From 8b1552d344a1ce42a36e8db66a98c8d9a8c2f9f9 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 3 Oct 2017 14:39:44 +0200
Subject: [PATCH] Added stringEquals to column
---
src/reader/cif/{binary-field.ts => binary/field.ts} | 0
src/reader/cif/{binary-parser.ts => binary/parser.ts} | 0
src/reader/cif/index.ts | 7 +++++--
src/reader/cif/schema.ts | 1 +
src/reader/cif/{text-field.ts => text/field.ts} | 10 +++++-----
src/reader/cif/{text-parser.ts => text/parser.ts} | 8 ++++----
src/reader/common/column.ts | 4 +++-
src/reader/common/text/column/fixed.ts | 1 +
src/reader/common/text/column/token.ts | 10 ++++++++++
src/reader/spec/cif.spec.ts | 2 +-
src/script.ts | 2 +-
11 files changed, 31 insertions(+), 14 deletions(-)
rename src/reader/cif/{binary-field.ts => binary/field.ts} (100%)
rename src/reader/cif/{binary-parser.ts => binary/parser.ts} (100%)
rename src/reader/cif/{text-field.ts => text/field.ts} (89%)
rename src/reader/cif/{text-parser.ts => text/parser.ts} (99%)
diff --git a/src/reader/cif/binary-field.ts b/src/reader/cif/binary/field.ts
similarity index 100%
rename from src/reader/cif/binary-field.ts
rename to src/reader/cif/binary/field.ts
diff --git a/src/reader/cif/binary-parser.ts b/src/reader/cif/binary/parser.ts
similarity index 100%
rename from src/reader/cif/binary-parser.ts
rename to src/reader/cif/binary/parser.ts
diff --git a/src/reader/cif/index.ts b/src/reader/cif/index.ts
index c7ba6c3d5..c3882b9e8 100644
--- a/src/reader/cif/index.ts
+++ b/src/reader/cif/index.ts
@@ -4,12 +4,15 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import parseText from './text-parser'
+import parseText from './text/parser'
+import { Block } from './data-model'
import { apply as applySchema } from './schema'
import mmCIF from './schema/mmcif'
export default {
parseText,
applySchema,
- schema: { mmCIF }
+ schema: {
+ mmCIF: (block: Block) => applySchema(mmCIF, block)
+ }
}
\ No newline at end of file
diff --git a/src/reader/cif/schema.ts b/src/reader/cif/schema.ts
index aea1576e9..f6c058f58 100644
--- a/src/reader/cif/schema.ts
+++ b/src/reader/cif/schema.ts
@@ -71,6 +71,7 @@ export namespace Field {
rowCount: field.rowCount,
value,
isValueDefined: row => presence(row) === Data.ValuePresence.Present,
+ stringEquals: field.stringEquals,
areValuesEqual: field.areValuesEqual,
toArray
};
diff --git a/src/reader/cif/text-field.ts b/src/reader/cif/text/field.ts
similarity index 89%
rename from src/reader/cif/text-field.ts
rename to src/reader/cif/text/field.ts
index c67cc8cf7..7f0951fb1 100644
--- a/src/reader/cif/text-field.ts
+++ b/src/reader/cif/text/field.ts
@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as Column from '../common/column'
-import * as TokenColumn from '../common/text/column/token'
-import { Tokens } from '../common/text/tokenizer'
-import * as Data from './data-model'
-import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../common/text/number-parser'
+import * as Column from '../../common/column'
+import * as TokenColumn from '../../common/text/column/token'
+import { Tokens } from '../../common/text/tokenizer'
+import * as Data from '../data-model'
+import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../../common/text/number-parser'
export default function CifTextField(tokens: Tokens, rowCount: number): Data.Field {
const { data, indices } = tokens;
diff --git a/src/reader/cif/text-parser.ts b/src/reader/cif/text/parser.ts
similarity index 99%
rename from src/reader/cif/text-parser.ts
rename to src/reader/cif/text/parser.ts
index 4e37ddb56..606fc02f7 100644
--- a/src/reader/cif/text-parser.ts
+++ b/src/reader/cif/text/parser.ts
@@ -22,10 +22,10 @@
*
*/
-import * as Data from './data-model'
-import Field from './text-field'
-import { Tokens, TokenBuilder } from '../common/text/tokenizer'
-import Result from '../result'
+import * as Data from '../data-model'
+import Field from './field'
+import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
+import Result from '../../result'
/**
* Types of supported mmCIF tokens.
