From f91c4cb5166c4729df87eba9372f716d68d2fe9a Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Tue, 30 Nov 2010 15:18:54 +0000
Subject: [PATCH] dynamic feature converter
SVN: 18942
---
.../feature_converter/CategoryOracle.java | 81 +++++++++
.../FeatureVectorConverter.java | 66 +++++++
.../tools/feature_converter/Features.java | 167 ++++++++++++++++++
.../tools/feature_converter/InputRow.java | 75 ++++++++
.../feature_converter/InputRowFactory.java | 33 ++++
.../feature_converter/InputRowsHelper.java | 78 ++++++++
.../InputRowsNamedCollection.java | 50 ++++++
.../tools/feature_converter/OutputRow.java | 81 +++++++++
.../tools/feature_converter/TsvBuilder.java | 62 +++++++
9 files changed, 693 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/CategoryOracle.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/FeatureVectorConverter.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/Features.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRow.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowFactory.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsHelper.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsNamedCollection.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/OutputRow.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/TsvBuilder.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/CategoryOracle.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/CategoryOracle.java
new file mode 100644
index 00000000000..d1f81eff1eb
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/CategoryOracle.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * @author Izabela Adamczyk
+ */
+class CategoryOracle
+{
+ private static final String DISCARD = "Discard";
+
+ private static final String UP = "up";
+
+ private static final String YES = "yes";
+
+ private static final String NO = "no";
+
+ private static final String CONSTANT = "Constant";
+
+ private static final String GOOD = "Good";
+
+ private enum Category
+ {
+ OTHER, DISCARDED_CHAMBER, GOOD_CHAMBER_INTENSITY_AND_LOCALIZATION_CHANGE,
+ GOOD_CHAMBER_LOCALIZATION_CHANGE, GOOD_CHAMBER_INTENSITY_UP, GOOD_CHAMBER_NO_CHANGE;
+ }
+
+ public static String calculateCategory(InputRow in)
+ {
+ String quality = in.getQuality();
+ String intensityChange = in.getIntensityChange();
+ String localizationChange = in.getLocalizationChange();
+ return calculateCategory(quality, intensityChange, localizationChange).toString();
+ }
+
+ private static Category calculateCategory(String quality, String intensityChange,
+ String localizationChange)
+ {
+ if (eq(quality, GOOD) && eq(intensityChange, CONSTANT) && eq(localizationChange, NO))
+ {
+ return Category.GOOD_CHAMBER_NO_CHANGE;
+ } else if (eq(quality, GOOD) && eq(intensityChange, UP) && eq(localizationChange, NO))
+ {
+ return Category.GOOD_CHAMBER_INTENSITY_UP;
+ } else if (eq(quality, GOOD) && eq(intensityChange, NO) && eq(localizationChange, YES))
+ {
+ return Category.GOOD_CHAMBER_LOCALIZATION_CHANGE;
+ } else if (eq(quality, GOOD) && eq(intensityChange, CONSTANT)
+ && eq(localizationChange, YES))
+ {
+ return Category.GOOD_CHAMBER_INTENSITY_AND_LOCALIZATION_CHANGE;
+ } else if (eq(quality, DISCARD))
+ {
+ return Category.DISCARDED_CHAMBER;
+ } else
+ {
+ return Category.OTHER;
+ }
+ }
+
+ private static boolean eq(String property, String value)
+ {
+ return StringUtils.equalsIgnoreCase(property, value);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/FeatureVectorConverter.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/FeatureVectorConverter.java
new file mode 100644
index 00000000000..dfa494b18ab
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/FeatureVectorConverter.java
@@ -0,0 +1,66 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.parser.IParserObjectFactory;
+import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
+import ch.systemsx.cisd.common.parser.IPropertyMapper;
+import ch.systemsx.cisd.common.parser.ParserException;
+import ch.systemsx.cisd.common.parser.ParsingException;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public class FeatureVectorConverter
+{
+
+ public static void main(String[] args) throws ParserException, ParsingException,
+ IllegalArgumentException, IOException
+ {
+ String in = args[0];
+ IParserObjectFactoryFactory<InputRow> parser = new IParserObjectFactoryFactory<InputRow>()
+ {
+ public IParserObjectFactory<InputRow> createFactory(IPropertyMapper propertyMapper)
+ throws ParserException
+ {
+ return new InputRowFactory(InputRow.class, propertyMapper);
+ }
+ };
+ BisTabFileLoader<InputRow> loader = new BisTabFileLoader<InputRow>(parser, false);
+ File inFile = new File(in);
+ List<InputRow> list = loader.load(FileUtils.openInputStream(inFile));
+ List<InputRowsNamedCollection> experiments = InputRowsHelper.extract(list);
+ for (InputRowsNamedCollection e : experiments)
+ {
+ String outName = e.getName() + "__" + inFile.getName();
+ File outFile =
+ FileUtilities.createNextNumberedFile(new File(inFile.getParent(), outName),
+ null);
