Changeset 2455


Ignore:
Timestamp:
03/14/07 17:06:15 (13 years ago)
Author:
curtis
Message:

Clean up comments, style and whitespace.

Location:
trunk/loci/formats
Files:
67 edited

Legend:

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

    r2320 r2455  
    409409    for (Iterator iter = delegates.iterator(); iter.hasNext();) { 
    410410      MetadataStore s = (MetadataStore) iter.next(); 
    411       s.setOTF(sizeX, sizeY, pixelType, path, opticalAxisAverage, instrumentNdx, 
    412       otfNdx, filterNdx, objectiveNdx); 
     411      s.setOTF(sizeX, sizeY, pixelType, path, opticalAxisAverage, 
     412        instrumentNdx, otfNdx, filterNdx, objectiveNdx); 
    413413    } 
    414414  } 
  • trunk/loci/formats/FormatHandler.java

    r2454 r2455  
    6565  } 
    6666 
    67   // -- Internal FormatHandler methods -- 
     67  // -- Internal FormatHandler API methods -- 
    6868 
    6969  /** Fires a status update event. */ 
  • trunk/loci/formats/FormatWriter.java

    r2453 r2455  
    4141  /** Debugging level. 1=basic, 2=extended, 3=everything, 4=insane. */ 
    4242  public static int debugLevel = 1; 
    43  
    4443 
    4544  // -- Fields -- 
  • trunk/loci/formats/IFormatReader.java

    r2453 r2455  
    254254  String[] getUsedFiles(String id) throws FormatException, IOException; 
    255255 
    256   /** Returns the current file */ 
     256  /** Returns the current file. */ 
    257257  String getCurrentFile(); 
    258258 
  • trunk/loci/formats/IRandomAccess.java

    r2178 r2455  
    2828 
    2929/** 
    30  * Interface for random access into structures (files or arrays). 
     30 * Interface for random access into structures (e.g., files or arrays). 
    3131 * 
    3232 * @author Curtis Rueden ctrueden at wisc.edu 
  • trunk/loci/formats/ImageTester.java

    r2178 r2455  
    8282  } 
    8383 
    84   // -- WindowListener methods -- 
     84  // -- WindowListener API methods -- 
    8585 
    8686  public void windowActivated(WindowEvent e) { } 
  • trunk/loci/formats/RABytes.java

    r2178 r2455  
    114114  // -- DataInput API methods -- 
    115115 
    116   /* @see DataInput.readBoolean() */ 
     116  /* @see java.io.DataInput.readBoolean() */ 
    117117  public boolean readBoolean() throws IOException { 
    118118    return readByte() != 0; 
    119119  } 
    120120 
    121   /* @see DataInput.readByte() */ 
     121  /* @see java.io.DataInput.readByte() */ 
    122122  public byte readByte() throws IOException { 
    123123    if (fp + 1 > array.length) throw new EOFException(); 
     
    125125  } 
    126126 
    127   /* @see DataInput.readChar() */ 
     127  /* @see java.io.DataInput.readChar() */ 
    128128  public char readChar() throws IOException { 
    129129    if (fp + 2 > array.length) throw new EOFException(); 
     
    133133  } 
    134134 
    135   /* @see DataInput.readDouble() */ 
     135  /* @see java.io.DataInput.readDouble() */ 
    136136  public double readDouble() throws IOException { 
    137137    if (fp + 8 > array.length) throw new EOFException(); 
     
    141141  } 
    142142 
    143   /* @see DataInput.readFloat() */ 
     143  /* @see java.io.DataInput.readFloat() */ 
    144144  public float readFloat() throws IOException { 
    145145    if (fp + 4 > array.length) throw new EOFException(); 
     
    149149  } 
    150150 
    151   /* @see DataInput.readFully(byte[]) */ 
     151  /* @see java.io.DataInput.readFully(byte[]) */ 
    152152  public void readFully(byte[] b) throws IOException { 
    153153    readFully(b, 0, b.length); 
    154154  } 
    155155 
    156   /* @see DataInput.readFully(byte[], int, int) */ 
     156  /* @see java.io.DataInput.readFully(byte[], int, int) */ 
    157157  public void readFully(byte[] b, int off, int len) throws IOException { 
    158158    if (fp + len > array.length) throw new EOFException(); 
     
    161161  } 
    162162 
    163   /* @see DataInput.readInt() */ 
     163  /* @see java.io.DataInput.readInt() */ 
    164164  public int readInt() throws IOException { 
    165165    if (fp + 4 > array.length) throw new EOFException(); 
     
    169169  } 
    170170 
    171   /* @see DataInput.readLine() */ 
     171  /* @see java.io.DataInput.readLine() */ 
    172172  public String readLine() throws IOException { 
    173173    throw new IOException("Unimplemented"); 
    174174  } 
    175175 
    176   /* @see DataInput.readLong() */ 
     176  /* @see java.io.DataInput.readLong() */ 
    177177  public long readLong() throws IOException { 
    178178    if (fp + 8 > array.length) throw new EOFException(); 
     
    182182  } 
    183183 
    184   /* @see DataInput.readShort() */ 
     184  /* @see java.io.DataInput.readShort() */ 
    185185  public short readShort() throws IOException { 
    186186    if (fp + 2 > array.length) throw new EOFException(); 
     
    190190  } 
    191191 
    192   /* @see DataInput.readUnsignedByte() */ 
     192  /* @see java.io.DataInput.readUnsignedByte() */ 
    193193  public int readUnsignedByte() throws IOException { 
    194194    if (fp + 1 > array.length) throw new EOFException(); 
     
    196196  } 
    197197 
    198   /* @see DataInput.readUnsignedShort() */ 
     198  /* @see java.io.DataInput.readUnsignedShort() */ 
    199199  public int readUnsignedShort() throws IOException { 
    200200    if (fp + 2 > array.length) throw new EOFException(); 
     
    204204  } 
    205205 
    206   /* @see DataInput.readUTF() */ 
     206  /* @see java.io.DataInput.readUTF() */ 
    207207  public String readUTF() throws IOException { 
    208208    throw new IOException("Unimplemented"); 
    209209  } 
    210210 
    211   /* @see DataInput.skipBytes(int) */ 
     211  /* @see java.io.DataInput.skipBytes(int) */ 
    212212  public int skipBytes(int n) { 
    213213    if (n < 0) n = 0; 
     
    219219  // -- DataOutput API metthods -- 
    220220 
    221   /* @see DataOutput.write(byte[]) */ 
     221  /* @see java.io.DataOutput.write(byte[]) */ 
    222222  public void write(byte[] b) throws IOException { 
    223223    write(b, 0, b.length); 
    224224  } 
    225225 
    226   /* @see DataOutput.write(byte[], int, int) */ 
     226  /* @see java.io.DataOutput.write(byte[], int, int) */ 
    227227  public void write(byte[] b, int off, int len) throws IOException { 
    228228    if (fp + len > array.length) setLength(fp + len); 
     
    231231  } 
    232232 
    233   /* @see DataOutput.write(int b) */ 
     233  /* @see java.io.DataOutput.write(int b) */ 
    234234  public void write(int b) throws IOException { 
    235235    if (fp + 1 > array.length) setLength(fp + 1); 
     
    237237  } 
    238238 
    239   /* @see DataOutput.writeBoolean(boolean) */ 
     239  /* @see java.io.DataOutput.writeBoolean(boolean) */ 
    240240  public void writeBoolean(boolean v) throws IOException { 
    241241    write(v ? 1 : 0); 
    242242  } 
    243243 
    244   /* @see DataOutput.writeByte(int) */ 
     244  /* @see java.io.DataOutput.writeByte(int) */ 
    245245  public void writeByte(int v) throws IOException { 
    246246    write(v); 
    247247  } 
    248248 
    249   /* @see DataOutput.writeBytes(String) */ 
     249  /* @see java.io.DataOutput.writeBytes(String) */ 
    250250  public void writeBytes(String s) throws IOException { 
    251251    char[] c = s.toCharArray(); 
     
    255255  } 
    256256 
    257   /* @see DataOutput.writeChar(int) */ 
     257  /* @see java.io.DataOutput.writeChar(int) */ 
    258258  public void writeChar(int v) throws IOException { 
    259259    if (fp + 2 > array.length) setLength(fp + 2); 
     
    262262  } 
    263263 
    264   /* @see DataOutput.writeChars(String) */ 
     264  /* @see java.io.DataOutput.writeChars(String) */ 
    265265  public void writeChars(String s) throws IOException { 
    266266    int len = 2 * s.length(); 
     
    274274  } 
    275275 
    276   /* @see DataOutput.writeDouble(double) */ 
     276  /* @see java.io.DataOutput.writeDouble(double) */ 
    277277  public void writeDouble(double v) throws IOException { 
    278278    writeLong(Double.doubleToLongBits(v)); 
    279279  } 
    280280 
    281   /* @see DataOutput.writeFloat(float) */ 
     281  /* @see java.io.DataOutput.writeFloat(float) */ 
    282282  public void writeFloat(float v) throws IOException { 
    283283    writeInt(Float.floatToIntBits(v)); 
    284284  } 
    285285 
    286   /* @see DataOutput.writeInt(int) */ 
     286  /* @see java.io.DataOutput.writeInt(int) */ 
    287287  public void writeInt(int v) throws IOException { 
    288288    if (fp + 4 > array.length) setLength(fp + 4); 
     
    293293  } 
    294294 
    295   /* @see DataOutput.writeLong(long) */ 
     295  /* @see java.io.DataOutput.writeLong(long) */ 
    296296  public void writeLong(long v) throws IOException { 
    297297    if (fp + 8 > array.length) setLength(fp + 8); 
     
    306306  } 
    307307 
    308   /* @see DataOutput.writeShort(int) */ 
     308  /* @see java.io.DataOutput.writeShort(int) */ 
    309309  public void writeShort(int v) throws IOException { 
    310310    if (fp + 2 > array.length) setLength(fp + 2); 
     
