cleanup, removed unused files

src/mol-io/reader/ply/parse_data/data-model.ts

@@ -1,6 +1,7 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
+ * @author Schäfer, Marco <marco.schaefer@uni-tuebingen.de>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
@@ -27,17 +28,11 @@ export interface ply_form {
     readonly vertices: number[],
     readonly colors: number[],
     readonly normals: number[],
-    readonly  faces: number[],
+    readonly faces: number[],
 }
 
 export function PlyStructure(vertexCount: number, faceCount: number, propertyCount: number, initialHead: string[], propertyNames: string[],  properties: number[],  vertices: number[],  colors: number[],  normals: number[], faces: number[]): ply_form {
     return {vertexCount, faceCount, propertyCount, initialHead: [...initialHead], propertyNames: [...propertyNames], properties: [...properties], vertices: [...vertices], colors: [...colors], normals: [...normals], faces: [...faces]};
 }
 
-export type PlyColumns = { [name: string]: PlyColumn }
-
-// export namespace CsvTable {
-//     export function empty(name: string): Table {
-//         return { rowCount: 0, name, fieldNames: [], getColumn(name: string) { return void 0; } };
-//     };
-// }
+export type PlyColumns = { [name: string]: PlyColumn }

src/mol-io/reader/ply/read_data/data-source.ts

@@ -1,58 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- *
- * Adapted from LiteMol
- */
-
-import { Task, RuntimeContext } from 'mol-task';
-
-export function readFromFile(file: File) {
-    return <Task<number | string>>readFromFileInternal(file);
-}
-
-
-async function processFile(ctx: RuntimeContext, e: any) {
-    const data = (e.target as FileReader).result;
-    return  data as string;
-}
-
-function readData(ctx: RuntimeContext, action: string, data: XMLHttpRequest | FileReader): Promise<any> {
-    return new Promise<any>((resolve, reject) => {
-        data.onerror = (e: any) => {
-            const error = (<FileReader>e.target).error;
-            reject(error ? error : 'Failed.');
-        };
-
-        data.onabort = () => reject(Task.Aborted(''));
-
-        data.onprogress = (e: ProgressEvent) => {
-            if (e.lengthComputable) {
-                ctx.update({ message: action, isIndeterminate: false, current: e.loaded, max: e.total });
-            } else {
-                ctx.update({ message: `${action} ${(e.loaded / 1024 / 1024).toFixed(2)} MB`, isIndeterminate: true });
-            }
-        }
-        data.onload = (e: any) => resolve(e);
-    });
-}
-
-function readFromFileInternal(file: File): Task<string | number> {
-    let reader: FileReader | undefined = void 0;
-    return Task.create('Read File', async ctx => {
-        try {
-            reader = new FileReader();
-            reader.readAsBinaryString(file);
-
-            ctx.update({ message: 'Opening file...', canAbort: true });
-            const e = await readData(ctx, 'Reading...', reader);
-            const result = processFile(ctx, e);
-            return result;
-        } finally {
-            reader = void 0;
-        }
-    }, () => {
-        if (reader) reader.abort();
-    });
-}

