Changeset 2648


Ignore:
Timestamp:
04/19/07 14:43:43 (13 years ago)
Author:
curtis
Message:

Fix javadoc generation warnings.

Location:
trunk/loci/formats
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/loci/formats/FileStitcher.java

    r2601 r2648  
    872872  // -- Deprecated IFormatReader API methods -- 
    873873 
    874   /** @deprecated Replaced by {@link getImageCount()} */ 
     874  /** @deprecated Replaced by {@link #getImageCount()} */ 
    875875  public int getImageCount(String id) throws FormatException, IOException { 
    876876    if (!id.equals(currentId)) setId(id); 
     
    878878  } 
    879879 
    880   /** @deprecated Replaced by {@link isRGB()} */ 
     880  /** @deprecated Replaced by {@link #isRGB()} */ 
    881881  public boolean isRGB(String id) throws FormatException, IOException { 
    882882    if (!id.equals(currentId)) setId(id); 
     
    884884  } 
    885885 
    886   /** @deprecated Replaced by {@link getSizeX()} */ 
     886  /** @deprecated Replaced by {@link #getSizeX()} */ 
    887887  public int getSizeX(String id) throws FormatException, IOException { 
    888888    if (!id.equals(currentId)) setId(id); 
     
    890890  } 
    891891 
    892   /** @deprecated Replaced by {@link getSizeY()} */ 
     892  /** @deprecated Replaced by {@link #getSizeY()} */ 
    893893  public int getSizeY(String id) throws FormatException, IOException { 
    894894    if (!id.equals(currentId)) setId(id); 
     
    896896  } 
    897897 
    898   /** @deprecated Replaced by {@link getSizeZ()} */ 
     898  /** @deprecated Replaced by {@link #getSizeZ()} */ 
    899899  public int getSizeZ(String id) throws FormatException, IOException { 
    900900    if (!id.equals(currentId)) setId(id); 
     
    902902  } 
    903903 
    904   /** @deprecated Replaced by {@link getSizeC()} */ 
     904  /** @deprecated Replaced by {@link #getSizeC()} */ 
    905905  public int getSizeC(String id) throws FormatException, IOException { 
    906906    if (!id.equals(currentId)) setId(id); 
     
    908908  } 
    909909 
    910   /** @deprecated Replaced by {@link getSizeT()} */ 
     910  /** @deprecated Replaced by {@link #getSizeT()} */ 
    911911  public int getSizeT(String id) throws FormatException, IOException { 
    912912    if (!id.equals(currentId)) setId(id); 
     
    914914  } 
    915915 
    916   /** @deprecated Replaced by {@link getPixelType()} */ 
     916  /** @deprecated Replaced by {@link #getPixelType()} */ 
    917917  public int getPixelType(String id) throws FormatException, IOException { 
    918918    if (!id.equals(currentId)) setId(id); 
     
    920920  } 
    921921 
    922   /** @deprecated Replaced by {@link getEffectiveSizeC()} */ 
     922  /** @deprecated Replaced by {@link #getEffectiveSizeC()} */ 
    923923  public int getEffectiveSizeC(String id) throws FormatException, IOException { 
    924924    if (!id.equals(currentId)) setId(id); 
     
    926926  } 
    927927 
    928   /** @deprecated Replaced by {@link getRGBChannelCount()} */ 
     928  /** @deprecated Replaced by {@link #getRGBChannelCount()} */ 
    929929  public int getRGBChannelCount(String id) throws FormatException, IOException { 
    930930    if (!id.equals(currentId)) setId(id); 
     
    932932  } 
    933933 
    934   /** @deprecated Replaced by {@link getChannelDimLengths()} */ 
     934  /** @deprecated Replaced by {@link #getChannelDimLengths()} */ 
    935935  public int[] getChannelDimLengths(String id) 
    936936    throws FormatException, IOException 
     
    944944  } 
    945945 
    946   /** @deprecated Replaced by {@link getChannelDimTypes()} */ 
     946  /** @deprecated Replaced by {@link #getChannelDimTypes()} */ 
    947947  public String[] getChannelDimTypes(String id) 
    948948    throws FormatException, IOException 
     
    956956  } 
    957957 
    958   /** @deprecated Replaced by {@link getThumbSizeX()} */ 
     958  /** @deprecated Replaced by {@link #getThumbSizeX()} */ 
    959959  public int getThumbSizeX(String id) throws FormatException, IOException { 
    960960    if (!id.equals(currentId)) setId(id); 
     
    962962  } 
    963963 
    964   /** @deprecated Replaced by {@link getThumbSizeY()} */ 
     964  /** @deprecated Replaced by {@link #getThumbSizeY()} */ 
    965965  public int getThumbSizeY(String id) throws FormatException, IOException { 
    966966    if (!id.equals(currentId)) setId(id); 
     
    968968  } 
    969969 
    970   /** @deprecated Replaced by {@link isLittleEndian()} */ 
     970  /** @deprecated Replaced by {@link #isLittleEndian()} */ 
    971971  public boolean isLittleEndian(String id) throws FormatException, IOException { 
    972972    if (!id.equals(currentId)) setId(id); 
     
    974974  } 
    975975 
    976   /** @deprecated Replaced by {@link getDimensionOrder()} */ 
     976  /** @deprecated Replaced by {@link #getDimensionOrder()} */ 
    977977  public String getDimensionOrder(String id) 
    978978    throws FormatException, IOException 
     
