diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/StringUtils.java b/openbis-common/source/java/ch/systemsx/cisd/bds/StringUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..0e6d79a290c6c1d4e968335195da789bcb7a86f9
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/StringUtils.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds;
+
+/**
+ * Operations on {@link java.lang.String} that are <code>null</code> safe.
+ *
+ * @author Christian Ribeaud
+ */
+public final class StringUtils
+{
+ public static final String EMPTY_STRING = "";
+
+ private StringUtils()
+ {
+ // Can not be instantiated
+ }
+
+ /**
+ * Whether given <var>value</var> is blank or not.
+ */
+ public final static boolean isBlank(final String value)
+ {
+ return value == null || value.trim().length() == 0;
+ }
+
+ /**
+ * Whether given <var>value</var> is empty or not.
+ */
+ public final static boolean isEmpty(final String value)
+ {
+ return value == null || value.length() == 0;
+ }
+
+ /** Returns an empty if given <var>stringOrNull</var> is <code>null</code>. */
+ public final static String emptyIfNull(final String stringOrNull)
+ {
+ return stringOrNull == null ? EMPTY_STRING : stringOrNull;
+ }
+}
diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Channel.java b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
new file mode 100644
index 0000000000000000000000000000000000000000..028e546ce3dd06c4de8df16b773f766ec5628305
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds.hcs;
+
+
+/**
+ * A channel is composed of only one child: <code>wavelength</code>.
+ * <p>
+ * Each channel has its <code>counter</code> which uniquely identifies it. It implements
+ * {@link Comparable} based on the <code>wavelength</code> value.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class Channel implements Comparable<Channel>
+{
+ static final String CHANNEL = "channel";
+
+ static final String WAVELENGTH = "wavelength";
+
+ private final int counter;
+
+ private final int wavelength;
+
+ public Channel(final int counter, final int wavelength)
+ {
+ assert counter > 0 : "Given counter must be > 0.";
+ this.counter = counter;
+ this.wavelength = wavelength;
+ }
+
+ public final int getCounter()
+ {
+ return counter;
+ }
+
+ public final int getWavelength()
+ {
+ return wavelength;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Channel == false)
+ {
+ return false;
+ }
+ final Channel channel = (Channel) obj;
+ return channel.counter == counter;
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return 17 * 37 + counter;
+ }
+
+ @Override
+ public final String toString()
+ {
+ return CHANNEL + counter + "[" + wavelength + "=" + getWavelength() + "]";
+ }
+
+ //
+ // Comparable
+ //
+
+ @Override
+ public final int compareTo(final Channel o)
+ {
+ assert o != null : "Unspecified Channel.";
+ return counter - o.counter;
+ }
+}
diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..31855a613aef87b614d18f8b8827b7aa0fe3f82b
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
@@ -0,0 +1,150 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds.hcs;
+
+
+/**
+ * A <code>Geometry</code> is composed of 2 dimensions:
+ * <ul>
+ * <li>rows</li>
+ * <li>columns</li>
+ * </ul>
+ * <p>
+ * This class is not <code>abstract</code> but {@link #getGeometryDirectoryName()} must be
+ * overridden by subclasses in order to work properly.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public class Geometry
+{
+ /**
+ * The <code>rows</code>-<code>columns</code> separator in the string representation of
+ * this object.
+ */
+ private static final String X = "x";
+
+ static final String NOT_POSITIVE = "Given geometry component '%s' must be > 0 (%d <= 0).";
+
+ final static String ROWS = "rows";
+
+ final static String COLUMNS = "columns";
+
+ private final int rows;
+
+ private final int columns;
+
+ public Geometry(final int rows, final int columns)
+ {
+ assert columns > 0 : String.format(NOT_POSITIVE, "columns", columns);
+ this.columns = columns;
+ assert rows > 0 : String.format(NOT_POSITIVE, "rows", rows);
+ this.rows = rows;
+ }
+
+ /** Return the number of columns this <code>Geometry</code> is composed of. */
+ public final int getColumns()
+ {
+ return columns;
+ }
+
+ /** Return the number of rows this <code>Geometry</code> is composed of. */
+ public final int getRows()
+ {
+ return rows;
+ }
+
+ /**
+ * Loads a <code>Geometry</code> from given <var>toString</var>.
+ *
+ * @param toString the output you get when calling {@link #toString()}.
+ * @return <code>null</code> if operation fails.