    315315  } 
    316316 
    317   /* @see DataOutput.writeUTF(String)  */ 
     317  /* @see java.io.DataOutput.writeUTF(String)  */ 
    318318  public void writeUTF(String str) throws IOException { 
    319319    throw new IOException("Unimplemented"); 
  • trunk/loci/formats/RAFile.java

    r2178 r2455  
    109109  // -- DataInput API methods -- 
    110110 
    111   /* @see DataInput.readBoolean() */ 
     111  /* @see java.io.DataInput.readBoolean() */ 
    112112  public boolean readBoolean() throws IOException { 
    113113    return raf.readBoolean(); 
    114114  } 
    115115 
    116   /* @see DataInput.readByte() */ 
     116  /* @see java.io.DataInput.readByte() */ 
    117117  public byte readByte() throws IOException { 
    118118    return raf.readByte(); 
    119119  } 
    120120 
    121   /* @see DataInput.readChar() */ 
     121  /* @see java.io.DataInput.readChar() */ 
    122122  public char readChar() throws IOException { 
    123123    return raf.readChar(); 
    124124  } 
    125125 
    126   /* @see DataInput.readDouble() */ 
     126  /* @see java.io.DataInput.readDouble() */ 
    127127  public double readDouble() throws IOException { 
    128128    return raf.readDouble(); 
    129129  } 
    130130 
    131   /* @see DataInput.readFloat() */ 
     131  /* @see java.io.DataInput.readFloat() */ 
    132132  public float readFloat() throws IOException { 
    133133    return raf.readFloat(); 
    134134  } 
    135135 
    136   /* @see DataInput.readFully(byte[]) */ 
     136  /* @see java.io.DataInput.readFully(byte[]) */ 
    137137  public void readFully(byte[] b) throws IOException { 
    138138    raf.readFully(b); 
    139139  } 
    140140 
    141   /* @see DataInput.readFully(byte[], int, int) */ 
     141  /* @see java.io.DataInput.readFully(byte[], int, int) */ 
    142142  public void readFully(byte[] b, int off, int len) throws IOException { 
    143143    raf.readFully(b, off, len); 
    144144  } 
    145145 
    146   /* @see DataInput.readInt() */ 
     146  /* @see java.io.DataInput.readInt() */ 
    147147  public int readInt() throws IOException { 
    148148    return raf.readInt(); 
    149149  } 
    150150 
    151   /* @see DataInput.readLine() */ 
     151  /* @see java.io.DataInput.readLine() */ 
    152152  public String readLine() throws IOException { 
    153153    return raf.readLine(); 
    154154  } 
    155155 
    156   /* @see DataInput.readLong() */ 
     156  /* @see java.io.DataInput.readLong() */ 
    157157  public long readLong() throws IOException { 
    158158    return raf.readLong(); 
    159159  } 
    160160 
    161   /* @see DataInput.readShort() */ 
     161  /* @see java.io.DataInput.readShort() */ 
    162162  public short readShort() throws IOException { 
    163163    return raf.readShort(); 
    164164  } 
    165165 
    166   /* @see DataInput.readUnsignedByte() */ 
     166  /* @see java.io.DataInput.readUnsignedByte() */ 
    167167  public int readUnsignedByte() throws IOException { 
    168168    return raf.readUnsignedByte(); 
    169169  } 
    170170 
    171   /* @see DataInput.readUnsignedShort() */ 
     171  /* @see java.io.DataInput.readUnsignedShort() */ 
    172172  public int readUnsignedShort() throws IOException { 
    173173    return raf.readUnsignedShort(); 
    174174  } 
    175175 
    176   /* @see DataInput.readUTF() */ 
     176  /* @see java.io.DataInput.readUTF() */ 
    177177  public String readUTF() throws IOException { 
    178178    return raf.readUTF(); 
    179179  } 
    180180 
    181   /* @see DataInput.skipBytes(int) */ 
     181  /* @see java.io.DataInput.skipBytes(int) */ 
    182182  public int skipBytes(int n) throws IOException { 
    183183    return raf.skipBytes(n); 
     
    186186  // -- DataOutput API metthods -- 
    187187 
    188   /* @see DataOutput.write(byte[]) */ 
     188  /* @see java.io.DataOutput.write(byte[]) */ 
    189189  public void write(byte[] b) throws IOException { 
    190190    raf.write(b); 
    191191  } 
    192192 
    193   /* @see DataOutput.write(byte[], int, int) */ 
     193  /* @see java.io.DataOutput.write(byte[], int, int) */ 
    194194  public void write(byte[] b, int off, int len) throws IOException { 
    195195    raf.write(b, off, len); 
    196196  } 
    197197 
    198   /* @see DataOutput.write(int b) */ 
     198  /* @see java.io.DataOutput.write(int b) */ 
    199199  public void write(int b) throws IOException { 
    200200    raf.write(b); 
    201201  } 
    202202 
    203   /* @see DataOutput.writeBoolean(boolean) */ 
     203  /* @see java.io.DataOutput.writeBoolean(boolean) */ 
    204204  public void writeBoolean(boolean v) throws IOException { 
    205205    raf.writeBoolean(v); 
    206206  } 
    207207 
    208   /* @see DataOutput.writeByte(int) */ 
     208  /* @see java.io.DataOutput.writeByte(int) */ 
    209209  public void writeByte(int v) throws IOException { 
    210210    raf.writeByte(v); 
    211211  } 
    212212 
    213   /* @see DataOutput.writeBytes(String) */ 
     213  /* @see java.io.DataOutput.writeBytes(String) */ 
    214214  public void writeBytes(String s) throws IOException { 
    215215    raf.writeBytes(s); 
    216216  } 
    217217 
    218   /* @see DataOutput.writeChar(int) */ 
     218  /* @see java.io.DataOutput.writeChar(int) */ 
    219219  public void writeChar(int v) throws IOException { 
    220220    raf.writeChar(v); 
    221221  } 
    222222 
    223   /* @see DataOutput.writeChars(String) */ 
     223  /* @see java.io.DataOutput.writeChars(String) */ 
    224224  public void writeChars(String s) throws IOException { 
    225225    raf.writeChars(s); 
    226226  } 
    227227 
    228   /* @see DataOutput.writeDouble(double) */ 
     228  /* @see java.io.DataOutput.writeDouble(double) */ 
    229229  public void writeDouble(double v) throws IOException { 
    230230    raf.writeDouble(v); 
    231231  } 
    232232 
    233   /* @see DataOutput.writeFloat(float) */ 
     233  /* @see java.io.DataOutput.writeFloat(float) */ 
    234234  public void writeFloat(float v) throws IOException { 
    235235    raf.writeFloat(v); 
    236236  } 
    237237 
    238   /* @see DataOutput.writeInt(int) */ 
     238  /* @see java.io.DataOutput.writeInt(int) */ 
    239239  public void writeInt(int v) throws IOException { 
    240240    raf.writeInt(v); 
    241241  } 
    242242 
    243   /* @see DataOutput.writeLong(long) */ 
     243  /* @see java.io.DataOutput.writeLong(long) */ 
    244244  public void writeLong(long v) throws IOException { 
    245245    raf.writeLong(v); 
    246246  } 
    247247 
    248   /* @see DataOutput.writeShort(int) */ 
     248  /* @see java.io.DataOutput.writeShort(int) */ 
    249249  public void writeShort(int v) throws IOException { 
    250250    raf.writeShort(v); 
    251251  } 
    252252 
    253   /* @see DataOutput.writeUTF(String)  */ 
     253  /* @see java.io.DataOutput.writeUTF(String)  */ 
    254254  public void writeUTF(String str) throws IOException { 
    255255    raf.writeUTF(str); 
  • trunk/loci/formats/RAUrl.java

    r2178 r2455  
    164164  // -- DataInput API methods -- 
    165165 
    166   /* @see DataInput#readBoolean() */ 
     166  /* @see java.io.DataInput#readBoolean() */ 
    167167  public boolean readBoolean() throws IOException { 
    168168    fp++; 
     
    170170  } 
    171171 
    172   /* @see DataInput#readByte() */ 
     172  /* @see java.io.DataInput#readByte() */ 
    173173  public byte readByte() throws IOException { 
    174174    fp++; 
     
    176176  } 
    177177 
    178   /* @see DataInput#readChar() */ 
     178  /* @see java.io.DataInput#readChar() */ 
    179179  public char readChar() throws IOException { 
    180180    fp++; 
     
    182182  } 
    183183 
    184   /* @see DataInput#readDouble() */ 
     184  /* @see java.io.DataInput#readDouble() */ 
    185185  public double readDouble() throws IOException { 
    186186    fp += 8; 
     
    188188  } 
    189189 
    190   /* @see DataInput#readFloat() */ 
     190  /* @see java.io.DataInput#readFloat() */ 
    191191  public float readFloat() throws IOException { 
    192192    fp += 4; 
     
    194194  } 
    195195 
    196   /* @see DataInput#readFully(byte[]) */ 
     196  /* @see java.io.DataInput#readFully(byte[]) */ 
    197197  public void readFully(byte[] b) throws IOException { 
    198198    fp += b.length; 
     
    200200  } 
    201201 
    202   /* @see DataInput#readFully(byte[], int, int) */ 
     202  /* @see java.io.DataInput#readFully(byte[], int, int) */ 
    203203  public void readFully(byte[] b, int off, int len) throws IOException { 
    204204    fp += len; 
     
    206206  } 
    207207 
    208   /* @see DataInput#readInt() */ 
     208  /* @see java.io.DataInput#readInt() */ 
    209209  public int readInt() throws IOException { 
    210210    fp += 4; 
     
    212212  } 
    213213 
    214   /* @see DataInput#readLine() */ 
     214  /* @see java.io.DataInput#readLine() */ 
    215215  public String readLine() throws IOException { 
    216216    throw new IOException("Unimplemented"); 
    217217  } 
    218218 
    219   /* @see DataInput#readLong() */ 
     219  /* @see java.io.DataInput#readLong() */ 
    220220  public long readLong() throws IOException { 
    221221    fp += 8; 
     
    223223  } 
    224224 
    225   /* @see DataInput#readShort() */ 
     225  /* @see java.io.DataInput#readShort() */ 
    226226  public short readShort() throws IOException { 
    227227    fp += 2; 
     
    229229  } 
    230230 
    231   /* @see DataInput#readUnsignedByte() */ 
     231  /* @see java.io.DataInput#readUnsignedByte() */ 
    232232  public int readUnsignedByte() throws IOException { 
    233233    fp++; 
     
    235235  } 
    236236 
    237   /* @see DataInput#readUnsignedShort() */ 
     237  /* @see java.io.DataInput#readUnsignedShort() */ 
    238238  public int readUnsignedShort() throws IOException { 
    239239    fp += 2; 
     
    241241  } 
    242242 
    243   /* @see DataInput#readUTF() */ 
     243  /* @see java.io.DataInput#readUTF() */ 
    244244  public String readUTF() throws IOException { 
    245245    fp += 2; 
     
    247247  } 
    248248 
    249   /* @see DataInput#skipBytes(int) */ 
     249  /* @see java.io.DataInput#skipBytes(int) */ 
    250250  public int skipBytes(int n) throws IOException { 
    251251    int skipped = 0; 
     
