/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on Nov 2, 2009
 * Author: Andreas Prlic
 *
 */

package org.biojava.nbio.structure.align.ce;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.MultiThreadedDBSearch;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.*;
import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.io.PDBFileReader;

import java.beans.Introspector;
import java.io.*;
import java.lang.reflect.InvocationTargetException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;


/**
 * Base class for a new structure alignment CLI.
 *
 * <p>To add a new StructureAlignment with a CLI similar to CE or FATCAT,
 * <ol>
 * <li>Implement StructureAlignment with the main algorithm
 * <li>Implement ConfigStrucAligParams. This provides the parameters for the GUI.
 * <li>Subclass StartupParameters (can be an inner class) with the same parameters
 *     described in the ConfigStrucAligParams.
 * <li>Subclass AbstractUserArgumentProcessor, with the getStartupParams() method
 *     returning a fresh instance of the custom StartupParameters
 * <li>Implement the getParameters() method to copy values from the StartupParameters
 *     to the ConfigStrucAligParams.
 * </ol>
 *
 * <p>Note that reflection is used in a number of places, so the CLI argument names
 * must match the get/set functions in both parameter beans.
 * <ul>
 * <li>AlignmentGUI automatically takes parameter names and types from the
 *     ConfigStrucAligParams
 * <li>AbstractUserArgumentProcessor also takes parameter names and help descriptions
 *     from ConfigStrucAligParams, but it saves arguments to the StartupParameter
 *     bean.
 * </ul>
 * This means that both beans should be kept in sync.
 *
 * @author Andreas
 * @author Spencer
 *
 */
public abstract class AbstractUserArgumentProcessor implements UserArgumentProcessor {

        public static String newline = System.getProperty("line.separator");

        protected StartupParameters params ;

        public static final List<String> mandatoryArgs= new ArrayList<String>();

        protected AbstractUserArgumentProcessor(){
                params = getStartupParametersInstance();
        }

        /**
         * StartupParameters is a bean to store all the possible
         * command line parameters.
         *
         * The `StartupParameter` class contains the basic set of CLI parameters
         * common to all `StructureAligmnent`s. This method should return a subclass
         * of StartupParameters which has been extended to store values for all
         * additional parameters.
         * @return A new instance of the correct StartupParameters subclass
         */
        protected abstract StartupParameters getStartupParametersInstance();

        public abstract StructureAlignment getAlgorithm();
        public abstract Object getParameters();
        public abstract String getDbSearchLegend();

        @Override
        public void process(String[] argv){

                printAboutMe();

//              if(argv.length == 0 ) {
//                      System.out.println(printHelp());
//                      return;
//              }

                for (int i = 0 ; i < argv.length; i++){
                        String arg   = argv[i];

                        // help string
                        if(arg.equalsIgnoreCase("-h") || arg.equalsIgnoreCase("-help")
                                        || arg.equalsIgnoreCase("--help") )
                        {
                                System.out.println(printHelp());
                                return;
                        }
                        // version
                        if(arg.equalsIgnoreCase("-version") || arg.equalsIgnoreCase("--version")) {
                                StructureAlignment alg = getAlgorithm();
                                System.out.println(alg.getAlgorithmName() + " v." + alg.getVersion() );
                                return;
                        }

                        String value = null;
                        if ( i < argv.length -1)
                                value = argv[i+1];

                        // if value starts with - then the arg does not have a value.
                        if (value != null && value.startsWith("-"))
                                value = null;
                        else
                                i++;


                        String[] tmp = {arg,value};

                        //System.out.println(arg + " " + value);

                        try {

                                CliTools.configureBean(params, tmp);

                        } catch (ConfigurationException e){
                                System.err.println("Error: "+e.getLocalizedMessage());
                                System.exit(1); return;
                        }
                }

                if ( params.getPdbFilePath() != null){
                        System.setProperty(UserConfiguration.PDB_DIR,params.getPdbFilePath());
                }

                if ( params.getCacheFilePath() != null){
                        System.setProperty(UserConfiguration.PDB_CACHE_DIR,params.getCacheFilePath());
                }

                if ( params.isShowMenu()){
                        System.err.println("showing menu...");
                        try {
                                GuiWrapper.showAlignmentGUI();
                        } catch (Exception e){
                                System.err.println(e.getMessage());
                                e.printStackTrace();
                        }
                }

                if ( params.getShowDBresult() != null){
                        // user wants to view DB search results:


