Flutter生物识别插件bio_flutter的使用

特性

小部件

• 投影数据可视化器：

生物数据类

• 蛋白质
• 序列：氨基酸序列、核苷酸序列
• 蛋白质-蛋白质相互作用
• 分类学

蛋白质表示和数据分析

• 嵌入：每个序列、每个残基
• UMAP

文件处理

使用

加载和写入蛋白质fasta文件

import 'package:flutter_test/flutter_test.dart';

Future<List<Protein>> readFastaFileProtein(String pathToFile) async {
  BioFileHandlerContext<Protein>? handler = BioFileHandler<Protein>().create(pathToFile);
  Map<String, Protein> proteins = await handler.read();
  return proteins.values.toList();
}

Future<void> saveProteins(List<Protein> proteins, String pathToFile) async {
  // 在桌面/移动设备上保存文件，在web上下载
  BioFileHandlerContext<Protein>? handler = BioFileHandler<Protein>().create(pathToFile);
  await handler.write(proteins.asMap().map((_, value) => MapEntry(value.id, value)));
}

添加自定义属性到蛋白质

import 'package:flutter_test/flutter_test.dart';

Future<List<Protein>> addCustomAttributes(List<Protein> proteins, String pathToFile) async {
  BioFileHandlerContext<CustomAttributes>? handler = BioFileHandler<CustomAttributes>().create(pathToFile);
  Map<String, CustomAttributes> attributes = await handler.read();
  List<Protein> updatedProteins = [];
  for (Protein protein in proteins) {
    if (attributes.containsKey(protein.id)) {
      Protein updated = protein.updateFromCustomAttributes(attributes[protein.id]!);
      updatedProteins.add(updated);
    }
  }
  return updatedProteins;
}

创建一个带有随机坐标的UMAP可视化小部件

Widget createProjectionWidget(List<ProteinProteinInteraction> interactionData) {
  return ProjectionVisualizer(
      projectionData: ProjectionData.random(interactionData.length),
      pointIdentifierKey: "id",
      pointData: interactionData.map((interaction) => interaction.toMap()).toList()); // 也适用于蛋白质数据
}

额外信息

该包的重点在于提供的操作的正确性，以便对科学家和研究人员在研究和发展中有所帮助。我们非常感谢在GitHub上报告的每一个错误和对代码库的贡献！

当前路线图

• 提高测试覆盖率
• 改进文档
• 支持更多文件格式用于所有数据类型
• 添加三维蛋白质可视化

完整示例代码

以下是一个完整的示例代码，展示了如何使用bio_flutter插件。

import 'package:bio_flutter/bio_flutter.dart';
import 'package:flutter/material.dart';

List<Protein> sampleData() {
  Taxonomy human = const Taxonomy(id: 9606, name: "Homo sapiens", family: "Hominidae");
  Taxonomy lyssaVirus = const Taxonomy(id: 11286, name: "Lyssavirus", family: "Rhabdoviridae");
  return [
    Protein("Seq1", sequence: Sequence.buildVerifiedFromString("SEQWENCE")!, taxonomy: human),
    Protein("Seq2", sequence: Sequence.buildVerifiedFromString("PRTEIN")!, taxonomy: lyssaVirus),
    Protein("Seq3", sequence: Sequence.buildVerifiedFromString("SEQVENCEPRTEI")!, taxonomy: human),
    Protein("Seq4", sequence: Sequence.buildVerifiedFromString("SEQ")!, taxonomy: lyssaVirus),
    Protein("Seq5", sequence: Sequence.buildVerifiedFromString("PRTEINSEQWENCE")!, taxonomy: lyssaVirus)
  ];
}

void main() {
  final List<Protein> proteinExampleData = sampleData();
  runApp(BioFlutterUMAPExample(
    proteinExampleData: proteinExampleData,
  ));
}

class BioFlutterUMAPExample extends StatelessWidget {
  final List<Protein> proteinExampleData;

  const BioFlutterUMAPExample({super.key, required this.proteinExampleData});

  [@override](/user/override)
  Widget build(BuildContext context) {
    return MaterialApp(
      title: 'bio_flutter UMAP Example',
      theme: ThemeData(
        useMaterial3: false,
        primaryColor: const Color(0xFF321F5D),
        fontFamily: 'Georgia',
      ),
      home: UMAPViewerPage(proteinExampleData: proteinExampleData),
    );
  }
}

class UMAPViewerPage extends StatelessWidget {
  final List<Protein> proteinExampleData;

  const UMAPViewerPage({super.key, required this.proteinExampleData});

  [@override](/user/override)
  Widget build(BuildContext context) {
    return Center(
        child: ProjectionVisualizer2D(
      projectionData: ProjectionData.random(proteinExampleData.length, 2),
      pointData: proteinExampleData
          .map((protein) =>
              Map.fromEntries(protein.toMap().entries.map((entry) => MapEntry(entry.key, entry.value.toString()))))
          .toList(),
      pointIdentifierKey: "id",
    ));
  }
}