    259259  // -- DataOutput API methods -- 
    260260 
    261   /* @see DataOutput#write(byte[]) */ 
     261  /* @see java.io.DataOutput#write(byte[]) */ 
    262262  public void write(byte[] b) throws IOException { 
    263263    os.write(b); 
    264264  } 
    265265 
    266   /* @see DataOutput#write(byte[], int, int) */ 
     266  /* @see java.io.DataOutput#write(byte[], int, int) */ 
    267267  public void write(byte[] b, int off, int len) throws IOException { 
    268268    os.write(b, off, len); 
    269269  } 
    270270 
    271   /* @see DataOutput#write(int b) */ 
     271  /* @see java.io.DataOutput#write(int b) */ 
    272272  public void write(int b) throws IOException { 
    273273    os.write(b); 
    274274  } 
    275275 
    276   /* @see DataOutput#writeBoolean(boolean) */ 
     276  /* @see java.io.DataOutput#writeBoolean(boolean) */ 
    277277  public void writeBoolean(boolean v) throws IOException { 
    278278    os.writeBoolean(v); 
    279279  } 
    280280 
    281   /* @see DataOutput#writeByte(int) */ 
     281  /* @see java.io.DataOutput#writeByte(int) */ 
    282282  public void writeByte(int v) throws IOException { 
    283283    os.writeByte(v); 
    284284  } 
    285285 
    286   /* @see DataOutput#writeBytes(String) */ 
     286  /* @see java.io.DataOutput#writeBytes(String) */ 
    287287  public void writeBytes(String s) throws IOException { 
    288288    os.writeBytes(s); 
    289289  } 
    290290 
    291   /* @see DataOutput#writeChar(int) */ 
     291  /* @see java.io.DataOutput#writeChar(int) */ 
    292292  public void writeChar(int v) throws IOException { 
    293293    os.writeChar(v); 
    294294  } 
    295295 
    296   /* @see DataOutput#writeChars(String) */ 
     296  /* @see java.io.DataOutput#writeChars(String) */ 
    297297  public void writeChars(String s) throws IOException { 
    298298    os.writeChars(s); 
    299299  } 
    300300 
    301   /* @see DataOutput#writeDouble(double) */ 
     301  /* @see java.io.DataOutput#writeDouble(double) */ 
    302302  public void writeDouble(double v) throws IOException { 
    303303    os.writeDouble(v); 
    304304  } 
    305305 
    306   /* @see DataOutput#writeFloat(float) */ 
     306  /* @see java.io.DataOutput#writeFloat(float) */ 
    307307  public void writeFloat(float v) throws IOException { 
    308308    os.writeFloat(v); 
    309309  } 
    310310 
    311   /* @see DataOutput#writeInt(int) */ 
     311  /* @see java.io.DataOutput#writeInt(int) */ 
    312312  public void writeInt(int v) throws IOException { 
    313313    os.writeInt(v); 
    314314  } 
    315315 
    316   /* @see DataOutput#writeLong(long) */ 
     316  /* @see java.io.DataOutput#writeLong(long) */ 
    317317  public void writeLong(long v) throws IOException { 
    318318    os.writeLong(v); 
    319319  } 
    320320 
    321   /* @see DataOutput#writeShort(int) */ 
     321  /* @see java.io.DataOutput#writeShort(int) */ 
    322322  public void writeShort(int v) throws IOException { 
    323323    os.writeShort(v); 
    324324  } 
    325325 
    326   /* @see DataOutput#writeUTF(String) */ 
     326  /* @see java.io.DataOutput#writeUTF(String) */ 
    327327  public void writeUTF(String str) throws IOException { 
    328328    os.writeUTF(str); 
  • trunk/loci/formats/RandomAccessStream.java

    r2320 r2455  
    138138  // -- RandomAccessStream API methods -- 
    139139 
    140   /** Return the underlying InputStream */ 
     140  /** Returns the underlying InputStream. */ 
    141141  public DataInputStream getInputStream() { 
    142142    try { 
  • trunk/loci/formats/codec/JPEGCodec.java

    r2450 r2455  
    5656 
    5757  /** 
    58    * Decodes an image strip using JPEG compression algorithm 
     58   * Decodes an image strip using JPEG compression algorithm. 
    5959   * 
    6060   * @param b input data to be decompressed 
     
    6767    try { 
    6868      b = ImageIO.read(new ByteArrayInputStream(input)); 
    69     } catch (IOException e) { 
     69    } 
     70    catch (IOException e) { 
    7071      System.err.println("An I/O Error occurred decompressing image." + 
    7172        " Stack dump follows:"); 
  • trunk/loci/formats/in/AVIReader.java

    r2430 r2455  
    102102  } 
    103103 
    104   /* @see IFormatReader#isRGB(String) */ 
     104  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    105105  public boolean isRGB(String id) throws FormatException, IOException { 
    106106    if (!id.equals(currentId)) initFile(id); 
     
    179179  } 
    180180 
    181   /* @see IFormatReader#close(boolean) */ 
     181  /* @see loci.formats.IFormatReader#close(boolean) */ 
    182182  public void close(boolean fileOnly) throws FormatException, IOException { 
    183183    if (fileOnly) { 
  • trunk/loci/formats/in/AliconaReader.java

    r2430 r2455  
    7474  } 
    7575 
    76   /* @see IFormatReader#isRGB(String) */ 
     76  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    7777  public boolean isRGB(String id) throws FormatException, IOException { 
    7878    return false; 
     
    137137  } 
    138138 
    139   /* @see IFormatReader#close(boolean) */ 
     139  /* @see loci.formats.IFormatReader#close(boolean) */ 
    140140  public void close(boolean fileOnly) throws FormatException, IOException { 
    141141    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/BMPReader.java

    r2430 r2455  
    9898  } 
    9999 
    100   /* @see IFormatReader#isRGB(String) */ 
     100  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    101101  public boolean isRGB(String id) throws FormatException, IOException { 
    102102    if (!id.equals(currentId)) initFile(id); 
     
    191191  } 
    192192 
    193   /* @see IFormatReader#close(boolean) */ 
     193  /* @see loci.formats.IFormatReader#close(boolean) */ 
    194194  public void close(boolean fileOnly) throws FormatException, IOException { 
    195195    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/BaseTiffReader.java

    r2438 r2455  
    664664  } 
    665665 
    666   /* @see IFormatReader#isRGB(String) */ 
     666  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    667667  public boolean isRGB(String id) throws FormatException, IOException { 
    668668    if (!id.equals(currentId)) initFile(id); 
     
    788788  } 
    789789 
    790   /* @see IFormatReader#close(boolean) */ 
     790  /* @see loci.formats.IFormatReader#close(boolean) */ 
    791791  public void close(boolean fileOnly) throws FormatException, IOException { 
    792792    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/BioRadReader.java

    r2430 r2455  
    9696  } 
    9797 
    98   /* @see IFormatReader#isRGB(String) */ 
     98  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    9999  public boolean isRGB(String id) throws FormatException, IOException { 
    100100    return false; 
     
    127127  } 
    128128 
    129   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     129  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    130130  public boolean isMinMaxPopulated(String id) 
    131131    throws FormatException, IOException 
     
    172172  } 
    173173 
    174   /* @see IFormatReader#close(boolean) */ 
     174  /* @see loci.formats.IFormatReader#close(boolean) */ 
    175175  public void close(boolean fileOnly) throws FormatException, IOException { 
    176176    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/CRC.java

    r2178 r2455  
    133133  } 
    134134 
    135   // -- CRC methods -- 
     135  // -- CRC API methods -- 
    136136 
    137137  public void initialiseCRC() { 
  • trunk/loci/formats/in/DeltavisionReader.java

    r2430 r2455  
    163163  } 
    164164 
    165   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     165  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    166166  public boolean isMinMaxPopulated(String id) 
    167167    throws FormatException, IOException 
     
    170170  } 
    171171 
    172   /* @see IFormatReader#isRGB(String) */ 
     172  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    173173  public boolean isRGB(String id) throws FormatException, IOException { 
    174174    return false; 
     
    225225  } 
    226226 
    227   /* @see IFormatReader#close(boolean) */ 
     227  /* @see loci.formats.IFormatReader#close(boolean) */ 
    228228  public void close(boolean fileOnly) throws FormatException, IOException { 
    229229    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/DicomReader.java

    r2430 r2455  
    175175  } 
    176176 
    177   /* @see IFormatReader#close(boolean) */ 
     177  /* @see loci.formats.IFormatReader#close(boolean) */ 
    178178  public void close(boolean fileOnly) throws FormatException, IOException { 
    179179    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/EPSReader.java

    r2430 r2455  
    160160  } 
    161161 
    162   /* @see IFormatReader#close(boolean) */ 
     162  /* @see loci.formats.IFormatReader#close(boolean) */ 
    163163  public void close(boolean fileOnly) throws FormatException, IOException { 
    164164    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/FluoviewReader.java

    r2418 r2455  
    118118  } 
    119119 
    120   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     120  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    121121  public boolean isMinMaxPopulated(String id) 
    122122    throws FormatException, IOException 
     
    126126  } 
    127127 
    128   // -- FormatHandler API methods -- 
     128  // -- IFormatHandler API methods -- 
    129129 
    130130  /** 
  • trunk/loci/formats/in/GIFReader.java

    r2430 r2455  
    214214  } 
    215215 
    216   /* @see IFormatReader#close(boolean) */ 
     216  /* @see loci.formats.IFormatReader#close(boolean) */ 
    217217  public void close(boolean fileOnly) throws FormatException, IOException { 
    218218    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/GatanReader.java

    r2430 r2455  
    118118  } 
    119119 
    120   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     120  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    121121  public boolean isMinMaxPopulated(String id) 
    122122    throws FormatException, IOException 
     
    166166  } 
    167167 
    168   /* @see IFormatReader#close(boolean) */ 
     168  /* @see loci.formats.IFormatReader#close(boolean) */ 
    169169  public void close(boolean fileOnly) throws FormatException, IOException { 
    170170    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/ICSReader.java

    r2450 r2455  
    226226  } 
    227227 
    228   /* @see IFormatReader#getUsedFiles(String) */ 
     228  /* @see loci.formats.IFormatReader#getUsedFiles(String) */ 
    229229  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    230230    if (!id.equals(currentIdsId) && !id.equals(currentIcsId)) initFile(id); 
     
    235235  } 
    236236 
    237   /* @see IFormatReader#close(boolean) */ 
     237  /* @see loci.formats.IFormatReader#close(boolean) */ 
    238238  public void close(boolean fileOnly) throws FormatException, IOException { 
    239239    if (fileOnly && idsIn != null) idsIn.close(); 
  • trunk/loci/formats/in/IPLabReader.java

    r2430 r2455  
    126126  } 
    127127 
    128   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     128  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    129129  public boolean isMinMaxPopulated(String id) 
    130130    throws FormatException, IOException 
     
    171171  } 
    172172 
    173   /* @see IFormatReader#close(boolean) */ 
     173  /* @see loci.formats.IFormatReader#close(boolean) */ 
    174174  public void close(boolean fileOnly) throws FormatException, IOException { 
    175175    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/IPWReader.java

    r2430 r2455  
    181181  } 
    182182 
    183   /* @see IFormatReader#close(boolean) */ 
     183  /* @see loci.formats.IFormatReader#close(boolean) */ 
    184184  public void close(boolean fileOnly) throws FormatException, IOException { 
    185185    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/ImageIOReader.java

    r2320 r2455  
    117117  } 
    118118 
    119   /* @see IFormatReader#close(boolean) */ 
     119  /* @see loci.formats.IFormatReader#close(boolean) */ 
    120120  public void close(boolean fileOnly) throws FormatException, IOException { } 
    121121 
  • trunk/loci/formats/in/ImageJReader.java

    r2320 r2455  
    184184  } 
    185185 
    186   /* @see IFormatReader#close(boolean) */ 
     186  /* @see loci.formats.IFormatReader#close(boolean) */ 
    187187  public void close(boolean fileOnly) throws FormatException, IOException { 
    188188    if (!fileOnly) close(); 
  • trunk/loci/formats/in/ImarisReader.java

    r2430 r2455  
    239239  } 
    240240 
    241   /* @see IFormatReader#close(boolean) */ 
     241  /* @see loci.formats.IFormatReader#close(boolean) */ 
    242242  public void close(boolean fileOnly) throws FormatException, IOException { 
    243243    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/ImarisTiffReader.java

    r2430 r2455  
    7777  } 
    7878 
    79   // -- FormatHandler API methods -- 
     79  // -- IFormatHandler API methods -- 
    8080 
    8181  /** 
  • trunk/loci/formats/in/LIFReader.java

    r2445 r2455  
    138138  } 
    139139 
    140   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     140  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    141141  public boolean isMinMaxPopulated(String id) 
    142142    throws FormatException, IOException 
     