                        System.err.println("showing DB results...");
                        try {
                                GuiWrapper.showDBResults(params);
                        } catch (Exception e){
                                System.err.println(e.getMessage());
                                e.printStackTrace();
                        }

                }

                String pdb1  = params.getPdb1();
                String file1 = params.getFile1();


                try {
                        if (pdb1 != null || file1 != null){
                                runPairwise();
                                return;
                        }

                        if ( params.getAlignPairs() != null){
                                runDBSearch();
                                return;
                        }

                        if ( params.getSearchFile() != null){
                                runDBSearch();
                                return;
                        }
                } catch (ConfigurationException e) {
                        System.err.println(e.getLocalizedMessage());
                        System.exit(1); return;
                }

                System.out.println(printHelp());
                System.err.println("Error: insufficient arguments.");
                System.exit(1); return;
        }





        public static void printAboutMe() {
                try {
                        ResourceManager about = ResourceManager.getResourceManager("about");

                        String version = about.getString("project_version");
                        String build   = about.getString("build");

                        System.out.println("Protein Comparison Tool " + version + " " + build);
                } catch (Exception e){
                        e.printStackTrace();
                }


        }


        private void runDBSearch() throws ConfigurationException{


                String pdbFilePath = params.getPdbFilePath();

                if ( pdbFilePath == null || pdbFilePath.equals("")){

                        UserConfiguration c = new UserConfiguration();
                        pdbFilePath = c.getPdbFilePath();
                        System.err.println("You did not specify the -pdbFilePath parameter. Defaulting to "+pdbFilePath+".");
                }

                String cacheFilePath = params.getCacheFilePath();

                if ( cacheFilePath == null || cacheFilePath.equals("")){
                        cacheFilePath = pdbFilePath;

                }


                AtomCache cache = new AtomCache(pdbFilePath, pdbFilePath);

                String alignPairs = params.getAlignPairs();

                String searchFile = params.getSearchFile();

                if ( alignPairs == null || alignPairs.equals("")) {
                        if ( searchFile == null || searchFile.equals("")){
                                throw new ConfigurationException("Please specify -alignPairs or -searchFile !");
                        }
                }

                String outputFile = params.getOutFile();

                if ( outputFile == null || outputFile.equals("")){
                        throw new ConfigurationException("Please specify the mandatory argument -outFile!");
                }

                System.out.println("running DB search with parameters: " + params);

                if ( alignPairs != null && ! alignPairs.equals("")) {
                        runAlignPairs(cache, alignPairs, outputFile);
                }  else {
                        // must be a searchFile request...

                        int useNrCPUs = params.getNrCPU();

                        runDbSearch(cache,searchFile, outputFile, useNrCPUs, params);
                }
        }


        /** Do a DB search with the input file against representative PDB domains
         *
         * @param cache
         * @param searchFile
         * @param outputFile
         * @throws ConfigurationException
         */
        private void runDbSearch(AtomCache cache, String searchFile,
                        String outputFile,int useNrCPUs, StartupParameters params) throws ConfigurationException {


                System.out.println("will use " + useNrCPUs + " CPUs.");

                PDBFileReader reader = new PDBFileReader();
                Structure structure1 = null ;
                try {
                        structure1 = reader.getStructure(searchFile);
                } catch (IOException e) {
                        throw new ConfigurationException("could not parse as PDB file: " + searchFile);
                }

                File searchF = new File(searchFile);
                String name1 = "CUSTOM";



                StructureAlignment algorithm =  getAlgorithm();

                MultiThreadedDBSearch dbSearch = new MultiThreadedDBSearch(name1,
                                structure1,
                                outputFile,
                                algorithm,
                                useNrCPUs,
                                params.isDomainSplit());

                dbSearch.setCustomFile1(searchF.getAbsolutePath());

                dbSearch.run();


