diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/AbstractTiffCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/AbstractTiffCompressionMethod.java
deleted file mode 100644
index 40850d973324cff56b77b3713c1da34cfe56e717..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/AbstractTiffCompressionMethod.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2008 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.common.compression.tiff;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.common.compression.file.InPlaceCompressionMethod;
-import ch.systemsx.cisd.common.exception.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exception.EnvironmentFailureException;
-import ch.systemsx.cisd.common.fileconverter.TiffCompressionStrategy;
-
-/**
- * A compression method for TIFF files using an <code>executable</code> utility with an option to
- * specify compression type.
- *
- * @deprecated Use {@link TiffCompressionStrategy} instead.
- * @author Piotr Buczek
- */
-@Deprecated
-public abstract class AbstractTiffCompressionMethod extends InPlaceCompressionMethod
-{
-
- abstract protected String getExecutableName();
-
- abstract protected File getExecutable();
-
- private final String compressionType;
-
- public AbstractTiffCompressionMethod(String compressionType)
- {
- assert compressionType != null;
- this.compressionType = compressionType;
- }
-
- public String getCompressionType()
- {
- return compressionType;
- }
-
- public void setCompressionType(String compressionType)
- {
-
- }
-
- @Override
- final protected List<String> getAcceptedExtensions()
- {
- return Arrays.asList(".tif", ".tiff");
- }
-
- @Override
- public void check() throws EnvironmentFailureException, ConfigurationFailureException
- {
- if (getExecutable() == null)
- {
- throw new ConfigurationFailureException("Cannot find executable of the "
- + getExecutableName() + " utility.");
- }
- }
-
- @Override
- public boolean isRemote()
- {
- return false;
- }
-
-}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java
deleted file mode 100644
index 37242443c3382fcdc6f7d962935d72cb51f49f9d..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * Copyright 2008 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.common.compression.tiff;
-
-import java.util.Collection;
-
-import ch.systemsx.cisd.common.compression.file.Compressor;
-import ch.systemsx.cisd.common.compression.file.FailureRecord;
-import ch.systemsx.cisd.common.compression.file.ICompressionMethod;
-import ch.systemsx.cisd.common.exception.EnvironmentFailureException;
-import ch.systemsx.cisd.common.fileconverter.FileConverter;
-
-/**
- * The main class for tiff file compression.
- *
- * @deprecated Use {@link FileConverter} instead.
- * @author Bernd Rinn
- */
-@Deprecated
-public class TiffCompressor extends Compressor
-{
- public static void main(String[] args)
- {
- if (args.length != 1)
- {
- System.err.println("Syntax: TiffCompressor <directory>");
- System.exit(1);
- }
-
- String errorMsgOrNull = tryCompress(args[0]);
- if (errorMsgOrNull != null)
- {
- System.err.print(errorMsgOrNull);
- }
- }
-
- private static String tryCompress(String path)
- {
- try
- {
- return compress(path, 1, TiffConvertCompressionMethod.create(null));
- } catch (InterruptedException ex)
- {
- return "Compression was interrupted:" + ex.getMessage();
- } catch (EnvironmentFailureException ex)
- {
- return ex.getMessage();
- }
- }
-
- /**
- * Compresses files in directory with given <var>path</var> with given tiff
- * <var>compressionMethod</var>.
