result != null) return result; 
     2289      } 
     2290    } 
     2291    return null; 
     2292  } 
     2293 
     2294  /* @see MetadataRetrieve#getWellID(int, int) */ 
     2295  public String getWellID(int plateIndex, int wellIndex) { 
     2296    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2297      Object o = iter.next(); 
     2298      if (o instanceof MetadataRetrieve) { 
     2299        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2300        String result = retrieve.getWellID(plateIndex, wellIndex); 
     2301        if (result != null) return result; 
     2302      } 
     2303    } 
     2304    return null; 
     2305  } 
     2306 
     2307  /* @see MetadataRetrieve#getWellRow(int, int) */ 
     2308  public Integer getWellRow(int plateIndex, int wellIndex) { 
     2309    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2310      Object o = iter.next(); 
     2311      if (o instanceof MetadataRetrieve) { 
     2312        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2313        Integer result = retrieve.getWellRow(plateIndex, wellIndex); 
     2314        if (result != null) return result; 
     2315      } 
     2316    } 
     2317    return null; 
     2318  } 
     2319 
     2320  /* @see MetadataRetrieve#getWellType(int, int) */ 
     2321  public String getWellType(int plateIndex, int wellIndex) { 
     2322    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2323      Object o = iter.next(); 
     2324      if (o instanceof MetadataRetrieve) { 
     2325        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2326        String result = retrieve.getWellType(plateIndex, wellIndex); 
    23272327        if (result != null) return result; 
    23282328      } 
     
    23332333  // - WellSample property retrieval - 
    23342334 
    2335   /* @see MetadataRetrieve#getWellSampleID(int, int) */ 
    2336   public String getWellSampleID(int wellIndex, int wellSampleIndex) { 
    2337     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2338       Object o = iter.next(); 
    2339       if (o instanceof MetadataRetrieve) { 
    2340         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2341         String result = retrieve.getWellSampleID(wellIndex, wellSampleIndex); 
    2342         if (result != null) return result; 
    2343       } 
    2344     } 
    2345     return null; 
    2346   } 
    2347  
    2348   /* @see MetadataRetrieve#getWellSampleIndex(int, int) */ 
    2349   public Integer getWellSampleIndex(int wellIndex, int wellSampleIndex) { 
    2350     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2351       Object o = iter.next(); 
    2352       if (o instanceof MetadataRetrieve) { 
    2353         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2354         Integer result = retrieve.getWellSampleIndex(wellIndex, wellSampleIndex); 
    2355         if (result != null) return result; 
    2356       } 
    2357     } 
    2358     return null; 
    2359   } 
    2360  
    2361   /* @see MetadataRetrieve#getWellSamplePosX(int, int) */ 
    2362   public Float getWellSamplePosX(int wellIndex, int wellSampleIndex) { 
    2363     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2364       Object o = iter.next(); 
    2365       if (o instanceof MetadataRetrieve) { 
    2366         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2367         Float result = retrieve.getWellSamplePosX(wellIndex, wellSampleIndex); 
    2368         if (result != null) return result; 
    2369       } 
    2370     } 
    2371     return null; 
    2372   } 
    2373  
    2374   /* @see MetadataRetrieve#getWellSamplePosY(int, int) */ 
    2375   public Float getWellSamplePosY(int wellIndex, int wellSampleIndex) { 
    2376     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2377       Object o = iter.next(); 
    2378       if (o instanceof MetadataRetrieve) { 
    2379         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2380         Float result = retrieve.getWellSamplePosY(wellIndex, wellSampleIndex); 
    2381         if (result != null) return result; 
    2382       } 
    2383     } 
    2384     return null; 
    2385   } 
    2386  
    2387   /* @see MetadataRetrieve#getWellSampleTimepoint(int, int) */ 
    2388   public Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex) { 
    2389     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    2390       Object o = iter.next(); 
    2391       if (o instanceof MetadataRetrieve) { 
    2392         MetadataRetrieve retrieve = (MetadataRetrieve) o; 
    2393         Integer result = retrieve.getWellSampleTimepoint(wellIndex, wellSampleIndex); 
     2335  /* @see MetadataRetrieve#getWellSampleID(int, int, int) */ 
     2336  public String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex) { 
     2337    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2338      Object o = iter.next(); 
     2339      if (o instanceof MetadataRetrieve) { 
     2340        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2341        String result = retrieve.getWellSampleID(plateIndex, wellIndex, wellSampleIndex); 
     2342        if (result != null) return result; 
     2343      } 
     2344    } 
     2345    return null; 
     2346  } 
     2347 
     2348  /* @see MetadataRetrieve#getWellSampleIndex(int, int, int) */ 
     2349  public Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex) { 
     2350    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2351      Object o = iter.next(); 
     2352      if (o instanceof MetadataRetrieve) { 
     2353        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2354        Integer result = retrieve.getWellSampleIndex(plateIndex, wellIndex, wellSampleIndex); 
     2355        if (result != null) return result; 
     2356      } 
     2357    } 
     2358    return null; 
     2359  } 
     2360 
     2361  /* @see MetadataRetrieve#getWellSamplePosX(int, int, int) */ 
     2362  public Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex) { 
     2363    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2364      Object o = iter.next(); 
     2365      if (o instanceof MetadataRetrieve) { 
     2366        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2367        Float result = retrieve.getWellSamplePosX(plateIndex, wellIndex, wellSampleIndex); 
     2368        if (result != null) return result; 
     2369      } 
     2370    } 
     2371    return null; 
     2372  } 
     2373 
     2374  /* @see MetadataRetrieve#getWellSamplePosY(int, int, int) */ 
     2375  public Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex) { 
     2376    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2377      Object o = iter.next(); 
     2378      if (o instanceof MetadataRetrieve) { 
     2379        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2380        Float result = retrieve.getWellSamplePosY(plateIndex, wellIndex, wellSampleIndex); 
     2381        if (result != null) return result; 
     2382      } 
     2383    } 
     2384    return null; 
     2385  } 
     2386 
     2387  /* @see MetadataRetrieve#getWellSampleTimepoint(int, int, int) */ 
     2388  public Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex) { 
     2389    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     2390      Object o = iter.next(); 
     2391      if (o instanceof MetadataRetrieve) { 
     2392        MetadataRetrieve retrieve = (MetadataRetrieve) o; 
     2393        Integer result = retrieve.getWellSampleTimepoint(plateIndex, wellIndex, wellSampleIndex); 
    23942394        if (result != null) return result; 
    23952395      } 
     
    40424042  // - Well property storage - 
    40434043 
    4044   /* @see MetadataStore#setWellColumn(Integer, int) */ 
    4045   public void setWellColumn(Integer column, int wellIndex) { 
    4046     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4047       Object o = iter.next(); 
    4048       if (o instanceof MetadataStore) { 
    4049         MetadataStore store = (MetadataStore) o; 
    4050         store.setWellColumn(column, wellIndex); 
    4051       } 
    4052     } 
    4053   } 
    4054  
    4055   /* @see MetadataStore#setWellExternalDescription(String, int) */ 
    4056   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
    4057     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4058       Object o = iter.next(); 
    4059       if (o instanceof MetadataStore) { 
    4060         MetadataStore store = (MetadataStore) o; 
    4061         store.setWellExternalDescription(externalDescription, wellIndex); 
    4062       } 
    4063     } 
    4064   } 
    4065  
    4066   /* @see MetadataStore#setWellExternalIdentifier(String, int) */ 
    4067   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
    4068     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4069       Object o = iter.next(); 
    4070       if (o instanceof MetadataStore) { 
    4071         MetadataStore store = (MetadataStore) o; 
    4072         store.setWellExternalIdentifier(externalIdentifier, wellIndex); 
    4073       } 
    4074     } 
    4075   } 
    4076  
    4077   /* @see MetadataStore#setWellID(String, int) */ 
    4078   public void setWellID(String id, int wellIndex) { 
    4079     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4080       Object o = iter.next(); 
    4081       if (o instanceof MetadataStore) { 
    4082         MetadataStore store = (MetadataStore) o; 
    4083         store.setWellID(id, wellIndex); 
    4084       } 
    4085     } 
    4086   } 
    4087  
    4088   /* @see MetadataStore#setWellRow(Integer, int) */ 
    4089   public void setWellRow(Integer row, int wellIndex) { 
    4090     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4091       Object o = iter.next(); 
    4092       if (o instanceof MetadataStore) { 
    4093         MetadataStore store = (MetadataStore) o; 
    4094         store.setWellRow(row, wellIndex); 
    4095       } 
    4096     } 
    4097   } 
    4098  
    4099   /* @see MetadataStore#setWellType(String, int) */ 
    4100   public void setWellType(String type, int wellIndex) { 
    4101     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4102       Object o = iter.next(); 
    4103       if (o instanceof MetadataStore) { 
    4104         MetadataStore store = (MetadataStore) o; 
    4105         store.setWellType(type, wellIndex); 
     4044  /* @see MetadataStore#setWellColumn(Integer, int, int) */ 
     4045  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
     4046    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4047      Object o = iter.next(); 
     4048      if (o instanceof MetadataStore) { 
     4049        MetadataStore store = (MetadataStore) o; 
     4050        store.setWellColumn(column, plateIndex, wellIndex); 
     4051      } 
     4052    } 
     4053  } 
     4054 
     4055  /* @see MetadataStore#setWellExternalDescription(String, int, int) */ 
     4056  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
     4057    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4058      Object o = iter.next(); 
     4059      if (o instanceof MetadataStore) { 
     4060        MetadataStore store = (MetadataStore) o; 
     4061        store.setWellExternalDescription(externalDescription, plateIndex, wellIndex); 
     4062      } 
     4063    } 
     4064  } 
     4065 
     4066  /* @see MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     4067  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
     4068    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4069      Object o = iter.next(); 
     4070      if (o instanceof MetadataStore) { 
     4071        MetadataStore store = (MetadataStore) o; 
     4072        store.setWellExternalIdentifier(externalIdentifier, plateIndex, wellIndex); 
     4073      } 
     4074    } 
     4075  } 
     4076 
     4077  /* @see MetadataStore#setWellID(String, int, int) */ 
     4078  public void setWellID(String id, int plateIndex, int wellIndex) { 
     4079    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4080      Object o = iter.next(); 
     4081      if (o instanceof MetadataStore) { 
     4082        MetadataStore store = (MetadataStore) o; 
     4083        store.setWellID(id, plateIndex, wellIndex); 
     4084      } 
     4085    } 
     4086  } 
     4087 
     4088  /* @see MetadataStore#setWellRow(Integer, int, int) */ 
     4089  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
     4090    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4091      Object o = iter.next(); 
     4092      if (o instanceof MetadataStore) { 
     4093        MetadataStore store = (MetadataStore) o; 
     4094        store.setWellRow(row, plateIndex, wellIndex); 
     4095      } 
     4096    } 
     4097  } 
     4098 
     4099  /* @see MetadataStore#setWellType(String, int, int) */ 
     4100  public void setWellType(String type, int plateIndex, int wellIndex) { 
     4101    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4102      Object o = iter.next(); 
     4103      if (o instanceof MetadataStore) { 
     4104        MetadataStore store = (MetadataStore) o; 
     4105        store.setWellType(type, plateIndex, wellIndex); 
    41064106      } 
    41074107    } 
     
