// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X 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 General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.potential.parsers;
  
  import ffx.potential.MolecularAssembly;
  import ffx.potential.Utilities.FileType;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.parameters.ForceField;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.io.File;
  import java.util.ArrayList;
  import java.util.HashSet;
  import java.util.List;
  import java.util.OptionalDouble;
  import java.util.Set;
  import java.util.Vector;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  import java.util.regex.Pattern;
  
  import static ffx.utilities.StringUtils.parseAtomRange;
  import static java.lang.String.format;
  
  /**
   * The SystemFilter class is the base class for most Force Field X file parsers.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public abstract class SystemFilter {
  
    protected static final Pattern lambdaPattern = Pattern.compile("Lambda: +([01]\\.\\d+)");
    private static final Logger logger = Logger.getLogger(SystemFilter.class.getName());
    private static Versioning vers = Versioning.TINKER;
    private static int absoluteCounter = 0;
    /**
     * Constant <code>dieOnMissingAtom=</code>
     */
    protected final boolean dieOnMissingAtom;
    /**
     * Standardize atom names to PDB standard by default.
     */
    protected boolean standardizeAtomNames;
    /**
     * True if atoms are to be printed to their van der Waals centers instead of nuclear centers
     * (applies primarily to hydrogen).
     */
    protected final boolean vdwH;
    /**
     * The atomList is filled by filters that extend SystemFilter.
     */
    protected List<Atom> atomList = null;
    /**
     * The bondList may be filled by the filters that extend SystemFilter.
     */
    protected List<Bond> bondList = null;
    /**
     * All MolecularAssembly instances defined. More than one MolecularAssembly should be defined for
     * PDB entries with alternate locations.
     */
    protected List<MolecularAssembly> systems = new Vector<>();
    /**
    * Append multiple files into one MolecularAssembly.
    */
   protected List<File> files;
   /**
    * The file format being handled.
    */
   protected FileType fileType = FileType.UNK;
   /**
    * Properties associated with this file.
    */
   protected CompositeConfiguration properties;
   /**
    * The molecular mechanics force field being used.
    */
   protected ForceField forceField;
   /**
    * True after the file has been read successfully.
    */
   protected boolean fileRead = false;
   /**
    * The current MolecularAssembly being populated. Note that more than one MolecularAssembly should
    * be defined for PDB files with alternate locations.
    */
   MolecularAssembly activeMolecularAssembly;
   /**
    * File currently being read.
    */
   File currentFile = null;
 
   /**
    * Initializations common to the all the constructors.
    *
    * @param forceField The force field.
    * @param properties The CompositeConfiguration properties.
    */
   private SystemFilter(ForceField forceField, CompositeConfiguration properties) {
     this.forceField = forceField;
     this.properties = properties;
     if (properties != null) {
       vdwH = properties.getBoolean("vdwHydrogens", false);
       dieOnMissingAtom = properties.getBoolean("trajectory-dieOnMissing", false);
       standardizeAtomNames = properties.getBoolean("standardizeAtomNames", true);
     } else {
       vdwH = false;
       dieOnMissingAtom = false;
       standardizeAtomNames = true;
     }
   }
 
   /**
    * Constructor for SystemFilter.
    *
    * @param files             a {@link java.util.List} object.
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    * @param forceField        a {@link ffx.potential.parameters.ForceField} object.
    * @param properties        a {@link org.apache.commons.configuration2.CompositeConfiguration}
    *                          object.
    */
   public SystemFilter(List<File> files, MolecularAssembly molecularAssembly, ForceField forceField,
                       CompositeConfiguration properties) {
     this(forceField, properties);
     this.files = files;
     if (files != null) {
       this.currentFile = files.get(0);
     }
     this.activeMolecularAssembly = molecularAssembly;
   }
 
   /**
    * Constructor for SystemFilter.
    *
    * @param file              a {@link java.io.File} object.
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    * @param forceField        a {@link ffx.potential.parameters.ForceField} object.
    * @param properties        a {@link org.apache.commons.configuration2.CompositeConfiguration}
    *                          object.
    */
   public SystemFilter(File file, MolecularAssembly molecularAssembly, ForceField forceField,
                       CompositeConfiguration properties) {
     this(forceField, properties);
     files = new ArrayList<>();
     if (file != null) {
       files.add(file);
     }
     this.currentFile = file;
     this.activeMolecularAssembly = molecularAssembly;
   }
 
