From b12f11af03393bcb15e2e1c6e9a2693c145583d6 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 13 Sep 2017 21:01:31 -0700
Subject: [PATCH] renamed table to category, added File and Block classes,
typed category and column objects
---
dist/molio.esm.js | 91 +++++++++++++-----
dist/molio.js | 1 -
package.json | 13 ++-
rollup.config.js | 18 ++--
src/index.d.ts | 3 +
src/index.ts | 3 +
src/reader/gro.ts | 94 +++++++++----------
src/reader/spec/gro.spec.ts | 6 +-
src/relational/block.ts | 24 +++++
src/relational/category.ts | 61 ++++++++++++
src/relational/file.ts | 10 ++
src/relational/table.ts | 36 -------
src/relational/text-block.ts | 39 ++++++++
.../{text-table.ts => text-category.ts} | 13 +--
src/relational/text-column.ts | 4 +-
src/relational/text-file.ts | 17 ++++
src/script.ts | 34 ++++---
17 files changed, 310 insertions(+), 157 deletions(-)
create mode 100644 src/relational/block.ts
create mode 100644 src/relational/category.ts
create mode 100644 src/relational/file.ts
delete mode 100644 src/relational/table.ts
create mode 100644 src/relational/text-block.ts
rename src/relational/{text-table.ts => text-category.ts} (90%)
create mode 100644 src/relational/text-file.ts
diff --git a/dist/molio.esm.js b/dist/molio.esm.js
index 913109a81..cce873658 100644
--- a/dist/molio.esm.js
+++ b/dist/molio.esm.js
@@ -72,6 +72,12 @@ function parseFloat(str, start, end) {
return neg * ret;
}
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
/**
* Eat everything until a newline occurs.
*/
@@ -150,6 +156,13 @@ function skipWhitespace(state) {
return prev;
}
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
var Tokens;
(function (Tokens) {
function resize(tokens) {
@@ -182,6 +195,12 @@ var Tokens;
Tokens.create = create;
})(Tokens || (Tokens = {}));
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
/**
* Represents a column that is not present.
*/
@@ -219,6 +238,13 @@ var ShortStringPool;
ShortStringPool.get = get;
})(ShortStringPool || (ShortStringPool = {}));
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
/**
* Represents a single column.
*/
@@ -328,10 +354,17 @@ var CifColumn = (function (TextColumn) {
return CifColumn;
}(TextColumn));
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
/**
- * Represents a table backed by a string.
+ * Represents a category backed by a string.
*/
-var TextTable = function TextTable(data, name, columns, tokens) {
+var TextCategory = function TextCategory(data, name, columns, tokens) {
this.name = name;
this.indices = tokens.indices;
this.data = data;
@@ -348,13 +381,13 @@ prototypeAccessors.columnNames.get = function () {
/**
* Get a column object that makes accessing data easier.
*/
-TextTable.prototype.getColumn = function getColumn (name) {
+TextCategory.prototype.getColumn = function getColumn (name) {
var i = this.columnIndices.get(name);
if (i !== void 0)
{ return new TextColumn(this, this.data, name, i); }
return UndefinedColumn;
};
-TextTable.prototype.initColumns = function initColumns (columns) {
+TextCategory.prototype.initColumns = function initColumns (columns) {
var this$1 = this;
this.columnIndices = new Map();
@@ -365,23 +398,23 @@ TextTable.prototype.initColumns = function initColumns (columns) {
}
};
-Object.defineProperties( TextTable.prototype, prototypeAccessors );
-var CifTable = (function (TextTable) {
- function CifTable () {
- TextTable.apply(this, arguments);
+Object.defineProperties( TextCategory.prototype, prototypeAccessors );
+var CifCategory = (function (TextCategory) {
+ function CifCategory () {
+ TextCategory.apply(this, arguments);
}
- if ( TextTable ) CifTable.__proto__ = TextTable;
- CifTable.prototype = Object.create( TextTable && TextTable.prototype );
- CifTable.prototype.constructor = CifTable;
+ if ( TextCategory ) CifCategory.__proto__ = TextCategory;
+ CifCategory.prototype = Object.create( TextCategory && TextCategory.prototype );
+ CifCategory.prototype.constructor = CifCategory;
- CifTable.prototype.getColumn = function getColumn (name) {
+ CifCategory.prototype.getColumn = function getColumn (name) {
var i = this.columnIndices.get(name);
if (i !== void 0)
{ return new CifColumn(this, this.data, name, i); }
return UndefinedColumn;
};
- CifTable.prototype.initColumns = function initColumns (columns) {
+ CifCategory.prototype.initColumns = function initColumns (columns) {
var this$1 = this;
this.columnIndices = new Map();
@@ -393,8 +426,8 @@ var CifTable = (function (TextTable) {
}
};
- return CifTable;
-}(TextTable));
+ return CifCategory;
+}(TextCategory));
/*
* Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
@@ -445,19 +478,19 @@ var GroFile = function GroFile(data) {
};
var GroBlock = function GroBlock(data) {
this.data = data;
- this.tableMap = new Map();
- this.tableList = [];
+ this.categoryMap = new Map();
+ this.categoryList = [];
};
-GroBlock.prototype.getTable = function getTable (name) {
- return this.tableMap.get(name);
+GroBlock.prototype.getCategory = function getCategory (name) {
+ return this.categoryMap.get(name);
};
/**
- * Adds a table.