        }


        private void runAlignPairs(AtomCache cache, String alignPairs,
                        String outputFile) {
                try {
                        File f = new File(alignPairs);

                        BufferedReader is = new BufferedReader (new InputStreamReader(new FileInputStream(f)));

                        BufferedWriter out = new BufferedWriter(new FileWriter(outputFile, true));

                        StructureAlignment algorithm =  getAlgorithm();

                        String header = "# algorithm:" + algorithm.getAlgorithmName();
                        out.write(header);
                        out.write(newline);

                        out.write("#Legend: " + newline );
                        String legend = getDbSearchLegend();
                        out.write(legend + newline );
                        System.out.println(legend);
                        String line = null;
                        while ( (line = is.readLine()) != null){
                                if ( line.startsWith("#"))
                                        continue;

                                String[] spl = line.split(" ");

                                if ( spl.length != 2) {
                                        System.err.println("wrongly formattted line. Expected format: 4hhb.A 4hhb.B but found " + line);
                                        continue;
                                }

                                String pdb1 = spl[0];
                                String pdb2 = spl[1];


                                Structure structure1 = cache.getStructure(pdb1);
                                Structure structure2 = cache.getStructure(pdb2);

                                Atom[] ca1;
                                Atom[] ca2;


                                ca1 = StructureTools.getRepresentativeAtomArray(structure1);
                                ca2 = StructureTools.getRepresentativeAtomArray(structure2);

                                Object jparams = getParameters();

                                AFPChain afpChain;

                                afpChain = algorithm.align(ca1, ca2, jparams);
                                afpChain.setName1(pdb1);
                                afpChain.setName2(pdb2);

                                String result = getDbSearchResult(afpChain);
                                out.write(result);
                                System.out.print(result);

                                checkWriteFile(afpChain,ca1,ca2,true);
                        }

                        out.close();
                        is.close();
                } catch(Exception e){
                        e.printStackTrace();
                }
        }


        private void runPairwise() throws ConfigurationException{

                String name1 = params.getPdb1();
                String file1 = params.getFile1();

                if ( name1 == null && file1 == null){
                        throw new ConfigurationException("You did not specify the -pdb1 or -file1 parameter. Can not find query PDB id for alignment.");
                }

                if ( file1 == null) {
                        if ( name1.length() < 4) {
                                throw new ConfigurationException("-pdb1 does not look like a PDB ID. Please specify PDB code or PDB.chainName.");
                        }
                }



                String name2 = params.getPdb2();
                String file2 = params.getFile2();
                if ( name2 == null && file2 == null ){
                        throw new ConfigurationException("You did not specify the -pdb2 or -file2 parameter. Can not find target PDB id for alignment.");
                }

                if ( file2 == null ){
                        if ( name2.length() < 4) {
                                throw new ConfigurationException("-pdb2 does not look like a PDB ID. Please specify PDB code or PDB.chainName.");
                        }
                }

                // first load two example structures

                Structure structure1 = null;
                Structure structure2 = null;

                String path = params.getPdbFilePath();

                if ( file1 == null || file2 == null) {
                        if ( path == null){
                                UserConfiguration c = new UserConfiguration();
                                path = c.getPdbFilePath();
                                System.err.println("You did not specify the -pdbFilePath parameter. Defaulting to "+path+".");
                        }

                        AtomCache cache = new AtomCache(path, path);
                        if(params.isAutoFetch()) {
                                cache.setFetchBehavior(FetchBehavior.DEFAULT);
                        } else {
                                cache.setFetchBehavior(FetchBehavior.LOCAL_ONLY);
                        }
                        structure1 = getStructure(cache, name1, file1);
                        structure2 = getStructure(cache, name2, file2);
                } else {

                        structure1 = getStructure(null, name1, file1);
                        structure2 = getStructure(null, name2, file2);
                }



                if ( structure1 == null){
                        System.err.println("structure 1 is null, can't run alignment.");
                        System.exit(1); return;
                }

                if ( structure2 == null){
                        System.err.println("structure 2 is null, can't run alignment.");
                        System.exit(1); return;
                }

                if ( name1 == null) {
                        name1 = structure1.getName();
                }
                if ( name2 == null) {
                        name2 = structure2.getName();
                }