    190190  } 
    191191 
    192   /* @see IFormatReader#close(boolean) */ 
     192  /* @see loci.formats.IFormatReader#close(boolean) */ 
    193193  public void close(boolean fileOnly) throws FormatException, IOException { 
    194194    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/LegacyPictReader.java

    r2430 r2455  
    132132  } 
    133133 
    134   /* @see IFormatReader#close(boolean) */ 
     134  /* @see loci.formats.IFormatReader#close(boolean) */ 
    135135  public void close(boolean fileOnly) throws FormatException, IOException { } 
    136136 
  • trunk/loci/formats/in/LegacyQTReader.java

    r2320 r2455  
    135135  } 
    136136 
    137   /* @see IFormatReader#close(boolean) */ 
     137  /* @see loci.formats.IFormatReader#close(boolean) */ 
    138138  public void close(boolean fileOnly) throws FormatException, IOException { 
    139139    if (fileOnly) { 
  • trunk/loci/formats/in/LegacyZVIReader.java

    r2430 r2455  
    162162  } 
    163163 
    164   /* @see IFormatReader#close(boolean) */ 
     164  /* @see loci.formats.IFormatReader#close(boolean) */ 
    165165  public void close(boolean fileOnly) throws FormatException, IOException { 
    166166    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/LeicaReader.java

    r2445 r2455  
    119119  } 
    120120 
    121   /* @see IFormatReader#getChannelGlobalMinimum(String, int) */ 
     121  /* @see loci.formats.IFormatReader#getChannelGlobalMinimum(String, int) */ 
    122122  public Double getChannelGlobalMinimum(String id, int theC) 
    123123    throws FormatException, IOException 
     
    128128  } 
    129129 
    130   /* @see IFormatReader#getChannelGlobalMaximum(Straxg, axt) */ 
     130  /* @see loci.formats.IFormatReader#getChannelGlobalMaximum(Straxg, axt) */ 
    131131  public Double getChannelGlobalMaximum(String id, int theC) 
    132132    throws FormatException, IOException 
     
    137137  } 
    138138 
    139   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     139  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    140140  public boolean isMinMaxPopulated(String id) 
    141141    throws FormatException, IOException 
     
    233233  } 
    234234 
    235   /* @see IFormatReader#getUsedFiles(String) */ 
     235  /* @see loci.formats.IFormatReader#getUsedFiles(String) */ 
    236236  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    237237    if (!id.equals(currentId) && !usedFile(id) && !id.equals(leiFilename)) { 
     
    248248  } 
    249249 
    250   /* @see IFormatReader#close(boolean) */ 
     250  /* @see loci.formats.IFormatReader#close(boolean) */ 
    251251  public void close(boolean fileOnly) throws FormatException, IOException { 
    252252    if (fileOnly) { 
     
    626626  } 
    627627 
    628   // -- FormatHandler API methods -- 
     628  // -- IFormatHandler API methods -- 
    629629 
    630630  /** 
  • trunk/loci/formats/in/MNGReader.java

    r2430 r2455  
    132132  } 
    133133 
    134   /* @see IFormatReader#close(boolean) */ 
     134  /* @see loci.formats.IFormatReader#close(boolean) */ 
    135135  public void close(boolean fileOnly) throws FormatException, IOException { 
    136136    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/MRCReader.java

    r2430 r2455  
    6565  // -- IFormatReader API methods -- 
    6666 
    67   /* @see IFormatReader#getChannelGlobalMinimum(String, int) */ 
     67  /* @see loci.formats.IFormatReader#getChannelGlobalMinimum(String, int) */ 
    6868  public Double getChannelGlobalMinimum(String id, int theC) 
    6969    throws FormatException, IOException 
     
    7373  } 
    7474 
    75   /* @see IFormatReader#getChannelGlobalMaximum(String, int) */ 
     75  /* @see loci.formats.IFormatReader#getChannelGlobalMaximum(String, int) */ 
    7676  public Double getChannelGlobalMaximum(String id, int theC) 
    7777    throws FormatException, IOException 
     
    8181  } 
    8282 
    83   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     83  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    8484  public boolean isMinMaxPopulated(String id) 
    8585    throws FormatException, IOException 
     
    149149  } 
    150150 
    151   /* @see IFormatReader#close(boolean) */ 
     151  /* @see loci.formats.IFormatReader#close(boolean) */ 
    152152  public void close(boolean fileOnly) throws FormatException, IOException { 
    153153    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/MetamorphReader.java

    r2377 r2455  
    105105  } 
    106106 
    107   /* @see IFormatReader#getChannelGlobalMinimum(String, int) */ 
     107  /* @see loci.formats.IFormatReader#getChannelGlobalMinimum(String, int) */ 
    108108  public Double getChannelGlobalMinimum(String id, int theC) 
    109109    throws FormatException, IOException 
     
    113113  } 
    114114 
    115   /* @see IFormatReader#getChannelGlobalMaximum(String, int) */ 
     115  /* @see loci.formats.IFormatReader#getChannelGlobalMaximum(String, int) */ 
    116116  public Double getChannelGlobalMaximum(String id, int theC) 
    117117    throws FormatException, IOException 
     
    121121  } 
    122122 
    123   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     123  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    124124  public boolean isMinMaxPopulated(String id) 
    125125    throws FormatException, IOException 
  • trunk/loci/formats/in/MicromanagerReader.java

    r2418 r2455  
    5050  // -- IFormatReader API methods -- 
    5151 
    52   /* @see IFormatReader#isThisType(byte[]) */ 
     52  /* @see loci.formats.IFormatReader#isThisType(byte[]) */ 
    5353  public boolean isThisType(byte[] b) { 
    5454    return tiffReader.isThisType(b); 
    5555  } 
    5656 
    57   /* @see IFormatReader#getImageCount(String) */ 
     57  /* @see loci.formats.IFormatReader#getImageCount(String) */ 
    5858  public int getImageCount(String id) throws FormatException, IOException { 
    5959    if (!id.equals(currentId)) initFile(id); 
     
    6161  } 
    6262 
    63   /* @see IFormatReader#isLittleEndian(String) */ 
     63  /* @see loci.formats.IFormatReader#isLittleEndian(String) */ 
    6464  public boolean isLittleEndian(String id) throws FormatException, IOException { 
    6565    if (!id.equals(currentId)) initFile(id); 
     
    6767  } 
    6868 
    69   /* @see IFormatReader#isInterleaved(String) */ 
     69  /* @see loci.formats.IFormatReader#isInterleaved(String) */ 
    7070  public boolean isInterleaved(String id) throws FormatException, IOException { 
    7171    return false; 
    7272  } 
    7373 
    74   /* @see IFormatReader#openBytes(String, int) */ 
     74  /* @see loci.formats.IFormatReader#openBytes(String, int) */ 
    7575  public byte[] openBytes(String id, int no) 
    7676    throws FormatException, IOException 
     
    8383  } 
    8484 
    85   /* @see IFormatReader#openBytes(String, int, byte[]) */ 
     85  /* @see loci.formats.IFormatReader#openBytes(String, int, byte[]) */ 
    8686  public byte[] openBytes(String id, int no, byte[] buf) 
    8787    throws FormatException, IOException 
     
    9494  } 
    9595 
    96   /* @see IFormatReader#openImage(String, int) */ 
     96  /* @see loci.formats.IFormatReader#openImage(String, int) */ 
    9797  public BufferedImage openImage(String id, int no) 
    9898    throws FormatException, IOException 
     
    105105  } 
    106106 
    107   /* @see IFormatReader#getChannelGlobalMinimum(String, int) */ 
     107  /* @see loci.formats.IFormatReader#getChannelGlobalMinimum(String, int) */ 
    108108  public Double getChannelGlobalMinimum(String id, int theC) 
    109109    throws FormatException, IOException 
     
    124124  } 
    125125 
    126   /* @see IFormatReader#getChannelGlobalMaximum(String, int) */ 
     126  /* @see loci.formats.IFormatReader#getChannelGlobalMaximum(String, int) */ 
    127127  public Double getChannelGlobalMaximum(String id, int theC) 
    128128    throws FormatException, IOException 
     
    143143  } 
    144144 
    145   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     145  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    146146  public boolean isMinMaxPopulated(String id) 
    147147    throws FormatException, IOException 
     
    151151  } 
    152152 
    153   /* @see IFormatReader#close() */ 
     153  /* @see loci.formats.IFormatReader#close() */ 
    154154  public void close() throws FormatException, IOException { 
    155155    if (tiffReader != null) tiffReader.close(); 
     
    159159  } 
    160160 
    161   /* @see IFormatReader#close(boolean) */ 
     161  /* @see loci.formats.IFormatReader#close(boolean) */ 
    162162  public void close(boolean fileOnly) throws FormatException, IOException { 
    163163    if (fileOnly) tiffReader.close(fileOnly); 
     
    165165  } 
    166166 
    167   /* @see IFormatReader#initFile(String) */ 
     167  /* @see loci.formats.IFormatReader#initFile(String) */ 
    168168  public void initFile(String id) throws FormatException, IOException { 
    169169    super.initFile(id); 
     
    260260  } 
    261261 
    262   // -- FormatHandler API methods -- 
    263  
    264   /* @see FormatHandler#isThisType(String, boolean) */ 
     262  // -- IFormatHandler API methods -- 
     263 
     264  /* @see loci.formats.IFormatHandler#isThisType(String, boolean) */ 
    265265  public boolean isThisType(String name, boolean open) { 
    266266    Location parent = new Location(name).getAbsoluteFile().getParentFile(); 
  • trunk/loci/formats/in/ND2Reader.java

    r2430 r2455  
    256256  } 
    257257 
    258   /* @see IFormatReader#close(boolean) */ 
     258  /* @see loci.formats.IFormatReader#close(boolean) */ 
    259259  public void close(boolean fileOnly) throws FormatException, IOException { 
    260260    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/NikonReader.java

    r2377 r2455  
    158158  } 
    159159 
    160   // -- FormatHandler API methods -- 
     160  // -- IFormatHandler API methods -- 
    161161 
    162162  /** 
  • trunk/loci/formats/in/OIBReader.java

    r2430 r2455  
    182182  } 
    183183 
    184   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     184  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    185185  public boolean isMinMaxPopulated(String id) 
    186186    throws FormatException, IOException 
     
    258258  } 
    259259 
    260   /* @see IFormatReader#close(boolean) */ 
     260  /* @see loci.formats.IFormatReader#close(boolean) */ 
    261261  public void close(boolean fileOnly) throws FormatException, IOException { 
    262262    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/OIFReader.java

    r2430 r2455  
    133133  } 
    134134 
    135   /* @see IFormatReader#isMinMaxPopulated(String) */ 
     135  /* @see loci.formats.IFormatReader#isMinMaxPopulated(String) */ 
    136136  public boolean isMinMaxPopulated(String id) 
    137137    throws FormatException, IOException 
     