+ * Adds a category.
*/
-GroBlock.prototype.addTable = function addTable (table) {
- this.tableList[this.tableList.length] = table;
- this.tableMap.set(table.name, table);
+GroBlock.prototype.addCategory = function addCategory (category) {
+ this.categoryList[this.categoryList.length] = category;
+ this.categoryMap.set(category.name, category);
};
function createTokenizer(data) {
return {
@@ -590,7 +623,7 @@ function handleAtoms(state, block) {
state.position = valueEnd;
eatLine(state);
}
- block.addTable(new TextTable(state.data, name, columns, tokens));
+ block.addCategory(new TextCategory(state.data, name, columns, tokens));
}
/**
* box vectors (free format, space separated reals), values:
@@ -626,8 +659,8 @@ function parseInternal(data) {
file.blocks.push(block);
var headerColumns = ['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ'];
var headerTokens = Tokens.create(2 * headerColumns.length);
- var header = new TextTable(state.data, 'header', headerColumns, headerTokens);
- block.addTable(header);
+ var header = new TextCategory(state.data, 'header', headerColumns, headerTokens);
+ block.addCategory(header);
handleTitleString(state, headerTokens);
handleNumberOfAtoms(state, headerTokens);
handleAtoms(state, block);
@@ -638,5 +671,11 @@ function parse(data) {
return parseInternal(data);
}
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
export { parse as groReader };
//# sourceMappingURL=molio.esm.js.map
diff --git a/dist/molio.js b/dist/molio.js
index 847442f65..e69de29bb 100644
--- a/dist/molio.js
+++ b/dist/molio.js
@@ -1 +0,0 @@
-!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?n(exports):"function"==typeof define&&define.amd?define(["exports"],n):n(t.MOLIO={})}(this,function(t){"use strict";function n(t,n,e){var i=0,r=1;for(45===t.charCodeAt(n)&&(r=-1,n++);n<e;n++){var o=t.charCodeAt(n)-48;if(o>9||o<0)return r*i|0;i=10*i+o|0}return r*i}function e(t,e,i,r){return 43===e.charCodeAt(i)&&i++,t*Math.pow(10,n(e,i,r))}function i(t,n,i){var r=1,o=0,s=0,u=1;for(45===t.charCodeAt(n)&&(r=-1,++n);n<i;){var a=t.charCodeAt(n)-48;if(!(a>=0&&a<10)){if(-2===a){for(++n;n<i;){if(!((a=t.charCodeAt(n)-48)>=0&&a<10))return 53===a||21===a?e(r*(o+s/u),t,n+1,i):r*(o+s/u);s=10*s+a,u*=10,++n}return r*(o+s/u)}if(53===a||21===a)return e(r*o,t,n+1,i);break}o=10*o+a,++n}return r*o}function r(t){for(;t.position<t.length;)switch(t.data.charCodeAt(t.position)){case 10:return t.currentTokenEnd=t.position,++t.position,void++t.currentLineNumber;case 13:return t.currentTokenEnd=t.position,++t.position,++t.currentLineNumber,void(10===t.data.charCodeAt(t.position)&&++t.position);default:++t.position}t.currentTokenEnd=t.position}function o(t){for(;t.position<t.length;)switch(t.data.charCodeAt(t.position)){case 9:case 10:case 13:case 32:return void(t.currentTokenEnd=t.position);default:++t.position}t.currentTokenEnd=t.position}function s(t){for(var n=10;t.position<t.length;){var e=t.data.charCodeAt(t.position);switch(e){case 9:case 32:n=e,++t.position;break;case 10:13!==n&&++t.currentLineNumber,n=e,++t.position;break;case 13:n=e,++t.position,++t.currentLineNumber;break;default:return n}}return n}function u(t){return{data:t,position:0,length:t.length,currentLineNumber:1,currentTokenStart:0,currentTokenEnd:0,numberOfAtoms:0,hasVelocities:!1,numberOfDecimalPlaces:3}}function a(t,n){r(t);for(var e=t.currentTokenStart,i=t.currentTokenEnd,o=t.currentTokenStart,s=e;s<i&&!d(t.data,s);)++s;if(d(t.data,s)){for(var u=s+2;s>e&&c(t.data,s-1);)--s;for(v.add(n,o,s);u<i&&32===t.data.charCodeAt(u);)++u;for(;s>u&&32===t.data.charCodeAt(s-1);)--s;v.add(n,u,i)}else v.add(n,o,s),v.add(n,s,s)}function c(t,n){var