    41104110  // - WellSample property storage - 
    41114111 
    4112   /* @see MetadataStore#setWellSampleID(String, int, int) */ 
    4113   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
    4114     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4115       Object o = iter.next(); 
    4116       if (o instanceof MetadataStore) { 
    4117         MetadataStore store = (MetadataStore) o; 
    4118         store.setWellSampleID(id, wellIndex, wellSampleIndex); 
    4119       } 
    4120     } 
    4121   } 
    4122  
    4123   /* @see MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    4124   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
    4125     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4126       Object o = iter.next(); 
    4127       if (o instanceof MetadataStore) { 
    4128         MetadataStore store = (MetadataStore) o; 
    4129         store.setWellSampleIndex(index, wellIndex, wellSampleIndex); 
    4130       } 
    4131     } 
    4132   } 
    4133  
    4134   /* @see MetadataStore#setWellSamplePosX(Float, int, int) */ 
    4135   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
    4136     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4137       Object o = iter.next(); 
    4138       if (o instanceof MetadataStore) { 
    4139         MetadataStore store = (MetadataStore) o; 
    4140         store.setWellSamplePosX(posX, wellIndex, wellSampleIndex); 
    4141       } 
    4142     } 
    4143   } 
    4144  
    4145   /* @see MetadataStore#setWellSamplePosY(Float, int, int) */ 
    4146   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
    4147     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4148       Object o = iter.next(); 
    4149       if (o instanceof MetadataStore) { 
    4150         MetadataStore store = (MetadataStore) o; 
    4151         store.setWellSamplePosY(posY, wellIndex, wellSampleIndex); 
    4152       } 
    4153     } 
    4154   } 
    4155  
    4156   /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    4157   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
    4158     for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    4159       Object o = iter.next(); 
    4160       if (o instanceof MetadataStore) { 
    4161         MetadataStore store = (MetadataStore) o; 
    4162         store.setWellSampleTimepoint(timepoint, wellIndex, wellSampleIndex); 
     4112  /* @see MetadataStore#setWellSampleID(String, int, int, int) */ 
     4113  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
     4114    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4115      Object o = iter.next(); 
     4116      if (o instanceof MetadataStore) { 
     4117        MetadataStore store = (MetadataStore) o; 
     4118        store.setWellSampleID(id, plateIndex, wellIndex, wellSampleIndex); 
     4119      } 
     4120    } 
     4121  } 
     4122 
     4123  /* @see MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     4124  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
     4125    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4126      Object o = iter.next(); 
     4127      if (o instanceof MetadataStore) { 
     4128        MetadataStore store = (MetadataStore) o; 
     4129        store.setWellSampleIndex(index, plateIndex, wellIndex, wellSampleIndex); 
     4130      } 
     4131    } 
     4132  } 
     4133 
     4134  /* @see MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     4135  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
     4136    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4137      Object o = iter.next(); 
     4138      if (o instanceof MetadataStore) { 
     4139        MetadataStore store = (MetadataStore) o; 
     4140        store.setWellSamplePosX(posX, plateIndex, wellIndex, wellSampleIndex); 
     4141      } 
     4142    } 
     4143  } 
     4144 
     4145  /* @see MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     4146  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
     4147    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4148      Object o = iter.next(); 
     4149      if (o instanceof MetadataStore) { 
     4150        MetadataStore store = (MetadataStore) o; 
     4151        store.setWellSamplePosY(posY, plateIndex, wellIndex, wellSampleIndex); 
     4152      } 
     4153    } 
     4154  } 
     4155 
     4156  /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     4157  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
     4158    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
     4159      Object o = iter.next(); 
     4160      if (o instanceof MetadataStore) { 
     4161        MetadataStore store = (MetadataStore) o; 
     4162        store.setWellSampleTimepoint(timepoint, plateIndex, wellIndex, wellSampleIndex); 
    41634163      } 
    41644164    } 
  • trunk/loci/formats/meta/DummyMetadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    140140  } 
    141141 
    142   /* @see MetadataRetrieve#getWellCount() */ 
    143   public int getWellCount() { 
    144     return -1; 
    145   } 
    146  
    147   /* @see MetadataRetrieve#getWellSampleCount(int) */ 
    148   public int getWellSampleCount(int wellIndex) { 
     142  /* @see MetadataRetrieve#getWellCount(int) */ 
     143  public int getWellCount(int plateIndex) { 
     144    return -1; 
     145  } 
     146 
     147  /* @see MetadataRetrieve#getWellSampleCount(int, int) */ 
     148  public int getWellSampleCount(int plateIndex, int wellIndex) { 
    149149    return -1; 
    150150  } 
     
    812812  // - Well property retrieval - 
    813813 
    814   /* @see MetadataRetrieve#getWellColumn(int) */ 
    815   public Integer getWellColumn(int wellIndex) { 
    816     return null; 
    817   } 
    818   /* @see MetadataRetrieve#getWellExternalDescription(int) */ 
    819   public String getWellExternalDescription(int wellIndex) { 
    820     return null; 
    821   } 
    822   /* @see MetadataRetrieve#getWellExternalIdentifier(int) */ 
    823   public String getWellExternalIdentifier(int wellIndex) { 
    824     return null; 
    825   } 
    826   /* @see MetadataRetrieve#getWellID(int) */ 
    827   public String getWellID(int wellIndex) { 
    828     return null; 
    829   } 
    830   /* @see MetadataRetrieve#getWellRow(int) */ 
    831   public Integer getWellRow(int wellIndex) { 
    832     return null; 
    833   } 
    834   /* @see MetadataRetrieve#getWellType(int) */ 
    835   public String getWellType(int wellIndex) { 
     814  /* @see MetadataRetrieve#getWellColumn(int, int) */ 
     815  public Integer getWellColumn(int plateIndex, int wellIndex) { 
     816    return null; 
     817  } 
     818  /* @see MetadataRetrieve#getWellExternalDescription(int, int) */ 
     819  public String getWellExternalDescription(int plateIndex, int wellIndex) { 
     820    return null; 
     821  } 
     822  /* @see MetadataRetrieve#getWellExternalIdentifier(int, int) */ 
     823  public String getWellExternalIdentifier(int plateIndex, int wellIndex) { 
     824    return null; 
     825  } 
     826  /* @see MetadataRetrieve#getWellID(int, int) */ 
     827  public String getWellID(int plateIndex, int wellIndex) { 
     828    return null; 
     829  } 
     830  /* @see MetadataRetrieve#getWellRow(int, int) */ 
     831  public Integer getWellRow(int plateIndex, int wellIndex) { 
     832    return null; 
     833  } 
     834  /* @see MetadataRetrieve#getWellType(int, int) */ 
     835  public String getWellType(int plateIndex, int wellIndex) { 
    836836    return null; 
    837837  } 
     
    839839  // - WellSample property retrieval - 
    840840 
    841   /* @see MetadataRetrieve#getWellSampleID(int, int) */ 
    842   public String getWellSampleID(int wellIndex, int wellSampleIndex) { 
    843     return null; 
    844   } 
    845   /* @see MetadataRetrieve#getWellSampleIndex(int, int) */ 
    846   public Integer getWellSampleIndex(int wellIndex, int wellSampleIndex) { 
    847     return null; 
    848   } 
    849   /* @see MetadataRetrieve#getWellSamplePosX(int, int) */ 
    850   public Float getWellSamplePosX(int wellIndex, int wellSampleIndex) { 
    851     return null; 
    852   } 
    853   /* @see MetadataRetrieve#getWellSamplePosY(int, int) */ 
    854   public Float getWellSamplePosY(int wellIndex, int wellSampleIndex) { 
    855     return null; 
    856   } 
    857   /* @see MetadataRetrieve#getWellSampleTimepoint(int, int) */ 
    858   public Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex) { 
     841  /* @see MetadataRetrieve#getWellSampleID(int, int, int) */ 
     842  public String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex) { 
     843    return null; 
     844  } 
     845  /* @see MetadataRetrieve#getWellSampleIndex(int, int, int) */ 
     846  public Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex) { 
     847    return null; 
     848  } 
     849  /* @see MetadataRetrieve#getWellSamplePosX(int, int, int) */ 
     850  public Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex) { 
     851    return null; 
     852  } 
     853  /* @see MetadataRetrieve#getWellSamplePosY(int, int, int) */ 
     854  public Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex) { 
     855    return null; 
     856  } 
     857  /* @see MetadataRetrieve#getWellSampleTimepoint(int, int, int) */ 
     858  public Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex) { 
    859859    return null; 
    860860  } 
     