    982982  } 
    983983 
    984   /** @deprecated Replaced by {@link isOrderCertain()} */ 
     984  /** @deprecated Replaced by {@link #isOrderCertain()} */ 
    985985  public boolean isOrderCertain(String id) throws FormatException, IOException { 
    986986    if (!id.equals(currentId)) setId(id); 
     
    988988  } 
    989989 
    990   /** @deprecated Replaced by {@link isInterleaved()} */ 
     990  /** @deprecated Replaced by {@link #isInterleaved()} */ 
    991991  public boolean isInterleaved(String id) throws FormatException, IOException { 
    992992    if (!id.equals(currentId)) setId(id); 
     
    994994  } 
    995995 
    996   /** @deprecated Replaced by {@link isInterleaved(int)} */ 
     996  /** @deprecated Replaced by {@link #isInterleaved(int)} */ 
    997997  public boolean isInterleaved(String id, int subC) 
    998998    throws FormatException, IOException 
     
    10021002  } 
    10031003 
    1004   /** @deprecated Replaced by {@link openImage(int)} */ 
     1004  /** @deprecated Replaced by {@link #openImage(int)} */ 
    10051005  public BufferedImage openImage(String id, int no) 
    10061006    throws FormatException, IOException 
     
    10101010  } 
    10111011 
    1012   /** @deprecated Replaced by {@link openBytes(int)} */ 
     1012  /** @deprecated Replaced by {@link #openBytes(int)} */ 
    10131013  public byte[] openBytes(String id, int no) 
    10141014    throws FormatException, IOException 
     
    10181018  } 
    10191019 
    1020   /** @deprecated Replaced by {@link openBytes(int, byte[]) */ 
     1020  /** @deprecated Replaced by {@link #openBytes(int, byte[])} */ 
    10211021  public byte[] openBytes(String id, int no, byte[] buf) 
    10221022    throws FormatException, IOException 
     
    10261026  } 
    10271027 
    1028   /** @deprecated Replaced by {@link openThumbImage(int)} */ 
     1028  /** @deprecated Replaced by {@link #openThumbImage(int)} */ 
    10291029  public BufferedImage openThumbImage(String id, int no) 
    10301030    throws FormatException, IOException 
     
    10341034  } 
    10351035 
    1036   /** @deprecated Replaced by {@link openThumbImage(int)} */ 
     1036  /** @deprecated Replaced by {@link #openThumbImage(int)} */ 
    10371037  public byte[] openThumbBytes(String id, int no) 
    10381038    throws FormatException, IOException 
     
    10421042  } 
    10431043 
    1044   /** @deprecated Replaced by {@link getSeriesCount()} */ 
     1044  /** @deprecated Replaced by {@link #getSeriesCount()} */ 
    10451045  public int getSeriesCount(String id) throws FormatException, IOException { 
    10461046    if (!id.equals(currentId)) setId(id); 
     
    10481048  } 
    10491049 
    1050   /** @deprecated Replaced by {@link setSeries(int)} */ 
     1050  /** @deprecated Replaced by {@link #setSeries(int)} */ 
    10511051  public void setSeries(String id, int no) throws FormatException, IOException { 
    10521052    if (!id.equals(currentId)) setId(id); 
     
    10541054  } 
    10551055 
    1056   /** @deprecated Replaced by {@link getSeries()} */ 
     1056  /** @deprecated Replaced by {@link #getSeries()} */ 
    10571057  public int getSeries(String id) throws FormatException, IOException { 
    10581058    if (!id.equals(currentId)) setId(id); 
     
    10601060  } 
    10611061 
    1062   /** @deprecated Replaced by {@link getUsedFiles()} */ 
     1062  /** @deprecated Replaced by {@link #getUsedFiles()} */ 
    10631063  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    10641064    if (!id.equals(currentId)) setId(id); 
     
    10661066  } 
    10671067 
    1068   /** @deprecated Replaced by {@link getIndex(int, int, int)} */ 
     1068  /** @deprecated Replaced by {@link #getIndex(int, int, int)} */ 
    10691069  public int getIndex(String id, int z, int c, int t) 
    10701070    throws FormatException, IOException 
     
    10741074  } 
    10751075 
    1076   /** @deprecated Replaced by {@link getZCTCoords(int)} */ 
     1076  /** @deprecated Replaced by {@link #getZCTCoords(int)} */ 
    10771077  public int[] getZCTCoords(String id, int index) 
    10781078    throws FormatException, IOException 
     
    10821082  } 
    10831083 
    1084   /** @deprecated Replaced by {@link getMetadataValue(String)} */ 
     1084  /** @deprecated Replaced by {@link #getMetadataValue(String)} */ 
    10851085  public Object getMetadataValue(String id, String field) 
    10861086    throws FormatException, IOException 
     
    10901090  } 
    10911091 
    1092   /** @deprecated Replaced by {@link getMetadata()} */ 
     1092  /** @deprecated Replaced by {@link #getMetadata()} */ 
    10931093  public Hashtable getMetadata(String id) throws FormatException, IOException { 
    10941094    if (!id.equals(currentId)) setId(id); 
     
    10961096  } 
    10971097 
    1098   /** @deprecated Replaced by {@link getCoreMetadata()} */ 
     1098  /** @deprecated Replaced by {@link #getCoreMetadata()} */ 
    10991099  public CoreMetadata getCoreMetadata(String id) 
    11001100    throws FormatException, IOException 
     