e=t.charCodeAt(n);return 32===e||44===e}function d(t,n){var e=t.charCodeAt(n);return(84===e||116===e)&&61===t.charCodeAt(n+1)}function h(t,e){s(t),t.currentTokenStart=t.position,o(t),t.numberOfAtoms=n(t.data,t.currentTokenStart,t.currentTokenEnd),v.add(e,t.currentTokenStart,t.currentTokenEnd),r(t)}function f(t,n){console.log("MOINMOIN");var e=["residueNumber","residueName","atomName","atomNumber","x","y","z"];t.hasVelocities&&e.push("vx","vy","vz");for(var i,o,s,u=[5,5,5,5,8,8,8,8,8,8],a=e.length,c=v.create(2*t.numberOfAtoms*a),d=t.position,h=0;h<t.numberOfAtoms;++h){t.currentTokenStart=t.position,o=t.currentTokenStart;for(var f=0;f<a;++f){for(s=i=o,d=o=i+u[f];s<d&&32===t.data.charCodeAt(s);)++s;for(;d>s&&32===t.data.charCodeAt(d-1);)--d;v.addUnchecked(c,s,d)}t.position=d,r(t)}n.addTable(new k(t.data,"atoms",e,c))}function p(t,n){for(var e=0;e<3;++e)s(t),t.currentTokenStart=t.position,o(t),v.add(n,t.currentTokenStart,t.currentTokenEnd)}function l(t){return w.success(t)}function m(t){var n=u(t),e=new x(t),i=new E(t);e.blocks.push(i);var r=["title","timeInPs","numberOfAtoms","boxX","boxY","boxZ"],o=v.create(2*r.length),s=new k(n.data,"header",r,o);return i.addTable(s),a(n,o),h(n,o),f(n,i),p(n,o),l(e)}var v;!function(t){function n(t){var n=new Int32Array(1.61*t.indices.length|0);n.set(t.indices),t.indices=n,t.indicesLenMinus2=n.length-2|0}t.add=function(t,e,i){t.count>t.indicesLenMinus2&&n(t),t.indices[t.count++]=e,t.indices[t.count++]=i},t.addUnchecked=function(t,n,e){t.indices[t.count++]=n,t.indices[t.count++]=e},t.create=function(t){return{indicesLenMinus2:t-2|0,count:0,indices:new Int32Array(t)}}}(v||(v={}));var g=function(){this.isDefined=!1};g.prototype.getString=function(t){return null},g.prototype.getInteger=function(t){return 0},g.prototype.getFloat=function(t){return 0},g.prototype.getValuePresence=function(t){return 1},g.prototype.areValuesEqual=function(t,n){return!0},g.prototype.stringEquals=function(t,n){return null===n};var b,y=new g;!function(t){t.create=function(){return Object.create(null)},t.get=function(t,n){if(n.length>6)return n;var e=t[n];return void 0!==e?e:(t[n]=n,n)}}(b||(b={}));var C=function(t,n,e,i){this.data=n,this.name=e,this.index=i,this.stringPool=b.create(),this.isDefined=!0,this.indices=t.indices,this.columnCount=t.columnCount};C.prototype.getString=function(t){var n=2*(t*this.columnCount+this.index);return b.get(this.stringPool,this.data.substring(this.indices[n],this.indices[n+1]))},C.prototype.getInteger=function(t){var e=2*(t*this.columnCount+this.index);return n(this.data,this.indices[e],this.indices[e+1])},C.prototype.getFloat=function(t){var n=2*(t*this.columnCount+this.index);return i(this.data,this.indices[n],this.indices[n+1])},C.prototype.stringEquals=function(t,n){var e=this,i=2*(t*this.columnCount+this.index),r=this.indices[i],o=n.length;if(o!==this.indices[i+1]-r)return!1;for(var s=0;s<o;s++)if(e.data.charCodeAt(s+r)!==n.charCodeAt(s))return!1;return!0},C.prototype.areValuesEqual=function(t,n){var e=this,i=2*(t*this.columnCount+this.index),r=2*(n*this.columnCount+this.index),o=this.indices[i],s=this.indices[r],u=this.indices[i+1]-o;if(u!==this.indices[r+1]-s)return!1;for(var a=0;a<u;a++)if(e.data.charCodeAt(a+o)!==e.data.charCodeAt(a+s))return!1;return!0},C.prototype.getValuePresence=function(t){var n=2*(t*this.columnCount+this.index);return this.indices[n]===this.indices[n+1]?1:0};var A=function(t){function n(){t.apply(this,arguments)}return t&&(n.__proto__=t),n.prototype=Object.create(t&&t.prototype),n.prototype.constructor=n,n.prototype.getString=function(n){var e=t.prototype.getString.call(this,n);return"."===e||"?"