                //                   default:      new:
                // 1buz - 1ali : time: 8.3s eqr 68 rmsd 3.1 score 161 | time 6.4 eqr 58 rmsd 3.0 scre 168
                // 5pti - 1tap : time: 6.2s eqr 48 rmsd 2.67 score 164 | time 5.2 eqr 49 rmsd 2.9 score 151
                // 1cdg - 8tim
                // 1jbe - 1ord
                // 1nbw.A - 1kid
                // 1t4y - 1rp5


                try {

                        Atom[] ca1;
                        Atom[] ca2;

                        ca1 = StructureTools.getRepresentativeAtomArray(structure1);
                        ca2 = StructureTools.getRepresentativeAtomArray(structure2);

                        StructureAlignment algorithm =  getAlgorithm();
                        Object jparams = getParameters();

                        AFPChain afpChain;

                        afpChain = algorithm.align(ca1, ca2, jparams);
                        afpChain.setName1(name1);
                        afpChain.setName2(name2);

                        if ( params.isShow3d()){

                                if (! GuiWrapper.isGuiModuleInstalled()) {
                                        System.err.println("The biojava-structure-gui module is not installed. Please install!");
                                } else {

                                        try {

                                                Object jmol = GuiWrapper.display(afpChain,ca1,ca2);

                                                GuiWrapper.showAlignmentImage(afpChain, ca1,ca2,jmol);

                                        } catch (Exception e){

                                                System.err.println(e.getMessage());
                                                e.printStackTrace();
                                        }
                                        //StructureAlignmentJmol jmol = algorithm.display(afpChain,ca1,ca2,hetatms1, nucs1, hetatms2, nucs2);

                                        //String result = afpChain.toFatcat(ca1, ca2);
                                        //String rot = afpChain.toRotMat();

                                        //DisplayAFP.showAlignmentImage(afpChain, ca1,ca2,jmol);
                                }
                        }


                        checkWriteFile(afpChain,ca1, ca2, false);




                        if ( params.isPrintXML()){
                                String fatcatXML = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
                                System.out.println(fatcatXML);
                        }
                        if ( params.isPrintFatCat()) {
                                // default output is to XML on sysout...
                                System.out.println(afpChain.toFatcat(ca1, ca2));
                        }
                        if ( params. isPrintCE()){
                                System.out.println(afpChain.toCE(ca1, ca2));
                        }

                } catch (IOException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                } catch (ClassNotFoundException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                } catch (NoSuchMethodException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                } catch (InvocationTargetException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                } catch (IllegalAccessException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                } catch (StructureException e) {
                        e.printStackTrace();
                        System.exit(1); return;
                }
        }

        /** check if the result should be written to the local file system
         *
         * @param params2
         * @param afpChain
         * @param ca1
         * @param ca2
         * @throws IOException If an error occurs when writing the afpChain to XML
         * @throws ClassNotFoundException If an error occurs when invoking jmol
         * @throws NoSuchMethodException If an error occurs when invoking jmol
         * @throws InvocationTargetException If an error occurs when invoking jmol
         * @throws IllegalAccessException If an error occurs when invoking jmol
         * @throws StructureException
         */
        private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException
                        {
                String output = null;
                if ( params.isOutputPDB()){
                        if (! GuiWrapper.isGuiModuleInstalled()) {
                                System.err.println("The biojava-structure-gui module is not installed. Please install!");
                                output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
                        } else {

                                Structure tmp = AFPAlignmentDisplay.createArtificalStructure(afpChain, ca1, ca2);
                                output = "TITLE  " + afpChain.getAlgorithmName() + " " + afpChain.getVersion()  + " ";
                                output += afpChain.getName1() + " vs. " + afpChain.getName2();
                                output += newline;
                                output += tmp.toPDB();
                        }
                } else  if ( params.getOutFile() != null) {
                        // output by default is XML
                        // write the XML to a file...
                        output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);

                } else if ( params.getSaveOutputDir() != null){
                        output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
                }

                // no output requested.
                if ( output == null)
                        return;

                String fileName = null;

                if ( dbsearch ){
                        if ( params.getSaveOutputDir() != null) {

