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Built with Vite.","homepage":"https://rcsb.github.io/rcsb-saguaro","keywords":["1D","sequence","annotations","gene","protein"],"repository":{"type":"git","url":"git://github.com/rcsb/rcsb-saguaro.git"},"bugs":{"url":"https://github.com/rcsb/rcsb-saguaro/issues"},"license":"MIT","readme":"# rcsb-saguaro\n\nRCSB Saguaro 1D Feature Viewer is an open-source TypeScript library used to display protein and genomic sequence annotations over the web.\nThe project is developed and maintained at [RCSB PDB](https://rcsb.org) and it is currently used to display protein features on its web site.\nThe package offers multiple types of data displays and a rich set of options to customize feature visualization.\n\nWhen using rcsb-saguaro, please cite:\n\nJoan Segura, Yana Rose, John Westbrook, Stephen K Burley, Jose M Duarte.\nRCSB Protein Data Bank 1D tools and services, Bioinformatics, 2020; https://doi.org/10.1093/bioinformatics/btaa1012\n\n<!---\n<div id=\"pfvSelect\" ></div>\n<div id=\"pfv\" ></div>\n<script type=\"text/javascript\" src=\"https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app/build/dist/app.js\" type=\"text/javascript\"></script>\n<script type=\"text/javascript\">\nRcsbFvWebApp.buildInstanceSequenceFv(\"pfv\", \"pfvSelect\",\"6M17\", {}, {\n    boardConfig:{\n        trackWidth:540,\n        rowTitleWidth:170\n    }\n});\n</script>\n--->\n\n### Node Module Installation\n\n`npm install @rcsb/rcsb-saguaro`\n\n### Testing\n\nDifferent testing example are available in the `src/examples` folder\n\n- `git clone git@github.com:rcsb/rcsb-saguaro.git`\n- `cd rcsb-saguaro`\n- `npm install`\n- `npm run devServer`\n\nGo to:\n\n- `http://localhost:9000/MultipleTracks.html`\n- `http://localhost:9000/MultipleAlignment.html`\n\n### CDN JavaScript\n\n`<script src=\"https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro@3.0.3/build/rcsb-saguaro.min.js\" type=\"text/javascript\"></script>`\n\n### Library Documentation\n\nTypeScript full classes documentation can be found [here](https://rcsb.github.io/rcsb-saguaro/index.html).\n\n### Main Classes and Interfaces\n\nThese are the most important elements if you are only interested in using RCSB Saguaro to visualise protein annotations\n\n- [RcsbFv](https://rcsb.github.io/rcsb-saguaro/classes/RcsbFv_RcsbFv.RcsbFv.html):\n  Main feature viewer class that can be used to create, configure and render a feature viewer object. It includes different methods to\n  change viewer configuration, add new tracks, replace or update track data or change track visibility\n- [RcsbFvBoardConfigInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbFv_RcsbFvConfig_RcsbFvConfigInterface.RcsbFvBoardConfigInterface.html):\n  Feature viewer configuration interface that defines the different properties to configure the feature viewer main panel\n  including track title and annotation cells width, activate tooltips flag and annotation click and hovering callbacks\n- [RcsbFvRowConfigInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbFv_RcsbFvConfig_RcsbFvConfigInterface.RcsbFvRowExtendedConfigInterface.html):\n  This interface can be used to set up the configuration for feature viewer tracks. It includes multiple properties that define how track features\n  are displayed (color, shape, overlap flag) and also different track attributes (background color, track height, track title, track visibility)\n- [RcsbFvTrackDataElementInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbDataManager_RcsbDataManager.RcsbFvTrackDataElementInterface.html)\n  Interface that defines properties of an specific annotation object. It includes the location where the annotation will be displayed\n  (begin, end) and additional properties to change the final representation and click-event behaviour\n\n## General Board and Track Configuration\n\n#### Board Configuration\n\nMain feature viewer board object configuration defines the coordinate range, track and title width and axis display.\nThe full set of attributes is defined in [RcsbFvBoardConfigInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbFv_RcsbFvConfig_RcsbFvConfigInterface.RcsbFvBoardConfigInterface.html)\ninterface.