    212212  } 
    213213 
    214   /* @see IFormatReader#getThumbSizeX(String) */ 
     214  /* @see loci.formats.IFormatReader#getThumbSizeX(String) */ 
    215215  public int getThumbSizeX(String id) throws FormatException, IOException { 
    216216    return openThumbImage(id, 0).getWidth(); 
    217217  } 
    218218 
    219   /* @see IFormatReader#getThumbSizeY(String) */ 
     219  /* @see loci.formats.IFormatReader#getThumbSizeY(String) */ 
    220220  public int getThumbSizeY(String id) throws FormatException, IOException { 
    221221    return openThumbImage(id, 0).getHeight(); 
    222222  } 
    223223 
    224   /* @see IFormatReader#getUsedFiles(String) */ 
     224  /* @see loci.formats.IFormatReader#getUsedFiles(String) */ 
    225225  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    226226    if (!id.equals(currentId)) initFile(id); 
     
    229229  } 
    230230 
    231   /* @see IFormatReader#close(boolean) */ 
     231  /* @see loci.formats.IFormatReader#close(boolean) */ 
    232232  public void close(boolean fileOnly) throws FormatException, IOException { 
    233233    if (fileOnly) { 
  • trunk/loci/formats/in/OMEXMLReader.java

    r2450 r2455  
    225225  } 
    226226 
    227   /* @see IFormatReader#close(boolean) */ 
     227  /* @see loci.formats.IFormatReader#close(boolean) */ 
    228228  public void close(boolean fileOnly) throws FormatException, IOException { 
    229229    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/OpenlabRawReader.java

    r2430 r2455  
    142142  } 
    143143 
    144   /* @see IFormatReader#close(boolean) */ 
     144  /* @see loci.formats.IFormatReader#close(boolean) */ 
    145145  public void close(boolean fileOnly) throws FormatException, IOException { 
    146146    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/OpenlabReader.java

    r2450 r2455  
    377377  } 
    378378 
    379   /* @see IFormatReader#close(boolean) */ 
     379  /* @see loci.formats.IFormatReader#close(boolean) */ 
    380380  public void close(boolean fileOnly) throws FormatException, IOException { 
    381381    if (fileOnly) { 
  • trunk/loci/formats/in/PerkinElmerReader.java

    r2430 r2455  
    149149  } 
    150150 
    151   /* @see IFormatReader#getUsedFiles(String) */ 
     151  /* @see loci.formats.IFormatReader#getUsedFiles(String) */ 
    152152  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    153153    if (!id.equals(currentId) && !isUsedFile(currentId, id)) { 
     
    157157  } 
    158158 
    159   /* @see IFormatReader#close(boolean) */ 
     159  /* @see loci.formats.IFormatReader#close(boolean) */ 
    160160  public void close(boolean fileOnly) throws FormatException, IOException { 
    161161    if (fileOnly) { 
  • trunk/loci/formats/in/PictReader.java

    r2450 r2455  
    176176  } 
    177177 
    178   /* @see IFormatReader#close(boolean) */ 
     178  /* @see loci.formats.IFormatReader#close(boolean) */ 
    179179  public void close(boolean fileOnly) throws FormatException, IOException { 
    180180    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/PrairieReader.java

    r2430 r2455  
    6868  } 
    6969 
    70   // -- FormatHandler API methods -- 
     70  // -- IFormatHandler API methods -- 
    7171 
    7272  /** 
     
    131131  } 
    132132 
    133   /* @see IFormatReader#getUsedFiles(String) */ 
     133  /* @see loci.formats.IFormatReader#getUsedFiles(String) */ 
    134134  public String[] getUsedFiles(String id) throws FormatException, IOException { 
    135135    if (!id.equals(currentId)) initFile(id); 
     
    141141  } 
    142142 
    143   /* @see IFormatReader#getImageCount(String) */ 
     143  /* @see loci.formats.IFormatReader#getImageCount(String) */ 
    144144  public int getImageCount(String id) throws FormatException, IOException { 
    145145    if (!id.equals(currentId)) initFile(id); 
     
    147147  } 
    148148 
    149   /* @see IFormatReader#isRGB(String) */ 
     149  /* @see loci.formats.IFormatReader#isRGB(String) */ 
    150150  public boolean isRGB(String id) throws FormatException, IOException { 
    151151    if (!id.equals(currentId)) initFile(id); 
     
    153153  } 
    154154 
    155   /* @see IFormatReader#isLittleEndian(String) */ 
     155  /* @see loci.formats.IFormatReader#isLittleEndian(String) */ 
    156156  public boolean isLittleEndian(String id) throws FormatException, IOException { 
    157157    if (!id.equals(currentId)) initFile(id); 
     
    159159  } 
    160160 
    161   /* @see IFormatReader#isInterleaved(String) */ 
     161  /* @see loci.formats.IFormatReader#isInterleaved(String) */ 
    162162  public boolean isInterleaved(String id) throws FormatException, IOException { 
    163163    if (!id.equals(currentId)) initFile(id); 
     
    165165  } 
    166166 
    167   /* @see IFormatReader#openBytes(String, int) */ 
     167  /* @see loci.formats.IFormatReader#openBytes(String, int) */ 
    168168  public byte[] openBytes(String id, int no) 
    169169    throws FormatException, IOException 
     
    190190  } 
    191191 
    192   /* @see IFormatReader#openImage(String, int) */ 
     192  /* @see loci.formats.IFormatReader#openImage(String, int) */ 
    193193  public BufferedImage openImage(String id, int no) 
    194194    throws FormatException, IOException 
     
    203203  } 
    204204 
    205   /* @see IFormatReader#close(boolean) */ 
     205  /* @see loci.formats.IFormatReader#close(boolean) */ 
    206206  public void close(boolean fileOnly) throws FormatException, IOException { 
    207207    if (fileOnly && tiff != null) tiff.close(fileOnly); 
     
    209209  } 
    210210 
    211   /* @see IFormatReader#close() */ 
     211  /* @see loci.formats.IFormatReader#close() */ 
    212212  public void close() throws FormatException, IOException { 
    213213    files = null; 
     
    219219  } 
    220220 
    221   /* @see IFormatReader#initFile(String) */ 
     221  /* @see loci.formats.IFormatReader#initFile(String) */ 
    222222  protected void initFile(String id) throws FormatException, IOException { 
    223223    if (debug) debug("PrairieReader.initFile(" + id + ")"); 
  • trunk/loci/formats/in/QTReader.java

    r2450 r2455  
    288288  } 
    289289 
    290   /* @see FormatReader#setMetadataStore(MetadataStore) */ 
     290  /* @see loci.formats.IFormatReader#setMetadataStore(MetadataStore) */ 
    291291  public void setMetadataStore(MetadataStore store) { 
    292292    super.setMetadataStore(store); 
     
    294294  } 
    295295 
    296   /* @see FormatReader#swapDimensions(String, String) */ 
     296  /* @see loci.formats.IFormatReader#swapDimensions(String, String) */ 
    297297  public void swapDimensions(String id, String order) 
    298298    throws FormatException, IOException 
     
    555555  } 
    556556 
    557   /* @see IFormatReader#close(boolean) */ 
     557  /* @see loci.formats.IFormatReader#close(boolean) */ 
    558558  public void close(boolean fileOnly) throws FormatException, IOException { 
    559559    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/SDTReader.java

    r2430 r2455  
    195195  } 
    196196 
    197   /* @see IFormatReader#close(boolean) */ 
     197  /* @see loci.formats.IFormatReader#close(boolean) */ 
    198198  public void close(boolean fileOnly) throws FormatException, IOException { 
    199199    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/SlidebookReader.java

    r2430 r2455  
    133133  } 
    134134 
    135   /* @see IFormatReader#close(boolean) */ 
     135  /* @see loci.formats.IFormatReader#close(boolean) */ 
    136136  public void close(boolean fileOnly) throws FormatException, IOException { 
    137137    if (fileOnly && in != null) in.close(); 
  • trunk/loci/formats/in/TiffReader.java

    r2430 r2455  
    478478  } 
    479479 
    480   // -- IFormatReader methods -- 
     480  // -- IFormatReader API methods -- 
    481481 
    482482  /* @see loci.formats.IFormatReader#getSeriesCount(String) */ 
  • trunk/loci/formats/in/ZeissLSMReader.java

    r2430 r2455  
    303303        int[] bps = TiffTools.getBitsPerSample(ifd); 
    304304        switch (bps[0]) { 
    305           case 8: pixelType[0] = FormatTools.UINT8; break; 
    306           case 16: pixelType[0] = FormatTools.UINT16; break; 
    307           case 32: pixelType[0] = FormatTools.FLOAT; break; 
    308           default: pixelType[0] = FormatTools.UINT8; 
     305          case 8: 
     306            pixelType[0] = FormatTools.UINT8; 
     307            break; 
     308          case 16: 
     309            pixelType[0] = FormatTools.UINT16; 
     310            break; 
     311          case 32: 
     312            pixelType[0] = FormatTools.FLOAT; 
     313            break; 
     314          default: 
     315            pixelType[0] = FormatTools.UINT8; 
    309316        } 
    310317      } 
     
    391398      int spectralScan = DataTools.read2UnsignedBytes(ras, little); 
    392399      switch (spectralScan) { 
    393         case 0: put("SpectralScan", "no spectral scan"); break; 
    394         case 1: put("SpectralScan", "acquired with spectral scan"); break; 
    395         default: put("SpectralScan", "no spectral scan"); 
     400        case 0: 
     401          put("SpectralScan", "no spectral scan"); 
     402          break; 
     403        case 1: 
     404          put("SpectralScan", "acquired with spectral scan"); 
     405          break; 
     406        default: 
     407          put("SpectralScan", "no spectral scan"); 
    396408      } 
    397409 
    398410      long type = DataTools.read4UnsignedBytes(ras, little); 
    399411      switch ((int) type) { 
    400         case 0: put("DataType2", "original scan data"); break; 
    401         case 1: put("DataType2", "calculated data"); break; 
    402         case 2: put("DataType2", "animation"); break; 
    403         default: put("DataType2", "original scan data"); 
     412        case 0: 
     413          put("DataType2", "original scan data"); 
     414          break; 
     415        case 1: 
     416          put("DataType2", "calculated data"); 
     417          break; 
     418        case 2: 
     419          put("DataType2", "animation"); 
     420          break; 
     421        default: 
     422          put("DataType2", "original scan data"); 
    404423      } 
    405424 
  • trunk/loci/formats/in/ZeissZVIReader.java

    r2430 r2455  
    128128  public ZeissZVIReader() { super("Zeiss Vision Image (ZVI)", "zvi"); } 
    129129 
    130   // -- FormatReader API methods -- 
     130  // -- IFormatReader API methods -- 
    131131 
    132132  /** Checks if the given block is a valid header for an Zeiss ZVI file. */ 
     