    15031503  // - Well property storage - 
    15041504 
    1505   /* @see MetadataStore#setWellColumn(Integer, int) */ 
    1506   public void setWellColumn(Integer column, int wellIndex) { 
    1507   } 
    1508  
    1509   /* @see MetadataStore#setWellExternalDescription(String, int) */ 
    1510   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
    1511   } 
    1512  
    1513   /* @see MetadataStore#setWellExternalIdentifier(String, int) */ 
    1514   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
    1515   } 
    1516  
    1517   /* @see MetadataStore#setWellID(String, int) */ 
    1518   public void setWellID(String id, int wellIndex) { 
    1519   } 
    1520  
    1521   /* @see MetadataStore#setWellRow(Integer, int) */ 
    1522   public void setWellRow(Integer row, int wellIndex) { 
    1523   } 
    1524  
    1525   /* @see MetadataStore#setWellType(String, int) */ 
    1526   public void setWellType(String type, int wellIndex) { 
     1505  /* @see MetadataStore#setWellColumn(Integer, int, int) */ 
     1506  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
     1507  } 
     1508 
     1509  /* @see MetadataStore#setWellExternalDescription(String, int, int) */ 
     1510  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
     1511  } 
     1512 
     1513  /* @see MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     1514  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
     1515  } 
     1516 
     1517  /* @see MetadataStore#setWellID(String, int, int) */ 
     1518  public void setWellID(String id, int plateIndex, int wellIndex) { 
     1519  } 
     1520 
     1521  /* @see MetadataStore#setWellRow(Integer, int, int) */ 
     1522  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
     1523  } 
     1524 
     1525  /* @see MetadataStore#setWellType(String, int, int) */ 
     1526  public void setWellType(String type, int plateIndex, int wellIndex) { 
    15271527  } 
    15281528 
    15291529  // - WellSample property storage - 
    15301530 
    1531   /* @see MetadataStore#setWellSampleID(String, int, int) */ 
    1532   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
    1533   } 
    1534  
    1535   /* @see MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    1536   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
    1537   } 
    1538  
    1539   /* @see MetadataStore#setWellSamplePosX(Float, int, int) */ 
    1540   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
    1541   } 
    1542  
    1543   /* @see MetadataStore#setWellSamplePosY(Float, int, int) */ 
    1544   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
    1545   } 
    1546  
    1547   /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    1548   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
     1531  /* @see MetadataStore#setWellSampleID(String, int, int, int) */ 
     1532  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
     1533  } 
     1534 
     1535  /* @see MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     1536  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
     1537  } 
     1538 
     1539  /* @see MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     1540  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
     1541  } 
     1542 
     1543  /* @see MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     1544  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
     1545  } 
     1546 
     1547  /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     1548  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
    15491549  } 
    15501550 
  • trunk/loci/formats/meta/FilterMetadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    916916  // -- Well property storage - 
    917917 
    918   /* @see MetadataStore#setWellColumn(Integer, int) */ 
    919   public void setWellColumn(Integer column, int wellIndex) { 
    920     store.setWellColumn(column, wellIndex); 
    921   } 
    922  
    923   /* @see MetadataStore#setWellExternalDescription(String, int) */ 
    924   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
     918  /* @see MetadataStore#setWellColumn(Integer, int, int) */ 
     919  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
     920    store.setWellColumn(column, plateIndex, wellIndex); 
     921  } 
     922 
     923  /* @see MetadataStore#setWellExternalDescription(String, int, int) */ 
     924  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
    925925    String value = filter ? DataTools.sanitize(externalDescription) : externalDescription; 
    926     store.setWellExternalDescription(value, wellIndex); 
    927   } 
    928  
    929   /* @see MetadataStore#setWellExternalIdentifier(String, int) */ 
    930   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
     926    store.setWellExternalDescription(value, plateIndex, wellIndex); 
     927  } 
     928 
     929  /* @see MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     930  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
    931931    String value = filter ? DataTools.sanitize(externalIdentifier) : externalIdentifier; 
    932     store.setWellExternalIdentifier(value, wellIndex); 
    933   } 
    934  
    935   /* @see MetadataStore#setWellID(String, int) */ 
    936   public void setWellID(String id, int wellIndex) { 
    937     String value = filter ? DataTools.sanitize(id) : id; 
    938     store.setWellID(value, wellIndex); 
    939   } 
    940  
    941   /* @see MetadataStore#setWellRow(Integer, int) */ 
    942   public void setWellRow(Integer row, int wellIndex) { 
    943     store.setWellRow(row, wellIndex); 
    944   } 
    945  
    946   /* @see MetadataStore#setWellType(String, int) */ 
    947   public void setWellType(String type, int wellIndex) { 
     932    store.setWellExternalIdentifier(value, plateIndex, wellIndex); 
     933  } 
     934 
     935  /* @see MetadataStore#setWellID(String, int, int) */ 
     936  public void setWellID(String id, int plateIndex, int wellIndex) { 
     937    String value = filter ? DataTools.sanitize(id) : id; 
     938    store.setWellID(value, plateIndex, wellIndex); 
     939  } 
     940 
     941  /* @see MetadataStore#setWellRow(Integer, int, int) */ 
     942  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
     943    store.setWellRow(row, plateIndex, wellIndex); 
     944  } 
     945 
     946  /* @see MetadataStore#setWellType(String, int, int) */ 
     947  public void setWellType(String type, int plateIndex, int wellIndex) { 
    948948    String value = filter ? DataTools.sanitize(type) : type; 
    949     store.setWellType(value, wellIndex); 
     949    store.setWellType(value, plateIndex, wellIndex); 
    950950  } 
    951951 
    952952  // -- WellSample property storage - 
    953953 
    954   /* @see MetadataStore#setWellSampleID(String, int, int) */ 
    955   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
    956     String value = filter ? DataTools.sanitize(id) : id; 
    957     store.setWellSampleID(value, wellIndex, wellSampleIndex); 
    958   } 
    959  
    960   /* @see MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    961   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
    962     store.setWellSampleIndex(index, wellIndex, wellSampleIndex); 
    963   } 
    964  
    965   /* @see MetadataStore#setWellSamplePosX(Float, int, int) */ 
    966   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
    967     store.setWellSamplePosX(posX, wellIndex, wellSampleIndex); 
    968   } 
    969  
    970   /* @see MetadataStore#setWellSamplePosY(Float, int, int) */ 
    971   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
    972     store.setWellSamplePosY(posY, wellIndex, wellSampleIndex); 
    973   } 
    974  
    975   /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    976   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
    977     store.setWellSampleTimepoint(timepoint, wellIndex, wellSampleIndex); 
     954  /* @see MetadataStore#setWellSampleID(String, int, int, int) */ 
     955  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
     956    String value = filter ? DataTools.sanitize(id) : id; 
     957    store.setWellSampleID(value, plateIndex, wellIndex, wellSampleIndex); 
     958  } 
     959 
     960  /* @see MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     961  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
     962    store.setWellSampleIndex(index, plateIndex, wellIndex, wellSampleIndex); 
     963  } 
     964 
     965  /* @see MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     966  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
     967    store.setWellSamplePosX(posX, plateIndex, wellIndex, wellSampleIndex); 
     968  } 
     969 
     970  /* @see MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     971  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
     972    store.setWellSamplePosY(posY, plateIndex, wellIndex, wellSampleIndex); 
     973  } 
     974 
     975  /* @see MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     976  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
     977    store.setWellSampleTimepoint(timepoint, plateIndex, wellIndex, wellSampleIndex); 
    978978  } 
    979979 
  • trunk/loci/formats/meta/MetadataConverter.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    352352      String plateStatusValue = src.getPlateStatus(plateIndex); 
    353353      if (plateStatusValue != null) dest.setPlateStatus(plateStatusValue, plateIndex); 
     354      int wellCount = src.getWellCount(plateIndex); 
     355      for (int wellIndex=0; wellIndex<wellCount; wellIndex++) { 
     356        Integer wellColumnValue = src.getWellColumn(plateIndex, wellIndex); 
     357        if (wellColumnValue != null) dest.setWellColumn(wellColumnValue, plateIndex, wellIndex); 
     358        String wellExternalDescriptionValue = src.getWellExternalDescription(plateIndex, wellIndex); 
     359        if (wellExternalDescriptionValue != null) dest.setWellExternalDescription(wellExternalDescriptionValue, plateIndex, wellIndex); 
     360        String wellExternalIdentifierValue = src.getWellExternalIdentifier(plateIndex, wellIndex); 
     361        if (wellExternalIdentifierValue != null) dest.setWellExternalIdentifier(wellExternalIdentifierValue, plateIndex, wellIndex); 
     362        String wellIDValue = src.getWellID(plateIndex, wellIndex); 
     363        if (wellIDValue != null) dest.setWellID(wellIDValue, plateIndex, wellIndex); 
     364        Integer wellRowValue = src.getWellRow(plateIndex, wellIndex); 
     365        if (wellRowValue != null) dest.setWellRow(wellRowValue, plateIndex, wellIndex); 
     366        String wellTypeValue = src.getWellType(plateIndex, wellIndex); 
     367        if (wellTypeValue != null) dest.setWellType(wellTypeValue, plateIndex, wellIndex); 
     368        int wellSampleCount = src.getWellSampleCount(plateIndex, wellIndex); 
     369        for (int wellSampleIndex=0; wellSampleIndex<wellSampleCount; wellSampleIndex++) { 
     370          String wellSampleIDValue = src.getWellSampleID(plateIndex, wellIndex, wellSampleIndex); 
     371          if (wellSampleIDValue != null) dest.setWellSampleID(wellSampleIDValue, plateIndex, wellIndex, wellSampleIndex); 
     372          Integer wellSampleIndexValue = src.getWellSampleIndex(plateIndex, wellIndex, wellSampleIndex); 
     373          if (wellSampleIndexValue != null) dest.setWellSampleIndex(wellSampleIndexValue, plateIndex, wellIndex, wellSampleIndex); 
     374          Float wellSamplePosXValue = src.getWellSamplePosX(plateIndex, wellIndex, wellSampleIndex); 
     375          if (wellSamplePosXValue != null) dest.setWellSamplePosX(wellSamplePosXValue, plateIndex, wellIndex, wellSampleIndex); 
     376          Float wellSamplePosYValue = src.getWellSamplePosY(plateIndex, wellIndex, wellSampleIndex); 
     377          if (wellSamplePosYValue != null) dest.setWellSamplePosY(wellSamplePosYValue, plateIndex, wellIndex, wellSampleIndex); 
     378          Integer wellSampleTimepointValue = src.getWellSampleTimepoint(plateIndex, wellIndex, wellSampleIndex); 
     379          if (wellSampleTimepointValue != null) dest.setWellSampleTimepoint(wellSampleTimepointValue, plateIndex, wellIndex, wellSampleIndex); 
     380        } 
     381      } 
    354382    } 
    355383    int screenCount = src.getScreenCount(); 
     