===e?null:e},n.prototype.getValuePresence=function(t){var n=2*(t*this.columnCount+this.index),e=this.indices[n];if(this.indices[n+1]-e!=1)return 0;var i=this.data.charCodeAt(e);return 46===i?1:63===i?2:0},n}(C),k=function(t,n,e,i){this.name=n,this.indices=i.indices,this.data=t,this.columnCount=e.length,this.rowCount=i.count/2/e.length|0,this.initColumns(e)},T={columnNames:{}};T.columnNames.get=function(){return this.columnNameList},k.prototype.getColumn=function(t){var n=this.columnIndices.get(t);return void 0!==n?new C(this,this.data,t,n):y},k.prototype.initColumns=function(t){var n=this;this.columnIndices=new Map,this.columnNameList=[];for(var e=0;e<t.length;e++)n.columnIndices.set(t[e],e),n.columnNameList.push(t[e])},Object.defineProperties(k.prototype,T);var w;!function(t){function n(){t.apply(this,arguments)}t&&(n.__proto__=t),n.prototype=Object.create(t&&t.prototype),n.prototype.constructor=n,n.prototype.getColumn=function(t){var n=this.columnIndices.get(t);return void 0!==n?new A(this,this.data,t,n):y},n.prototype.initColumns=function(t){var n=this;this.columnIndices=new Map,this.columnNameList=[];for(var e=0;e<t.length;e++){var i=t[e].substr(n.name.length+1);n.columnIndices.set(i,e),n.columnNameList.push(i)}}}(k);!function(t){t.error=function(t,n){return void 0===n&&(n=-1),new L(t,n)},t.success=function(t,n){return void 0===n&&(n=[]),new N(t,n)}}(w||(w={}));var L=function(t,n){this.message=t,this.line=n,this.isError=!0};L.prototype.toString=function(){return this.line>=0?"[Line "+this.line+"] "+this.message:this.message};var N=function(t,n){this.result=t,this.warnings=n,this.isError=!1},x=function(t){this.blocks=[],this.data=t},E=function(t){this.data=t,this.tableMap=new Map,this.tableList=[]};E.prototype.getTable=function(t){return this.tableMap.get(t)},E.prototype.addTable=function(t){this.tableList[this.tableList.length]=t,this.tableMap.set(t.name,t)},t.groReader=function(t){return m(t)},Object.defineProperty(t,"__esModule",{value:!0})});
diff --git a/package.json b/package.json
index 639b0d963..c1de25f15 100644
--- a/package.json
+++ b/package.json
@@ -23,19 +23,18 @@
"license": "MIT",
"devDependencies": {
"@types/jest": "latest",
- "@types/node": "^8.0.25",
- "jest": "^20.0.4",
- "rollup": "^0.49.2",
+ "@types/node": "^8.0.28",
+ "jest": "^21.1.0",
+ "rollup": "^0.49.3",
"rollup-plugin-buble": "^0.15.0",
- "rollup-plugin-commonjs": "^8.2.0",
+ "rollup-plugin-commonjs": "^8.2.1",
"rollup-plugin-json": "^2.3.0",
"rollup-plugin-node-resolve": "^3.0.0",
"rollup-watch": "^4.3.1",
- "ts-jest": "^20.0.14",
+ "ts-jest": "^21.0.0",
"tslint": "^5.7.0",
"typescript": "^2.5.1",
- "uglify-js": "^3.0.28",
- "webpack": "^3.5.5"
+ "uglify-js": "^3.1.0"
},
"dependencies": {}
}
diff --git a/rollup.config.js b/rollup.config.js
index 29e505326..577c39346 100644
--- a/rollup.config.js
+++ b/rollup.config.js
@@ -1,4 +1,4 @@
-import buble from 'rollup-plugin-buble';
+// import buble from 'rollup-plugin-buble';
import json from 'rollup-plugin-json';
import resolve from 'rollup-plugin-node-resolve';
import commonjs from 'rollup-plugin-commonjs';
@@ -16,21 +16,21 @@ export default {
}),
commonjs(),
json(),
- buble()
+ // buble()
],
output: [
{
file: "build/js/molio.dev.js",
format: 'umd',
name: 'MOLIO',
- sourcemap: true
+ sourcemap: false
},
- {
- file: "build/js/molio.esm.js",
- format: 'es',
- sourcemap: true
- }
+ // {
+ // file: "build/js/molio.esm.js",
+ // format: 'es',
+ // sourcemap: false
+ // }
],
external: external,
- sourcemap: true
+ sourcemap: false
};
\ No newline at end of file
diff --git a/src/index.d.ts b/src/index.d.ts
index f4e7f3c9a..8e857ee33 100644
--- a/src/index.d.ts