+ FileUtils.writeLines(outFile, InputRowsHelper.toTsv(e.getRows()));
+ System.out.println(outFile.getPath());
+ }
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/Features.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/Features.java
new file mode 100644
index 00000000000..852980a331f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/Features.java
@@ -0,0 +1,167 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.util.Arrays;
+import java.util.List;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public class Features
+{
+
+ private static final String POSITION = "position";
+
+ private static final String SIDE = "side";
+
+ private static final String QUALITY = "quality";
+
+ private static final String QUALITY_DESC = "quality_desc";
+
+ private static final String INTENSITY_CHANGE = "intensity_change";
+
+ private static final String LOCALIZATION_CHANGE = "localization_change";
+
+ private static final String END_LOCALIZATION = "end_localization";
+
+ private static final String INITIAL_LOCALIZATION = "initial_localization";
+
+ private String position;
+
+ private String side;
+
+ private String quality;
+
+ private String qualityDesc;
+
+ private String intensityChange;
+
+ private String localizationChange;
+
+ private String initialLocalization;
+
+ private String endLocalization;
+
+ public Features()
+ {
+ }
+
+ public String getPosition()
+ {
+ return position;
+ }
+
+ @BeanProperty(label = POSITION)
+ public void setPosition(String position)
+ {
+ this.position = position;
+ }
+
+ public String getSide()
+ {
+ return side;
+ }
+
+ @BeanProperty(label = SIDE)
+ public void setSide(String side)
+ {
+ this.side = side;
+ }
+
+ public String getQuality()
+ {
+ return quality;
+ }
+
+ @BeanProperty(label = QUALITY)
+ public void setQuality(String quality)
+ {
+ this.quality = quality;
+ }
+
+ public String getQualityDesc()
+ {
+ return qualityDesc;
+ }
+
+ @BeanProperty(label = QUALITY_DESC)
+ public void setQualityDesc(String qualityDesc)
+ {
+ this.qualityDesc = qualityDesc;
+ }
+
+ public String getIntensityChange()
+ {
+ return intensityChange;
+ }
+
+ @BeanProperty(label = INTENSITY_CHANGE)
+ public void setIntensityChange(String intensityChange)
+ {
+ this.intensityChange = intensityChange;
+ }
+
+ public String getLocalizationChange()
+ {
+ return localizationChange;
+ }
+
+ @BeanProperty(label = LOCALIZATION_CHANGE)
+ public void setLocalizationChange(String localizationChange)
+ {
+ this.localizationChange = localizationChange;
+ }
+
+ public String getInitialLocalization()
+ {
+ return initialLocalization;
+ }
+
+ @BeanProperty(label = INITIAL_LOCALIZATION)
+ public void setInitialLocalization(String initialLocalization)
+ {
+ this.initialLocalization = initialLocalization;
+ }
+
+ public String getEndLocalization()
+ {
+ return endLocalization;
+ }
+
+ @BeanProperty(label = END_LOCALIZATION)
+ public void setEndLocalization(String endLocalization)
+ {
+ this.endLocalization = endLocalization;
+ }
+
+ /** NOTE: Order strictly connected with {@link #getColumns()} */
+ public static List<String> getHeaderColumns()
+ {
+ return Arrays.asList(END_LOCALIZATION, INITIAL_LOCALIZATION, INTENSITY_CHANGE,
+ LOCALIZATION_CHANGE, POSITION, QUALITY, QUALITY_DESC, SIDE);
+ }
+
+ /** NOTE: Order strictly connected with {@link #getHeaderColumns()} */
+ public List<String> getColumns()
+ {
+ return Arrays.asList(getEndLocalization(), getInitialLocalization(), getIntensityChange(),
+ getLocalizationChange(), getPosition(), getQuality(), getQualityDesc(), getSide());
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRow.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRow.java
new file mode 100644
index 00000000000..e60c3fdab8b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRow.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public final class InputRow extends Features
+{
+ private static final String IDENTIFIER = "identifier";
+
+ private static final String CONTAINER = "container";
+
+ private static final String YORF = "yorf";
+
+ private String yorf;
+
+ private String container;
+
+ private String identifier;
+
+ public InputRow()
+ {
+ }
+
+ public String getContainer()
+ {
+ return container;
+ }
+
+ @BeanProperty(label = CONTAINER)
+ public void setContainer(String container)
+ {
+ this.container = container;
+ }
+
+ public String getIdentifier()
+ {
+ return identifier;
+ }
+
+ @BeanProperty(label = IDENTIFIER)
+ public void setIdentifier(String identifier)
+ {
+ this.identifier = identifier;
+ }
+
+ public String getYorf()
+ {
+ return yorf;
+ }
+
+ @BeanProperty(label = YORF)
+ public void setYorf(String yorf)
+ {
+ this.yorf = yorf;
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowFactory.java
new file mode 100644
index 00000000000..009fab2c86f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowFactory.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import ch.systemsx.cisd.common.parser.AbstractParserObjectFactory;
+import ch.systemsx.cisd.common.parser.IPropertyMapper;
+
+/**
+ * @author Izabela Adamczyk