    393421      } 
    394422    } 
    395     int wellCount = src.getWellCount(); 
    396     for (int wellIndex=0; wellIndex<wellCount; wellIndex++) { 
    397       Integer wellColumnValue = src.getWellColumn(wellIndex); 
    398       if (wellColumnValue != null) dest.setWellColumn(wellColumnValue, wellIndex); 
    399       String wellExternalDescriptionValue = src.getWellExternalDescription(wellIndex); 
    400       if (wellExternalDescriptionValue != null) dest.setWellExternalDescription(wellExternalDescriptionValue, wellIndex); 
    401       String wellExternalIdentifierValue = src.getWellExternalIdentifier(wellIndex); 
    402       if (wellExternalIdentifierValue != null) dest.setWellExternalIdentifier(wellExternalIdentifierValue, wellIndex); 
    403       String wellIDValue = src.getWellID(wellIndex); 
    404       if (wellIDValue != null) dest.setWellID(wellIDValue, wellIndex); 
    405       Integer wellRowValue = src.getWellRow(wellIndex); 
    406       if (wellRowValue != null) dest.setWellRow(wellRowValue, wellIndex); 
    407       String wellTypeValue = src.getWellType(wellIndex); 
    408       if (wellTypeValue != null) dest.setWellType(wellTypeValue, wellIndex); 
    409       int wellSampleCount = src.getWellSampleCount(wellIndex); 
    410       for (int wellSampleIndex=0; wellSampleIndex<wellSampleCount; wellSampleIndex++) { 
    411         String wellSampleIDValue = src.getWellSampleID(wellIndex, wellSampleIndex); 
    412         if (wellSampleIDValue != null) dest.setWellSampleID(wellSampleIDValue, wellIndex, wellSampleIndex); 
    413         Integer wellSampleIndexValue = src.getWellSampleIndex(wellIndex, wellSampleIndex); 
    414         if (wellSampleIndexValue != null) dest.setWellSampleIndex(wellSampleIndexValue, wellIndex, wellSampleIndex); 
    415         Float wellSamplePosXValue = src.getWellSamplePosX(wellIndex, wellSampleIndex); 
    416         if (wellSamplePosXValue != null) dest.setWellSamplePosX(wellSamplePosXValue, wellIndex, wellSampleIndex); 
    417         Float wellSamplePosYValue = src.getWellSamplePosY(wellIndex, wellSampleIndex); 
    418         if (wellSamplePosYValue != null) dest.setWellSamplePosY(wellSamplePosYValue, wellIndex, wellSampleIndex); 
    419         Integer wellSampleTimepointValue = src.getWellSampleTimepoint(wellIndex, wellSampleIndex); 
    420         if (wellSampleTimepointValue != null) dest.setWellSampleTimepoint(wellSampleTimepointValue, wellIndex, wellSampleIndex); 
    421       } 
    422     } 
    423423  } 
    424424 
  • trunk/loci/formats/meta/MetadataRetrieve.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    8282  int getTiffDataCount(int imageIndex, int pixelsIndex); 
    8383 
    84   int getWellCount(); 
    85  
    86   int getWellSampleCount(int wellIndex); 
     84  int getWellCount(int plateIndex); 
     85 
     86  int getWellSampleCount(int plateIndex, int wellIndex); 
    8787 
    8888  // - Entity retrieval - 
     
    11181118  /** 
    11191119   * For a particular Well, gets column index of the well, where top-left is 0. 
     1120   * @param plateIndex index of the Plate 
    11201121   * @param wellIndex index of the Well 
    11211122   */ 
    1122   Integer getWellColumn(int wellIndex); 
     1123  Integer getWellColumn(int plateIndex, int wellIndex); 
    11231124 
    11241125  /** 
    11251126   * For a particular Well, gets description of the externally defined ID for this plate. 
     1127   * @param plateIndex index of the Plate 
    11261128   * @param wellIndex index of the Well 
    11271129   */ 
    1128   String getWellExternalDescription(int wellIndex); 
     1130  String getWellExternalDescription(int plateIndex, int wellIndex); 
    11291131 
    11301132  /** 
    11311133   * For a particular Well, gets reference to this well in an external database. 
     1134   * @param plateIndex index of the Plate 
    11321135   * @param wellIndex index of the Well 
    11331136   */ 
    1134   String getWellExternalIdentifier(int wellIndex); 
     1137  String getWellExternalIdentifier(int plateIndex, int wellIndex); 
    11351138 
    11361139  /** 
    11371140   * For a particular Well, gets TODO. 
     1141   * @param plateIndex index of the Plate 
    11381142   * @param wellIndex index of the Well 
    11391143   */ 
    1140   String getWellID(int wellIndex); 
     1144  String getWellID(int plateIndex, int wellIndex); 
    11411145 
    11421146  /** 
    11431147   * For a particular Well, gets row index of the well, where top-left is 0. 
     1148   * @param plateIndex index of the Plate 
    11441149   * @param wellIndex index of the Well 
    11451150   */ 
    1146   Integer getWellRow(int wellIndex); 
     1151  Integer getWellRow(int plateIndex, int wellIndex); 
    11471152 
    11481153  /** 
    11491154   * For a particular Well, gets human-readable identifier of the screen status, e.g. empty, control. 
     1155   * @param plateIndex index of the Plate 
    11501156   * @param wellIndex index of the Well 
    11511157   */ 
    1152   String getWellType(int wellIndex); 
     1158  String getWellType(int plateIndex, int wellIndex); 
    11531159 
    11541160  // - WellSample property retrieval - 
     