    215215  } 
    216216 
    217   /* @see FormatReader#setMetadataStore(MetadataStore) */ 
     217  /* @see loci.formats.IFormatReader#setMetadataStore(MetadataStore) */ 
    218218  public void setMetadataStore(MetadataStore store) { 
    219219    super.setMetadataStore(store); 
     
    221221  } 
    222222 
    223   /* @see FormatReader#swapDimensions(String, String) */ 
     223  /* @see loci.formats.IFormatReader#swapDimensions(String, String) */ 
    224224  public void swapDimensions(String id, String order) 
    225225    throws FormatException, IOException 
     
    272272        // reverse bytes in groups of 3 to account for BGR storage 
    273273        for (int i=0; i<buf.length; i+=3) { 
    274           byte r = buf[i + 2]; 
     274          byte b = buf[i + 2]; 
    275275          buf[i + 2] = buf[i]; 
    276           buf[i] = r; 
     276          buf[i] = b; 
    277277        } 
    278278      } 
     
    297297  } 
    298298 
    299   /* @see IFormatReader#close(boolean) */ 
     299  /* @see loci.formats.IFormatReader#close(boolean) */ 
    300300  public void close(boolean fileOnly) throws FormatException, IOException { 
    301301    if (fileOnly) { 
  • trunk/loci/formats/ome/OMEReader.java

    r2430 r2455  
    3939 * The 'id' parameter should take one of the following forms: 
    4040 * 
    41  * <server>?user=<username>&password=<password>&id=<image id> 
    42  * <server>?key=<session key>&id=<image id> 
     41 * [server]?user=[username]&password=[password]&id=[image id] 
     42 * [server]?key=[session key]&id=[image id] 
    4343 * 
    44  * where <server> is the URL of the OME data server (not the image server). 
     44 * where [server] is the URL of the OME data server (not the image server). 
    4545 */ 
    4646public class OMEReader extends FormatReader { 
     
    4848  // -- Fields -- 
    4949 
    50   /** String containing authentication information */ 
     50  /** String containing authentication information. */ 
    5151  private String loginString; 
    5252 
    53   /** Number of images */ 
     53  /** Number of images. */ 
    5454  private int numImages; 
    5555 
    56   /** Current server */ 
     56  /** Current server. */ 
    5757  private String server; 
    5858 
    59   /** Session key for authentication */ 
     59  /** Session key for authentication. */ 
    6060  private String sessionKey; 
    6161 
    62   /** OME image ID */ 
     62  /** OME image ID. */ 
    6363  private String imageId; 
    6464 
    65   /** Thumbnail associated with the current dataset */ 
     65  /** Thumbnail associated with the current dataset. */ 
    6666  private BufferedImage thumb; 
    6767 
    68   /** Download helpers */ 
     68  /** Download helpers. */ 
    6969  private DataServices rs; 
    7070  private RemoteCaller rc; 
     
    7575  // -- Constructor -- 
    7676 
    77   /** Constructs a new OME reader */ 
     77  /** Constructs a new OME reader. */ 
    7878  public OMEReader() { super("Open Microscopy Environment (OME)", "*"); } 
    7979 
    80   // -- FormatHandler API methods -- 
    81  
    82   /* @see IFormatHandler#isThisType(String) */ 
    83   public boolean isThisType(String id) { 
    84     return id.indexOf("id") != -1 && (id.indexOf("password") != -1 || 
    85       id.indexOf("sessionKey") != -1); 
    86   } 
    87  
    88   // -- FormatReader API methods -- 
    89  
    90   /* @see IFormatReader#isThisType(byte[]) */ 
    91   public boolean isThisType(byte[] block) { 
    92     return true; 
    93   } 
    94  
    95   /* @see IFormatReader#getImageCount(String) */ 
    96   public int getImageCount(String id) throws FormatException, IOException { 
    97     if (!id.equals(currentId)) initFile(id); 
    98     return numImages; 
    99   } 
    100  
    101   /* @see IFormatReader#isRGB(String) */ 
    102   public boolean isRGB(String id) throws FormatException, IOException { 
    103     if (!id.equals(currentId)) initFile(id); 
    104     return false; 
    105   } 
    106  
    107   /* @see IFormatReader#getThumbSizeX(String) */ 
    108   public int getThumbSizeX(String id) throws FormatException, IOException { 
    109     if (!id.equals(currentId)) initFile(id); 
    110     return thumb.getWidth(); 
    111   } 
    112  
    113   /* @see IFormatReader#getThumbSizeY(String) */ 
    114   public int getThumbSizeY(String id) throws FormatException, IOException { 
    115     if (!id.equals(currentId)) initFile(id); 
    116     return thumb.getHeight(); 
    117   } 
    118  
    119   /* @see IFormatReader#isLittleEndian(String) */ 
    120   public boolean isLittleEndian(String id) throws FormatException, IOException { 
    121     return true; 
    122   } 
    123  
    124   /* @see IFormatReader#isInterleaved(String) */ 
    125   public boolean isInterleaved(String id) throws FormatException, IOException { 
    126     return false; 
    127   } 
    128  
    129   /* @see IFormatReader#openBytes(String, int) */ 
    130   public byte[] openBytes(String id, int no) throws FormatException, IOException 
    131   { 
    132     if (!id.equals(currentId)) initFile(id); 
    133     if (no < 0 || no >= numImages) { 
    134       throw new FormatException("Invalid image number: " + no); 
    135     } 
    136     int[] indices = getZCTCoords(id, no); 
    137     try { 
    138       byte[] b = pf.getPlane(pixels, indices[0], indices[1], indices[2], false); 
    139       updateMinMax(b, no); 
    140       return b; 
    141     } 
    142     catch (ImageServerException e) { 
    143       throw new FormatException(e); 
    144     } 
    145   } 
    146  
    147   /* @see IFormatReader#openImage(String, int) */ 
    148   public BufferedImage openImage(String id, int no) 
    149     throws FormatException, IOException 
    150   { 
    151     BufferedImage b = ImageTools.makeImage(openBytes(id, no), sizeX[0], 
    152       sizeY[0], 1, false, FormatTools.getBytesPerPixel(pixelType[0]), true); 
    153     updateMinMax(b, no); 
    154     return b; 
    155   } 
    156  
    157   /* @see IFormatReader#openThumbBytes(String, int) */ 
    158   public byte[] openThumbBytes(String id, int no) 
    159     throws FormatException, IOException 
    160   { 
    161     if (!id.equals(currentId)) initFile(id); 
    162     if (no < 0 || no >= numImages) { 
    163       throw new FormatException("Invalid image number: " + no); 
    164     } 
    165     byte[][] b = ImageTools.getPixelBytes(openThumbImage(id, no), true); 
    166     byte[] rtn = new byte[b.length * b[0].length]; 
    167     for (int i=0; i<b.length; i++) { 
    168       System.arraycopy(b[i], 0, rtn, i*b[0].length, b[i].length); 
    169     } 
    170     return rtn; 
    171   } 
    172  
    173   /* @see IFormatReader#openThumbImage(String, int) */ 
    174   public BufferedImage openThumbImage(String id, int no) 
    175     throws FormatException, IOException 
    176   { 
    177     if (!id.equals(currentId)) initFile(id); 
    178     if (no < 0 || no >= numImages) { 
    179       throw new FormatException("Invalid image number: " + no); 
    180     } 
    181     return thumb; 
    182   } 
    183  
    184   /* @see IFormatReader#close(boolean) */ 
    185   public void close(boolean fileOnly) throws FormatException, IOException { 
    186     if (fileOnly && rc != null) rc.logout(); 
    187     else close(); 
    188   } 
    189  
    190   /* @see IFormatReader#close() */ 
    191   public void close() throws FormatException, IOException { 
    192     if (rc != null) rc.logout(); 
    193     thumb = null; 
    194     rs = null; 
    195     rc = null; 
    196     df = null; 
    197     pf = null; 
    198     pixels = null; 
    199     currentId = null; 
    200     loginString = null; 
    201   } 
    202  
    203   /* @see IFormatReader#initFile(String) */ 
     80  // -- Internal FormatReader API methods -- 
     81 
     82  /* @see loci.formats.FormatReader#initFile(String) */ 
    20483  protected void initFile(String id) throws FormatException, IOException { 
    20584    if (id.equals(loginString)) return; 
     
    306185  } 
    307186 
     187  // -- IFormatReader API methods -- 
     188 
     189  /* @see loci.formats.IFormatReader#isThisType(byte[]) */ 
     190  public boolean isThisType(byte[] block) { 
     191    return true; 
     192  } 
     193 
     194  /* @see loci.formats.IFormatReader#getImageCount(String) */ 
     195  public int getImageCount(String id) throws FormatException, IOException { 
     196    if (!id.equals(currentId)) initFile(id); 
     197    return numImages; 
     198  } 
     199 
     200  /* @see loci.formats.IFormatReader#isRGB(String) */ 
     201  public boolean isRGB(String id) throws FormatException, IOException { 
     202    if (!id.equals(currentId)) initFile(id); 
     203    return false; 
     204  } 
     205 
     206  /* @see loci.formats.IFormatReader#getThumbSizeX(String) */ 
     207  public int getThumbSizeX(String id) throws FormatException, IOException { 
     208    if (!id.equals(currentId)) initFile(id); 
     209    return thumb.getWidth(); 
     210  } 
     211 
     212  /* @see loci.formats.IFormatReader#getThumbSizeY(String) */ 
     213  public int getThumbSizeY(String id) throws FormatException, IOException { 
     214    if (!id.equals(currentId)) initFile(id); 
     215    return thumb.getHeight(); 
     216  } 
     217 
     218  /* @see loci.formats.IFormatReader#isLittleEndian(String) */ 
     219  public boolean isLittleEndian(String id) throws FormatException, IOException { 
     220    return true; 
     221  } 
     222 
     223  /* @see loci.formats.IFormatReader#isInterleaved(String) */ 
     224  public boolean isInterleaved(String id) throws FormatException, IOException { 
     225    return false; 
     226  } 
     227 
     228  /* @see loci.formats.IFormatReader#openBytes(String, int) */ 
     229  public byte[] openBytes(String id, int no) throws FormatException, IOException 
     230  { 
     231    if (!id.equals(currentId)) initFile(id); 
     232    if (no < 0 || no >= numImages) { 
     233      throw new FormatException("Invalid image number: " + no); 
     234    } 
     235    int[] indices = getZCTCoords(id, no); 
     236    try { 
     237      byte[] b = pf.getPlane(pixels, indices[0], indices[1], indices[2], false); 
     238      updateMinMax(b, no); 
     239      return b; 
     240    } 
     241    catch (ImageServerException e) { 
     242      throw new FormatException(e); 
     243    } 
     244  } 
     245 
     246  /* @see loci.formats.IFormatReader#openImage(String, int) */ 
     247  public BufferedImage openImage(String id, int no) 
     248    throws FormatException, IOException 
     249  { 
     250    BufferedImage b = ImageTools.makeImage(openBytes(id, no), sizeX[0], 
     251      sizeY[0], 1, false, FormatTools.getBytesPerPixel(pixelType[0]), true); 
     252    updateMinMax(b, no); 
     253    return b; 
     254  } 
     255 
     256  /* @see loci.formats.IFormatReader#openThumbBytes(String, int) */ 
     257  public byte[] openThumbBytes(String id, int no) 
     258    throws FormatException, IOException 
     259  { 
     260    if (!id.equals(currentId)) initFile(id); 
     261    if (no < 0 || no >= numImages) { 
     262      throw new FormatException("Invalid image number: " + no); 
     263    } 
     264    byte[][] b = ImageTools.getPixelBytes(openThumbImage(id, no), true); 
     265    byte[] rtn = new byte[b.length * b[0].length]; 
     266    for (int i=0; i<b.length; i++) { 
     267      System.arraycopy(b[i], 0, rtn, i*b[0].length, b[i].length); 
     268    } 
     269    return rtn; 
     270  } 
     271 
     272  /* @see loci.formats.IFormatReader#openThumbImage(String, int) */ 
     273  public BufferedImage openThumbImage(String id, int no) 
     274    throws FormatException, IOException 
     275  { 
     276    if (!id.equals(currentId)) initFile(id); 
     277    if (no < 0 || no >= numImages) { 
     278      throw new FormatException("Invalid image number: " + no); 
     279    } 
     280    return thumb; 
     281  } 
     282 
     283  /* @see loci.formats.IFormatReader#close(boolean) */ 
     284  public void close(boolean fileOnly) throws FormatException, IOException { 
     285    if (fileOnly && rc != null) rc.logout(); 
     286    else close(); 
     287  } 
     288 
     289  /* @see loci.formats.IFormatReader#close() */ 
     290  public void close() throws FormatException, IOException { 
     291    if (rc != null) rc.logout(); 
     292    thumb = null; 
     293    rs = null; 
     294    rc = null; 
     295    df = null; 
     296    pf = null; 
     297    pixels = null; 
     298    currentId = null; 
     299    loginString = null; 
     300  } 
     301 
     302  // -- IFormatHandler API methods -- 
     303 
     304  /* @see loci.formats.IFormatHandler#isThisType(String) */ 
     305  public boolean isThisType(String id) { 
     306    return id.indexOf("id") != -1 && (id.indexOf("password") != -1 || 
     307      id.indexOf("sessionKey") != -1); 
     308  } 
     309 
    308310  // -- Main method -- 
    309311 
  • trunk/loci/formats/ome/OMEUploader.java

