├── .github ├── dependabot.yml └── workflows │ └── ci.yml ├── .gitignore ├── .mvn └── wrapper │ ├── maven-wrapper.jar │ └── maven-wrapper.properties ├── .travis.yml ├── DockerPostgres └── docker-compose.yml ├── Dockerfile ├── LICENSE ├── README.md ├── archive.sh ├── docker-compose.yml ├── docs ├── index.md └── start.md ├── generate-war ├── grasp ├── docs │ └── index.md ├── mkdocs.yml └── site │ ├── 404.html │ ├── css │ ├── fonts │ │ ├── Roboto-Slab-Bold.woff │ │ ├── Roboto-Slab-Bold.woff2 │ │ ├── Roboto-Slab-Regular.woff │ │ ├── Roboto-Slab-Regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── lato-bold-italic.woff │ │ ├── lato-bold-italic.woff2 │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-normal-italic.woff │ │ ├── lato-normal-italic.woff2 │ │ ├── lato-normal.woff │ │ └── lato-normal.woff2 │ ├── theme.css │ └── theme_extra.css │ ├── img │ └── favicon.ico │ ├── index.html │ ├── js │ ├── html5shiv.min.js │ ├── jquery-3.6.0.min.js │ ├── theme.js │ └── theme_extra.js │ ├── search.html │ ├── search │ ├── lunr.js │ ├── main.js │ ├── search_index.json │ └── worker.js │ ├── sitemap.xml │ └── sitemap.xml.gz ├── mkdocs.yml ├── mvnw ├── mvnw.cmd ├── pom-dev.xml ├── pom-release.xml ├── pom-test.xml ├── pom.xml ├── run-dev ├── run-test ├── src ├── main │ ├── java │ │ └── com │ │ │ └── asr │ │ │ └── grasp │ │ │ ├── ASRThread.java │ │ │ ├── GraspApplication.java │ │ │ ├── GraspConfig.java │ │ │ ├── controller │ │ │ ├── ASRController.java │ │ │ ├── ConsensusController.java │ │ │ ├── EmailController.java │ │ │ ├── ReconstructionController.java │ │ │ ├── SaveController.java │ │ │ ├── SeqController.java │ │ │ ├── TaxaController.java │ │ │ ├── TreeController.java │ │ │ └── UserController.java │ │ │ ├── model │ │ │ ├── BaseModel.java │ │ │ ├── ColumnEntry.java │ │ │ ├── GroupsModel.java │ │ │ ├── InferenceModel.java │ │ │ ├── QueryEntry.java │ │ │ ├── ReconstructionsModel.java │ │ │ ├── SeqModel.java │ │ │ ├── ShareGroupsModel.java │ │ │ ├── ShareUsersModel.java │ │ │ ├── TaxaModel.java │ │ │ ├── TreeModel.java │ │ │ └── UsersModel.java │ │ │ ├── objects │ │ │ ├── ASRObject.java │ │ │ ├── EmailObject.java │ │ │ ├── GeneralObject.java │ │ │ ├── ReconstructionObject.java │ │ │ ├── ShareObject.java │ │ │ └── UserObject.java │ │ │ ├── utils │ │ │ ├── Defines.java │ │ │ └── NaturalOrderComparator.java │ │ │ ├── validator │ │ │ ├── LoginValidator.java │ │ │ └── UserValidator.java │ │ │ └── view │ │ │ └── AccountView.java │ └── resources │ │ ├── application-example.properties │ │ ├── application.properties │ │ ├── data │ │ ├── app │ │ │ ├── CYP2U1_10.aln │ │ │ ├── CYP2U1_10.nwk │ │ │ ├── clifton.aln │ │ │ ├── clifton.nwk │ │ │ ├── cyp2u1.aln │ │ │ ├── cyp2u1.nwk │ │ │ ├── default.aln │ │ │ ├── default.nwk │ │ │ ├── hudson.aln │ │ │ ├── hudson.nwk │ │ │ ├── tawfik.aln │ │ │ ├── tawfik.nwk │ │ │ └── tutorial │ │ │ │ ├── GRASPTutorial.fasta │ │ │ │ ├── GRASPTutorial_Final.aln │ │ │ │ ├── GRASPTutorial_Final.nwk │ │ │ │ ├── tpswb_v5.aln │ │ │ │ ├── tpswb_v5.zip │ │ │ │ ├── tpswb_v5r.nwk │ │ │ │ └── tutorial.zip │ │ └── test │ │ │ ├── 0_10_dhad_28102018.aln │ │ │ ├── 0_10_dhad_28102018.nwk │ │ │ ├── 10.aln │ │ │ ├── 10.nwk │ │ │ ├── 