    11561162  /** 
    11571163   * For a particular WellSample, gets TODO. 
     1164   * @param plateIndex index of the Plate 
    11581165   * @param wellIndex index of the Well 
    11591166   * @param wellSampleIndex index of the WellSample 
    11601167   */ 
    1161   String getWellSampleID(int wellIndex, int wellSampleIndex); 
     1168  String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex); 
    11621169 
    11631170  /** 
    11641171   * For a particular WellSample, gets link to the Image element. 
     1172   * @param plateIndex index of the Plate 
    11651173   * @param wellIndex index of the Well 
    11661174   * @param wellSampleIndex index of the WellSample 
    11671175   */ 
    1168   Integer getWellSampleIndex(int wellIndex, int wellSampleIndex); 
     1176  Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex); 
    11691177 
    11701178  /** 
    11711179   * For a particular WellSample, gets X position of the image within the well. 
     1180   * @param plateIndex index of the Plate 
    11721181   * @param wellIndex index of the Well 
    11731182   * @param wellSampleIndex index of the WellSample 
    11741183   */ 
    1175   Float getWellSamplePosX(int wellIndex, int wellSampleIndex); 
     1184  Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex); 
    11761185 
    11771186  /** 
    11781187   * For a particular WellSample, gets Y position of the image within the well. 
     1188   * @param plateIndex index of the Plate 
    11791189   * @param wellIndex index of the Well 
    11801190   * @param wellSampleIndex index of the WellSample 
    11811191   */ 
    1182   Float getWellSamplePosY(int wellIndex, int wellSampleIndex); 
     1192  Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex); 
    11831193 
    11841194  /** 
    11851195   * For a particular WellSample, gets time-point at which the image started to be collected. 
     1196   * @param plateIndex index of the Plate 
    11861197   * @param wellIndex index of the Well 
    11871198   * @param wellSampleIndex index of the WellSample 
    11881199   */ 
    1189   Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex); 
     1200  Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex); 
    11901201 
    11911202} 
  • trunk/loci/formats/meta/MetadataStore.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    12401240   * For a particular Well, sets column index of the well, where top-left is 0. 
    12411241   * @param column column index of the well, where top-left is 0 
     1242   * @param plateIndex index of the Plate 
    12421243   * @param wellIndex index of the Well 
    12431244   */ 
    1244   void setWellColumn(Integer column, int wellIndex); 
     1245  void setWellColumn(Integer column, int plateIndex, int wellIndex); 
    12451246 
    12461247  /** 
    12471248   * For a particular Well, sets description of the externally defined ID for this plate. 
    12481249   * @param externalDescription description of the externally defined ID for this plate 
     1250   * @param plateIndex index of the Plate 
    12491251   * @param wellIndex index of the Well 
    12501252   */ 
    1251   void setWellExternalDescription(String externalDescription, int wellIndex); 
     1253  void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex); 
    12521254 
    12531255  /** 
    12541256   * For a particular Well, sets reference to this well in an external database. 
    12551257   * @param externalIdentifier reference to this well in an external database 
     1258   * @param plateIndex index of the Plate 
    12561259   * @param wellIndex index of the Well 
    12571260   */ 
    1258   void setWellExternalIdentifier(String externalIdentifier, int wellIndex); 
     1261  void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex); 
    12591262 
    12601263  /** 
    12611264   * For a particular Well, sets TODO. 
    12621265   * @param id TODO 
     1266   * @param plateIndex index of the Plate 
    12631267   * @param wellIndex index of the Well 
    12641268   */ 
    1265   void setWellID(String id, int wellIndex); 
     1269  void setWellID(String id, int plateIndex, int wellIndex); 
    12661270 
    12671271  /** 
    12681272   * For a particular Well, sets row index of the well, where top-left is 0. 
    12691273   * @param row row index of the well, where top-left is 0 
     1274   * @param plateIndex index of the Plate 
    12701275   * @param wellIndex index of the Well 
    12711276   */ 
    1272   void setWellRow(Integer row, int wellIndex); 
     1277  void setWellRow(Integer row, int plateIndex, int wellIndex); 
    12731278 
    12741279  /** 
    12751280   * For a particular Well, sets human-readable identifier of the screen status, e.g. empty, control. 
    12761281   * @param type human-readable identifier of the screen status, e.g. empty, control 
     1282   * @param plateIndex index of the Plate 
    12771283   * @param wellIndex index of the Well 
    12781284   */ 
    1279   void setWellType(String type, int wellIndex); 
     1285  void setWellType(String type, int plateIndex, int wellIndex); 
    12801286 
    12811287  // - WellSample property storage - 
     
    12841290   * For a particular WellSample, sets TODO. 
    12851291   * @param id TODO 
     1292   * @param plateIndex index of the Plate 
    12861293   * @param wellIndex index of the Well 
    12871294   * @param wellSampleIndex index of the WellSample 
    12881295   */ 
    1289   void setWellSampleID(String id, int wellIndex, int wellSampleIndex); 
     1296  void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex); 
    12901297 
    12911298  /** 
    12921299   * For a particular WellSample, sets link to the Image element. 
    12931300   * @param index link to the Image element 
     1301   * @param plateIndex index of the Plate 
    12941302   * @param wellIndex index of the Well 
    12951303   * @param wellSampleIndex index of the WellSample 
    12961304   */ 
    1297   void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex); 
     1305  void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex); 
    12981306 
    12991307  /** 
    13001308   * For a particular WellSample, sets X position of the image within the well. 
    13011309   * @param posX X position of the image within the well 
     1310   * @param plateIndex index of the Plate 
    13021311   * @param wellIndex index of the Well 
    13031312   * @param wellSampleIndex index of the WellSample 
    13041313   */ 
    1305   void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex); 
     1314  void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex); 
    13061315 
    13071316  /** 
    13081317   * For a particular WellSample, sets Y position of the image within the well. 
    13091318   * @param posY Y position of the image within the well 
     1319   * @param plateIndex index of the Plate 
    13101320   * @param wellIndex index of the Well 
    13111321   * @param wellSampleIndex index of the WellSample 
    13121322   */ 
    1313   void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex); 
     1323  void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex); 
    13141324 
    13151325  /** 
    13161326   * For a particular WellSample, sets time-point at which the image started to be collected. 
    13171327   * @param timepoint time-point at which the image started to be collected 
     1328   * @param plateIndex index of the Plate 
    13181329   * @param wellIndex index of the Well 
    13191330   * @param wellSampleIndex index of the WellSample 
    13201331   */ 
    1321   void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex); 
     1332  void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex); 
    13221333 
    13231334} 
  • trunk/loci/formats/ome/OMEXML2003FCMetadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    203203  } 
    204204 
    205   /* @see loci.formats.meta.MetadataRetrieve#getWellCount() */ 
    206   public int getWellCount() { 
     205  /* @see loci.formats.meta.MetadataRetrieve#getWellCount(int) */ 
     206  public int getWellCount(int plateIndex) { 
    207207    // NB: Well unsupported for schema version 2003-FC 
    208208    return -1; 
    209209  } 
    210210 
    211   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int) */ 
    212   public int getWellSampleCount(int wellIndex) { 
     211  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int, int) */ 
     212  public int getWellSampleCount(int plateIndex, int wellIndex) { 
    213213    // NB: WellSample unsupported for schema version 2003-FC 
    214214    return -1; 
     
    11231123  // - Well property retrieval - 
    11241124 
    1125   /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int) */ 
    1126   public Integer getWellColumn(int wellIndex) { 
     1125  /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int, int) */ 
     1126  public Integer getWellColumn(int plateIndex, int wellIndex) { 
    11271127    // NB: Column unsupported for schema version 2003-FC 
    11281128    return null; 
    11291129  } 
    11301130 
    1131   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int) */ 
    1132   public String getWellExternalDescription(int wellIndex) { 
     1131  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int, int) */ 
     1132  public String getWellExternalDescription(int plateIndex, int wellIndex) { 
    11331133    // NB: ExternalDescription unsupported for schema version 2003-FC 
    11341134    return null; 
    11351135  } 
    11361136 
    1137   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int) */ 
    1138   public String getWellExternalIdentifier(int wellIndex) { 
     1137  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int, int) */ 
     1138  public String getWellExternalIdentifier(int plateIndex, int wellIndex) { 
    11391139    // NB: ExternalIdentifier unsupported for schema version 2003-FC 
    11401140    return null; 
    11411141  } 
    11421142 
    1143   /* @see loci.formats.meta.MetadataRetrieve#getWellID(int) */ 
    1144   public String getWellID(int wellIndex) { 
     1143  /* @see loci.formats.meta.MetadataRetrieve#getWellID(int, int) */ 
     1144  public String getWellID(int plateIndex, int wellIndex) { 
    11451145    // NB: ID unsupported for schema version 2003-FC 
    11461146    return null; 
    11471147  } 
    11481148 
    1149   /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int) */ 
    1150   public Integer getWellRow(int wellIndex) { 
     1149  /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int, int) */ 
     1150  public Integer getWellRow(int plateIndex, int wellIndex) { 
    11511151    // NB: Row unsupported for schema version 2003-FC 
    11521152    return null; 
    11531153  } 
    11541154 
    1155   /* @see loci.formats.meta.MetadataRetrieve#getWellType(int) */ 
    1156   public String getWellType(int wellIndex) { 
     1155  /* @see loci.formats.meta.MetadataRetrieve#getWellType(int, int) */ 
     1156  public String getWellType(int plateIndex, int wellIndex) { 
    11571157    // NB: Type unsupported for schema version 2003-FC 
    11581158    return null; 
     
    11611161  // - WellSample property retrieval - 
    11621162 
    1163   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int) */ 
    1164   public String getWellSampleID(int wellIndex, int wellSampleIndex) { 
     1163  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int, int) */ 
     1164  public String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex) { 
    11651165    // NB: ID unsupported for schema version 2003-FC 
    11661166    return null; 
    11671167  } 
    11681168 
    1169   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int) */ 
    1170   public Integer getWellSampleIndex(int wellIndex, int wellSampleIndex) { 
     1169  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int, int) */ 
     1170  public Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex) { 
    11711171    // NB: Index unsupported for schema version 2003-FC 
    11721172    return null; 
    11731173  } 
    11741174 
    1175   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int) */ 
    1176   public Float getWellSamplePosX(int wellIndex, int wellSampleIndex) { 
     1175  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int, int) */ 
     1176  public Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex) { 
    11771177    // NB: PosX unsupported for schema version 2003-FC 
    11781178    return null; 
    11791179  } 
    11801180 
    1181   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int) */ 
    1182   public Float getWellSamplePosY(int wellIndex, int wellSampleIndex) { 
     1181  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int, int) */ 
     1182  public Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex) { 
    11831183    // NB: PosY unsupported for schema version 2003-FC 
    11841184    return null; 
    11851185  } 
    11861186 
    1187   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int) */ 
    1188   public Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex) { 
     1187  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int, int) */ 
     1188  public Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex) { 
    11891189    // NB: Timepoint unsupported for schema version 2003-FC 
    11901190    return null; 
     