   /**
    * Constructor for SystemFilter.
    *
    * @param file                a {@link java.io.File} object.
    * @param molecularAssemblies a {@link java.util.List} object.
    * @param forceField          a {@link ffx.potential.parameters.ForceField} object.
    * @param properties          a {@link org.apache.commons.configuration2.CompositeConfiguration}
    *                            object.
    */
   public SystemFilter(File file, List<MolecularAssembly> molecularAssemblies, ForceField forceField,
                       CompositeConfiguration properties) {
     this(forceField, properties);
     files = new ArrayList<>();
     if (file != null) {
       files.add(file);
     }
     this.currentFile = file;
     this.systems = new ArrayList<>(molecularAssemblies);
     this.activeMolecularAssembly = systems.get(0);
   }
 
   /**
    * previousVersion
    *
    * @param file a {@link java.io.File} object.
    * @return a {@link java.io.File} object.
    */
   public static File previousVersion(File file) {
     if (file == null) {
       return null;
     }
     String fileName = file.getAbsolutePath();
     int dot = file.getAbsolutePath().lastIndexOf(".");
     int under = file.getAbsolutePath().lastIndexOf("_");
     File newFile = file;
     if (under > dot) {
       String name = fileName.substring(0, under);
       newFile = new File(name);
     }
     File baseFile = newFile;
     File previousFile = null;
     int i = 1;
     while (newFile.exists()) {
       i = i + 1;
       previousFile = newFile;
       newFile = baseFile;
       int thousand = i / 1000;
       int hundred = (i - 1000 * thousand) / 100;
       int tens = (i - 1000 * thousand - 100 * hundred) / 10;
       int ones = i - 1000 * thousand - 100 * hundred - 10 * tens;
       StringBuilder newFileString = new StringBuilder(baseFile.getAbsolutePath());
       if (thousand != 0) {
         newFileString.append('_').append(thousand).append(hundred).append(tens).append(ones);
       } else if (hundred != 0) {
         newFileString.append('_').append(hundred).append(tens).append(ones);
       } else if (tens != 0) {
         newFileString.append('_').append(tens).append(ones);
       } else {
         newFileString.append('_').append(ones);
       }
       newFile = new File(newFileString.toString());
     }
     return previousFile;
   }
 
   /**
    * Negative: prefix a version number; Positive: postfix; Zero: TINKER-style.
    *
    * @param vers a {@link ffx.potential.parsers.SystemFilter.Versioning} object.
    */
   public static void setVersioning(Versioning vers) {
     SystemFilter.vers = vers;
   }
 
   /**
    * Use setVersioning() to choose between prefix/postfix.
    *
    * @param file a {@link java.io.File} object.
    * @return a {@link java.io.File} object.
    */
   public static File version(File file) {
     if (vers == Versioning.TINKER) {
       return versionTinker(file);
     } else {
       if (vers == Versioning.PREFIX_ABSOLUTE || vers == Versioning.POSTFIX_ABSOLUTE) {
         return versionAbsolute(file, (vers == Versioning.PREFIX_ABSOLUTE));
       } else {
         return version(file, (vers == Versioning.PREFIX));
       }
     }
   }
 
   private static File version(File file, boolean prefix) {
     if (file == null || !(file.exists())) {
       return file;
     }
     String fn = file.getAbsolutePath();
     int dot = fn.lastIndexOf(".");
     int under = fn.lastIndexOf("_");
     if (dot < 0) {
       fn += ".unk";
       dot = fn.lastIndexOf(".");
     }
     if (under < 0) {
       under = dot;
     }
     String name = (prefix) ? fn.substring(0, under) : fn.substring(0, dot);
     String extension = (prefix) ? fn.substring(dot + 1) : fn.substring(dot + 1, under);
     int number = 0;
     String newFn = (prefix) ? format("%s_%d.%s", name, number, extension)
         : format("%s.%s_%d", name, extension, number);
     if (prefix && under < dot) {
       try {
         number = Integer.parseInt(fn.substring(under + 1, dot));
       } catch (NumberFormatException ex) {
         // Then we have something like "AKA_dyn.pdb"
         name = fn.substring(0, dot);
         number++;
         newFn = format("%s_%d.%s", name, number, extension);
       }
     } else if (!prefix && under > dot) {
       try {
         number = Integer.parseInt(fn.substring(under + 1));
         number++;
       } catch (NumberFormatException ex) {
         //
       }
     }
     File newFile = new File(newFn);
     while (newFile.exists()) {
       ++number;
       newFn = (prefix) ? format("%s_%d.%s", name, number, extension)
           : format("%s.%s_%d", name, extension, number);
       newFile = new File(newFn);
     }
     return newFile;
   }
 