+++ b/src/index.d.ts
@@ -6,4 +6,7 @@
export { ParserResult, ParserError, ParserSuccess } from './parser'
+export { Category } from './relational/category'
+export { Column } from './relational/column'
+
export { parse as groReader } from './reader/gro'
diff --git a/src/index.ts b/src/index.ts
index cbcdecf1e..3a7b1225e 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -4,4 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
+export { Category } from './relational/category'
+export { Column } from './relational/column'
+
export { parse as groReader } from './reader/gro'
diff --git a/src/reader/gro.ts b/src/reader/gro.ts
index ede2ac342..d148f3ebc 100644
--- a/src/reader/gro.ts
+++ b/src/reader/gro.ts
@@ -9,7 +9,9 @@ import { eatLine, eatValue, skipWhitespace } from '../utils/helper'
import { Tokens } from '../utils/tokens'
import { TokenizerState } from '../utils/tokenizer-state'
-import { TextTable } from '../relational/text-table'
+import { TextFile } from '../relational/text-file'
+import { TextBlock } from '../relational/text-block'
+import { TextCategory } from '../relational/text-category'
import { ParserResult } from '../parser'
@@ -17,53 +19,40 @@ import { ParserResult } from '../parser'
* http://manual.gromacs.org/current/online/gro.html
*/
-export interface GroFile {
- data: string;
- blocks: GroBlock[];
+export const GroCategories = {
+ 'header': '',
+ 'atoms': ''
}
-export interface GroBlock {
- getTable(name: string): TextTable
- addTable(table: TextTable): void
-}
-
-export class GroFile implements GroFile {
- data: string;
- blocks: GroBlock[] = [];
+// type GroCategories = keyof typeof GroCategories
- constructor(data: string) {
- this.data = data;
- }
+export const GroAtomBasicColumns = {
+ 'residueNumber': '',
+ 'residueName': '',
+ 'atomName': '',
+ 'atomNumber': '',
+ 'x': '',
+ 'y': '',
+ 'z': ''
}
-
-export class GroBlock implements GroBlock {
- private tableMap: Map<string, TextTable>;
- private tableList: TextTable[];
-
- data: string;
-
- /**
- * Gets a table by its name.
- */
- getTable(name: string) {
- return this.tableMap.get(name);
- }
-
- /**
- * Adds a table.
- */
- addTable(table: TextTable) {
- this.tableList[this.tableList.length] = table;
- this.tableMap.set(table.name, table);
- }
-
- constructor(data: string) {
- this.data = data;
-
- this.tableMap = new Map()
- this.tableList = []
- }
+export type GroAtomBasicColumns = keyof typeof GroAtomBasicColumns
+
+export const GroAtomVelocityColumns = Object.assign({
+ 'vx': '',
+ 'vy': '',
+ 'vz': ''
+}, GroAtomBasicColumns)
+export type GroAtomVelocityColumns = keyof typeof GroAtomVelocityColumns
+
+export const GroHeaderColumns = {
+ 'title': '',
+ 'timeInPs': '',
+ 'numberOfAtoms': '',
+ 'boxX': '',
+ 'boxY': '',
+ 'boxZ': ''
}
+export type GroHeaderColumns = keyof typeof GroHeaderColumns
export interface GroState extends TokenizerState {
numberOfAtoms: number
@@ -181,7 +170,7 @@ function handleNumberOfAtoms (state: GroState, tokens: Tokens) {
* position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places)
* velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
*/
-function handleAtoms (state: GroState, block: GroBlock) {
+function handleAtoms (state: GroState, block: TextBlock) {
console.log('MOINMOIN')
const name = 'atoms'
@@ -218,7 +207,7 @@ function handleAtoms (state: GroState, block: GroBlock) {
eatLine(state)
}
- block.addTable(new TextTable(state.data, name, columns, tokens));
+ block.addCategory(new TextCategory(state.data, name, columns, tokens));
}
/**
@@ -241,27 +230,28 @@ function handleBoxVectors (state: GroState, tokens: Tokens) {
* Creates an error result.