    r2454 r2455  
    535535  } 
    536536 
    537  
    538537  // -- Helper methods -- 
    539538 
     
    566565 
    567566  /** Build an XML-RPC request. */ 
    568   private String buildXML(String method, Vector params) throws UploadException 
    569   { 
     567  private String buildXML(String method, Vector params) throws UploadException { 
    570568    try { 
    571569      String request = "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>" + 
  • trunk/loci/formats/ome/OMEXMLMetadataStore.java

    r2445 r2455  
    6969  public OMEXMLMetadataStore() { createRoot(); } 
    7070 
    71   // -- OMEXMLMetadataStore methods -- 
     71  // -- OMEXMLMetadataStore API methods -- 
    7272 
    7373  /** Constructs a new OME-XML root node with the given XML block. */ 
     
    313313  } 
    314314 
    315   // -- MetadataStore methods -- 
    316  
    317   /* @see MetadataStore#createRoot() */ 
     315  // -- MetadataStore API methods -- 
     316 
     317  /* @see loci.formats.MetadataStore#createRoot() */ 
    318318  public void createRoot() { createRoot(null); } 
    319319 
    320   /* @see MetadataStore#setRoot(Object) */ 
     320  /* @see loci.formats.MetadataStore#setRoot(Object) */ 
    321321  public void setRoot(Object root) { 
    322322    if (!(root instanceof OMENode)) { 
     
    327327  } 
    328328 
    329   /* @see MetadataStore#getRoot() */ 
     329  /* @see loci.formats.MetadataStore#getRoot() */ 
    330330  public Object getRoot() { return root; } 
    331331 
    332   /* @see MetadataStore#setImage(String, String, String, Integer) */ 
     332  /* 
     333   * @see loci.formats.MetadataStore#setImage(String, 
     334   *   String, String, Integer) 
     335   */ 
    333336  public void setImage(String name, 
    334337    String creationDate, String description, Integer i) 
     
    342345 
    343346  /* 
    344    * @see MetadataStore#setExperimenter(String, String, 
     347   * @see loci.formats.MetadataStore#setExperimenter(String, String, 
    345348   *   String, String, String, Object, Integer) 
    346349   */ 
     
    361364  } 
    362365 
    363   /* @see MetadataStore#setGroup(String, Object, Object, Integer) */ 
     366  /* 
     367   * @see loci.formats.MetadataStore#setGroup(String, Object, Object, Integer) 
     368   */ 
    364369  public void setGroup(String name, Object leader, Object contact, Integer i) { 
    365370    int ndx = i == null ? 0 : i.intValue(); 
     
    373378 
    374379  /* 
    375    * @see MetadataStore#setInstrument(String, String, String, String, Integer) 
     380   * @see loci.formats.MetadataStore#setInstrument(String, 
     381   *   String, String, String, Integer) 
    376382   */ 
    377383  public void setInstrument(String manufacturer, 
     
    390396 
    391397  /* 
    392    * @see MetadataStore#setDimensions(Float, 
     398   * @see loci.formats.MetadataStore#setDimensions(Float, 
    393399   *   Float, Float, Float, Float, Integer) 
    394400   */ 
     
    415421 
    416422  /* 
    417    * @see MetadataStore#setDisplayROI(Integer, Integer, Integer, 
     423   * @see loci.formats.MetadataStore#setDisplayROI(Integer, Integer, Integer, 
    418424   *   Integer, Integer, Integer, Integer, Integer, Object, Integer) 
    419425   */ 
     
    441447 
    442448  /* 
    443    * @see MetadataStore#setPixels(Integer, Integer, Integer, 
     449   * @see loci.formats.MetadataStore#setPixels(Integer, Integer, Integer, 
    444450   *   Integer, Integer, String, Boolean, String, Integer, Integer) 
    445451   */ 
     
    468474  } 
    469475 
    470   /* @see MetadataStore#setStageLabel(String, Float, Float, Float, Integer) */ 
     476  /* 
     477   * @see loci.formats.MetadataStore#setStageLabel(String, 
     478   *   Float, Float, Float, Integer) 
     479   */ 
    471480  public void setStageLabel(String name, Float x, Float y, Float z, Integer i) { 
    472481    int ndx = i == null ? 0 : i.intValue(); 
     
    484493 
    485494  /* 
    486    * @see MetadataStore#setLogicalChannel(int, String, 
     495   * @see loci.formats.MetadataStore#setLogicalChannel(int, String, 
    487496   *   Float, Integer, Integer, String, String, Integer) 
    488497   */ 
     
    524533  } 
    525534 
    526   /* @see MetadataStore#setChannelGlobalMinMax(int, Double, Double, Integer) */ 
     535  /* 
     536   * @see loci.formats.MetadataStore#setChannelGlobalMinMax(int, 
     537   *   Double, Double, Integer) 
     538   */ 
    527539  public void setChannelGlobalMinMax(int channel, 
    528540    Double globalMin, Double globalMax, Integer i) 
     
    556568  } 
    557569 
    558   /* @see MetadataStore#setPlaneInfo(int, int, int, Float, Float, Integer) */ 
     570  /* 
     571   * @see loci.formats.MetadataStore#setPlaneInfo(int, 
     572   *   int, int, Float, Float, Integer) 
     573   */ 
    559574  public void setPlaneInfo(int theZ, int theC, int theT, Float timestamp, 
    560575    Float exposureTime, Integer i) 
     
    565580  } 
    566581 
    567   /* @see MetadataStore#setDefaultDisplaySettings(Integer) */ 
     582  /* @see loci.formats.MetadataStore#setDefaultDisplaySettings(Integer) */ 
    568583  public void setDefaultDisplaySettings(Integer i) { 
    569584    int ndx = i == null ? 0 : i.intValue(); 
     
    622637  } 
    623638 
    624   /* @see MetadataStore#setImagingEnvironment(Float, Float, Float, 
    625    * Float, Integer) 
     639  /* 
     640   * @see loci.formats.MetadataStore#setImagingEnvironment(Float, 
     641   *   Float, Float, Float, Integer) 
    626642   */ 
    627643  public void setImagingEnvironment(Float temperature, Float airPressure, 
     
    640656  } 
    641657 
    642   /* @see MetadataStore#setDisplayChannel(Integer, Double, Double, Float, 
    643    * Integer) 
     658  /* 
     659   * @see loci.formats.MetadataStore#setDisplayChannel(Integer, 
     660   *   Double, Double, Float, Integer) 
    644661   */ 
    645662  public void setDisplayChannel(Integer channelNumber, Double blackLevel, 
     
    658675  } 
    659676 
    660   /* @see MetadataStore#setDisplayOptions(Float, Boolean, Boolean, Boolean, 
    661    * Boolean, String, Integer, Integer, Integer, Integer, Integer, Integer, 
    662    * Integer, Integer, Integer, Integer) 
     677  /* 
     678   * @see loci.formats.MetadataStore#setDisplayOptions(Float, Boolean, 
     679   *   Boolean, Boolean, Boolean, String, Integer, Integer, Integer, 
     680   *   Integer, Integer, Integer, Integer, Integer, Integer, Integer) 
    663681   */ 
    664682  public void setDisplayOptions(Float zoom, Boolean redChannelOn, 
     
    678696      getChild(ca, "DisplayChannel", redChannel.intValue()); 
    679697    DisplayChannelNode green = greenChannel == null ? null : 
    680       (DisplayChannelNode) getChild(ca, "DisplayChannel", 
    681       greenChannel.intValue()); 
     698      (DisplayChannelNode) 
     699      getChild(ca, "DisplayChannel", greenChannel.intValue()); 
    682700    DisplayChannelNode blue = blueChannel == null ? null : (DisplayChannelNode) 
    683701      getChild(ca, "DisplayChannel", blueChannel.intValue()); 
     
    704722  } 
    705723 
    706   /* @see MetadataStore#setLightSource(String, String, String, 
    707    * Integer, Integer) 
     724  /* 
     725   * @see loci.formats.MetadataStore#setLightSource(String, 
     726   *   String, String, Integer, Integer) 
    708727   */ 
    709728  public void setLightSource(String manufacturer, String model, 
     
    723742  } 
    724743 
    725   /* @see MetadataStore#setLaser(String, String, Integer, Boolean, Boolean, 
    726    * String, Float, Integer, Integer, Integer, Integer) 
     744  /* 
     745   * @see loci.formats.MetadataStore#setLaser(String, String, Integer, 
     746   *   Boolean, Boolean, String, Float, Integer, Integer, Integer, Integer) 
    727747   */ 
    728748  public void setLaser(String type, String medium, Integer wavelength, 
     
    754774  } 
    755775 
    756   /* @see MetadataStore#setFilament(String, Float, Integer, Integer) */ 
     776  /* 
     777   * @see loci.formats.MetadataStore#setFilament(String, 
     778   *   Float, Integer, Integer) 
     779   */ 
    757780  public void setFilament(String type, Float power, Integer lightSource, 
    758781    Integer num) 
     