+ */
+ public static Geometry createFromString(final String toString)
+ {
+ assert toString != null : "Given string can not be null.";
+ final int index = toString.indexOf(X);
+ if (index > -1)
+ {
+ try
+ {
+ int rows = Integer.parseInt(toString.substring(0, index));
+ int columns = Integer.parseInt(toString.substring(index + X.length()));
+ return new Geometry(rows, columns);
+ } catch (NumberFormatException ex)
+ {
+ // Nothing to do here.
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Whether this <code>Geometry</code> contains given <var>location</var>, meaning that it is
+ * a valid <code>Location</code>.
+ */
+ public final boolean contains(final Location location)
+ {
+ assert location != null : "Given location can not be null.";
+ return location.getX() <= getColumns() && location.getY() <= getRows();
+ }
+
+ /**
+ * Returns the directory name where this <code>Geometry</code> is saved.
+ * <p>
+ * Currently this method is not supported and must be implemented.
+ * </p>
+ */
+ protected String getGeometryDirectoryName()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Geometry == false)
+ {
+ return false;
+ }
+ final Geometry geometry = (Geometry) obj;
+ return geometry.rows == rows && geometry.columns == columns;
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ int hashCode = 17;
+ hashCode = hashCode * 37 + getRows();
+ hashCode = hashCode * 37 + getColumns();
+ return hashCode;
+ }
+
+ @Override
+ public final String toString()
+ {
+ return getRows() + X + getColumns();
+ }
+}
\ No newline at end of file
diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Location.java b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Location.java
new file mode 100644
index 0000000000000000000000000000000000000000..d55369d7de3d8ff1e36d1743d89ffbd9d4df1916
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/Location.java
@@ -0,0 +1,205 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds.hcs;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.geometry.ConversionUtils;
+import ch.systemsx.cisd.common.geometry.Point;
+
+/**
+ * A location in (x, y) coordinate space, specified in integer precision. X and Y start from 1. *
+ *
+ * @author Christian Ribeaud
+ */
+public final class Location implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ static final String NOT_POSITIVE = "Given coordinate '%s' must be > 0 (%d <= 0).";
+
+ /**
+ * The <i>x</i> (or <i>column</i>) coordinate.
+ */
+ private final int x;
+
+ /**
+ * The <i>y</i> (or <i>row</i>) coordinate.
+ */
+ private final int y;
+
+ public Location(final int x, final int y)
+ {
+ assert x > 0 : String.format(NOT_POSITIVE, "x", x);
+ this.x = x;
+ assert y > 0 : String.format(NOT_POSITIVE, "y", y);
+ this.y = y;
+ }
+
+ public static final Location createLocationFromRowAndColumn(final int row, final int column)
+ {
+ return new Location(column, row);
+ }
+
+ /**
+ * For given <var>position</var> in given <code>geometry</code> returns corresponding
+ * <code>Location</code>. Position should be greater than 0.<br>
+ * Assumes that element index grows as column/row numbers grow, so for a 3x2 geometry elements
+ * would be numbered like:<br>
+ * 1 2 3<br>
+ * 4 5 6<br>
+ *
+ * @return <code>null</code> if position is out of range.
+ */
+ public static final Location tryCreateLocationFromRowwisePosition(final int position,
+ final Geometry geometry)
+ {
+ return tryCreateLocationFromPosition(position, geometry, false);
+ }
+
+ /**
+ * For given <var>position</var> in given <code>geometry</code> returns corresponding
+ * <code>Location</code>. Position should be greater than 0.<br>
+ * Assumes that element index grows as row/column numbers grow, so for a 3x2 geometry elements
+ * would be numbered like:<br>
+ * 1 3 5<br>
+ * 2 4 6<br>
+ *
+ * @return <code>null</code> if position is out of range.
+ */
+ public static final Location tryCreateLocationFromColumnwisePosition(final int position,
+ final Geometry geometry)
+ {
+ return tryCreateLocationFromPosition(position, geometry, true);
+ }
+
+ private static final Location tryCreateLocationFromPosition(final int position,
+ final Geometry geometry, boolean isColumnwise)
+ {
+ assert geometry != null : "Given geometry can not be null.";
+ int rows = geometry.getRows();
+ int columns = geometry.getColumns();
+ int divisor = (isColumnwise ? rows : columns);
+ final int max = columns * rows;
+ // Given position is within the range.
+ if (position > 0 && position <= max)
+ {
+ final int modulo = position % divisor;
+ final int x = modulo == 0 ? divisor : modulo;
+ final int y = (int) Math.ceil(position / (float) divisor);
+ if (isColumnwise)
+ {
+ return new Location(y, x);
+ } else
+ {
+ return new Location(x, y);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * For given matrix <var>coordinate</var> (<strong>which is given in transposed form</strong>)
+ * returns corresponding <code>Location</code>.