   private static synchronized File versionAbsolute(File file, boolean prefix) {
     if (file == null || !(file.exists())) {
       return file;
     }
     String fn = file.getAbsolutePath();
     int dot = fn.lastIndexOf(".");
     int under = fn.lastIndexOf("_");
     if (dot < 0) {
       fn += ".unk";
       dot = fn.lastIndexOf(".");
     }
     if (under < 0) {
       under = dot;
     }
     String name = (prefix) ? fn.substring(0, under) : fn.substring(0, dot);
     String extension = (prefix) ? fn.substring(dot + 1) : fn.substring(dot + 1, under);
     String newFn = (prefix) ? format("%s_%d.%s", name, absoluteCounter, extension)
         : format("%s.%s_%d", name, extension, absoluteCounter);
     File newFile = new File(newFn);
     while (newFile.exists()) {
       absoluteCounter++;
       newFn = (prefix) ? format("%s_%d.%s", name, absoluteCounter, extension)
           : format("%s.%s_%d", name, extension, absoluteCounter);
       newFile = new File(newFn);
     }
     return newFile;
   }
 
   /**
    * This follows the TINKER file versioning scheme.
    *
    * @param file File to find a version for.
    * @return File Versioned File.
    */
   private static File versionTinker(File file) {
     if (file == null) {
       return null;
     }
     if (!file.exists()) {
       return file;
     }
     String fileName = file.getAbsolutePath();
     int dot = file.getAbsolutePath().lastIndexOf(".");
     int under = file.getAbsolutePath().lastIndexOf("_");
     File newFile = file;
     if (under > dot) {
       String name = fileName.substring(0, under);
       newFile = new File(name);
     }
     File oldFile = newFile;
     int i = 1;
     while (newFile.exists()) {
       i = i + 1;
       String newFileString = format("%s_%d", oldFile.getAbsolutePath(), i);
       newFile = new File(newFileString);
     }
     return newFile;
   }
 
   /**
    * Converts a list of atom indices to an array of atoms.
    *
    * @param atomList List of atom indices.
    * @param atoms    Array of atoms.
    * @return Array of atoms.
    */
   public static Set<Atom> atomListToSet(List<Integer> atomList, Atom[] atoms) {
     Set<Atom> atomSet = new HashSet<>();
     for (int i = 0; i < atomList.size(); i++) {
       atomSet.add(atoms[atomList.get(i)]);
     }
     return atomSet;
   }
 
   /**
    * Automatically sets atom-specific flags, particularly nouse and inactive, and apply harmonic
    * restraints. Intended to be called at the end of readFile() implementations.
    *
    * <p>Supported syntax: "(\\d+)-(\\d+)"
    */
   public void applyAtomProperties() {
     /*
       What may be a more elegant implementation is to make readFile() a
       public concrete, but skeletal method, and then have readFile() call a
       protected abstract readFile method for each implementation.
     */
     Atom[] atomArray = activeMolecularAssembly.getAtomArray();
     int nAtoms = atomArray.length;
     String[] nouseKeys = properties.getStringArray("nouse");
     for (String nouseKey : nouseKeys) {
       String[] toks = nouseKey.split("\\s+");
       for (String tok : toks) {
         try {
           List<Integer> nouseRange = parseAtomRange("nouse", tok, nAtoms);
           for (int j : nouseRange) {
             atomArray[j].setUse(false);
           }
         } catch (IllegalArgumentException ex) {
           boolean atomFound = false;
           for (Atom atom : atomArray) {
             if (atom.getName().equalsIgnoreCase(tok)) {
               atomFound = true;
               atom.setUse(false);
             }
           }
           if (atomFound) {
             logger.info(format(" Setting atoms with name %s to not be used", tok));
           } else {
             logger.log(Level.INFO, ex.getLocalizedMessage());
           }
         }
       }
     }
 
