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35 /*! \defgroup module_coordinateio Handling of writing new coordinate files
36 * \ingroup group_analysismodules
37 * \brief
38 * Provides basic functions to handle writing of new coordinate files.
39 *
40 * The methods included in the coordinateio module implement the basics
41 * for manipulating and writing coordinate trajectory files
42 * and changing metadata in the underlying datastructures. Included are a container for storing
43 * modules that change trajectory data, as well as a manager to write output files that uses
44 * those methods. It can be used from within \ref module_trajectoryanalysis, and uses
45 * methods from:
46 * - \ref module_options
47 * - \ref module_selection
48 *
49 * <H3>Overview</H3>
50 * The methods in coordinateio provide the infrastructure to perform operations on coordinate data files
51 * and structures during data analysis. It implements ways to change the information
52 * in coordinate data structures as well as checking that both input data and output
53 * method are matching for a given coordinate file writing operation. For this
54 * components verify first that all the requirements can be satisfied. Then
55 * components are build that will change the coordinate information accordingly.
56 *
57 * The main parts are the outputadapters implemented using the
58 * IOutputAdapter interface to change information in a local (deep) copy of t_trxframes
59 * stored in the coordinatefile.
60 *
61 * <H3>Outputadapter</H3>
62 * Each OutputAdapter module implements the same IOutputAdapter interface and
63 * has to set its requirements for final
64 * processing as a flag from the enum in requirementflags. During processing, they implement a custom
65 * version of the processFrame directive that modifies the stored trajectory data before writing
66 * a new file to disk.
67 *
68 *
69 * The interaction between the CoordinateFile and the OutputAdapter modules derived from
70 * IOutputAdapter is shown in the diagram below.
71 *
72 * \msc
73 wordwraparcs=true,
74 hscale="2";
76 analysistool,
77 builder [ label="CoordinateFileBuilder" ],
78 coordinatefile [ label="CoordinateFile" ],
79 container [ label="OutputAdapterStorage" ],
80 outputadapters [ label="OutputAdapters" ];
82 analysistool => builder [ label="Requests new coordinate output" ];
83 analysistool => builder [ label="Specifies required OutputAdapters" ];
84 builder => outputadapters [ label="Tries to construct new outputadapters" ];
85 outputadapters => builder [ label="Return or give error for wrong preconditions" ];
86 outputadapters => container [ label="Outputadapters are stored" ];
87 container => builder [ label="Gives error if storage conditions are violated" ];
88 builder => coordinatefile [ label="Constructs new manager according to specifications" ];
89 builder => container [ label="Requests storage object with registered outputadapters" ];
90 container => builder [ label="Gives ownership of stored outputadapters" ];
91 builder box builder [ label="Tests preconditions of storage object and new coordinatefile" ];
92 builder => analysistool [ label="Raise error if preconditions don't match" ];
93 builder => coordinatefile [ label="Add storage object to new coordinatefile" ];
94 coordinatefile => analysistool [ label="Returns finished coordinatefile" ];
95 builder box builder [ label="coordinatefile created, can start to work on input data" ];
97 * \endmsc
98 *
99 * Once the CoordinateFile object and its registered modules are created, they can be used to
100 * iterate over input data to write new coordinate frames.
101 *
102 * \msc
103 wordwraparcs=true,
104 hscale="2";
106 analysistool,
107 analysisloop,
108 coordinatefile [ label="CoordinateFile" ],
109 outputadapters [ label="OutputAdapters" ] ,
110 filewriting;
112 --- [ label="Setup of coordinatefile complete, analysis phase begins" ];
113 analysistool => analysisloop [ label="Starts iteration over frames" ];
114 analysisloop => coordinatefile [ label="Provides coordinates" ];
115 coordinatefile => outputadapters [ label="Provide coordinate frames for changing" ];
116 outputadapters => coordinatefile [ label="Return after changing data" ];
117 coordinatefile => filewriting [ label="Send new coordinates for writing" ];
118 filewriting => coordinatefile [ label="Continue after writing to disk" ];
119 coordinatefile => analysisloop [ label="Returns after writing" ];
120 analysisloop box analysisloop [ label="Iterates over frames" ];
121 --- [ label="Analysis complete, object is destructed and files are closed" ];
123 * \endmsc
124 *
125 *
126 *
127 * \if libapi
128 * <H3>Preparing new OutputAdapters</H3>
129 *
130 * If additional methods are needed to perform changes to the t_trxframe metadata,
131 * new OutputAdapters can be written that again implement the IOutputAdapter interface.
132 * The new method should follow the approach of the other modules that are present
133 * in changing a minimal set of t_trxframe data.
134 * \endif
135 *
136 * \author Paul Bauer <paul.bauer.q@gmail.com>
137 */
138 /*! \file
139 * \libinternal
140 * \brief
141 * Public API convenience header for coordinate file output.
142 *
143 * \author Paul Bauer <paul.bauer.q@gmail.com>
144 * \inlibraryapi
145 * \ingroup module_coordinateio
146 */
147 #ifndef GMX_COORDINATEIO_H
148 #define GMX_COORDINATEIO_H
165 #endif