\n\nMain Board Configuration properties are:\n\n- **range**: Object that defines the 1D domain coordinates segment as a range of sequential integer values\n  - **min**: Numerical value that defines the coordinates start position\n  - **max**: Numerical value that defines the coordinates end position\n- **trackWidth**: Numerical value that defines the width of the board cells that contains the feature\n- **rowTitleWidth**: Numerical value that defines the width of the row title cells\n- **includeAxis**: Boolean flag used to include a 1D horizontal axis on the top part of the board\n\n```javascript\nconst boardConfig = {\n  range: {\n    min: 20,\n    max: 110,\n  },\n  trackWidth: 940,\n  rowTitleWidth: 260,\n  includeAxis: true,\n};\n```\n\n#### Track Configuration\n\nRow configuration object defines format and content of feature viewer rows. The full set of board row configuration attributes is defined in [RcsbFvRowConfigInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbFv_RcsbFvConfig_RcsbFvConfigInterface.RcsbFvRowExtendedConfigInterface.html).\n\nMain Row Configuration properties are:\n\n- **trackHeight**: Defines the board row height\n- **trackColor**: Color in which row data will be displayed\n- **rowTitle**: Board track title, text displayed next to the board row\n- **displayType**: Enumerated value used to define how the data is displayed\n  - Values: sequence, block, pin, line, area, bond, vline\n- **trackData**: List of data displayed in the board row. The full set o data attributes are defined in [RcsbFvTrackDataElementInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbDataManager_RcsbDataManager.RcsbFvTrackDataElementInterface.html). Most important data elements attributes are\n  - **begin**: Start position of the feature\n  - **end**: End position of the feature (optional value). When no end value is available the feature is located on a single position defined by _begin_\n  - **value**: Numerical or string value of the feature in this range (optional value)\n  - **gaps**: List of empty regions in the feature. These regions are displayed as a dashed line between blocks. This attribute is only available when displayType is \"block\"\n    - Attributes: begin, end\n\n#### Track Configuration Examples\n\n- Sequence Track\n\n```javascript\nconst sequence =\n  \"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQ\" +\n  \"EEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAA\" +\n  \"RTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMS\";\n```\n\n```javascript\nconst sequenceTrack = {\n  trackHeight: 20,\n  trackColor: \"#F9F9F9\",\n  displayType: \"sequence\",\n  rowTitle: \"SEQUENCE\",\n  trackData: [\n    {\n      begin: 1,\n      label: sequence,\n    },\n  ],\n};\n```\n\n- Block Track\n\n```javascript\nconst blockTrack = {\n  trackId: \"blockTrack\",\n  trackHeight: 20,\n  trackColor: \"#F9F9F9\",\n  displayType: \"block\",\n  displayColor: \"#FF0000\",\n  rowTitle: \"BLOCK\",\n  trackData: [\n    {\n      begin: 30,\n      end: 60,\n      gaps: [\n        {\n          begin: 40,\n          end: 50,\n        },\n      ],\n    },\n    {\n      begin: 80,\n      end: 90,\n      openEnd: true,\n    },\n  ],\n};\n```\n\n#### Feature View Constructor\n\n```javascript\nconst pfv = new RcsbFv.Create({\n  boardConfigData: boardConfig,\n  rowConfigData: [sequenceTrack, blockTrack],\n  elementId: \"htmlElementId\",\n});\n```\n\nSee this expanded example online [here](https://rcsb.github.io/rcsb-saguaro/examples/board_track_configuration.html)\n\n### More Examples\n\n- [Single Tracks](https://rcsb.github.io/rcsb-saguaro/examples/simple_tracks.html)\n- [Composite Track](https://rcsb.github.io/rcsb-saguaro/examples/composite_track.html)\n- [Dynamic Tracks](https://rcsb.github.io/rcsb-saguaro/examples/dynamic_track_loading.html)\n- [Track Visibility](https://rcsb.github.io/rcsb-saguaro/examples/change_track_visibility.html)\n- [Update Track Data](https://rcsb.github.io/rcsb-saguaro/examples/update_track_data.html)\n- [Click Callback](https://rcsb.github.io/rcsb-saguaro/examples/click_callback.html)\n\nThe full collection of examples can be edited and modified at [CODEPEN](https://codepen.io/collection/njrBOR?grid_type=list)\n\n### rcsb-saguaro-app\n\nWe also provide a library ([rcsb-saguaro-app](https://rcsb.github.io/rcsb-saguaro-app)) to build preconfigured 1D Protein Feature Views of RCSB PDB and UniProtKB annotations.\n\n## Contributing\n\nAll contributions are welcome. Please, make a pull request or open an issue.\n\n## License\n\nThe MIT License\n\n    Copyright (c) 2019 - now, RCSB PDB and contributors\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n","readmeFilename":"README.md","author":{"name":"Joan Segura Mora","email":"joan.segura@rcsb.org"}}