    22022202  // - Well property storage - 
    22032203 
    2204   /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int) */ 
    2205   public void setWellColumn(Integer column, int wellIndex) { 
     2204  /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int, int) */ 
     2205  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
    22062206    // NB: Column unsupported for schema version 2003-FC 
    22072207  } 
    22082208 
    2209   /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int) */ 
    2210   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
     2209  /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int, int) */ 
     2210  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
    22112211    // NB: ExternalDescription unsupported for schema version 2003-FC 
    22122212  } 
    22132213 
    2214   /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int) */ 
    2215   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
     2214  /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     2215  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
    22162216    // NB: ExternalIdentifier unsupported for schema version 2003-FC 
    22172217  } 
    22182218 
    2219   /* @see loci.formats.meta.MetadataStore#setWellID(String, int) */ 
    2220   public void setWellID(String id, int wellIndex) { 
     2219  /* @see loci.formats.meta.MetadataStore#setWellID(String, int, int) */ 
     2220  public void setWellID(String id, int plateIndex, int wellIndex) { 
    22212221    // NB: ID unsupported for schema version 2003-FC 
    22222222  } 
    22232223 
    2224   /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int) */ 
    2225   public void setWellRow(Integer row, int wellIndex) { 
     2224  /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int, int) */ 
     2225  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
    22262226    // NB: Row unsupported for schema version 2003-FC 
    22272227  } 
    22282228 
    2229   /* @see loci.formats.meta.MetadataStore#setWellType(String, int) */ 
    2230   public void setWellType(String type, int wellIndex) { 
     2229  /* @see loci.formats.meta.MetadataStore#setWellType(String, int, int) */ 
     2230  public void setWellType(String type, int plateIndex, int wellIndex) { 
    22312231    // NB: Type unsupported for schema version 2003-FC 
    22322232  } 
     
    22342234  // - WellSample property storage - 
    22352235 
    2236   /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int) */ 
    2237   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
     2236  /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int, int) */ 
     2237  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
    22382238    // NB: ID unsupported for schema version 2003-FC 
    22392239  } 
    22402240 
    2241   /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    2242   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
     2241  /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     2242  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
    22432243    // NB: Index unsupported for schema version 2003-FC 
    22442244  } 
    22452245 
    2246   /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int) */ 
    2247   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
     2246  /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     2247  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
    22482248    // NB: PosX unsupported for schema version 2003-FC 
    22492249  } 
    22502250 
    2251   /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int) */ 
    2252   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
     2251  /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     2252  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
    22532253    // NB: PosY unsupported for schema version 2003-FC 
    22542254  } 
    22552255 
    2256   /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    2257   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
     2256  /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     2257  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
    22582258    // NB: Timepoint unsupported for schema version 2003-FC 
    22592259  } 
  • trunk/loci/formats/ome/OMEXML200706Metadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    216216  } 
    217217 
    218   /* @see loci.formats.meta.MetadataRetrieve#getWellCount() */ 
    219   public int getWellCount() { 
     218  /* @see loci.formats.meta.MetadataRetrieve#getWellCount(int) */ 
     219  public int getWellCount(int plateIndex) { 
    220220    for (int i=0; i<Integer.MAX_VALUE; i++) { 
    221       if (getWellNode(i, false) == null) return i; 
     221      if (getWellNode(plateIndex, i, false) == null) return i; 
    222222    } 
    223223    return -1; 
    224224  } 
    225225 
    226   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int) */ 
    227   public int getWellSampleCount(int wellIndex) { 
     226  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int, int) */ 
     227  public int getWellSampleCount(int plateIndex, int wellIndex) { 
    228228    for (int i=0; i<Integer.MAX_VALUE; i++) { 
    229       if (getWellSampleNode(wellIndex, i, false) == null) return i; 
     229      if (getWellSampleNode(plateIndex, wellIndex, i, false) == null) return i; 
    230230    } 
    231231    return -1; 
     
    11401140  // - Well property retrieval - 
    11411141 
    1142   /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int) */ 
    1143   public Integer getWellColumn(int wellIndex) { 
    1144     WellNode well = getWellNode(wellIndex, false); 
     1142  /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int, int) */ 
     1143  public Integer getWellColumn(int plateIndex, int wellIndex) { 
     1144    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11451145      return well == null ? null : well.getColumn(); 
    11461146    } 
    11471147 
    1148   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int) */ 
    1149   public String getWellExternalDescription(int wellIndex) { 
    1150     WellNode well = getWellNode(wellIndex, false); 
     1148  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int, int) */ 
     1149  public String getWellExternalDescription(int plateIndex, int wellIndex) { 
     1150    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11511151      return well == null ? null : well.getExternalDescription(); 
    11521152    } 
    11531153 
    1154   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int) */ 
    1155   public String getWellExternalIdentifier(int wellIndex) { 
    1156     WellNode well = getWellNode(wellIndex, false); 
     1154  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int, int) */ 
     1155  public String getWellExternalIdentifier(int plateIndex, int wellIndex) { 
     1156    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11571157      return well == null ? null : well.getExternalIdentifier(); 
    11581158    } 
    11591159 
    1160   /* @see loci.formats.meta.MetadataRetrieve#getWellID(int) */ 
    1161   public String getWellID(int wellIndex) { 
    1162     WellNode well = getWellNode(wellIndex, false); 
     1160  /* @see loci.formats.meta.MetadataRetrieve#getWellID(int, int) */ 
     1161  public String getWellID(int plateIndex, int wellIndex) { 
     1162    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11631163      return well == null ? null : well.getNodeID(); 
    11641164    } 
    11651165 
    1166   /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int) */ 
    1167   public Integer getWellRow(int wellIndex) { 
    1168     WellNode well = getWellNode(wellIndex, false); 
     1166  /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int, int) */ 
     1167  public Integer getWellRow(int plateIndex, int wellIndex) { 
     1168    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11691169      return well == null ? null : well.getRow(); 
    11701170    } 
    11711171 
    1172   /* @see loci.formats.meta.MetadataRetrieve#getWellType(int) */ 
    1173   public String getWellType(int wellIndex) { 
    1174     WellNode well = getWellNode(wellIndex, false); 
     1172  /* @see loci.formats.meta.MetadataRetrieve#getWellType(int, int) */ 
     1173  public String getWellType(int plateIndex, int wellIndex) { 
     1174    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11751175      return well == null ? null : well.getType(); 
    11761176    } 
     
    11781178  // - WellSample property retrieval - 
    11791179 
    1180   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int) */ 
    1181   public String getWellSampleID(int wellIndex, int wellSampleIndex) { 
    1182     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1180  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int, int) */ 
     1181  public String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1182    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11831183      return wellSample == null ? null : wellSample.getNodeID(); 
    11841184    } 
    11851185 
    1186   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int) */ 
    1187   public Integer getWellSampleIndex(int wellIndex, int wellSampleIndex) { 
    1188     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1186  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int, int) */ 
     1187  public Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1188    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11891189      return wellSample == null ? null : wellSample.getIndex(); 
    11901190    } 
    11911191 
    1192   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int) */ 
    1193   public Float getWellSamplePosX(int wellIndex, int wellSampleIndex) { 
    1194     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1192  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int, int) */ 
     1193  public Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1194    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11951195      return wellSample == null ? null : wellSample.getPosX(); 
    11961196    } 
    11971197 
    1198   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int) */ 
    1199   public Float getWellSamplePosY(int wellIndex, int wellSampleIndex) { 
    1200     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1198  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int, int) */ 
     1199  public Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1200    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    12011201      return wellSample == null ? null : wellSample.getPosY(); 
    12021202    } 
    12031203 
    1204   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int) */ 
    1205   public Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex) { 
    1206     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1204  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int, int) */ 
     1205  public Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1206    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    12071207      return wellSample == null ? null : wellSample.getTimepoint(); 
    12081208    } 
     
    22832283  // - Well property storage - 
    22842284 
    2285   /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int) */ 
    2286   public void setWellColumn(Integer column, int wellIndex) { 
     2285  /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int, int) */ 
     2286  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
    22872287    if (column == null) return; 
    2288     WellNode wellNode = getWellNode(wellIndex, true); 
     2288    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    22892289      wellNode.setColumn(column); 
    22902290    } 
    22912291 
    2292   /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int) */ 
    2293   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
     2292  /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int, int) */ 
     2293  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
    22942294    if (externalDescription == null) return; 
    2295     WellNode wellNode = getWellNode(wellIndex, true); 
     2295    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    22962296      wellNode.setExternalDescription(externalDescription); 
    22972297    } 
    22982298 
    2299   /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int) */ 
    2300   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
     2299  /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     2300  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
    23012301    if (externalIdentifier == null) return; 
    2302     WellNode wellNode = getWellNode(wellIndex, true); 
     2302    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23032303      wellNode.setExternalIdentifier(externalIdentifier); 
    23042304    } 
    23052305 
    2306   /* @see loci.formats.meta.MetadataStore#setWellID(String, int) */ 
    2307   public void setWellID(String id, int wellIndex) { 
     2306  /* @see loci.formats.meta.MetadataStore#setWellID(String, int, int) */ 
     2307  public void setWellID(String id, int plateIndex, int wellIndex) { 
    23082308    if (id == null) return; 
    2309     WellNode wellNode = getWellNode(wellIndex, true); 
     2309    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23102310      wellNode.setNodeID(id); 
    23112311    } 
    23122312 
    2313   /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int) */ 
    2314   public void setWellRow(Integer row, int wellIndex) { 
     2313  /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int, int) */ 
     2314  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
    23152315    if (row == null) return; 
    2316     WellNode wellNode = getWellNode(wellIndex, true); 
     2316    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23172317      wellNode.setRow(row); 
    23182318    } 
    23192319 
    2320   /* @see loci.formats.meta.MetadataStore#setWellType(String, int) */ 
    2321   public void setWellType(String type, int wellIndex) { 
     2320  /* @see loci.formats.meta.MetadataStore#setWellType(String, int, int) */ 
     2321  public void setWellType(String type, int plateIndex, int wellIndex) { 
    23222322    if (type == null) return; 
    2323     WellNode wellNode = getWellNode(wellIndex, true); 
     2323    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23242324      wellNode.setType(type); 
    23252325    } 
     
