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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.chem.io;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Properties;
import java.util.TreeMap;
import com.actelion.research.chem.SSSearcherWithIndex;
import com.actelion.research.chem.descriptor.DescriptorConstants;
import com.actelion.research.chem.descriptor.DescriptorHandlerFFP512;
public class ODEFileParser extends CompoundFileParser implements CompoundTableConstants,DescriptorConstants {
private BufferedReader mReader;
private String[] mFieldName;
private String[] mFieldData;
private String mIDCodeColumnName,mCoordinateColumnName,mFragFpColumnName;
private int[] mFieldIndex;
private int mIDCodeColumn, mCoordinateColumn,
mIndexColumn,mOutdatedIndexColumn;
public ODEFileParser(String fileName) {
try {
mReader = new BufferedReader(new FileReader(fileName));
}
catch (FileNotFoundException e) {}
init();
}
public ODEFileParser(File file) {
try {
mReader = new BufferedReader(new FileReader(file));
}
catch (FileNotFoundException e) {}
init();
}
public ODEFileParser(Reader reader) {
mReader = new BufferedReader(reader);
init();
}
private void init() {
mIDCodeColumn = -1;
mCoordinateColumn = -1;
mIndexColumn = -1;
mOutdatedIndexColumn = -1;
ArrayList columnNameList = new ArrayList();
ArrayList columnIndexList = new ArrayList();
String header = null;
if (mReader != null)
try {
header = mReader.readLine();
// skip file header in case of '.dwar' file
if (header != null && header.equals(cNativeFileHeaderStart)) {
header = mReader.readLine();
while (header != null
&& !header.equals(cNativeFileHeaderEnd))
header = mReader.readLine();
header = mReader.readLine();
}
// interpret column properties in case of '.dwar' file
if (header != null && header.equals(cColumnPropertyStart)) {
TreeMap columnProperties = new TreeMap();
header = mReader.readLine();
Properties properties = null;
String columnName = null;
while (header != null
&& !header.equals(cColumnPropertyEnd)) {
if (header.startsWith("<"+cColumnName)) {
columnName = extractValue(header);
properties = new Properties();
}
else if (header.startsWith("<"+cColumnProperty)) {
String keyAndValue = extractValue(header);
if (keyAndValue.equals("isIDCode\ttrue")
|| keyAndValue.equals(cColumnPropertySpecialType
+"\t"+cColumnTypeIDCode)) {
mIDCodeColumnName = columnName;
}
else {
int index = keyAndValue.indexOf('\t');
properties.put(keyAndValue.substring(0, index), keyAndValue.substring(index+1));
}
}
header = mReader.readLine();
if (header.startsWith("<"+cColumnName)
|| header.equals(cColumnPropertyEnd)) {
columnProperties.put(columnName, properties);
}
}
if (mIDCodeColumnName != null) {
for (String key:columnProperties.keySet()) {
Properties props = columnProperties.get(key);
if (cColumnType2DCoordinates.equals(props.get(cColumnPropertySpecialType))
&& mIDCodeColumnName.equals(props.get(cColumnPropertyParentColumn)))
mCoordinateColumnName = key;
else if (DESCRIPTOR_FFP512.shortName.equals(props.get(cColumnPropertySpecialType))
&& DescriptorHandlerFFP512.VERSION.equals(props.get(cColumnPropertyDescriptorVersion))
&& mIDCodeColumnName.equals(props.get(cColumnPropertyParentColumn)))
mFragFpColumnName = key;
}
}
header = mReader.readLine();
}
}
catch (IOException e) {}
if (header == null) {
mReader = null;
return;
}
int fromIndex = 0;
int toIndex = 0;
int sourceColumn = 0;
do {
String columnName;
toIndex = header.indexOf('\t', fromIndex);
if (toIndex == -1) {
columnName = header.substring(fromIndex);
}
else {
columnName = header.substring(fromIndex, toIndex);
fromIndex = toIndex+1;
}
if (mIDCodeColumn == -1 && columnName.equals(mIDCodeColumnName))
mIDCodeColumn = sourceColumn;
else if (mCoordinateColumn == -1 && columnName.equals(mCoordinateColumnName))
mCoordinateColumn = sourceColumn;
else if (mIndexColumn == -1 && columnName.equals(mFragFpColumnName))
mIndexColumn = sourceColumn;
else if (columnName.equalsIgnoreCase("idcode") && mIDCodeColumn == -1)
mIDCodeColumn = sourceColumn;
else if (columnName.equalsIgnoreCase("idcoordinates") && mCoordinateColumn == -1)
mCoordinateColumn = sourceColumn;
else if (columnName.startsWith("fingerprint") && mIndexColumn == -1) {
if (columnName.endsWith(SSSearcherWithIndex.cIndexVersion))
mIndexColumn = sourceColumn;
else
mOutdatedIndexColumn = sourceColumn;
}
if (sourceColumn != mIDCodeColumn
&& sourceColumn != mCoordinateColumn
&& sourceColumn != mIndexColumn
&& sourceColumn != mOutdatedIndexColumn) {
columnNameList.add(columnName);
columnIndexList.add(new Integer(sourceColumn));
}
sourceColumn++;
} while (toIndex != -1);
mFieldName = new String[columnNameList.size()];
mFieldIndex = new int[columnNameList.size()];
for (int i=0; i