                                // we currently don't have a naming convention for how to store results for custom files
                                // they will be re-created on the fly
                                if ( afpChain.getName1().startsWith("file:") || afpChain.getName2().startsWith("file:"))
                                        return;
                                fileName = params.getSaveOutputDir();
                                fileName += getAutoFileName(afpChain);

                        } else {
                                return;
                        }

                        //
                        //else {
                        //      fileName = getAutoFileName(afpChain);
                        //}
                } else

                        if ( params.getOutFile() != null) {
                                fileName = params.getOutFile();
                        }

                if (fileName == null) {
                        System.err.println("Can't write outputfile. Either provide a filename using -outFile or set -autoOutputFile to true .");
                        System.exit(1); return;
                }
                //System.out.println("writing results to " + fileName + " " + params.getSaveOutputDir());

                FileOutputStream out; // declare a file output object
                PrintStream p; // declare a print stream object

                        // Create a new file output stream
                        out = new FileOutputStream(fileName);

                        // Connect print stream to the output stream
                        p = new PrintStream( out );

                        p.println (output);

                        p.close();



        }


        private String getAutoFileName(AFPChain afpChain){
                String fileName =afpChain.getName1()+"_" + afpChain.getName2()+"_"+afpChain.getAlgorithmName();

                if (params.isOutputPDB() )
                        fileName += ".pdb";
                else
                        fileName += ".xml";
                return fileName;
        }


        private Structure getStructure(AtomCache cache, String name1, String file)
        {

                PDBFileReader reader = new PDBFileReader();
                if ( file != null ){
                        try {
                                // check if it is a URL:
                                try {
                                        URL url = new URL(file);
                                        System.out.println(url);

                                        Structure s = reader.getStructure(url);

                                        return fixStructureName(s,file);

                                } catch ( Exception e){
                                        System.err.println(e.getMessage());
                                }
                                File f= new File(file);
                                System.out.println("file from local " + f.getAbsolutePath());
                                Structure s= reader.getStructure(f);
                                return fixStructureName(s, file);
                        } catch (Exception e){
                                System.err.println("general exception:" + e.getMessage());
                                System.err.println("unable to load structure from " + file);
                                return null;
                        }
                }
                try {
                        Structure s = cache.getStructure(name1);
                        return s;
                } catch ( Exception e){
                        System.err.println(e.getMessage());
                        System.err.println("unable to load structure from dir: " + cache.getPath() + "/"+ name1);
                        return null;
                }

        }

        /** apply a number of rules to fix the name of the structure if it did not get set during loading.
         *
         * @param s
         * @param file
         * @return
         */
        private Structure fixStructureName(Structure s, String file) {

                if ( s.getName() != null && (! s.getName().equals("")))
                        return s;

                s.setName(s.getPDBCode());

                if ( s.getName() == null || s.getName().equals("")){
                        File f = new File(file);
                        s.setName(f.getName());
                }
                return s;
        }

        public String getDbSearchResult(AFPChain afpChain){
                return afpChain.toDBSearchResult();
        }

        @Override
        public String printHelp() {
                StringBuffer buf = new StringBuffer();
                StructureAlignment alg = getAlgorithm();

                buf.append("-------------------").append(newline);
                buf.append(alg.getAlgorithmName() + " v." + alg.getVersion() + " help: " + newline);
                buf.append("-------------------").append(newline);
                buf.append(newline);

                buf.append(alg.getAlgorithmName()).append(" accepts the following parameters:").append(newline);
                buf.append(newline);

                buf.append("--- pairwise alignments ---").append(newline);
                buf.append(" two files to align can be specified by providing a path to a file, or a URL:").append(newline);
                buf.append("   -file1 the first file to align").append(newline);
                buf.append("   -file2 the second file to align").append(newline);
                buf.append(" alternatively you can specify PDB files by their PDB ids:").append(newline);
                buf.append("   -pdbFilePath  Path to the directory in your file system that contains the PDB files.").append(newline);
                buf.append("   -pdb1  PDB ID of target structure. Chain IDs are optional. In order to specify chain IDs write e.g: 5pti.A").append(newline);
                buf.append("   -pdb2  PDB ID of query structure. Chain IDs are optional. In order to specify chain IDs write e.g: 5pti.A").append(newline);
                buf.append(newline);