    11041104  } 
    11051105 
    1106   /** @deprecated Replaced by {@link getMetadataStore()} */ 
     1106  /** @deprecated Replaced by {@link #getMetadataStore()} */ 
    11071107  public MetadataStore getMetadataStore(String id) 
    11081108    throws FormatException, IOException 
     
    11121112  } 
    11131113 
    1114   /** @deprecated Replaced by {@link getMetadataStoreRoot()} */ 
     1114  /** @deprecated Replaced by {@link #getMetadataStoreRoot()} */ 
    11151115  public Object getMetadataStoreRoot(String id) 
    11161116    throws FormatException, IOException 
  • trunk/loci/formats/FormatReader.java

    r2631 r2648  
    516516  // -- Deprecated IFormatReader API methods -- 
    517517 
    518   /** @deprecated Replaced by {@link getImageCount()} */ 
     518  /** @deprecated Replaced by {@link #getImageCount()} */ 
    519519  public int getImageCount(String id) throws FormatException, IOException { 
    520520    if (!id.equals(currentId)) setId(id); 
     
    522522  } 
    523523 
    524   /** @deprecated Replaced by {@link isRGB()} */ 
     524  /** @deprecated Replaced by {@link #isRGB()} */ 
    525525  public boolean isRGB(String id) throws FormatException, IOException { 
    526526    return getRGBChannelCount(id) > 1; 
    527527  } 
    528528 
    529   /** @deprecated Replaced by {@link getSizeX()} */ 
     529  /** @deprecated Replaced by {@link #getSizeX()} */ 
    530530  public int getSizeX(String id) throws FormatException, IOException { 
    531531    if (!id.equals(currentId)) setId(id); 
     
    533533  } 
    534534 
    535   /** @deprecated Replaced by {@link getSizeY()} */ 
     535  /** @deprecated Replaced by {@link #getSizeY()} */ 
    536536  public int getSizeY(String id) throws FormatException, IOException { 
    537537    if (!id.equals(currentId)) setId(id); 
     
    539539  } 
    540540 
    541   /** @deprecated Replaced by {@link getSizeZ()} */ 
     541  /** @deprecated Replaced by {@link #getSizeZ()} */ 
    542542  public int getSizeZ(String id) throws FormatException, IOException { 
    543543    if (!id.equals(currentId)) setId(id); 
     
    545545  } 
    546546 
    547   /** @deprecated Replaced by {@link getSizeC()} */ 
     547  /** @deprecated Replaced by {@link #getSizeC()} */ 
    548548  public int getSizeC(String id) throws FormatException, IOException { 
    549549    if (!id.equals(currentId)) setId(id); 
     
    551551  } 
    552552 
    553   /** @deprecated Replaced by {@link getSizeT()} */ 
     553  /** @deprecated Replaced by {@link #getSizeT()} */ 
    554554  public int getSizeT(String id) throws FormatException, IOException { 
    555555    if (!id.equals(currentId)) setId(id); 
     
    557557  } 
    558558 
    559   /** @deprecated Replaced by {@link getPixelType()} */ 
     559  /** @deprecated Replaced by {@link #getPixelType()} */ 
    560560  public int getPixelType(String id) throws FormatException, IOException { 
    561561    if (!id.equals(currentId)) setId(id); 
     
    563563  } 
    564564 
    565   /** @deprecated Replaced by {@link getEffectiveSizeC()} */ 
     565  /** @deprecated Replaced by {@link #getEffectiveSizeC()} */ 
    566566  public int getEffectiveSizeC(String id) throws FormatException, IOException { 
    567567    // NB: by definition, imageCount == effectiveSizeC * sizeZ * sizeT 
     
    569569  } 
    570570 
    571   /** @deprecated Replaced by {@link getRGBChannelCount()} */ 
     571  /** @deprecated Replaced by {@link #getRGBChannelCount()} */ 
    572572  public int getRGBChannelCount(String id) throws FormatException, IOException { 
    573573    return getSizeC(id) / getEffectiveSizeC(id); 
    574574  } 
    575575 
    576   /** @deprecated Replaced by {@link getChannelDimLengths()} */ 
     576  /** @deprecated Replaced by {@link #getChannelDimLengths()} */ 
    577577  public int[] getChannelDimLengths(String id) 
    578578    throws FormatException, IOException 
     
    585585  } 
    586586 
    587   /** @deprecated Replaced by {@link getChannelDimTypes()} */ 
     587  /** @deprecated Replaced by {@link #getChannelDimTypes()} */ 
    588588  public String[] getChannelDimTypes(String id) 
    589589    throws FormatException, IOException 
     
    596596  } 
    597597 
    598   /** @deprecated Replaced by {@link getThumbSizeX()} */ 
     598  /** @deprecated Replaced by {@link #getThumbSizeX()} */ 
    599599  public int getThumbSizeX(String id) throws FormatException, IOException { 
    600600    int sx = getSizeX(id); 
     
    603603  } 
    604604 
    605   /** @deprecated Replaced by {@link getThumbSizeY()} */ 
     605  /** @deprecated Replaced by {@link #getThumbSizeY()} */ 
    606606  public int getThumbSizeY(String id) throws FormatException, IOException { 
    607607    int sx = getSizeX(id); 
     