     if (properties.containsKey("active")) {
       for (Atom atom : atomArray) {
         atom.setActive(false);
       }
       String[] activeKeys = properties.getStringArray("active");
       for (String inactiveKey : activeKeys) {
         try {
           List<Integer> inactiveRange = parseAtomRange("inactive", inactiveKey, nAtoms);
           for (int i : inactiveRange) {
             atomArray[i].setActive(false);
           }
         } catch (IllegalArgumentException ex) {
           logger.log(Level.INFO, ex.getLocalizedMessage());
         }
       }
     } else if (properties.containsKey("inactive")) {
       for (Atom atom : atomArray) {
         atom.setActive(true);
       }
       String[] inactiveKeys = properties.getStringArray("inactive");
       for (String inactiveKey : inactiveKeys) {
         try {
           List<Integer> inactiveRange = parseAtomRange("inactive", inactiveKey, nAtoms);
           for (int i : inactiveRange) {
             atomArray[i].setActive(false);
           }
         } catch (IllegalArgumentException ex) {
           logger.log(Level.INFO, ex.getLocalizedMessage());
         }
       }
     }
 
     String[] noElStrings = properties.getStringArray("noElectro");
     for (String noE : noElStrings) {
       String[] toks = noE.split("\\s+");
       for (String tok : toks) {
         try {
           List<Integer> noERange = parseAtomRange("noElectro", tok, nAtoms);
           for (int i : noERange) {
             atomArray[i].setElectrostatics(false);
           }
         } catch (IllegalArgumentException ex) {
           boolean atomFound = false;
           for (Atom atom : atomArray) {
             if (atom.getName().equalsIgnoreCase(tok)) {
               atomFound = true;
               atom.setElectrostatics(false);
             }
           }
           if (atomFound) {
             logger.info(format(" Disabled electrostatics for atoms with name %s", tok));
           } else {
             logger.log(Level.INFO, format(" No electrostatics input %s could not be parsed as a numerical "
                 + "range or atom type present in assembly", tok));
           }
         }
       }
     }
   }
 
   /**
    * Attempts to close any open resources associated with the underlying file; primarily to be used
    * when finished reading a trajectory.
    */
   public abstract void closeReader();
 
   public int countNumModels() {
     return -1;
   }
 
   /**
    * Returns true if the read was successful
    *
    * @return a boolean.
    */
   public boolean fileRead() {
     return fileRead;
   }
 
   /**
    * Return the MolecularSystem that has been read in
    *
    * @return a {@link ffx.potential.MolecularAssembly} object.
    */
   public MolecularAssembly getActiveMolecularSystem() {
     return activeMolecularAssembly;
   }
 
   /**
    * Getter for the field <code>atomList</code>.
    *
    * @return a {@link java.util.List} object.
    */
   public List<Atom> getAtomList() {
     return atomList;
   }
 
   /**
    * getFile
    *
    * @return a {@link java.io.File} object.
    */
   public File getFile() {
     return currentFile;
   }
 
   /**
    * setFile
    *
    * @param file a {@link java.io.File} object.
    */
   public void setFile(File file) {
     this.currentFile = file;
     files = new ArrayList<>();
     if (file != null) {
       files.add(file);
     }
   }
 
   /**
    * Getter for the field <code>files</code>.
    *
    * @return a {@link java.util.List} object.
    */
   public List<File> getFiles() {
     return files;
   }
 
   /**
    * Setter for the field <code>files</code>.
    *
    * @param files a {@link java.util.List} object.
    */
   public void setFiles(List<File> files) {
     this.files = files;
     if (files != null && !files.isEmpty()) {
       this.currentFile = files.get(0);
     } else {
       this.currentFile = null;
     }
   }
 
   /**
    * Gets the last read lambda value read by the filter, if any.
    *
    * @return Last lambda value read by this filter.
    */
   public OptionalDouble getLastReadLambda() {
     return OptionalDouble.empty();
   }
 