                buf.append("   -h / -help / --help : print this help string.").append(newline);
                buf.append("   -version: print version info").append(newline);
                buf.append("   -printXML true/false print the XML representation of the alignment on stdout.").append(newline);
                buf.append("   -printFatCat true/false print the original FATCAT output to stdout.").append(newline);
                buf.append("   -printCE true/false print the result in CE style").append(newline);
                buf.append("   -show3d print a 3D visualisation of the alignment (requires jmolapplet.jar in classpath)").append(newline);
                buf.append("   -outFile file to write the output to (default: writes XML representation).").append(newline);
                buf.append("   -outputPDB use this flag together with -outFile to dump the PDB file of the aligned structures, instead of the XML representation, instead of XML").append(newline);
                buf.append("   -autoFetch true/false if set to true PDB files will automatically get downloaded and stored in the right location. (default: false)").append(newline);
                buf.append("   -showMenu displays the menu that allows to run alignments through a user interface.").append(newline);
                buf.append(newline);

                buf.append("--- custom searches ---").append(newline);
                buf.append("   -alignPairs (mandatory) path to a file that contains a set of pairs to compair").append(newline);
                buf.append("   -outFile (mandatory) a file that will contain the summary of all the pairwise alignments").append(newline);
                buf.append(newline);

                buf.append("--- database searches ---").append(newline);
                buf.append("   -searchFile (mandatory) path to a PDB file that should be used in the search").append(newline);
                buf.append("   -outFile (mandatory) a directory that will contain the results of the DB search").append(newline);
                buf.append("   -nrCPU (optional) Number of CPUs to use for the database search. By default will use the all, but one CPU in the system.").append(newline);
                buf.append("   -pdbFilePath (mandatory) Path to the directory in your file system that contains the PDB files.").append(newline);
                buf.append("   -saveOutputDir (optional) a directory that will contain the detailed outputs of the alignments. By default will write XML files, if used together with -outputPDB, will write PDB files of the alignment.").append(newline);
                buf.append(newline);

                buf.append(" Once DB seaches are complete it is possible to view the results with:").append(newline);
                buf.append("   -showDBresult (optional) path to a DB outFile to show. Also provide the -pdbFilePath parameter to enable visualisation of results.").append(newline);
                buf.append(newline);

                ConfigStrucAligParams params = alg.getParameters();
                List<String> paramNames = params.getUserConfigParameters();
                List<String> paramHelp = params.getUserConfigHelp();

                assert(paramNames.size() == paramHelp.size());

                int size = Math.min(paramNames.size(), paramHelp.size());
                if(size > 0) {
                        Iterator<String> namesIt = paramNames.iterator();
                        Iterator<String> helpIt = paramHelp.iterator();

                        buf.append("--- ").append(alg.getAlgorithmName()).append(" parameters: ---").append(newline);
                        for(int i = 0; i< size; i++) {
                                String name = namesIt.next();
                                buf.append("   -").append(Introspector.decapitalize(name));
                                buf.append(" ").append(helpIt.next());
                                buf.append(newline);
                        }
                }
                buf.append(newline);

                buf.append(" For boolean arguments: if neither the text >true< or >false< is provided it is assumed to mean >true<. Instead of >-argument false< it is also possible to write -noArgument.").append(newline);
                buf.append(newline);

                buf.append("--- How to specify what to align ---").append(newline);
                buf.append(" If only a PDB code is provided, the whole structure will be used for the alignment.").append(newline);
                buf.append(" To specify a particular chain write as: 4hhb.A (chain IDs are case sensitive, PDB ids are not)").append(newline);
                buf.append(" To specify that the 1st chain in a structure should be used write: 4hhb:0 .").append(newline);
                buf.append(" In order to align SCOP domains, provide pdb1/pdb2 as: d4hhba_ Note: if SCOP is not installed at the -pdbFilePath, will automatically download and install.").append(newline);
                buf.append(newline);

                return buf.toString();
        }

}