    610610  } 
    611611 
    612   /** @deprecated Replaced by {@link isLittleEndian()} */ 
     612  /** @deprecated Replaced by {@link #isLittleEndian()} */ 
    613613  public boolean isLittleEndian(String id) throws FormatException, IOException { 
    614614    if (!id.equals(currentId)) setId(id); 
     
    616616  } 
    617617 
    618   /** @deprecated Replaced by {@link getDimensionOrder()} */ 
     618  /** @deprecated Replaced by {@link #getDimensionOrder()} */ 
    619619  public String getDimensionOrder(String id) throws FormatException, IOException 
    620620  { 
     
    623623  } 
    624624 
    625   /** @deprecated Replaced by {@link isOrderCertain()} */ 
     625  /** @deprecated Replaced by {@link #isOrderCertain()} */ 
    626626  public boolean isOrderCertain(String id) throws FormatException, IOException { 
    627627    if (!id.equals(currentId)) setId(id); 
     
    629629  } 
    630630 
    631   /** @deprecated Replaced by {@link isInterleaved()} */ 
     631  /** @deprecated Replaced by {@link #isInterleaved()} */ 
    632632  public boolean isInterleaved(String id) 
    633633    throws FormatException, IOException 
     
    636636  } 
    637637 
    638   /** @deprecated Replaced by {@link isInterleaved(int)} */ 
     638  /** @deprecated Replaced by {@link #isInterleaved(int)} */ 
    639639  public boolean isInterleaved(String id, int subC) 
    640640    throws FormatException, IOException 
     
    644644  } 
    645645 
    646   /** @deprecated Replaced by {@link openImage(int)} */ 
     646  /** @deprecated Replaced by {@link #openImage(int)} */ 
    647647  public BufferedImage openImage(String id, int no) 
    648648    throws FormatException, IOException 
     
    652652  } 
    653653 
    654   /** @deprecated Replaced by {@link openBytes(int)} */ 
     654  /** @deprecated Replaced by {@link #openBytes(int)} */ 
    655655  public byte[] openBytes(String id, int no) 
    656656    throws FormatException, IOException 
     
    660660  } 
    661661 
    662   /** @deprecated Replaced by {@link openBytes(int, byte[])} */ 
     662  /** @deprecated Replaced by {@link #openBytes(int, byte[])} */ 
    663663  public byte[] openBytes(String id, int no, byte[] buf) 
    664664    throws FormatException, IOException 
     
    667667  } 
    668668 
    669   /** @deprecated Replaced by {@link openThumbImage(int)} */ 
     669  /** @deprecated Replaced by {@link #openThumbImage(int)} */ 
    670670  public BufferedImage openThumbImage(String id, int no) 
    671671    throws FormatException, IOException 
     
    675675  } 
    676676 
    677   /** @deprecated Replaced by {@link openThumbBytes(int)} */ 
     677  /** @deprecated Replaced by {@link #openThumbBytes(int)} */ 
    678678  public byte[] openThumbBytes(String id, int no) 
    679679    throws FormatException, IOException 
     
    689689  } 
    690690 
    691   /** @deprecated Replaced by {@link getSeriesCount()} */ 
     691  /** @deprecated Replaced by {@link #getSeriesCount()} */ 
    692692  public int getSeriesCount(String id) throws FormatException, IOException { 
    693693    if (!id.equals(currentId)) setId(id); 
     
    695695  } 
    696696 
    697   /** @deprecated Replaced by {@link setSeries(int)} */ 
     697  /** @deprecated Replaced by {@link #setSeries(int)} */ 
    698698  public void setSeries(String id, int no) throws FormatException, IOException { 
    699699    if (no < 0 || no >= getSeriesCount(id)) { 
     
    703703  } 
    704704 
    705   /** @deprecated Replaced by {@link getSeries()} */ 
     705  /** @deprecated Replaced by {@link #getSeries()} */ 
    706706  public int getSeries(String id) throws FormatException, IOException { 
    707707    if (!id.equals(currentId)) setId(id); 
     
    709709  } 
    710710 
    711   /** @deprecated Replaced by {@link getUsedFiles()} */ 
     711  /** @deprecated Replaced by {@link #getUsedFiles()} */ 
    712712  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    713713    if (!id.equals(currentId)) setId(id); 
     
    715715  } 
    716716 
    717   /** @deprecated Replaced by {@link getIndex(int, int, int)} */ 
     717  /** @deprecated Replaced by {@link #getIndex(int, int, int)} */ 
    718718  public int getIndex(String id, int z, int c, int t) 
    719719    throws FormatException, IOException 
     
    723723  } 
    724724 
    725   /** @deprecated Replaced by {@link getZCTCoords(int)} */ 
     725  /** @deprecated Replaced by {@link #getZCTCoords(int)} */ 
    726726  public int[] getZCTCoords(String id, int index) 
    727727    throws FormatException, IOException 
     
    731731  } 
    732732 
    733   /** @deprecated Replaced by {@link getMetadataValue(String)} */ 
     733  /** @deprecated Replaced by {@link #getMetadataValue(String)} */ 
    734734  public Object getMetadataValue(String id, String field) 
    735735    throws FormatException, IOException 
     
    739739  } 
    740740 
    741   /** @deprecated Replaced by {@link getMetadata()} */ 
     741  /** @deprecated Replaced by {@link #getMetadata()} */ 
    742742  public Hashtable getMetadata(String id) throws FormatException, IOException { 
    743743    if (!id.equals(currentId)) setId(id); 
     