*/
// function error(line: number, message: string) {
-// return ParserResult.error<GroFile>(message, line);
+// return ParserResult.error<TextFile>(message, line);
// }
/**
* Creates a data result.
*/
-function result(data: GroFile) {
+function result(data: TextFile) {
return ParserResult.success(data);
}
-function parseInternal(data: string): ParserResult<GroFile> {
+function parseInternal(data: string): ParserResult<TextFile> {
const state = createTokenizer(data)
- const file = new GroFile(data)
+ const file = new TextFile(data)
+ file.blocks
- let block = new GroBlock(data)
+ let block = new TextBlock(data)
file.blocks.push(block)
const headerColumns = ['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ']
const headerTokens = Tokens.create(2 * headerColumns.length)
- let header = new TextTable(state.data, 'header', headerColumns, headerTokens)
- block.addTable(header)
+ let header = new TextCategory(state.data, 'header', headerColumns, headerTokens)
+ block.addCategory(header)
handleTitleString(state, headerTokens)
handleNumberOfAtoms(state, headerTokens)
diff --git a/src/reader/spec/gro.spec.ts b/src/reader/spec/gro.spec.ts
index db611f56f..0071a447c 100644
--- a/src/reader/spec/gro.spec.ts
+++ b/src/reader/spec/gro.spec.ts
@@ -5,7 +5,7 @@
*/
import { parse } from '../gro'
-// import { Table } from '../../relational/table'
+// import { Category } from '../../relational/category'
const groString = `MD of 2 waters, t= 4.2
6
@@ -33,7 +33,7 @@ describe('gro reader', () => {
} else {
const groFile = parsed.result
- const header = groFile.blocks[0].getTable('header')
+ const header = groFile.blocks[0].getCategory('header')
if (header) {
expect(header.columnNames).toEqual(['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ'])
@@ -58,7 +58,7 @@ describe('gro reader', () => {
} else {
const groFile = parsed.result
- const header = groFile.blocks[0].getTable('header')
+ const header = groFile.blocks[0].getCategory('header')
if (header) {
expect(header.columnNames).toEqual(['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ'])
diff --git a/src/relational/block.ts b/src/relational/block.ts
new file mode 100644
index 000000000..d8c212bff
--- /dev/null
+++ b/src/relational/block.ts
@@ -0,0 +1,24 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Category, UndefinedCategory } from './category'
+
+export abstract class Block<T> {
+ abstract getCategory(name: string): T|undefined
+ abstract addCategory(category: T): void
+
+ getCategoriesFromSchema<T extends object> (schema: T) {
+ return BlockCategories(this, schema)
+ }
+}
+
+export type BlockCategories<Categories extends string> = { readonly [name in Categories]: Category }
+export function BlockCategories<T extends object>(block: Block<any> | undefined, categories: T): BlockCategories<keyof T> {
+ const ret = Object.create(null);
+ if (!block) for (const c of Object.keys(categories)) ret[c] = UndefinedCategory;
+ else for (const c of Object.keys(categories)) ret[c] = block.getCategory(c);
+ return ret;
+}
diff --git a/src/relational/category.ts b/src/relational/category.ts
new file mode 100644
index 000000000..0d387b49d
--- /dev/null
+++ b/src/relational/category.ts
@@ -0,0 +1,61 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * from https://github.com/dsehnal/CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, UndefinedColumn } from './column'
+
+/**
+ * Represents a tabular category with multiple fields represented as columns.
+ *
+ * Example:
+ * _category.field1
+ * _category.field2
+ * ...
+ */
+export abstract class Category {
+ name: string;
+ rowCount: number;
+ columnCount: number;
+ columnNames: string[];
+
+ /**
+ * If a field with the given name is not present, returns UndefinedColumn.