- *
- * @param threadsPerProcessor number of threads performing compression per processor (>0)
- * @return error message or null if no error occurred
- * @throws InterruptedException if compression was interrupted
- * @throws EnvironmentFailureException if there is a problem with specified path
- */
- public static String compress(String path, int threadsPerProcessor,
- ICompressionMethod compressionMethod) throws InterruptedException,
- EnvironmentFailureException
- {
- assert path != null;
- assert compressionMethod != null;
- assert threadsPerProcessor > 0;
-
- final StringBuilder errorMsgBuilder = new StringBuilder();
- final Collection<FailureRecord> failed;
- failed = start(path, compressionMethod, threadsPerProcessor);
- if (failed.size() > 0)
- {
- errorMsgBuilder.append("The following files could not bee successfully compressed:\n");
- for (FailureRecord r : failed)
- {
- errorMsgBuilder.append(String.format("%s (%s)\n", r.getFailedFile().getName(), r
- .getFailureStatus()));
- }
- return errorMsgBuilder.toString();
- }
- return null;
- }
-}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffConvertCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffConvertCompressionMethod.java
deleted file mode 100644
index 685908053adcd0c7ebaace08d9691a246737cc37..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffConvertCompressionMethod.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Copyright 2008 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.common.compression.tiff;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.base.utilities.OSUtilities;
-import ch.systemsx.cisd.common.Constants;
-import ch.systemsx.cisd.common.exception.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exception.EnvironmentFailureException;
-import ch.systemsx.cisd.common.fileconverter.TiffCompressionStrategy;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
-import ch.systemsx.cisd.common.process.ProcessIOStrategy;
-import ch.systemsx.cisd.common.process.ProcessResult;
-
-/**
- * A compression method for TIFF files using the ImageMagick <code>convert</code> utility with
- * specified compression type parameter (by default: <code>LZW</code>).
- *
- * @deprecated Use {@link TiffCompressionStrategy} instead.
- * @author Bernd Rinn
- */
-@Deprecated
-public class TiffConvertCompressionMethod extends AbstractTiffCompressionMethod
-{
-
- private final static String executableName = "convert";
-
- private final static File executable = OSUtilities.findExecutable(executableName);
-
- private final static String DEFAULT_COMPRESSION_TYPE = "LZW";
-
- private static String getImageMagickVersion(String convertExecutableToCheck)
- {
- final ProcessResult result =
- ProcessExecutionHelper.run(Arrays.asList(convertExecutableToCheck, "--version"),
- operationLog, machineLog, Constants.MILLIS_TO_WAIT_BEFORE_TIMEOUT,
- ProcessIOStrategy.DEFAULT_IO_STRATEGY, true);
- result.log();
- final String versionString = extractImageMagickVersion(result.getOutput().get(0));
- return versionString;
- }
-
- private static String extractImageMagickVersion(String imageMagickVersionLine)
- {
- if (imageMagickVersionLine.startsWith("Version: ImageMagick") == false)
- {
- return null;
- } else
- {
- final String[] versionStringParts = imageMagickVersionLine.split("\\s+");
- if (versionStringParts.length < 3)
- {
- return null;
- }
- return versionStringParts[2];
- }
- }
-
- /**
- * @returns compression method using specified compression type
- * @param compressionTypeOrNull compression type to use (if <code>null</code> default
- * compression type will be used)
- */
- public static TiffConvertCompressionMethod create(String compressionTypeOrNull)
- {
- return compressionTypeOrNull == null ? new TiffConvertCompressionMethod()
- : new TiffConvertCompressionMethod(compressionTypeOrNull);
- }
-
- /** Constructs compression method using default compression type. */
- private TiffConvertCompressionMethod()
- {
- this(DEFAULT_COMPRESSION_TYPE);
- }
-
- /** Constructs compression method using specified <var>compressonType</var>. */
- private TiffConvertCompressionMethod(String compressionType)
- {
- super(compressionType);
- }
-
- @Override
- protected List<String> createCommandLine(File fileToCompress, File inProgressFile)
- {
- assert executable != null;
- assert fileToCompress != null;
- assert fileToCompress.isFile();
- assert inProgressFile != null;
- assert inProgressFile.exists() == false;