    745745  } 
    746746 
    747   /** @deprecated Replaced by {@link getCoreMetadata()} */ 
     747  /** @deprecated Replaced by {@link #getCoreMetadata()} */ 
    748748  public CoreMetadata getCoreMetadata(String id) 
    749749    throws FormatException, IOException 
     
    753753  } 
    754754 
    755   /** @deprecated Replaced by {@link getMetadataStore()} */ 
     755  /** @deprecated Replaced by {@link #getMetadataStore()} */ 
    756756  public MetadataStore getMetadataStore(String id) 
    757757    throws FormatException, IOException 
     
    761761  } 
    762762 
    763   /** @deprecated Replaced by {@link getMetadataStoreRoot()} */ 
     763  /** @deprecated Replaced by {@link #getMetadataStoreRoot()} */ 
    764764  public Object getMetadataStoreRoot(String id) 
    765765    throws FormatException, IOException 
  • trunk/loci/formats/IFormatReader.java

    r2601 r2648  
    284284  // -- Deprecated API methods -- 
    285285 
    286   /** @deprecated Replaced by {@link getImageCount()} */ 
     286  /** @deprecated Replaced by {@link #getImageCount()} */ 
    287287  int getImageCount(String id) throws FormatException, IOException; 
    288288 
    289   /** @deprecated Replaced by {@link isRGB()} */ 
     289  /** @deprecated Replaced by {@link #isRGB()} */ 
    290290  boolean isRGB(String id) throws FormatException, IOException; 
    291291 
    292   /** @deprecated Replaced by {@link getSizeX()} */ 
     292  /** @deprecated Replaced by {@link #getSizeX()} */ 
    293293  int getSizeX(String id) throws FormatException, IOException; 
    294294 
    295   /** @deprecated Replaced by {@link getSizeY()} */ 
     295  /** @deprecated Replaced by {@link #getSizeY()} */ 
    296296  int getSizeY(String id) throws FormatException, IOException; 
    297297 
    298   /** @deprecated Replaced by {@link getSizeZ()} */ 
     298  /** @deprecated Replaced by {@link #getSizeZ()} */ 
    299299  int getSizeZ(String id) throws FormatException, IOException; 
    300300 
    301   /** @deprecated Replaced by {@link getSizeC()} */ 
     301  /** @deprecated Replaced by {@link #getSizeC()} */ 
    302302  int getSizeC(String id) throws FormatException, IOException; 
    303303 
    304   /** @deprecated Replaced by {@link getSizeT()} */ 
     304  /** @deprecated Replaced by {@link #getSizeT()} */ 
    305305  int getSizeT(String id) throws FormatException, IOException; 
    306306 
    307   /** @deprecated Replaced by {@link getPixelType()} */ 
     307  /** @deprecated Replaced by {@link #getPixelType()} */ 
    308308  int getPixelType(String id) throws FormatException, IOException; 
    309309 
    310   /** @deprecated Replaced by {@link getEffectiveSizeC()} */ 
     310  /** @deprecated Replaced by {@link #getEffectiveSizeC()} */ 
    311311  int getEffectiveSizeC(String id) throws FormatException, IOException; 
    312312 
    313   /** @deprecated Replaced by {@link getRGBChannelCount()} */ 
     313  /** @deprecated Replaced by {@link #getRGBChannelCount()} */ 
    314314  int getRGBChannelCount(String id) throws FormatException, IOException; 
    315315 
    316   /** @deprecated Replaced by {@link getChannelDimLengths()} */ 
     316  /** @deprecated Replaced by {@link #getChannelDimLengths()} */ 
    317317  int[] getChannelDimLengths(String id) throws FormatException, IOException; 
    318318 
    319   /** @deprecated Replaced by {@link getChannelDimTypes()} */ 
     319  /** @deprecated Replaced by {@link #getChannelDimTypes()} */ 
    320320  String[] getChannelDimTypes(String id) throws FormatException, IOException; 
    321321 
    322   /** @deprecated Replaced by {@link getThumbSizeX()} */ 
     322  /** @deprecated Replaced by {@link #getThumbSizeX()} */ 
    323323  int getThumbSizeX(String id) throws FormatException, IOException; 
    324324 
    325   /** @deprecated Replaced by {@link getThumbSizeY()} */ 
     325  /** @deprecated Replaced by {@link #getThumbSizeY()} */ 
    326326  int getThumbSizeY(String id) throws FormatException, IOException; 
    327327 
    328   /** @deprecated Replaced by {@link isLittleEndian()} */ 
     328  /** @deprecated Replaced by {@link #isLittleEndian()} */ 
    329329  boolean isLittleEndian(String id) throws FormatException, IOException; 
    330330 
    331   /** @deprecated Replaced by {@link getDimensionOrder()} */ 
     331  /** @deprecated Replaced by {@link #getDimensionOrder()} */ 
    332332  String getDimensionOrder(String id) throws FormatException, IOException; 
    333333 
    334   /** @deprecated Replaced by {@link isOrderCertain()} */ 
     334  /** @deprecated Replaced by {@link #isOrderCertain()} */ 
    335335  boolean isOrderCertain(String id) throws FormatException, IOException; 
    336336 
    337   /** @deprecated Replaced by {@link isInterleaved()} */ 
     337  /** @deprecated Replaced by {@link #isInterleaved()} */ 