+ *
+ * Columns are accessed by their field name only, i.e.
+ * _category.field is accessed by
+ * category.getColumn('field')
+ *
+ * Note that columns are created on demand and there is some computational
+ * cost when creating a new column. Therefore, if you need to reuse a column,
+ * it is a good idea to cache it.
+ */
+ abstract getColumn(name: string): Column;
+
+ getColumnsFromSchema<T extends object> (schema: T) {
+ return CategoryColumns(this, schema)
+ }
+}
+
+/**
+ * Represents a category that is not present.
+ */
+class _UndefinedCategory extends Category { // tslint:disable-line:class-name
+ name: ''
+ rowCount = 0
+ columnCount = 0
+ columnNames = []
+ getColumn(name: string) { return UndefinedColumn }
+}
+export const UndefinedCategory = new _UndefinedCategory() as Category;
+
+
+export type CategoryColumns<Columns extends string> = { readonly [name in Columns]: Column }
+export function CategoryColumns<T extends object>(category: Category | undefined, columns: T): CategoryColumns<keyof T> {
+ const ret = Object.create(null);
+ if (!category) for (const c of Object.keys(columns)) ret[c] = UndefinedColumn;
+ else for (const c of Object.keys(columns)) ret[c] = category.getColumn(c);
+ return ret;
+}
diff --git a/src/relational/file.ts b/src/relational/file.ts
new file mode 100644
index 000000000..80bf53205
--- /dev/null
+++ b/src/relational/file.ts
@@ -0,0 +1,10 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export interface File<T> {
+ blocks: T[];
+}
+
diff --git a/src/relational/table.ts b/src/relational/table.ts
deleted file mode 100644
index ebf6f88f7..000000000
--- a/src/relational/table.ts
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { Column } from './column'
-
-/**
- * Represents that CIF category with multiple fields represented as columns.
- *
- * Example:
- * _category.field1
- * _category.field2
- * ...
- */
-export interface Table {
- name: string;
- rowCount: number;
- columnCount: number;
- columnNames: string[];
-
- /**
- * If a field with the given name is not present, returns UndefinedColumn.
- *
- * Columns are accessed by their field name only, i.e.
- * _category.field is accessed by
- * category.getColumn('field')
- *
- * Note that columns are created on demand and there is some computational
- * cost when creating a new column. Therefore, if you need to reuse a column,
- * it is a good idea to cache it.
- */
- getColumn(name: string): Column;
-}
diff --git a/src/relational/text-block.ts b/src/relational/text-block.ts
new file mode 100644
index 000000000..c4ef35b76
--- /dev/null
+++ b/src/relational/text-block.ts
@@ -0,0 +1,39 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Block } from './block'
+import { TextCategory } from './text-category'
+
+export class TextBlock extends Block<TextCategory> {
+ private categoryMap: Map<string, TextCategory>;
+ private categoryList: TextCategory[];
+
+ data: string;
+
+ /**
+ * Gets a category by its name.
+ */
+ getCategory(name: string) {
+ return this.categoryMap.get(name);
+ }
+
+ /**
+ * Adds a category.
+ */
+ addCategory(category: TextCategory) {
+ this.categoryList[this.categoryList.length] = category;
+ this.categoryMap.set(category.name, category);
+ }
+
+ constructor(data: string) {
+ super()
+
+ this.data = data;
+
+ this.categoryMap = new Map()
+ this.categoryList = []
+ }
+}
\ No newline at end of file
diff --git a/src/relational/text-table.ts b/src/relational/text-category.ts
similarity index 90%
rename from src/relational/text-table.ts
rename to src/relational/text-category.ts
index c4ca29a8c..f550213df 100644
--- a/src/relational/text-table.ts
+++ b/src/relational/text-category.ts
@@ -6,16 +6,16 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Table } from './table'
+import { Category } from './category'
import { UndefinedColumn } from './column'
import { TextColumn, CifColumn } from './text-column'
import { Tokens } from '../utils/tokens'
/**
- * Represents a table backed by a string.
+ * Represents a category backed by a string.