    23272327  // - WellSample property storage - 
    23282328 
    2329   /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int) */ 
    2330   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
     2329  /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int, int) */ 
     2330  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23312331    if (id == null) return; 
    2332     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2332    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23332333      wellSampleNode.setNodeID(id); 
    23342334    } 
    23352335 
    2336   /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    2337   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
     2336  /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     2337  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23382338    if (index == null) return; 
    2339     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2339    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23402340      wellSampleNode.setIndex(index); 
    23412341    } 
    23422342 
    2343   /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int) */ 
    2344   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
     2343  /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     2344  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23452345    if (posX == null) return; 
    2346     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2346    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23472347      wellSampleNode.setPosX(posX); 
    23482348    } 
    23492349 
    2350   /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int) */ 
    2351   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
     2350  /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     2351  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23522352    if (posY == null) return; 
    2353     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2353    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23542354      wellSampleNode.setPosY(posY); 
    23552355    } 
    23562356 
    2357   /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    2358   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
     2357  /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     2358  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23592359    if (timepoint == null) return; 
    2360     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2360    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23612361      wellSampleNode.setTimepoint(timepoint); 
    23622362    } 
     
    27062706  } 
    27072707 
     2708  // Plate+/Well+ 
     2709  private WellNode getWellNode(int plateIndex, int wellIndex, boolean create) { 
     2710    // get Plate+ node 
     2711    PlateNode plate = getPlateNode(plateIndex, create); 
     2712    if (plate == null) return null; 
     2713    // get Well+ node 
     2714    int count = plate.getWellCount(); 
     2715    if (!create && count <= wellIndex) return null; 
     2716    for (int i=count; i<=wellIndex; i++) new WellNode(plate); 
     2717    List list = plate.getWellList(); 
     2718    return (WellNode) list.get(wellIndex); 
     2719  } 
     2720 
     2721  // Plate+/Well+/WellSample+ 
     2722  private WellSampleNode getWellSampleNode(int plateIndex, int wellIndex, int wellSampleIndex, boolean create) { 
     2723    // get Plate+/Well+ node 
     2724    WellNode well = getWellNode(plateIndex, wellIndex, create); 
     2725    if (well == null) return null; 
     2726    // get WellSample+ node 
     2727    int count = well.getWellSampleCount(); 
     2728    if (!create && count <= wellSampleIndex) return null; 
     2729    for (int i=count; i<=wellSampleIndex; i++) new WellSampleNode(well); 
     2730    List list = well.getWellSampleList(); 
     2731    return (WellSampleNode) list.get(wellSampleIndex); 
     2732  } 
     2733 
    27082734  // Screen+ 
    27092735  private ScreenNode getScreenNode(int screenIndex, boolean create) { 
     
    27562782  } 
    27572783 
    2758   // Well+ 
    2759   private WellNode getWellNode(int wellIndex, boolean create) { 
    2760     OMENode ome = (OMENode) root; 
    2761     // get Well+ node 
    2762     int count = ome.getWellCount(); 
    2763     if (!create && count <= wellIndex) return null; 
    2764     for (int i=count; i<=wellIndex; i++) new WellNode(ome); 
    2765     List list = ome.getWellList(); 
    2766     return (WellNode) list.get(wellIndex); 
    2767   } 
    2768  
    2769   // Well+/WellSample+ 
    2770   private WellSampleNode getWellSampleNode(int wellIndex, int wellSampleIndex, boolean create) { 
    2771     // get Well+ node 
    2772     WellNode well = getWellNode(wellIndex, create); 
    2773     if (well == null) return null; 
    2774     // get WellSample+ node 
    2775     int count = well.getWellSampleCount(); 
    2776     if (!create && count <= wellSampleIndex) return null; 
    2777     for (int i=count; i<=wellSampleIndex; i++) new WellSampleNode(well); 
    2778     List list = well.getWellSampleList(); 
    2779     return (WellSampleNode) list.get(wellSampleIndex); 
    2780   } 
    2781  
    27822784} 
  • trunk/loci/formats/ome/OMEXML200802Metadata.java

    r4117 r4146  
    2525 * 
    2626 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY. 
    27  * Created by melissa via MetadataAutogen on Jun 16, 2008 1:24:43 PM PDT 
     27 * Created by melissa via MetadataAutogen on Jul 1, 2008 8:53:09 AM PDT 
    2828 * 
    2929 *----------------------------------------------------------------------------- 
     
    216216  } 
    217217 
    218   /* @see loci.formats.meta.MetadataRetrieve#getWellCount() */ 
    219   public int getWellCount() { 
     218  /* @see loci.formats.meta.MetadataRetrieve#getWellCount(int) */ 
     219  public int getWellCount(int plateIndex) { 
    220220    for (int i=0; i<Integer.MAX_VALUE; i++) { 
    221       if (getWellNode(i, false) == null) return i; 
     221      if (getWellNode(plateIndex, i, false) == null) return i; 
    222222    } 
    223223    return -1; 
    224224  } 
    225225 
    226   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int) */ 
    227   public int getWellSampleCount(int wellIndex) { 
     226  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleCount(int, int) */ 
     227  public int getWellSampleCount(int plateIndex, int wellIndex) { 
    228228    for (int i=0; i<Integer.MAX_VALUE; i++) { 
    229       if (getWellSampleNode(wellIndex, i, false) == null) return i; 
     229      if (getWellSampleNode(plateIndex, wellIndex, i, false) == null) return i; 
    230230    } 
    231231    return -1; 
     
    11401140  // - Well property retrieval - 
    11411141 
    1142   /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int) */ 
    1143   public Integer getWellColumn(int wellIndex) { 
    1144     WellNode well = getWellNode(wellIndex, false); 
     1142  /* @see loci.formats.meta.MetadataRetrieve#getWellColumn(int, int) */ 
     1143  public Integer getWellColumn(int plateIndex, int wellIndex) { 
     1144    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11451145      return well == null ? null : well.getColumn(); 
    11461146    } 
    11471147 
    1148   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int) */ 
    1149   public String getWellExternalDescription(int wellIndex) { 
    1150     WellNode well = getWellNode(wellIndex, false); 
     1148  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalDescription(int, int) */ 
     1149  public String getWellExternalDescription(int plateIndex, int wellIndex) { 
     1150    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11511151      return well == null ? null : well.getExternalDescription(); 
    11521152    } 
    11531153 
    1154   /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int) */ 
    1155   public String getWellExternalIdentifier(int wellIndex) { 
    1156     WellNode well = getWellNode(wellIndex, false); 
     1154  /* @see loci.formats.meta.MetadataRetrieve#getWellExternalIdentifier(int, int) */ 
     1155  public String getWellExternalIdentifier(int plateIndex, int wellIndex) { 
     1156    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11571157      return well == null ? null : well.getExternalIdentifier(); 
    11581158    } 
    11591159 
    1160   /* @see loci.formats.meta.MetadataRetrieve#getWellID(int) */ 
    1161   public String getWellID(int wellIndex) { 
    1162     WellNode well = getWellNode(wellIndex, false); 
     1160  /* @see loci.formats.meta.MetadataRetrieve#getWellID(int, int) */ 
     1161  public String getWellID(int plateIndex, int wellIndex) { 
     1162    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11631163      return well == null ? null : well.getNodeID(); 
    11641164    } 
    11651165 
    1166   /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int) */ 
    1167   public Integer getWellRow(int wellIndex) { 
    1168     WellNode well = getWellNode(wellIndex, false); 
     1166  /* @see loci.formats.meta.MetadataRetrieve#getWellRow(int, int) */ 
     1167  public Integer getWellRow(int plateIndex, int wellIndex) { 
     1168    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11691169      return well == null ? null : well.getRow(); 
    11701170    } 
    11711171 
    1172   /* @see loci.formats.meta.MetadataRetrieve#getWellType(int) */ 
    1173   public String getWellType(int wellIndex) { 
    1174     WellNode well = getWellNode(wellIndex, false); 
     1172  /* @see loci.formats.meta.MetadataRetrieve#getWellType(int, int) */ 
     1173  public String getWellType(int plateIndex, int wellIndex) { 
     1174    WellNode well = getWellNode(plateIndex, wellIndex, false); 
    11751175      return well == null ? null : well.getType(); 
    11761176    } 
     