+ */
+final class InputRowFactory extends AbstractParserObjectFactory<InputRow>
+{
+
+ protected InputRowFactory(Class<InputRow> beanClass, IPropertyMapper propertyMapper)
+ {
+ super(beanClass, propertyMapper);
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsHelper.java
new file mode 100644
index 00000000000..c870a359fbb
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsHelper.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.utilities.BeanUtils;
+
+/**
+ * @author Izabela Adamczyk
+ */
+class InputRowsHelper
+{
+
+ public static List<InputRowsNamedCollection> extract(List<InputRow> list)
+ {
+ Map<String, List<InputRow>> map = new HashMap<String, List<InputRow>>();
+ for (InputRow r : list)
+ {
+ String name = r.getContainer();
+ if (map.get(name) == null)
+ {
+ map.put(name, new ArrayList<InputRow>());
+ }
+ map.get(name).add(r);
+ }
+ ArrayList<InputRowsNamedCollection> result = new ArrayList<InputRowsNamedCollection>();
+ for (String key : map.keySet())
+ {
+ InputRowsNamedCollection exp = new InputRowsNamedCollection();
+ exp.setName(key);
+ exp.setRows(map.get(key));
+ result.add(exp);
+ }
+ return result;
+ }
+
+ public static List<String> toTsv(List<InputRow> list)
+ {
+ ArrayList<String> result = new ArrayList<String>();
+ result.add(new TsvBuilder(OutputRow.getHeaderColumns()).toString());
+ for (InputRow r : list)
+ {
+ result.add(new TsvBuilder(convert(r).getColumns()).toString());
+ }
+ return result;
+ }
+
+ private static OutputRow convert(InputRow in)
+ {
+ OutputRow outputRow = new OutputRow();
+ BeanUtils.fillBean(OutputRow.class, outputRow, in);
+ outputRow.setWellName(StringUtils.split(in.getIdentifier(), ":")[1]);
+ String category = CategoryOracle.calculateCategory(in);
+ outputRow.setCategory(category);
+ return outputRow;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsNamedCollection.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsNamedCollection.java
new file mode 100644
index 00000000000..7c2f9820a28
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/InputRowsNamedCollection.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.util.List;
+
+/**
+ * @author Izabela Adamczyk
+ */
+class InputRowsNamedCollection
+{
+ String name;
+
+ List<InputRow> rows;
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public List<InputRow> getRows()
+ {
+ return rows;
+ }
+
+ public void setRows(List<InputRow> rows)
+ {
+ this.rows = rows;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/OutputRow.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/OutputRow.java
new file mode 100644
index 00000000000..625d358947f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/OutputRow.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+
+/**
+ * @author Izabela Adamczyk
+ */
+final class OutputRow extends Features
+{
+
+ private static final String CATEGORY = "category";
+
+ private static final String WELL_NAME = "well_name";
+
+ private String wellName;
+
+ private String category;
+
+ public String getWellName()
+ {
+ return wellName;
+ }
+
+ @BeanProperty(label = WELL_NAME)
+ public void setWellName(String wellName)
+ {
+ this.wellName = wellName;
+ }
+
+ public String getCategory()
+ {
+ return category;
+ }
+
+ @BeanProperty(label = CATEGORY)
+ public void setCategory(String category)
+ {
+ this.category = category;
+ }
+
+ /** NOTE: Order strictly connected with {@link #getColumns()} */
+ public static List<String> getHeaderColumns()
+ {
+ ArrayList<String> list = new ArrayList<String>();
+ list.add(WELL_NAME);
+ list.add(CATEGORY);
+ list.addAll(Features/* super class */.getHeaderColumns());
+ return list;
+ }
+
+ /** NOTE: Order strictly connected with {@link #getHeaderColumns()} */
+ @Override
+ public List<String> getColumns()
+ {
+ ArrayList<String> list = new ArrayList<String>();
+ list.add(getWellName());
+ list.add(getCategory());
+ list.addAll(super.getColumns());
+ return list;
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/TsvBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/TsvBuilder.java
new file mode 100644
index 00000000000..8cd21d55e93
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/tools/feature_converter/TsvBuilder.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright 2010 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.openbis.dss.etl.dynamix.tools.feature_converter;
+
+import java.util.List;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public class TsvBuilder
+{
+ static final String TSV_SEPARATOR = ";";
+
+ StringBuilder builder = new StringBuilder();
+
+ boolean empty = true;
+
+ public TsvBuilder()
+ {
+ }
+
+ public TsvBuilder(List<String> columns)
+ {
+ addColumns(columns.toArray(new String[0]));
+ }
+
+ public void addColumns(String... columns)
+ {
+ for (String c : columns)
+ {
+ if (empty)
+ {
+ empty = false;
+ } else
+ {
+ builder.append(TsvBuilder.TSV_SEPARATOR);
+ }
+ builder.append(c);
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return builder.toString();
+ }
+
+}
--
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