Java tutorial
/* * * * Copyright (C) 2009-2015 Syed Asad Rahman <asad@ebi.ac.uk> * * Contact: cdk-devel@lists.sourceforge.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * All we ask is that proper credit is given for our work, which includes * - but is not limited to - adding the above copyright notice to the beginning * of your source code files, and to any copyright notice that you may distribute * with programs based on this work. * * 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 Lesser General Public License for more details. * * You should have received query copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. * */ package uk.ac.ebi.smsd.cmd; import java.io.Writer; import java.util.Properties; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; /** * * @author Syed Asad Rahman <asad@ebi.ac.uk> */ public class ArgumentHandler { final static String NEW_LINE = System.getProperty("line.separator"); /** * Get any arguments that were left over. * * @return the remaining arguments */ public String[] getRemainingArgs() { return remainingArgs; } /** * @return the matchFile */ public String getMatchFile() { return matchFile; } /** * @return the fingerFile */ public String getFingerFile() { return fingerFile; } /** * @return the descriptorFile */ public String getDescriptorFile() { return descriptorFile; } /* Boolean Options */ private boolean applyHAdding = false; private boolean applyHRemoval = false; private boolean applyTest = false; private boolean applySuffix = false; private boolean appendMode = false; private boolean matchBondType = false; private boolean matchRingType = false; private boolean allMapping = false; private boolean image = false; private boolean substructureMode = false; private boolean isNMCS = false; private boolean outputSubgraph = false; private boolean matchAtomType = false; /* */ private final String matchFile = "mcs"; private final String fingerFile = "finger"; private final String descriptorFile = "molDescriptors"; private String queryOutfileName; private String targetOutfileName; private String suffix = ""; private int chemFilter = 3; private String outputFilepath; private Writer outputWriter; private String outputFiletype; private String queryFilepath; private String targetFilepath; private String queryType; private String targetType; private int imageWidth = -1; private int imageHeight = -1; private boolean helpRequested = false; private Options options; private String[] remainingArgs; private Properties imageProperties; private boolean isImageOptionHelp = false; protected void printError(String errmessg) { System.err.println(errmessg); System.exit(-1); } /** * Parses the options in the command line arguments and returns an array of * strings corresponding to the filenames given as arguments only * * @param args * @throws org.apache.commons.cli.ParseException */ @SuppressWarnings("static-access") public void parseCommandLineOptions(String[] args) throws ParseException { options = new Options(); options.addOption("h", "help", false, "Help page for command usage"); options.addOption("s", false, "SubStructure detection"); options.addOption("a", false, "Add Hydrogen"); options.addOption("x", false, "Match Atom Type"); options.addOption("r", false, "Remove Hydrogen"); options.addOption("z", false, "Ring matching"); options.addOption("b", false, "Match Bond types (Single, Double etc)"); options.addOption(Option.builder("q").argName("query_file").hasArg().desc("Query filename").build()); options.addOption(Option.builder("t").argName("target_file").hasArg().desc("Target filename").build()); options.addOption(Option.builder("S").argName("suffix").hasArg().desc("Add suffix to the files").build()); options.addOption("g", false, "create png of the mapping"); options.addOption(Option.builder("d").argName("WIDTHxHEIGHT").hasArg() .desc("Dimension of the image in pixels").build()); options.addOption("m", false, "Report all Mappings"); String filterDescr = "Default: 0, Stereo: 1, " + "Stereo+Fragment: 2, Stereo+Fragment+Energy: 3"; options.addOption(Option.builder("f").argName("filter_number").hasArg().desc(filterDescr).build()); options.addOption("A", false, "Appends output to existing files, else creates new files"); options.addOption(Option.builder("N").desc("Do N-way MCS on the target SD file").build()); options.addOption( Option.builder("Q").argName("query_type").hasArg().desc("Query type (MOL, SMI, etc.)").build()); options.addOption(Option.builder("T").argName("target_type").hasArg() .desc("Target type (MOL, SMI, SMIF, etc.)").build()); options.addOption( Option.builder("o").argName("filename").hasArg().desc("Output the substructure to a file").build()); options.addOption(Option.builder("O").argName("type").hasArg().desc("Output type (SMI, MOL)").build()); options.addOption(Option.builder("I").argName("option=value").hasArg().desc("Image options").build()); DefaultParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args, true); if (line.hasOption('Q')) { queryType = line.getOptionValue("Q"); } //else { // queryType = "MOL"; // } //XXX default type? if (line.hasOption('T')) { targetType = line.getOptionValue("T"); } else { targetType = "MOL"; } if (line.hasOption('a')) { this.setApplyHAdding(true); } if (line.hasOption('r')) { this.setApplyHRemoval(true); } if (line.hasOption('m')) { this.setAllMapping(true); } if (line.hasOption('s')) { this.setSubstructureMode(true); } if (line.hasOption('g')) { this.setImage(true); } if (line.hasOption('b')) { this.setMatchBondType(true); } if (line.hasOption('z')) { this.setMatchRingType(true); } if (line.hasOption('x')) { this.setMatchAtomType(true); } remainingArgs = line.getArgs(); if (line.hasOption('h') || line.getOptions().length == 0) { // System.out.println("Hello"); helpRequested = true; } if (line.hasOption('S')) { String[] suffix_reader = line.getOptionValues('S'); if (suffix_reader.length < 1) { System.out.println("Suffix required!"); helpRequested = true; } setSuffix(suffix_reader[0]); setApplySuffix(true); } if (line.hasOption('f')) { String[] filters = line.getOptionValues('f'); if (filters.length < 1) { System.out.println("Chemical filter required (Ranges: 0 to 3)!"); helpRequested = true; } setChemFilter((int) new Integer(filters[0])); } if (line.hasOption('q')) { queryFilepath = line.getOptionValue('q'); } if (line.hasOption('t')) { targetFilepath = line.getOptionValue('t'); } if (line.hasOption("A")) { this.setAppendMode(true); } if (line.hasOption("N")) { setNMCS(true); } if (line.hasOption("o")) { outputSubgraph = true; outputFilepath = line.getOptionValue("o"); } if (line.hasOption("O")) { outputFiletype = line.getOptionValue("O"); } else { outputFiletype = "MOL"; } if (line.hasOption("d")) { String dimensionString = line.getOptionValue("d"); if (dimensionString.contains("x")) { String[] parts = dimensionString.split("x"); try { setImageWidth(Integer.parseInt(parts[0])); setImageHeight(Integer.parseInt(parts[1])); System.out.println("set image dim to " + getImageWidth() + "x" + getImageHeight()); } catch (NumberFormatException nfe) { throw new ParseException("Malformed dimension string " + dimensionString); } } else { throw new ParseException("Malformed dimension string " + dimensionString); } } if (line.hasOption("I")) { imageProperties = line.getOptionProperties("I"); if (imageProperties.isEmpty()) { // used just "-I" by itself isImageOptionHelp = true; } } } public Properties getImageProperties() { return imageProperties; } public void setImageProperties(Properties imageProperties) { this.imageProperties = imageProperties; } public Options getOptions() { return options; } public void printHelp() { printHelp(options); } public void printHelp(Options options) { HelpFormatter formatter = new HelpFormatter(); System.out.println(NEW_LINE + "++++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE + "Small Molecule Similarity Detector (SMSD)" + NEW_LINE + "+++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE + "Contact: Syed Asad Rahman," + NEW_LINE + "\t EMBL-EBI, Hinxton " + NEW_LINE + "\t Cambridge CB10 1SD" + NEW_LINE + "\t United Kingdom " + NEW_LINE + "e-mail: asad@ebi.ac.uk" + NEW_LINE + "++++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE + NEW_LINE + "SMSD can calculate similarity between small molecules" + NEW_LINE + "by using an inhouse algorithm developed at EMBL-EBI. It" + NEW_LINE + "reports similarity scores and highlights the matched " + NEW_LINE + "substructure." + NEW_LINE + NEW_LINE + "It uses CDK library for handling chemistry. " + NEW_LINE + "++++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE + "Publication:" + NEW_LINE + " S.A. Rahman et.al, (2009), Journal of Cheminformatics" + NEW_LINE + " (http://www.jcheminf.com/content/1/1/12)" + NEW_LINE + "++++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE); formatter.printHelp(NEW_LINE, options); System.out.println(getExamples()); System.out.println(NEW_LINE + "++++++++++++++++++++++++++++++++++++++++++++++" + NEW_LINE); } private StringBuilder getExamples() { StringBuilder sb = new StringBuilder(); sb.append(NEW_LINE); sb.append("Usage examples: "); sb.append(NEW_LINE); sb.append("To start the GUI: java -jar SMSD.jar ").append(NEW_LINE).append(NEW_LINE); sb.append("Java Command: ").append("java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd") .append(NEW_LINE).append(NEW_LINE); sb.append("Help Command: ").append("java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd -h") .append(NEW_LINE).append(NEW_LINE); sb.append("Shell Command Line Options (recommended flags):") .append("\n -r -z -b will remove hydrogens, match rings, match bond types respectively.") .append(NEW_LINE).append(NEW_LINE); sb.append("a) Find MCS between two molecules and write the output as a MOL file:").append(NEW_LINE) .append("\tsh SMSD.sh -Q SMI -q \"CCC\" -T PDB -t ATP.pdb -O MOL -o subgraph.mol -r -z -b") .append(NEW_LINE); sb.append("b) Find MCS between two molecules and print the output:").append(NEW_LINE) .append("\tsh SMSD.sh -Q SMI -q \"CCC\" -T SMI -t \"CCN\" -O SMI -o - -r -z -b").append(NEW_LINE); sb.append("c) Find MCS between two molecules and generate an image highlighting the matched parts:") .append(NEW_LINE).append("\tsh SMSD.sh -Q MOL -q ADP.mol -T MOL -t ATP.mol -g -r -z -b") .append(NEW_LINE); sb.append("d) Find MCS between N-molecules and print the common substructure between them:") .append(NEW_LINE).append("\tsh SMSD.sh -T SDF -t arom.sdf -N -O SMI -o - -r -z -b") .append(NEW_LINE); sb.append("e) Find MCS between N-molecules and highlighting the common