-
- final List<String> parameters =
- Arrays.asList(executable.getAbsolutePath(), fileToCompress.getAbsolutePath(),
- "-compress", getCompressionType(), inProgressFile.getAbsolutePath());
- return parameters;
- }
-
- @Override
- public void check() throws EnvironmentFailureException, ConfigurationFailureException
- {
- super.check();
- final String imageMagickVersionOrNull = getImageMagickVersion(executable.getAbsolutePath());
- if (imageMagickVersionOrNull == null)
- {
- throw new ConfigurationFailureException("Invalid convert utility");
- }
- String[] imageMagickVersionParts = imageMagickVersionOrNull.split("\\.");
- if (imageMagickVersionParts.length != 3)
- {
- throw new ConfigurationFailureException("Invalid convert utility");
- }
- final int imageMagickMajorVersion = Integer.parseInt(imageMagickVersionParts[0]);
- final int imageMagickMinorVersion = Integer.parseInt(imageMagickVersionParts[1]);
- if (imageMagickMajorVersion < 6 || imageMagickMinorVersion < 2)
- {
- throw ConfigurationFailureException.fromTemplate(
- "Convert utility is too old (expected: v6.2 or newer, found: v%s)",
- imageMagickVersionOrNull);
- }
- if (machineLog.isInfoEnabled())
- {
- machineLog.info(String.format("Using convert executable '%s', ImageMagick version %s",
- executable, imageMagickVersionOrNull));
- }
- }
-
- public static void main(String[] args)
- {
- LogInitializer.init();
- final TiffConvertCompressionMethod compressor = new TiffConvertCompressionMethod();
- compressor.check();
- }
-
- @Override
- protected File getExecutable()
- {
- return executable;
- }
-
- @Override
- protected String getExecutableName()
- {
- return executableName;
- }
-
-}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCpCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCpCompressionMethod.java
deleted file mode 100644
index c9ddf4163ec56ddc4888f48f8af99ac817405496..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCpCompressionMethod.java
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- * Copyright 2008 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.common.compression.tiff;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.base.utilities.OSUtilities;
-import ch.systemsx.cisd.common.fileconverter.TiffCompressionStrategy;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-
-/**
- * A compression method for TIFF files using the <code>tiffcp</code> utility with specified
- * compression type parameter (by default: <code>lzw:2</code>).
- *
- * @deprecated Use {@link TiffCompressionStrategy} instead.
- * @author Piotr Buczek
- */
-@Deprecated
-public class TiffCpCompressionMethod extends AbstractTiffCompressionMethod
-{
-
- private final static String executableName = "tiffcp";
-
- private final static File executable = OSUtilities.findExecutable(executableName);
-
- private final static String DEFAULT_COMPRESSION_TYPE = "lzw:2";
-
- /**
- * @returns compression method using specified compression type
- * @param compressionTypeOrNull compression type to use (if <code>null</code> default
- * compression type will be used)
- */
- public static TiffCpCompressionMethod create(String compressionTypeOrNull)
- {
- return compressionTypeOrNull == null ? new TiffCpCompressionMethod()
- : new TiffCpCompressionMethod(compressionTypeOrNull);
- }
-
- /** Constructs compression method using default compression type. */
- private TiffCpCompressionMethod()
- {
- this(DEFAULT_COMPRESSION_TYPE);
- }
-
- /** Constructs compression method using specified <var>compressonType</var>. */
- private TiffCpCompressionMethod(String compressionType)
- {
- super(compressionType);
- }
-
- @Override
- protected List<String> createCommandLine(File fileToCompress, File inProgressFile)
- {
- assert executable != null;
- assert fileToCompress != null;
- assert fileToCompress.isFile();
- assert inProgressFile != null;
- assert inProgressFile.exists() == false;
-
- final List<String> parameters =
- Arrays.asList(executable.getAbsolutePath(), "-c", getCompressionType(),
- fileToCompress.getAbsolutePath(), inProgressFile.getAbsolutePath());
- return parameters;
- }
-
- public static void main(String[] args)
- {
- LogInitializer.init();
- final TiffCpCompressionMethod compressor = new TiffCpCompressionMethod();
- compressor.check();
- }
-
- @Override
- protected File getExecutable()
- {
- return executable;
- }
-
- @Override
- protected String getExecutableName()
- {
- return executableName;
- }
-
-}