src/mol-io/reader/ply/read_data/data.ts

@@ -1,60 +0,0 @@
-// /**
-//  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-//  *
-//  * @author David Sehnal <david.sehnal@gmail.com>
-//  */
-
-// import { PluginStateTransform } from '../../../../mol-plugin/state/objects';
-// import { PluginStateObject as SO } from '../../../../mol-plugin/state/objects';
-// import { Task } from 'mol-task';
-// import PLY from 'mol-io/reader/ply/parse_data/ply_parser'
-// import { ParamDefinition as PD } from 'mol-util/param-definition';
-// import { Transformer } from 'mol-state';
-// import { readFromFile } from './data-source';
-
-// export { ReadFile_ascii }
-// type ReadFile_ascii = typeof ReadFile_ascii
-// const ReadFile_ascii = PluginStateTransform.BuiltIn({
-//     name: 'ReadFile_ascii',
-//     display: { name: 'ReadFile_ascii', description: 'Read string data from the specified file' },
-//     from: SO.Root,
-//     to: [SO.Data.String],
-//     params: {
-//         file: PD.File(),
-//         label: PD.Optional(PD.Text('')),
-//         isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)' }))
-//     }
-// })({
-//     apply({ params: p }) {
-//         return Task.create('Open File', async ctx => {
-//             const data = await readFromFile(p.file).runInContext(ctx);
-//             return  new SO.Data.String(data as string, { label: p.label ? p.label : p.file.name });
-//         });
-//     },
-//     update({ oldParams, newParams, b }) {
-//         if (oldParams.label !== newParams.label) {
-//             (b.label as string) = newParams.label || oldParams.file.name;
-//             return Transformer.UpdateResult.Updated;
-//         }
-//         return Transformer.UpdateResult.Unchanged;
-//     },
-//     isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user loaded files.' })
-// });
-
-
-// export { ParsePLY }
-// type ParsePLY = typeof ParsePLY
-// const ParsePLY = PluginStateTransform.BuiltIn({
-//     name: 'parse-ply',
-//     display: { name: 'Parse PLY', description: 'Parse PLY from String' },
-//     from: [SO.Data.String],
-//     to: SO.Format.Ply
-// })({
-//     apply({ a }) {
-//         return Task.create('Parse PLY', async ctx => {
-//             const parsed = await (PLY(a.data).runInContext(ctx));
-//             if (parsed.isError) throw new Error(parsed.message);
-//             return new SO.Format.Ply(parsed.result);
-//         });
-//     }
-// });

src/mol-model/shape/formarts/ply/plyData_to_shape.ts

@@ -1,3 +1,10 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Schäfer, Marco <marco.schaefer@uni-tuebingen.de>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
 import {ply_form, PlyFile} from '../../../../mol-io/reader/ply/parse_data/data-model';
 import {RuntimeContext, Task} from 'mol-task';
 import {Mesh} from '../../../../mol-geo/geometry/mesh/mesh';
@@ -13,7 +20,6 @@ export interface MyData {
     faces: number[],
     colors: Color[],
     labels: string[],
-    transforms: number[]
 }
 
 function collectData_for_Shape(parsedData: ply_form): MyData {
@@ -26,13 +32,12 @@ function collectData_for_Shape(parsedData: ply_form): MyData {
         faces: faces,
         colors: [],
         labels: [],
-        transforms: []
     }
 
     for (let i = 0; i<parsedData.faceCount; i++) {
         data.colors[i] = Color.fromRgb(colors[faces[4*i+1]*3+0], colors[faces[4*i+1]*3+1], colors[faces[4*i+1]*3+2]);
         data.labels[i] = parsedData.properties[parsedData.propertyCount * faces[4*i+1] + 10].toString();
-            //i.toString();
+        // i.toString();
         // data.transforms[i] = 0;
     }
     console.log('data', data);
@@ -55,8 +60,8 @@ async function getSphereMesh(ctx: RuntimeContext, centers: number[], normals: nu
         triangle_normals = [ normals[faces[4*i+1]*3], normals[faces[4*i+1]*3+1], normals[faces[4*i+1]*3+2],
                              normals[faces[4*i+2]*3], normals[faces[4*i+2]*3+1], normals[faces[4*i+2]*3+2],
                              normals[faces[4*i+3]*3], normals[faces[4*i+3]*3+1], normals[faces[4*i+3]*3+2]];
-        triangle_indices = [0,1,2];
-        //console.log(triangle_vertices)
+        triangle_indices = [0, 1, 2];
+        // console.log(triangle_vertices)
         addTriangle(builderState, triangle_vertices, triangle_normals, triangle_indices)
     }
     let a = MeshBuilder.getMesh(builderState);