    338338  boolean isInterleaved(String id) throws FormatException, IOException; 
    339339 
    340   /** @deprecated Replaced by {@link isInterleaved(int)} */ 
     340  /** @deprecated Replaced by {@link #isInterleaved(int)} */ 
    341341  boolean isInterleaved(String id, int subC) 
    342342    throws FormatException, IOException; 
    343343 
    344   /** @deprecated Replaced by {@link openImage(int)} */ 
     344  /** @deprecated Replaced by {@link #openImage(int)} */ 
    345345  BufferedImage openImage(String id, int no) 
    346346    throws FormatException, IOException; 
    347347 
    348   /** @deprecated Replaced by {@link openBytes(int)} */ 
     348  /** @deprecated Replaced by {@link #openBytes(int)} */ 
    349349  byte[] openBytes(String id, int no) throws FormatException, IOException; 
    350350 
    351   /** @deprecated Replaced by {@link openBytes(int, byte[])} */ 
     351  /** @deprecated Replaced by {@link #openBytes(int, byte[])} */ 
    352352  byte[] openBytes(String id, int no, byte[] buf) 
    353353    throws FormatException, IOException; 
    354354 
    355   /** @deprecated Replaced by {@link openThumbImage(int)} */ 
     355  /** @deprecated Replaced by {@link #openThumbImage(int)} */ 
    356356  BufferedImage openThumbImage(String id, int no) 
    357357    throws FormatException, IOException; 
    358358 
    359   /** @deprecated Replaced by {@link openThumbBytes(int)} */ 
     359  /** @deprecated Replaced by {@link #openThumbBytes(int)} */ 
    360360  byte[] openThumbBytes(String id, int no) throws FormatException, IOException; 
    361361 
    362   /** @deprecated Replaced by {@link getSeriesCount()} */ 
     362  /** @deprecated Replaced by {@link #getSeriesCount()} */ 
    363363  int getSeriesCount(String id) throws FormatException, IOException; 
    364364 
    365   /** @deprecated Replaced by {@link setSeries(int)} */ 
     365  /** @deprecated Replaced by {@link #setSeries(int)} */ 
    366366  void setSeries(String id, int no) throws FormatException, IOException; 
    367367 
    368   /** @deprecated Replaced by {@link getSeries()} */ 
     368  /** @deprecated Replaced by {@link #getSeries()} */ 
    369369  int getSeries(String id) throws FormatException, IOException; 
    370370 
    371   /** @deprecated Replaced by {@link getUsedFiles()} */ 
     371  /** @deprecated Replaced by {@link #getUsedFiles()} */ 
    372372  String[] getUsedFiles(String id) throws FormatException, IOException; 
    373373 
    374   /** @deprecated Replaced by {@link getIndex(int, int, int)} */ 
     374  /** @deprecated Replaced by {@link #getIndex(int, int, int)} */ 
    375375  int getIndex(String id, int z, int c, int t) 
    376376    throws FormatException, IOException; 
    377377 
    378   /** @deprecated Replaced by {@link getZCTCoords(int)} */ 
     378  /** @deprecated Replaced by {@link #getZCTCoords(int)} */ 
    379379  int[] getZCTCoords(String id, int index) 
    380380    throws FormatException, IOException; 
    381381 
    382   /** @deprecated Replaced by {@link getMetadataValue(String)} */ 
     382  /** @deprecated Replaced by {@link #getMetadataValue(String)} */ 
    383383  Object getMetadataValue(String id, String field) 
    384384    throws FormatException, IOException; 
    385385 
    386   /** @deprecated Replaced by {@link getMetadata()} */ 
     386  /** @deprecated Replaced by {@link #getMetadata()} */ 
    387387  Hashtable getMetadata(String id) throws FormatException, IOException; 
    388388 
    389   /** @deprecated Replaced by {@link getCoreMetadata()} */ 
     389  /** @deprecated Replaced by {@link #getCoreMetadata()} */ 
    390390  CoreMetadata getCoreMetadata(String id) throws FormatException, IOException; 
    391391 
    392   /** @deprecated Replaced by {@link getMetadataStore()} */ 
     392  /** @deprecated Replaced by {@link #getMetadataStore()} */ 
    393393  MetadataStore getMetadataStore(String id) throws FormatException, IOException; 
    394394 
    395   /** @deprecated Replaced by {@link getMetadataStoreRoot()} */ 
     395  /** @deprecated Replaced by {@link #getMetadataStoreRoot()} */ 
    396396  Object getMetadataStoreRoot(String id) throws FormatException, IOException; 
    397397 
  • trunk/loci/formats/ImageReader.java

    r2601 r2648  
    475475  // -- Deprecated IFormatReader API methods -- 
    476476 
    477   /** @deprecated Replaced by {@link getImageCount()} */ 
     477  /** @deprecated Replaced by {@link #getImageCount()} */ 
    478478  public int getImageCount(String id) throws FormatException, IOException { 
    479479    setId(id); 
     
    481481  } 
    482482 
    483   /** @deprecated Replaced by {@link isRGB()} */ 
     483  /** @deprecated Replaced by {@link #isRGB()} */ 
    484484  public boolean isRGB(String id) throws FormatException, IOException { 
    485485    setId(id); 
     