substructure between them:") .append(NEW_LINE); sb.append("\tWARNING: This option might require large virtual machine memory allocation").append(NEW_LINE) .append("\tsh SMSD.sh -T SDF -t arom.sdf -N -O SMI -o - -g -r -z -b").append(NEW_LINE) .append(NEW_LINE); sb.append("Note: You could use various file formats").append(NEW_LINE); return sb; } public boolean isHelp() { return helpRequested; } public void setOutputWriter(Writer writer) { outputWriter = writer; } public Writer getOutputWriter() { return outputWriter; } public boolean shouldOutputSubgraph() { return outputSubgraph; } public String getOutputFilepath() { return outputFilepath; } public String getOutputFiletype() { return outputFiletype; } public String getQueryFilepath() { return queryFilepath; } public void setQueryFilepath(String filepath) { queryFilepath = filepath; } public String getTargetFilepath() { return targetFilepath; } public void setTargetFilepath(String filepath) { targetFilepath = filepath; } /** * Use N-way MCS. * * @return True if condition meet else False */ public boolean isNMCS() { return isNMCS; } /** * Set the use of N-MCS for finding the MCS of N molecules from an SDF file. * * @param value true if N-MCS should be used */ public void setNMCS(boolean value) { isNMCS = value; } /** * @return the applyHAdding */ public boolean isApplyHAdding() { return applyHAdding; } /** * @param applyHAdding the applyHAdding to set */ public void setApplyHAdding(boolean applyHAdding) { this.applyHAdding = applyHAdding; } /** * @return the applyHRemoval */ public boolean isApplyHRemoval() { return applyHRemoval; } /** * @param applyHRemoval the applyHRemoval to set */ public void setApplyHRemoval(boolean applyHRemoval) { this.applyHRemoval = applyHRemoval; } /** * @return the applyTest */ public boolean isApplyTest() { return applyTest; } /** * @param applyTest the applyTest to set */ public void setApplyTest(boolean applyTest) { this.applyTest = applyTest; } /** * @return the applySuffix */ public boolean isApplySuffix() { return applySuffix; } /** * @param applySuffix the applySuffix to set */ public void setApplySuffix(boolean applySuffix) { this.applySuffix = applySuffix; } /** * @return the appendMode */ public boolean isAppendMode() { return appendMode; } /** * @param appendMode the appendMode to set */ public void setAppendMode(boolean appendMode) { this.appendMode = appendMode; } /** * @return the matchBondType */ public boolean isMatchBondType() { return matchBondType; } /** * @return the matchRingType */ public boolean isMatchRingType() { return matchRingType; } /** * @param matchBondType the matchBondType to set */ public void setMatchBondType(boolean matchBondType) { this.matchBondType = matchBondType; } /** * @param matchRingType the match ring size and ring atom */ public void setMatchRingType(boolean matchRingType) { this.matchRingType = matchRingType; } /** * @return the suffix */ public String getSuffix() { return suffix; } /** * @param suffix the suffix to set */ public void setSuffix(String suffix) { this.suffix = suffix; } /** * @return the chemFilter */ public int getChemFilter() { return chemFilter; } /** * @return the Target */ public String getTargetMolOutName() { return targetOutfileName; } /** * @return the Query */ public String getQueryMolOutName() { return queryOutfileName; } /** * @param name */ public void setTargetMolOutName(String name) { this.targetOutfileName = name; } /** * @param name */ public void setQueryMolOutName(String name) { this.queryOutfileName = name; } /** * @param chemFilter the chemFilter to set */ public void setChemFilter(int chemFilter) { this.chemFilter = chemFilter; } /** * @return the allMapping */ public boolean isAllMapping() { return allMapping; } /** * @param allMapping the allMapping to set */ public void setAllMapping(boolean allMapping) { this.allMapping = allMapping; } /** * @return the image */ public boolean isImage() { return image; } /** * @param image the image to set */ public void setImage(boolean image) { this.image = image; } /** * @return the substructureMode */ public boolean isSubstructureMode() { return substructureMode; } /** * @param substructureMode the substructureMode to set */ public void setSubstructureMode(boolean substructureMode) { this.substructureMode = substructureMode; } public String getQueryType() { return queryType; } public String getTargetType() { return targetType; } public void setQueryType(String queryType) { this.queryType = queryType; } public void setTargetType(String targetType) { this.targetType = targetType; } public void setOutputSubgraph(boolean value) { outputSubgraph = value; } public void setOutputFilepath(String filepath) { outputFilepath = filepath; } public void setOutputFiletype(String filetype) { outputFiletype = filetype; } public int getImageWidth() { return imageWidth; } public void setImageWidth(int imageWidth) { this.imageWidth = imageWidth; } public int getImageHeight() { return imageHeight; } public void setImageHeight(int imageHeight) { this.imageHeight = imageHeight; } public boolean isImageOptionHelp() { return isImageOptionHelp; } private void setMatchAtomType(boolean x) { this.matchAtomType = x; } /** * @return the matchAtomType */ public boolean isMatchAtomType() { return matchAtomType; } }