    772795  } 
    773796 
    774   /* @see MetadataStore#setArc(String, Float, Integer, Integer) */ 
     797  /* @see loci.formats.MetadataStore#setArc(String, Float, Integer, Integer) */ 
    775798  public void setArc(String type, Float power, Integer lightSource, 
    776799    Integer num) 
     
    789812  } 
    790813 
    791   /* @see MetadataStore#setDetector(String, String, String, String, Float, 
    792    * Float, Float, Integer, Integer) 
     814  /* 
     815   * @see loci.formats.MetadataStore#setDetector(String, String, 
     816   *   String, String, Float, Float, Float, Integer, Integer) 
    793817   */ 
    794818  public void setDetector(String manufacturer, String model, 
     
    813837  } 
    814838 
    815   /* @see MetadataStore#setObjective(String, String, String, Float, Float, 
    816    * Integer, Integer) 
     839  /* 
     840   * @see loci.formats.MetadataStore#setObjective(String, 
     841   *   String, String, Float, Float, Integer, Integer) 
    817842   */ 
    818843  public void setObjective(String manufacturer, String model, 
     
    835860  } 
    836861 
    837   /* @see MetadataStore#setExcitationFilter(String, String, String, 
    838    * String, Integer) 
     862  /* 
     863   * @see loci.formats.MetadataStore#setExcitationFilter(String, 
     864   *   String, String, String, Integer) 
    839865   */ 
    840866  public void setExcitationFilter(String manufacturer, String model, 
     
    853879  } 
    854880 
    855   /* @see MetadataStore#setDichroic(String, String, String, Integer) */ 
     881  /* 
     882   * @see loci.formats.MetadataStore#setDichroic(String, 
     883   *   String, String, Integer) 
     884   */ 
    856885  public void setDichroic(String manufacturer, String model, String lotNumber, 
    857886    Integer dichroic) 
     
    867896  } 
    868897 
    869   /* @see MetadataStore#setEmissionFilter(String, String, String, 
    870    * String, Integer) 
     898  /* 
     899   * @see loci.formats.MetadataStore#setEmissionFilter(String, 
     900   *   String, String, String, Integer) 
    871901   */ 
    872902  public void setEmissionFilter(String manufacturer, String model, 
     
    885915  } 
    886916 
    887   /* @see MetadataStore#setFilterSet(String, String, String, Integer, 
    888    * Integer) 
     917  /* 
     918   * @see loci.formats.MetadataStore#setFilterSet(String, 
     919   *   String, String, Integer, Integer) 
    889920   */ 
    890921  public void setFilterSet(String manufacturer, String model, String lotNumber, 
     
    904935  } 
    905936 
    906   /* @see MetadataStore#setOTF(Integer, Integer, String, String, 
    907    * Boolean, Integer, Integer, Integer, Integer) 
     937  /* 
     938   * @see loci.formats.MetadataStore#setOTF(Integer, Integer, 
     939   *   String, String, Boolean, Integer, Integer, Integer, Integer) 
    908940   */ 
    909941  public void setOTF(Integer sizeX, Integer sizeY, String pixelType, 
  • trunk/loci/formats/out/AVIWriter.java

    r2430 r2455  
    8888  public AVIWriter() { super("Audio Video Interleave", "avi"); } 
    8989 
    90   // -- FormatWriter API methods -- 
     90  // -- IFormatWriter API methods -- 
    9191 
    9292  /** 
     
    513513  } 
    514514 
    515   /* @see IFormatWriter#close() */ 
     515  /* @see loci.formats.IFormatWriter#close() */ 
    516516  public void close() throws FormatException, IOException { 
    517517    if (raFile != null) raFile.close(); 
     
    523523  public boolean canDoStacks(String id) { return true; } 
    524524 
    525   /* @see IFormatWriter#getPixelTypes(String) */ 
     525  /* @see loci.formats.IFormatWriter#getPixelTypes(String) */ 
    526526  public int[] getPixelTypes(String id) throws FormatException, IOException { 
    527527    return new int[] {FormatTools.UINT8}; 
  • trunk/loci/formats/out/EPSWriter.java

    r2430 r2455  
    4646  } 
    4747 
    48   // -- FormatWriter API methods -- 
     48  // -- IFormatWriter API methods -- 
    4949 
    5050  /** 
     
    144144  } 
    145145 
    146   /* @see IFormatWriter#close() */ 
     146  /* @see loci.formats.IFormatWriter#close() */ 
    147147  public void close() throws FormatException, IOException { 
    148148    if (out != null) out.close(); 
     
    154154  public boolean canDoStacks(String id) { return false; } 
    155155 
    156   /* @see IFormatWriter#getPixelTypes(String) */ 
     156  /* @see loci.formats.IFormatWriter#getPixelTypes(String) */ 
    157157  public int[] getPixelTypes(String id) throws FormatException, IOException { 
    158158    return new int[] {FormatTools.UINT8}; 
  • trunk/loci/formats/out/ImageIOWriter.java

    r2430 r2455  
    6666  } 
    6767 
    68   // -- FormatWriter API methods -- 
     68  // -- IFormatWriter API methods -- 
    6969 
    7070  /** 
     
    8585  } 
    8686 
    87   /* @see IFormatWriter#close() */ 
     87  /* @see loci.formats.IFormatWriter#close() */ 
    8888  public void close() throws FormatException, IOException { 
    8989    if (out != null) out.close(); 
     
    9595  public boolean canDoStacks(String id) { return false; } 
    9696 
    97   /* @see IFormatWriter#getPixelTypes(String) */ 
     97  /* @see loci.formats.IFormatWriter#getPixelTypes(String) */ 
    9898  public int[] getPixelTypes(String id) throws FormatException, IOException { 
    9999    return new int[] {FormatTools.UINT8, FormatTools.UINT16}; 
  • trunk/loci/formats/out/JPEGWriter.java

    r2430 r2455  
    4040  } 
    4141 
    42   // -- FormatWriter API methods -- 
     42  // -- IFormatWriter API methods -- 
    4343 
    44   /* @see ImageIOWriter#save(String, Image, boolean) */ 
     44  /* @see loci.formats.IFormatWriter#save(String, Image, boolean) */ 
    4545  public void save(String id, Image image, boolean last) 
    4646    throws FormatException, IOException 
     
    5555  } 
    5656 
    57   /* @see IFormatWriter#getPixelTypes(String) */ 
     57  /* @see loci.formats.IFormatWriter#getPixelTypes(String) */ 
    5858  public int[] getPixelTypes(String id) throws FormatException, IOException { 
    5959    return new int[] {FormatTools.UINT8}; 
  • trunk/loci/formats/out/LegacyQTWriter.java

    r2178 r2455  
    104104  public void setQuality(int quality) { this.quality = quality; } 
    105105 
    106   // -- FormatWriter API methods -- 
     106  // -- IFormatWriter API methods -- 
    107107 
    108108  /** 
     
    276276  } 
    277277 
    278   /* @see IFormatWriter#close() */ 
     278  /* @see loci.formats.IFormatWriter#close() */ 
    279279  public void close() throws FormatException, IOException { 
    280280    r = null; 
  • trunk/loci/formats/out/QTWriter.java

    r2430 r2455  
    148148  public void setQuality(int quality) { this.quality = quality; } 
    149149 
    150   // -- FormatWriter API methods -- 
     150  // -- IFormatWriter API methods -- 
    151151 
    152152  /** 
     
    579579  } 
    580580 
    581   /* @see IFormatWriter#close() */ 
     581  /* @see loci.formats.IFormatWriter#close() */ 
    582582  public void close() throws FormatException, IOException { 
    583583    if (out != null) out.close(); 
     
    593593  public boolean canDoStacks(String id) { return true; } 
    594594 
    595   /* @see IFormatWriter#getPixelTypes(String) */ 
     595  /* @see loci.formats.IFormatWriter#getPixelTypes(String) */ 
    596596  public int[] getPixelTypes(String id) throws FormatException, IOException { 
    597597    return new int[] {FormatTools.UINT8, FormatTools.UINT16}; 
  • trunk/loci/formats/out/TiffWriter.java

    r2178 r2455  
    101101  } 
    102102 
    103   // -- FormatWriter API methods -- 
     103  // -- IFormatWriter API methods -- 
    104104 
    105105  /** 
     
    117117  } 
    118118 
    119   /* @see IFormatWriter#close() */ 
     119  /* @see loci.formats.IFormatWriter#close() */ 
    120120  public void close() throws FormatException, IOException { 
    121121    if (out != null) out.close(); 
  • trunk/loci/formats/test/ConfigurationFiles.java

    r2430 r2455  
    2929import loci.formats.*; 
    3030 
    31 /** Stores data from a set of config files */ 
     31/** Stores data from a set of config files. */ 
    3232public class ConfigurationFiles { 
     33 
     34  // -- Fields -- 
     35 
    3336  private Hashtable entries = new Hashtable(); 
    3437 
    35   public Vector parsedFiles = new Vector(); 
     38  private Vector parsedFiles = new Vector(); 
    3639 
    3740  private int currentSeries = 0; 
     41 
     42  // -- Static ConfigurationFiles API methods -- 
    3843 
    3944  public static ConfigurationFiles newInstance() { 
     
    4146  } 
    4247 
     48  // -- ConfigurationFiles API methods -- 
     49 
    4350  public int numFiles() { return entries.size(); } 
     51 
     52  public boolean isParsed(String file) { return parsedFiles.contains(file); } 
    4453 
    4554  public boolean initialized(String id) { 
     
    232241  } 
    233242 
    234   // -- Helper class -- 
    235  
     243  // -- Helper classes -- 
     244 
     245  /** Helper class representing a configuration entry for a dataset. */ 
    236246  public class ConfigEntry { 
    237     public int numSeries; 
    238     public int[][] dimensions; 
    239     public String[] orders; 
    240     public boolean[] interleaved; 
    241     public boolean[] rgb; 
    242     public int[][] thumbs; 
    243     public int[] type; 
    244     public boolean[] littleEndian; 
    245     public float access; 
    246     public int mem; 
    247     public boolean test; 
    248   } 
     247    private int numSeries; 
     248    private int[][] dimensions; 
     249    private String[] orders; 
     250    private boolean[] interleaved; 
     251    private boolean[] rgb; 
     252    private int[][] thumbs; 
     253    private int[] type; 
     254    private boolean[] littleEndian; 
     255    private float access; 
     256    private int mem; 
     257    private boolean test; 
     258  } 
     259 
    249260} 
  • trunk/loci/formats/test/ReaderTest.java

    r2452 r2455  
    6060  // -- Static fields -- 
    6161 
    62   public static boolean writeConfigFiles = false; 
    63   public static float timeMultiplier = 1f; 
     62  private static boolean writeConfigFiles = false; 
     63  private static float timeMultiplier = 1f; 
    6464 
    6565  private static StringBuffer configLine; 
     
    651651      try { 
    652652        String s = (String) configFiles.get(i); 
    653         if (!config.parsedFiles.contains(s)) { 
    654           config.addFile(s); 
    655         } 
     653        if (!config.isParsed(s)) config.addFile(s); 
    656654      } 
    657655      catch (IOException e) { 
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