    11781178  // - WellSample property retrieval - 
    11791179 
    1180   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int) */ 
    1181   public String getWellSampleID(int wellIndex, int wellSampleIndex) { 
    1182     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1180  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleID(int, int, int) */ 
     1181  public String getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1182    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11831183      return wellSample == null ? null : wellSample.getNodeID(); 
    11841184    } 
    11851185 
    1186   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int) */ 
    1187   public Integer getWellSampleIndex(int wellIndex, int wellSampleIndex) { 
    1188     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1186  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleIndex(int, int, int) */ 
     1187  public Integer getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1188    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11891189      return wellSample == null ? null : wellSample.getIndex(); 
    11901190    } 
    11911191 
    1192   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int) */ 
    1193   public Float getWellSamplePosX(int wellIndex, int wellSampleIndex) { 
    1194     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1192  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosX(int, int, int) */ 
     1193  public Float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1194    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    11951195      return wellSample == null ? null : wellSample.getPosX(); 
    11961196    } 
    11971197 
    1198   /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int) */ 
    1199   public Float getWellSamplePosY(int wellIndex, int wellSampleIndex) { 
    1200     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1198  /* @see loci.formats.meta.MetadataRetrieve#getWellSamplePosY(int, int, int) */ 
     1199  public Float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1200    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    12011201      return wellSample == null ? null : wellSample.getPosY(); 
    12021202    } 
    12031203 
    1204   /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int) */ 
    1205   public Integer getWellSampleTimepoint(int wellIndex, int wellSampleIndex) { 
    1206     WellSampleNode wellSample = getWellSampleNode(wellIndex, wellSampleIndex, false); 
     1204  /* @see loci.formats.meta.MetadataRetrieve#getWellSampleTimepoint(int, int, int) */ 
     1205  public Integer getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex) { 
     1206    WellSampleNode wellSample = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, false); 
    12071207      return wellSample == null ? null : wellSample.getTimepoint(); 
    12081208    } 
     
    22892289  // - Well property storage - 
    22902290 
    2291   /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int) */ 
    2292   public void setWellColumn(Integer column, int wellIndex) { 
     2291  /* @see loci.formats.meta.MetadataStore#setWellColumn(Integer, int, int) */ 
     2292  public void setWellColumn(Integer column, int plateIndex, int wellIndex) { 
    22932293    if (column == null) return; 
    2294     WellNode wellNode = getWellNode(wellIndex, true); 
     2294    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    22952295      wellNode.setColumn(column); 
    22962296    } 
    22972297 
    2298   /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int) */ 
    2299   public void setWellExternalDescription(String externalDescription, int wellIndex) { 
     2298  /* @see loci.formats.meta.MetadataStore#setWellExternalDescription(String, int, int) */ 
     2299  public void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex) { 
    23002300    if (externalDescription == null) return; 
    2301     WellNode wellNode = getWellNode(wellIndex, true); 
     2301    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23022302      wellNode.setExternalDescription(externalDescription); 
    23032303    } 
    23042304 
    2305   /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int) */ 
    2306   public void setWellExternalIdentifier(String externalIdentifier, int wellIndex) { 
     2305  /* @see loci.formats.meta.MetadataStore#setWellExternalIdentifier(String, int, int) */ 
     2306  public void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex) { 
    23072307    if (externalIdentifier == null) return; 
    2308     WellNode wellNode = getWellNode(wellIndex, true); 
     2308    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23092309      wellNode.setExternalIdentifier(externalIdentifier); 
    23102310    } 
    23112311 
    2312   /* @see loci.formats.meta.MetadataStore#setWellID(String, int) */ 
    2313   public void setWellID(String id, int wellIndex) { 
     2312  /* @see loci.formats.meta.MetadataStore#setWellID(String, int, int) */ 
     2313  public void setWellID(String id, int plateIndex, int wellIndex) { 
    23142314    if (id == null) return; 
    2315     WellNode wellNode = getWellNode(wellIndex, true); 
     2315    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23162316      wellNode.setNodeID(id); 
    23172317    } 
    23182318 
    2319   /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int) */ 
    2320   public void setWellRow(Integer row, int wellIndex) { 
     2319  /* @see loci.formats.meta.MetadataStore#setWellRow(Integer, int, int) */ 
     2320  public void setWellRow(Integer row, int plateIndex, int wellIndex) { 
    23212321    if (row == null) return; 
    2322     WellNode wellNode = getWellNode(wellIndex, true); 
     2322    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23232323      wellNode.setRow(row); 
    23242324    } 
    23252325 
    2326   /* @see loci.formats.meta.MetadataStore#setWellType(String, int) */ 
    2327   public void setWellType(String type, int wellIndex) { 
     2326  /* @see loci.formats.meta.MetadataStore#setWellType(String, int, int) */ 
     2327  public void setWellType(String type, int plateIndex, int wellIndex) { 
    23282328    if (type == null) return; 
    2329     WellNode wellNode = getWellNode(wellIndex, true); 
     2329    WellNode wellNode = getWellNode(plateIndex, wellIndex, true); 
    23302330      wellNode.setType(type); 
    23312331    } 
     
    23332333  // - WellSample property storage - 
    23342334 
    2335   /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int) */ 
    2336   public void setWellSampleID(String id, int wellIndex, int wellSampleIndex) { 
     2335  /* @see loci.formats.meta.MetadataStore#setWellSampleID(String, int, int, int) */ 
     2336  public void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23372337    if (id == null) return; 
    2338     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2338    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23392339      wellSampleNode.setNodeID(id); 
    23402340    } 
    23412341 
    2342   /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int) */ 
    2343   public void setWellSampleIndex(Integer index, int wellIndex, int wellSampleIndex) { 
     2342  /* @see loci.formats.meta.MetadataStore#setWellSampleIndex(Integer, int, int, int) */ 
     2343  public void setWellSampleIndex(Integer index, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23442344    if (index == null) return; 
    2345     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2345    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23462346      wellSampleNode.setIndex(index); 
    23472347    } 
    23482348 
    2349   /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int) */ 
    2350   public void setWellSamplePosX(Float posX, int wellIndex, int wellSampleIndex) { 
     2349  /* @see loci.formats.meta.MetadataStore#setWellSamplePosX(Float, int, int, int) */ 
     2350  public void setWellSamplePosX(Float posX, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23512351    if (posX == null) return; 
    2352     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2352    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23532353      wellSampleNode.setPosX(posX); 
    23542354    } 
    23552355 
    2356   /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int) */ 
    2357   public void setWellSamplePosY(Float posY, int wellIndex, int wellSampleIndex) { 
     2356  /* @see loci.formats.meta.MetadataStore#setWellSamplePosY(Float, int, int, int) */ 
     2357  public void setWellSamplePosY(Float posY, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23582358    if (posY == null) return; 
    2359     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2359    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23602360      wellSampleNode.setPosY(posY); 
    23612361    } 
    23622362 
    2363   /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int) */ 
    2364   public void setWellSampleTimepoint(Integer timepoint, int wellIndex, int wellSampleIndex) { 
     2363  /* @see loci.formats.meta.MetadataStore#setWellSampleTimepoint(Integer, int, int, int) */ 
     2364  public void setWellSampleTimepoint(Integer timepoint, int plateIndex, int wellIndex, int wellSampleIndex) { 
    23652365    if (timepoint == null) return; 
    2366     WellSampleNode wellSampleNode = getWellSampleNode(wellIndex, wellSampleIndex, true); 
     2366    WellSampleNode wellSampleNode = getWellSampleNode(plateIndex, wellIndex, wellSampleIndex, true); 
    23672367      wellSampleNode.setTimepoint(timepoint); 
    23682368    } 
     
    27262726  } 
    27272727 
     2728  // Plate+/Well+ 
     2729  private WellNode getWellNode(int plateIndex, int wellIndex, boolean create) { 
     2730    // get Plate+ node 
     2731    PlateNode plate = getPlateNode(plateIndex, create); 
     2732    if (plate == null) return null; 
     2733    // get Well+ node 
     2734    int count = plate.getWellCount(); 
     2735    if (!create && count <= wellIndex) return null; 
     2736    for (int i=count; i<=wellIndex; i++) new WellNode(plate); 
     2737    List list = plate.getWellList(); 
     2738    return (WellNode) list.get(wellIndex); 
     2739  } 
     2740 
     2741  // Plate+/Well+/WellSample+ 
     2742  private WellSampleNode getWellSampleNode(int plateIndex, int wellIndex, int wellSampleIndex, boolean create) { 
     2743    // get Plate+/Well+ node 
     2744    WellNode well = getWellNode(plateIndex, wellIndex, create); 
     2745    if (well == null) return null; 
     2746    // get WellSample+ node 
     2747    int count = well.getWellSampleCount(); 
     2748    if (!create && count <= wellSampleIndex) return null; 
     2749    for (int i=count; i<=wellSampleIndex; i++) new WellSampleNode(well); 
     2750    List list = well.getWellSampleList(); 
     2751    return (WellSampleNode) list.get(wellSampleIndex); 
     2752  } 
     2753 
    27282754  // Screen+ 
    27292755  private ScreenNode getScreenNode(int screenIndex, boolean create) { 
     
    27762802  } 
    27772803 
    2778   // Well+ 
    2779   private WellNode getWellNode(int wellIndex, boolean create) { 
    2780     OMENode ome = (OMENode) root; 
    2781     // get Well+ node 
    2782     int count = ome.getWellCount(); 
    2783     if (!create && count <= wellIndex) return null; 
    2784     for (int i=count; i<=wellIndex; i++) new WellNode(ome); 
    2785     List list = ome.getWellList(); 
    2786     return (WellNode) list.get(wellIndex); 
    2787   } 
    2788  
    2789   // Well+/WellSample+ 
    2790   private WellSampleNode getWellSampleNode(int wellIndex, int wellSampleIndex, boolean create) { 
    2791     // get Well+ node 
    2792     WellNode well = getWellNode(wellIndex, create); 
    2793     if (well == null) return null; 
    2794     // get WellSample+ node 
    2795     int count = well.getWellSampleCount(); 
    2796     if (!create && count <= wellSampleIndex) return null; 
    2797     for (int i=count; i<=wellSampleIndex; i++) new WellSampleNode(well); 
    2798     List list = well.getWellSampleList(); 
    2799     return (WellSampleNode) list.get(wellSampleIndex); 
    2800   } 
    2801  
    28022804} 
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