*/
-export class TextTable implements Table {
+export class TextCategory extends Category {
protected data: string;
protected columnNameList: string[];
protected columnIndices: Map<string, number>;
@@ -66,8 +66,9 @@ export class TextTable implements Table {
}
}
- constructor(
- data: string, name: string, columns: string[], tokens: Tokens) {
+ constructor(data: string, name: string, columns: string[], tokens: Tokens) {
+ super()
+
this.name = name;
this.indices = tokens.indices;
this.data = data;
@@ -79,7 +80,7 @@ export class TextTable implements Table {
}
}
-export class CifTable extends TextTable {
+export class CifCategory extends TextCategory {
getColumn(name: string): CifColumn {
let i = this.columnIndices.get(name);
if (i !== void 0) return new CifColumn(this, this.data, name, i);
diff --git a/src/relational/text-column.ts b/src/relational/text-column.ts
index d6cb87c79..7c04c09d6 100644
--- a/src/relational/text-column.ts
+++ b/src/relational/text-column.ts
@@ -8,7 +8,7 @@
import { Column } from './column'
import { ValuePresence } from './constants'
-import { TextTable } from './text-table'
+import { TextCategory } from './text-category'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../utils/number-parser'
import { ShortStringPool } from '../utils/short-string-pool'
@@ -89,7 +89,7 @@ export class TextColumn implements Column {
return ValuePresence.Present
}
- constructor(table: TextTable, protected data: string, public name: string, public index: number) {
+ constructor(table: TextCategory, protected data: string, public name: string, public index: number) {
this.indices = table.indices;
this.columnCount = table.columnCount;
}
diff --git a/src/relational/text-file.ts b/src/relational/text-file.ts
new file mode 100644
index 000000000..6058531cc
--- /dev/null
+++ b/src/relational/text-file.ts
@@ -0,0 +1,17 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { File } from './file'
+import { TextBlock } from './text-block'
+
+export class TextFile implements File<TextBlock> {
+ data: string;
+ blocks: TextBlock[] = [];
+
+ constructor(data: string) {
+ this.data = data;
+ }
+}
diff --git a/src/script.ts b/src/script.ts
index d5520faea..013e07921 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -7,17 +7,17 @@
// import * as util from 'util'
import * as fs from 'fs'
-import { parse } from './reader/gro'
-import { Table } from './relational/table'
+import { parse, GroCategories, GroAtomBasicColumns } from './reader/gro'
+import { Category } from './relational/category'
const file = '1crn.gro'
// const file = 'water.gro'
// const file = 'test.gro'
// const file = 'md_1u19_trj.gro'
-function getFloatArray(table: Table, name: string) {
- const column = table.getColumn(name)
- const n = table.rowCount
+function getFloatArray(category: Category, name: string) {
+ const column = category.getColumn(name)
+ const n = category.rowCount
const array = new Float32Array(n)
for (let i = 0; i < n; ++i) {
array[i] = column.getFloat(i)
@@ -25,9 +25,9 @@ function getFloatArray(table: Table, name: string) {
return array
}
-function getIntArray(table: Table, name: string) {
- const column = table.getColumn(name)
- const n = table.rowCount
+function getIntArray(category: Category, name: string) {
+ const column = category.getColumn(name)
+ const n = category.rowCount
const array = new Int32Array(n)
for (let i = 0; i < n; ++i) {
array[i] = column.getInteger(i)
@@ -48,8 +48,10 @@ fs.readFile(`./examples/${file}`, 'utf8', function (err,data) {
console.log(parsed)
} else {
const groFile = parsed.result
+ const categories = groFile.blocks[0].getCategoriesFromSchema(GroCategories)
- const header = groFile.blocks[0].getTable('header')
+ // const header = groFile.blocks[0].getCategory('header')
+ const header = categories.header
if (header) {
console.log(header.columnNames)
@@ -63,15 +65,17 @@ fs.readFile(`./examples/${file}`, 'utf8', function (err,data) {
console.error('no header')
}
- const atoms = groFile.blocks[0].getTable('atoms')
+ const atoms = categories.atoms
if (atoms) {
console.log(atoms.columnNames)
- console.log(`'${atoms.getColumn('residueNumber').getString(1)}'`)
- console.log(`'${atoms.getColumn('residueName').getString(1)}'`)
- console.log(`'${atoms.getColumn('atomName').getString(1)}'`)
- console.log(atoms.getColumn('z').getFloat(1))
- console.log(`'${atoms.getColumn('z').getString(1)}'`)
+ const columns = atoms.getColumnsFromSchema(GroAtomBasicColumns)
+
+ console.log(`'${columns.residueNumber.getString(1)}'`)
+ console.log(`'${columns.residueName.getString(1)}'`)
+ console.log(`'${columns.atomName.getString(1)}'`)
+ console.log(columns.z.getFloat(1))
+ console.log(`'${columns.z.getString(1)}'`)
const n = atoms.rowCount
console.log('rowCount', n)
--
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