diff --git a/src/reader/common/column.ts b/src/reader/common/column.ts
index 1c27a911e..5f9fb03cd 100644
--- a/src/reader/common/column.ts
+++ b/src/reader/common/column.ts
@@ -27,6 +27,7 @@ export interface Column<T> {
value(row: number): T,
isValueDefined(row: number): boolean,
toArray(params?: ToArrayParams): ReadonlyArray<T>,
+ stringEquals(row: number, value: string): boolean,
areValuesEqual(rowA: number, rowB: number): boolean
}
@@ -42,7 +43,8 @@ export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T)
for (let i = 0, _i = array.length; i < _i; i++) array[i] = value(0)
return array;
},
- areValuesEqual() { return true; }
+ stringEquals(row, value) { return !value; },
+ areValuesEqual(rowA, rowB) { return true; }
}
}
diff --git a/src/reader/common/text/column/fixed.ts b/src/reader/common/text/column/fixed.ts
index 7caf97e35..84a0f561c 100644
--- a/src/reader/common/text/column/fixed.ts
+++ b/src/reader/common/text/column/fixed.ts
@@ -47,6 +47,7 @@ export function FixedColumn<T extends ColumnType>(lines: Tokens, offset: number,
value,
isValueDefined(row) { return true; },
toArray(params) { return createAndFillArray(rowCount, value, params); },
+ stringEquals(row, v) { return value(row) === v; },
areValuesEqual(rowA, rowB) {
return value(rowA) === value(rowB);
}
diff --git a/src/reader/common/text/column/token.ts b/src/reader/common/text/column/token.ts
index c78ccc794..0c5bb682f 100644
--- a/src/reader/common/text/column/token.ts
+++ b/src/reader/common/text/column/token.ts
@@ -35,6 +35,16 @@ export function TokenColumn<T extends ColumnType>(tokens: Tokens, type: T): Colu
value,
isValueDefined(row) { return true; },
toArray(params) { return createAndFillArray(rowCount, value, params); },
+ stringEquals(row, v) {
+ const s = indices[2 * row];
+ const value = v || '';
+ const len = value.length;
+ if (len !== indices[2 * row + 1] - s) return false;
+ for (let i = 0; i < len; i++) {
+ if (data.charCodeAt(i + s) !== value.charCodeAt(i)) return false;
+ }
+ return true;
+ },
areValuesEqual: areValuesEqualProvider(tokens)
};
}
diff --git a/src/reader/spec/cif.spec.ts b/src/reader/spec/cif.spec.ts
index 8a9cf8277..6e3824bd8 100644
--- a/src/reader/spec/cif.spec.ts
+++ b/src/reader/spec/cif.spec.ts
@@ -5,7 +5,7 @@
*/
import * as Data from '../cif/data-model'
-import TextField from '../cif/text-field'
+import TextField from '../cif/text/field'
import * as Schema from '../cif/schema'
const columnData = `123abc`;
diff --git a/src/script.ts b/src/script.ts
index 06615a362..0ac94deb9 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -94,7 +94,7 @@ export function _cif() {
console.log(atom_site.getField('Cartn_x')!.float(0));
//console.log(atom_site.getField('label_atom_id')!.toStringArray());
- const mmcif = CIF.applySchema(CIF.schema.mmCIF, data);
+ const mmcif = CIF.schema.mmCIF(data);
console.log(mmcif.atom_site.Cartn_x.value(0));
console.log(mmcif.entity.type.toArray());
console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
--
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