    487487  } 
    488488 
    489   /** @deprecated Replaced by {@link getSizeX()} */ 
     489  /** @deprecated Replaced by {@link #getSizeX()} */ 
    490490  public int getSizeX(String id) throws FormatException, IOException { 
    491491    setId(id); 
     
    493493  } 
    494494 
    495   /** @deprecated Replaced by {@link getSizeY()} */ 
     495  /** @deprecated Replaced by {@link #getSizeY()} */ 
    496496  public int getSizeY(String id) throws FormatException, IOException { 
    497497    setId(id); 
     
    499499  } 
    500500 
    501   /** @deprecated Replaced by {@link getSizeZ()} */ 
     501  /** @deprecated Replaced by {@link #getSizeZ()} */ 
    502502  public int getSizeZ(String id) throws FormatException, IOException { 
    503503    setId(id); 
     
    505505  } 
    506506 
    507   /** @deprecated Replaced by {@link getSizeC()} */ 
     507  /** @deprecated Replaced by {@link #getSizeC()} */ 
    508508  public int getSizeC(String id) throws FormatException, IOException { 
    509509    setId(id); 
     
    511511  } 
    512512 
    513   /** @deprecated Replaced by {@link getSizeT()} */ 
     513  /** @deprecated Replaced by {@link #getSizeT()} */ 
    514514  public int getSizeT(String id) throws FormatException, IOException { 
    515515    setId(id); 
     
    517517  } 
    518518 
    519   /** @deprecated Replaced by {@link getPixelType()} */ 
     519  /** @deprecated Replaced by {@link #getPixelType()} */ 
    520520  public int getPixelType(String id) throws FormatException, IOException { 
    521521    setId(id); 
     
    523523  } 
    524524 
    525   /** @deprecated Replaced by {@link getEffectiveSizeC()} */ 
     525  /** @deprecated Replaced by {@link #getEffectiveSizeC()} */ 
    526526  public int getEffectiveSizeC(String id) throws FormatException, IOException { 
    527527    setId(id); 
     
    529529  } 
    530530 
    531   /** @deprecated Replaced by {@link getRGBChannelCount()} */ 
     531  /** @deprecated Replaced by {@link #getRGBChannelCount()} */ 
    532532  public int getRGBChannelCount(String id) throws FormatException, IOException { 
    533533    setId(id); 
     
    535535  } 
    536536 
    537   /** @deprecated Replaced by {@link getChannelDimLengths()} */ 
     537  /** @deprecated Replaced by {@link #getChannelDimLengths()} */ 
    538538  public int[] getChannelDimLengths(String id) 
    539539    throws FormatException, IOException 
     
    543543  } 
    544544 
    545   /** @deprecated Replaced by {@link getChannelDimTypes()} */ 
     545  /** @deprecated Replaced by {@link #getChannelDimTypes()} */ 
    546546  public String[] getChannelDimTypes(String id) 
    547547    throws FormatException, IOException 
     
    551551  } 
    552552 
    553   /** @deprecated Replaced by {@link getThumbSizeX()} */ 
     553  /** @deprecated Replaced by {@link #getThumbSizeX()} */ 
    554554  public int getThumbSizeX(String id) throws FormatException, IOException { 
    555555    setId(id); 
     
    557557  } 
    558558 
    559   /** @deprecated Replaced by {@link getThumbSizeY()} */ 
     559  /** @deprecated Replaced by {@link #getThumbSizeY()} */ 
    560560  public int getThumbSizeY(String id) throws FormatException, IOException { 
    561561    setId(id); 
     
    563563  } 
    564564 
    565   /** @deprecated Replaced by {@link isLittleEndian()} */ 
     565  /** @deprecated Replaced by {@link #isLittleEndian()} */ 
    566566  public boolean isLittleEndian(String id) throws FormatException, IOException { 
    567567    setId(id); 
     
    569569  } 
    570570 
    571   /** @deprecated Replaced by {@link getDimensionOrder()} */ 
     571  /** @deprecated Replaced by {@link #getDimensionOrder()} */ 
    572572  public String getDimensionOrder(String id) 
    573573    throws FormatException, IOException 
     
    577577  } 
    578578 
    579   /** @deprecated Replaced by {@link isOrderCertain()} */ 
     579  /** @deprecated Replaced by {@link #isOrderCertain()} */ 
    580580  public boolean isOrderCertain(String id) throws FormatException, IOException { 
    581581    setId(id); 
     
    583583  } 
    584584 
    585   /** @deprecated Replaced by {@link isInterleaved()} */ 
     585  /** @deprecated Replaced by {@link #isInterleaved()} */ 
    586586  public boolean isInterleaved(String id) throws FormatException, IOException { 
    587587    setId(id); 
     
    589589  } 
    590590 
    591   /** @deprecated Replaced by {@link isInterleaved(int)} */ 
     591  /** @deprecated Replaced by {@link #isInterleaved(int)} */ 
    592592  public boolean isInterleaved(String id, int subC) 
    593593    throws FormatException, IOException 
     
    597597  } 
    598598 
    599   /** @deprecated Replaced by {@link openImage(int)} */ 
     599  /** @deprecated Replaced by {@link #openImage(int)} */ 
    600600  public BufferedImage openImage(String id, int no) 
    601601    throws FormatException, IOException 
     