   /**
    * Get the MolecularAssembly array.
    *
    * @return an array of {@link ffx.potential.MolecularAssembly} objects.
    */
   public MolecularAssembly[] getMolecularAssemblyArray() {
     if (!systems.isEmpty()) {
       return systems.toArray(new MolecularAssembly[0]);
     } else {
       return new MolecularAssembly[]{activeMolecularAssembly};
     }
   }
 
   /**
    * Gets all remark lines read by the last readFile or readNext call.
    *
    * @return Array of Strings representing remark lines, if any.
    */
   public String[] getRemarkLines() {
     return new String[0];
   }
 
   /**
    * Return snapshot number.
    *
    * @return The snapshot number.
    */
   public int getSnapshot() {
     return -1;
   }
 
   /**
    * getType
    *
    * @return a {@link ffx.potential.Utilities.FileType} object.
    */
   public FileType getType() {
     return fileType;
   }
 
   /**
    * setType
    *
    * @param fileType a {@link ffx.potential.Utilities.FileType} object.
    */
   public void setType(FileType fileType) {
     this.fileType = fileType;
   }
 
   /**
    * This method is different for each subclass and must be overridden.
    *
    * @return a boolean.
    */
   public abstract boolean readFile();
 
   /**
    * Reads the next model if applicable (currently, ARC and PDB files only).
    *
    * @return If next model read.
    */
   public abstract boolean readNext();
 
   /**
    * Reads the next model if applicable (currently, ARC files only).
    *
    * @param resetPosition Resets to first frame.
    * @return If next model read.
    */
   public abstract boolean readNext(boolean resetPosition);
 
   /**
    * Reads the next model if applicable (currently, ARC files only).
    *
    * @param resetPosition Resets to first frame.
    * @param print         Flag to print.
    * @return If next model read.
    */
   public abstract boolean readNext(boolean resetPosition, boolean print);
 
   /**
    * Reads the next model if applicable (currently, ARC files only).
    *
    * @param resetPosition Resets to first frame.
    * @param print         Flag to print.
    * @param parse         Parse data in file. May want to skip structures for parallel jobs.
    * @return If next model read.
    */
   public abstract boolean readNext(boolean resetPosition, boolean print, boolean parse);
 
   /**
    * Setter for the field <code>forceField</code>.
    *
    * @param forceField a {@link ffx.potential.parameters.ForceField} object.
    */
   public void setForceField(ForceField forceField) {
     this.forceField = forceField;
   }
 
   /**
    * Setter for the field <code>properties</code>.
    *
    * @param properties a {@link org.apache.commons.configuration2.CompositeConfiguration}
    *                   object.
    */
   public void setProperties(CompositeConfiguration properties) {
     this.properties = properties;
   }
 
   /**
    * This method is different for each subclass and must be overridden.
    *
    * <p>If the append flag is true, "saveFile" will be appended to. Otherwise, the default
    * versioning
    * scheme will be applied.
    *
    * @param saveFile a {@link java.io.File} object.
    * @param append   a boolean.
    * @return a boolean.
    */
   public boolean writeFile(File saveFile, boolean append) {
     return writeFile(saveFile, append, null);
   }
 
   /**
    * This method is different for each subclass and must be overridden.
    *
    * <p>If the append flag is true, "saveFile" will be appended to. Otherwise, the default
    * versioning
    * scheme will be applied.
    *
    * @param saveFile   a {@link java.io.File} object.
    * @param append     a boolean.
    * @param extraLines Additional lines to append to a comments section, or null.
    * @return a boolean.
    */
   public abstract boolean writeFile(File saveFile, boolean append, String[] extraLines);
 
   /**
    * Setter for the field <code>fileRead</code>.
    *
    * @param fileRead a boolean.
    */
   protected void setFileRead(boolean fileRead) {
     this.fileRead = fileRead;
   }
 
   /**
    * setMolecularSystem
    *
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    */
   void setMolecularSystem(MolecularAssembly molecularAssembly) {
     activeMolecularAssembly = molecularAssembly;
   }
 
   public enum Versioning {
     TINKER, PREFIX, POSTFIX, PREFIX_ABSOLUTE, POSTFIX_ABSOLUTE, NONE
   }
 }