meshi.util
Class CommandList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Command>
              meshi.util.CommandList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Command>, java.util.Collection<Command>, java.util.List<Command>, java.util.RandomAccess, KeyWords

public class CommandList
extends java.util.ArrayList<Command>
implements KeyWords

Command File Parser.

 MESHI programs require a large number of user defined parameters (e.g. weights for the 
 energy terms). The user provide these parameters through a single command file encoded in 
 a very simple format. The CommandList class reads this file, parses it, stores the commands and 
 provide them to the other classes.
 

See Also:

Serialized Form

Field Summary

private CommandsException	commandsException
private java.lang.String	comment The file from which the comands were read.
private boolean	debug

Fields inherited from class java.util.AbstractList

modCount

Fields inherited from interface meshi.util.KeyWords

AA_SEQUENCE, ACCESIBILITY_SEQUENCE, ALINMENT_FILE_PATH, ALL_CA, ALPHA_ANGLE_ENERGY, ALPHA_TORSION_ENERGY, ANGLE_ENERGY, ANGLE_X, ANGLE_Z, ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, BEAUTIFY_PROBLEMATIC_RANGE, BFGS, BOND_ENERGY, BUFFER_SIZE, CA_CLASH_DISTANCE, CA_LONG_DISTANCE, CA_MODEL, CA_SHORT_DISTANCE, CA_TETHER_ENERGY, CALPHA_HYDROGEN_BONDS, CALPHA_HYDROGEN_BONDS_PLANE, CASP_GROUP, CG, CHECK_INTERLOOP_DISTANCE, CLASH_DISTANCE, COMPOSITE_PROPENSITY_ENERGY, CONSENSUS_ENERGY, CONSTRICT, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME, COOPERATIVE_PERATOM_SUMMA_ENERGY, COOPERATIVE_PERATOM_SUMMA_FILENAME, COOPERATIVE_PROPENSITY_ENERGY, COOPERATIVE_PROPENSITY_FILENAME, COOPERATIVE_RAMACHANDRAN_ENERGY, COOPERATIVE_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_PROPENSITY_ENERGY, COOPERATIVE_Z_PROPENSITY_FILENAME, COOPERATIVE_Z_RAMACHANDRAN_ENERGY, COOPERATIVE_Z_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_SUMMA_ENERGY, COOPERATIVE_Z_SUMMA_FILENAME, CORPUS_FILE_NAME, CSAonly_FILES_LOCATION_PATH, CUTOFF, CYLINDER_ENERGY, DICTIONARY_KEY, DIELECTRIC_CONSTANT, DISTANCE_CONSTRAINT_PCA, DISTANCE_CONSTRAINTS_ENERGY, DISTANCE_CONSTRAINTS_MASK, DISTANCE_FROM_CENTROID_ENERGY, DRESSER_FRAGMENTS, EDM_ENERGY, EDM_ENERGY_FILE_NAME, ELECTROSTATICS, END, EXCLUDED_VOL, FINAL_TEMPERATURE, FIX_C_TERMINAL, FIX_N_TERMINAL, FLAT_RAMACH_ENERGY, FREE_FINAL_MINIMIZATION, GRID_EDGE, HYDROGEN_BONDS, HYDROGEN_BONDS_ANGLES, HYDROGEN_BONDS_PAIRS, HYDROGEN_BONDS_PLANE, INFLATE_ENERGY, INITIAL_TEMPERATURE, INPUT_FILE, INTER_SEGMENT_FACTOR, INTER_SEGMENT_TOLERANCE, INTRA_SEGMENT_FACTOR, INTRA_SEGMENT_TOLERANCE, ITERATIONS_ALLATOM, ITERATIONS_BACKBONE, ITERATIONS_CA, KEY_KEY, KOEHL_FILE, LBFGS, LENNARD_JONES, LENNARD_JONES_CA, LINEAR_RG, LOOP1, LOOP2, LOOSEN_EDGE_LENGTH, MAX_ANGLE, MAX_CLASHES, MAX_DISTANCE, MAX_RUN_TIME, MAX_STEPS, MAX_WIDTH_OF_HAIRPIN, MCM, MCM_PERTURBATION, MESHILOG_KEY, METHOD, MIN_WIDTH_OF_HAIRPIN, MINIMIZATION_LOOP, MINIMIZE, MODE, MODEL, MODEL_DSSP, MODEL_NUMBER, N_ATOMS, N_TRIES, NON_FROZEN_BOND_DEPTH, NON_FROZEN_RADIUS, NONE, NUMBER, NUMBER_OF_CA_ITERATIONS, NUMBER_OF_CHAINS, NUMBER_OF_MODELS, NUMBER_OF_RUNS, OFF, ON, OPTIMIZER, OUT_OFPLANE_ENERGY, OUTPUT_FILE_NAME, OUTPUT_FILE_PATH, PARAMETERS_DIRECTORY, PDB_FILE, PLANE_ENERGY, PROPENSITY_TORSION_ENERGY, R_MAX, RAMACHANDRAN_SIDECHAIN_ENERGY, REFERENCE, RELAX, REPORT_EVERY, RESTART_EVERY, RMS_TARGET, ROTAMER_LIBRARY, SATURATION, SECONDARY_STRUCTURE, SEED, SEQUENCE, SHOTGUN_MODEL, SMOOTH_ROTAMER_LIBRARY_ENERGY, SOLVATE_ENERGY, SS_NAME, SS_SEQUENCE, STEEPEST_DECENT, STEPS, STRICT_CLASHES, STRUCTURE_NAMES, SUPERIMPOSE, SYMMETRY_ENERGY, TARGET_FILE_PATH, TARGET_NAME, TARGET_SEQUENCE, TEMPLATE_DISTANCE_CONSTRAINTS, TEMPLATE_DSSP, TEMPLATE_ENERGY, TEMPLATE_FILE_PATH, TEMPLATE_NAME, TEMPLATE_STRUCTURE, TEMPLATE_TARGET_ALIGNMENT, TETHER_ENERGY, TOLERANCE, TOPOLOGY_MAP, TWO_TORSIONS_ENERGY, UN_WARP_ENERGY, UNSATISFIED_CUTTOF, UP_TO_CUTOFF, USE_FAST_ARCCOS, VALUE_KEY, VOLUME_CONSTRAINT, WARP_ENERGY, WARP_STEP_SIZE, WARP_THRESHOLD, WEIGHT, WIDTH_OF_HAIRPIN