+ *
+ * @return <code>null</code> if given <var>coordinate</var> is not a matrix coordinate.
+ */
+ public static final Location tryCreateLocationFromTransposedMatrixCoordinate(
+ final String coordinate)
+ {
+ try
+ {
+ Point point = ConversionUtils.parseSpreadsheetLocation(coordinate);
+ return new Location(point.getY() + 1, point.getX() + 1);
+ } catch (IllegalArgumentException ex)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Do the matrix coordinate conversion for coordinates that are specified this way, but in two
+ * columns. <strong>Note that first the <var>columnCoord</var> is given and then the
+ * <var>rowCoord</var>.
+ *
+ * @return <code>null</code> if given <var>coordinate</var> is not a matrix coordinate.
+ */
+ public static final Location tryCreateLocationFromTransposedSplitMatrixCoordinate(
+ final String columnCoord, final String rowCoord)
+ {
+ return tryCreateLocationFromTransposedMatrixCoordinate(columnCoord + rowCoord);
+ }
+
+ /**
+ * For given location returns corresponding matrix coordinate.
+ */
+ public final String createMatrixCoordinateFromLocation()
+ {
+ Point point = new Point(getY() - 1, getX() - 1);
+ return ConversionUtils.convertToSpreadsheetLocation(point);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Location == false)
+ {
+ return false;
+ }
+ final Location location = (Location) obj;
+ return location.x == x && location.y == y;
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ int hashCode = 17;
+ hashCode = hashCode * 37 + x;
+ hashCode = hashCode * 37 + y;
+ return hashCode;
+ }
+
+ @Override
+ public final String toString()
+ {
+ return "[x=" + x + ",y=" + y + "]";
+ }
+
+ /**
+ * Returns the <i>x</i> (or <i>column</i>) coordinate.
+ */
+ public int getX()
+ {
+ return x;
+ }
+
+ /**
+ * Returns the <i>y</i> (or <i>row</i>) coordinate.
+ */
+ public int getY()
+ {
+ return y;
+ }
+}
\ No newline at end of file
diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..6396ec2342cb3f75eb45f07974e4334cf8cb7a5d
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds.hcs;
+
+
+/**
+ * An <code>AbstractGeometry</code> implementation suitable for <i>Plate</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class PlateGeometry extends Geometry
+{
+
+ /**
+ * Directory name which contains the plate geometry.
+ * <p>
+ */
+ public static final String PLATE_GEOMETRY = "plate_geometry";
+
+ public PlateGeometry(final Geometry geometry)
+ {
+ this(geometry.getRows(), geometry.getColumns());
+ }
+
+ public PlateGeometry(final int rows, final int columns)
+ {
+ super(rows, columns);
+ }
+
+ /**
+ * Creates a new <code>WellGeometry</code> from given <var>toString</var>.
+ */
+ public final static Geometry createFromString(final String toString)
+ {
+ return new PlateGeometry(Geometry.createFromString(toString));
+ }
+
+ //
+ // Geometry
+ //
+
+ @Override
+ protected final String getGeometryDirectoryName()
+ {
+ return PLATE_GEOMETRY;
+ }
+
+}
diff --git a/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java
new file mode 100644
index 0000000000000000000000000000000000000000..55830ba4c77f6f60a47fa3c6e7f52c3c1e4b5ccd
--- /dev/null
+++ b/openbis-common/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.bds.hcs;
+
+
+/**
+ * An <code>AbstractGeometry</code> implementation suitable for <i>Well</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class WellGeometry extends Geometry
+{
+
+ /**
+ * Directory name which contains the well geometry.
+ * <p>
+ */
+ public static final String WELL_GEOMETRY = "well_geometry";
+
+ public WellGeometry(final Geometry geometry)
+ {
+ this(geometry.getRows(), geometry.getColumns());
+ }
+
+ public WellGeometry(final int rows, final int columns)
+ {
+ super(rows, columns);
+ }
+
+ /**
+ * Creates a new <code>WellGeometry</code> from given <var>toString</var>.
+ */
+ public final static Geometry createFromString(final String toString)
+ {
+ return new WellGeometry(Geometry.createFromString(toString));
+ }
+
+ //
+ // Geometry
+ //
+
+ @Override
+ protected final String getGeometryDirectoryName()
+ {
+ return WELL_GEOMETRY;
+ }
+
+}