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A library for reading Metakit database files.
There is a newer version: 5.3.7
/*
 * #%L
 * OME Metakit package for reading Metakit database files.
 * %%
 * Copyright (C) 2011 - 2016 Open Microscopy Environment:
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 *   - University of Dundee
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as
 * published by the Free Software Foundation, either version 2 of the 
 * License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public 
 * License along with this program.  If not, see
 * .
 * #L%
 */

package ome.metakit;

import java.io.IOException;
import java.util.ArrayList;

import loci.common.Constants;
import loci.common.RandomAccessInputStream;

/**
 * Class representating a column mapping in a Metakit database file.
 *
 * @author Melissa Linkert melissa at glencoesoftware.com
 */
public class ColumnMap {

  // -- Fields --

  private ArrayList values = new ArrayList();
  private Column col;
  private RandomAccessInputStream stream;
  private int rowCount;

  // -- Constructors --

  public ColumnMap(Column col, RandomAccessInputStream stream, int rowCount) {
    this.col = col;
    this.stream = stream;
    this.rowCount = rowCount;
    try {
      setup();
    }
    catch (IOException e) {

    }
  }

  // -- ColumnMap API methods --

  /** Return the list of values in this map's column. */
  public ArrayList getValueList() {
    return values;
  }

  /** Return an array of the values in this map's column. */
  public Object[] getValues() {
    return values.toArray(new Object[values.size()]);
  }

  /**
   * Return whether or not this map represents a fixed-type column.
   * Fixed-type columns have type "I", "F", "D", or "L".
   */
  public boolean isFixedMap() {
    char type = col.getTypeString().charAt(0);
    return type != 'S' && type != 'B';
  }

  // -- Helper methods --

  /**
   * Read the data values for the current column.
   */
  private void setup() throws IOException {
    if (isFixedMap()) {
      // read a single IVecRef

      int ivecSize = MetakitTools.readBpInt(stream);
      if (ivecSize > 0) {
        int ivecPointer = MetakitTools.readBpInt(stream);
        long fp = stream.getFilePointer();
        stream.seek(ivecPointer);

        for (int i=0; i 0) {
        catalogIvecPointer = MetakitTools.readBpInt(stream);
      }

      long fp = stream.getFilePointer();

      stream.seek(mapIvecPointer);
      int[] byteCounts = new int[rowCount];

      int bits = (mapIvecSize * 8) / rowCount;
      for (int i=0; i= 32) {
      return stream.readInt();
    }

    long fp = stream.getFilePointer();
    stream.skipBytes((index * bits) / 8);
    int b = stream.read();
    int mask = (int) Math.pow(2, bits) - 1;

    int bitIndex = index % (8 / bits);
    int value = b & (mask << (bitIndex * bits));
    value >>= ((8 - (bitIndex * bits)) % 8);

    stream.seek(fp);
    return value;
  }

}