    605605  } 
    606606 
    607   /** @deprecated Replaced by {@link openBytes(int)} */ 
     607  /** @deprecated Replaced by {@link #openBytes(int)} */ 
    608608  public byte[] openBytes(String id, int no) 
    609609    throws FormatException, IOException 
     
    613613  } 
    614614 
    615   /** @deprecated Replaced by {@link openBytes(int, byte[])} */ 
     615  /** @deprecated Replaced by {@link #openBytes(int, byte[])} */ 
    616616  public byte[] openBytes(String id, int no, byte[] buf) 
    617617    throws FormatException, IOException 
     
    621621  } 
    622622 
    623   /** @deprecated Replaced by {@link openThumbImage(int)} */ 
     623  /** @deprecated Replaced by {@link #openThumbImage(int)} */ 
    624624  public BufferedImage openThumbImage(String id, int no) 
    625625    throws FormatException, IOException 
     
    629629  } 
    630630 
    631   /** @deprecated Replaced by {@link openThumbBytes(int)} */ 
     631  /** @deprecated Replaced by {@link #openThumbBytes(int)} */ 
    632632  public byte[] openThumbBytes(String id, int no) 
    633633    throws FormatException, IOException 
     
    637637  } 
    638638 
    639   /** @deprecated Replaced by {@link getSeriesCount()} */ 
     639  /** @deprecated Replaced by {@link #getSeriesCount()} */ 
    640640  public int getSeriesCount(String id) throws FormatException, IOException { 
    641641    setId(id); 
     
    643643  } 
    644644 
    645   /** @deprecated Replaced by {@link setSeries(int)} */ 
     645  /** @deprecated Replaced by {@link #setSeries(int)} */ 
    646646  public void setSeries(String id, int no) throws FormatException, IOException { 
    647647    setId(id); 
     
    649649  } 
    650650 
    651   /** @deprecated Replaced by {@link getSeries()} */ 
     651  /** @deprecated Replaced by {@link #getSeries()} */ 
    652652  public int getSeries(String id) throws FormatException, IOException { 
    653653    setId(id); 
     
    655655  } 
    656656 
    657   /** @deprecated Replaced by {@link getUsedFiles()} */ 
     657  /** @deprecated Replaced by {@link #getUsedFiles()} */ 
    658658  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    659659    setId(id); 
     
    661661  } 
    662662 
    663   /** @deprecated Replaced by {@link getIndex(int, int, int)} */ 
     663  /** @deprecated Replaced by {@link #getIndex(int, int, int)} */ 
    664664  public int getIndex(String id, int z, int c, int t) 
    665665    throws FormatException, IOException 
     
    669669  } 
    670670 
    671   /** @deprecated Replaced by {@link getZCTCoords(int)} */ 
     671  /** @deprecated Replaced by {@link #getZCTCoords(int)} */ 
    672672  public int[] getZCTCoords(String id, int index) 
    673673    throws FormatException, IOException 
     
    677677  } 
    678678 
    679   /** @deprecated Replaced by {@link getMetadataValue(String)} */ 
     679  /** @deprecated Replaced by {@link #getMetadataValue(String)} */ 
    680680  public Object getMetadataValue(String id, String field) 
    681681    throws FormatException, IOException 
     
    685685  } 
    686686 
    687   /** @deprecated Replaced by {@link getMetadata()} */ 
     687  /** @deprecated Replaced by {@link #getMetadata()} */ 
    688688  public Hashtable getMetadata(String id) throws FormatException, IOException { 
    689689    setId(id); 
     
    691691  } 
    692692 
    693   /** @deprecated Replaced by {@link getCoreMetadata()} */ 
     693  /** @deprecated Replaced by {@link #getCoreMetadata()} */ 
    694694  public CoreMetadata getCoreMetadata(String id) 
    695695    throws FormatException, IOException 
     
    699699  } 
    700700 
    701   /** @deprecated Replaced by {@link getMetadataStore()} */ 
     701  /** @deprecated Replaced by {@link #getMetadataStore()} */ 
    702702  public MetadataStore getMetadataStore(String id) 
    703703    throws FormatException, IOException 
     
    707707  } 
    708708 
    709   /** @deprecated Replaced by {@link getMetadataStoreRoot()} */ 
     709  /** @deprecated Replaced by {@link #getMetadataStoreRoot()} */ 
    710710  public Object getMetadataStoreRoot(String id) 
    711711    throws FormatException, IOException 
  • trunk/loci/formats/MinMaxCalculator.java

    r2628 r2648  
    368368  // -- Deprecated IFormatReader API methods -- 
    369369 
    370   /** @deprecated Replaced by {@link openImage(int)} */ 
     370  /** @deprecated Replaced by {@link #openImage(int)} */ 
    371371  public BufferedImage openImage(String id, int no) 
    372372    throws FormatException, IOException 
     
    378378  } 
    379379 
    380   /** @deprecated Replaced by {@link openBytes(int)} */ 
     380  /** @deprecated Replaced by {@link #openBytes(int)} */ 
    381381  public byte[] openBytes(String id, int no) throws FormatException, IOException 
    382382  { 
     
    387387  } 
    388388 
    389   /** @deprecated Replaced by {@link openBytes(int, byte[])} */ 
     389  /** @deprecated Replaced by {@link #openBytes(int, byte[])} */ 
    390390  public byte[] openBytes(String id, int no, byte[] buf) 
    391391    throws FormatException, IOException 
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