Constructor Summary

CommandList(CommandsException commandsException)
An empty commands List,

CommandList(java.lang.String[] args, CommandsException commandsException)
Constract a CommandList object from a file.

CommandList(java.lang.String fileName, CommandsException commandsException)

Method Summary

java.lang.String	comment()
private void	comment(java.lang.String s)
Command	firstWord(Key key) Returns the first command that start with the given keyword.
Command	firstWord(java.lang.String key) Returns the first command that start with the given keyword.
CommandList	firstWordFilter(Key key)
CommandList	firstWordFilter(java.lang.String key) Generates a list including only the commands starting with a given keyword.
double	getWeight(Key key) Gets energy term weight getWeight.
double	getWeight(java.lang.String key) Gets energy term weight getWeight.
boolean	keyExists(Key key) Testing if some key exists
boolean	keyExists(Key key, Key key2) Testing if a combined key exists
boolean	keyExists(java.lang.String key) Testing if some key is exists
boolean	keyExists(java.lang.String key, java.lang.String key2) Testing if a combined key exists
void	printCommandsLines(MeshiWriter writer)
Command	secondWord(Key key) Returns the first command that whose second word is the given keyword.
Command	secondWord(java.lang.String key) Returns the first command that whose second word is the given keyword.

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

comment

private java.lang.String comment

The file from which the comands were read. Usefull for debugging.

debug

private boolean debug

commandsException

private CommandsException commandsException

Constructor Detail

CommandList

public CommandList(CommandsException commandsException)

An empty commands List,

CommandList

public CommandList(java.lang.String[] args,
                   CommandsException commandsException)

Constract a CommandList object from a file. The rules for the command file format are: empty lines - ignored line starting with the "#" char - ignored, and used for commenting other cases - the first word in the line serves as the key word

Parameters:

args - A String array (typicaly the main parameter). The Commands file name is expected to be the first element in this array. If the array is of length zero or strats with the String "-help", the method usageMessage() of the commandsException is called.

commandsException - will take care of problems that arise during commands processing.

CommandList

public CommandList(java.lang.String fileName,
                   CommandsException commandsException)

Method Detail

comment

private void comment(java.lang.String s)

firstWordFilter

public CommandList firstWordFilter(Key key)

firstWordFilter

public CommandList firstWordFilter(java.lang.String key)

Generates a list including only the commands starting with a given keyword. Used to extract all the commands relevant to some module.

keyExists

public boolean keyExists(Key key)

Testing if some key exists

keyExists

public boolean keyExists(java.lang.String key)

Testing if some key is exists

keyExists

public boolean keyExists(Key key,
                         Key key2)

Testing if a combined key exists

keyExists

public boolean keyExists(java.lang.String key,
                         java.lang.String key2)

Testing if a combined key exists

firstWord

public Command firstWord(Key key)

Returns the first command that start with the given keyword.

firstWord

public Command firstWord(java.lang.String key)

Returns the first command that start with the given keyword.

secondWord

public Command secondWord(Key key)

Returns the first command that whose second word is the given keyword.

secondWord

public Command secondWord(java.lang.String key)

Returns the first command that whose second word is the given keyword.

getWeight

public double getWeight(Key key)

Gets energy term weight getWeight. If the following line occur in the command file: VDW weight 8.5 then getWeight("VDW") returns 8.5

getWeight

public double getWeight(java.lang.String key)

Gets energy term weight getWeight. If the following line occur in the command file: VDW weight 8.5 then getWeight("VDW") returns 8.5

comment

public java.lang.String comment()

printCommandsLines

public void printCommandsLines(MeshiWriter writer)