10_20_dhad_28102018.aln │ │ │ ├── 10_20_dhad_28102018.nwk │ │ │ ├── 20_40_dhad_28102018.aln │ │ │ ├── 20_40_dhad_28102018.nwk │ │ │ ├── CYP2U1_10.aln │ │ │ ├── CYP2U1_10.nwk │ │ │ ├── CYP2U1_10_no_spaces.aln │ │ │ ├── CYP2U1_10_no_spaces.nwk │ │ │ ├── CYP2U1_just_IDs_10.aln │ │ │ ├── CYP2U1_just_IDs_10.nwk │ │ │ ├── Edge_parsimony_example_10.nwk │ │ │ ├── Edge_parsimony_example_with_non_bi_directional_transition_10.aln │ │ │ ├── Name_test_with_no_error_9.aln │ │ │ ├── Name_test_with_no_error_9.nwk │ │ │ ├── Name_test_with_one_error_10.aln │ │ │ ├── Name_test_with_one_error_10.nwk │ │ │ ├── Nexus_simple_6.nexus │ │ │ ├── Nexus_with_labels_and_annotations_64.nexus │ │ │ ├── input_test_aln_diff_length_4.aln │ │ │ ├── input_test_aln_diff_length_4.nwk │ │ │ ├── input_test_diff_names.aln │ │ │ ├── input_test_diff_names.nwk │ │ │ ├── resources_explanation.md │ │ │ ├── tawfik.aln │ │ │ └── tawfik.nwk │ │ ├── database │ │ └── create_grasp_schema.sql │ │ ├── grasp-repo │ │ └── com │ │ │ └── asr │ │ │ └── bnkit │ │ │ └── 1.0 │ │ │ ├── bnkit-1.0.jar │ │ │ ├── bnkit-1.0.jar.md5 │ │ │ ├── bnkit-1.0.jar.sha1 │ │ │ ├── bnkit-1.0.pom │ │ │ ├── bnkit-1.0.pom.md5 │ │ │ └── bnkit-1.0.pom.sha1 │ │ ├── lib │ │ ├── bnkit.jar │ │ ├── bnkit_20190911.jar │ │ ├── bnkit_20191109.jar │ │ ├── bnkit_20200430.jar │ │ └── bnkit_28112018.jar │ │ ├── logback-spring.xml │ │ ├── messages.properties │ │ ├── public │ │ ├── css │ │ │ ├── asr.css │ │ │ ├── bootstrap_override.css │ │ │ ├── lib │ │ │ │ ├── bootstrap-switch.min.css │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── font-awesome.min.css │ │ │ │ └── phyd3.min.css │ │ │ └── phylotree.css │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ └── glyphicons-halflings-regular.woff2 │ │ ├── images │ │ │ ├── GRASP_MSA.png │ │ │ ├── GRASP_POAGs.png │ │ │ ├── bg_tmp.jpeg │ │ │ ├── dark_edge.png │ │ │ ├── dark_light_edges.jpg │ │ │ ├── dark_light_edges.png │ │ │ ├── dashed_edge.png │ │ │ ├── download_pane.jpg │ │ │ ├── download_pane.png │ │ │ ├── edit │ │ │ │ ├── dark_light_edges.ai │ │ │ │ ├── download_pane.ai │ │ │ │ ├── graph_view.ai │ │ │ │ ├── graph_view_marginal.ai │ │ │ │ ├── home_page.ai │ │ │ │ ├── merged_graph.ai │ │ │ │ ├── msa_pie_chart.ai │ │ │ │ ├── phylo_tree.ai │ │ │ │ ├── phylo_tree_right_click.ai │ │ │ │ └── taxonomic_annotation.ai │ │ │ ├── graph_view.jpg │ │ │ ├── graph_view.png │ │ │ ├── graph_view_marginal.jpg │ │ │ ├── graph_view_marginal.png │ │ │ ├── home_page.jpg │ │ │ ├── home_page.png │ │ │ ├── light_edge.png │ │ │ ├── loading.gif │ │ │ ├── loading_licenced.gif │ │ │ ├── loadingbw.gif │ │ │ ├── merged_graph.jpg │ │ │ ├── merged_graph.png │ │ │ ├── msa_pie_chart.jpg │ │ │ ├── msa_pie_chart.png │ │ │ ├── phylo_tree.jpg │ │ │ ├── phylo_tree.png │ │ │ ├── phylo_tree_right_click.jpg │ │ │ ├── phylo_tree_right_click.png │ │ │ ├── taxonomic_annotation.jpg │ │ │ ├── taxonomic_annotation.png │ │ │ ├── thick_edge.png │ │ │ ├── tree_howtoroot.png │ │ │ ├── tutorial4.aln │ │ │ ├── tutorial4.aln.png │ │ │ ├── tutorial4.nwk │ │ │ ├── tutorial4.nwk.png │ │ │ ├── tutorial4_pos17.nwk.png │ │ │ └── tutorial4_pos6.nwk.png │ │ └── js │ │ │ ├── actions.js │ │ │ ├── annot.js │ │ │ ├── asr.js │ │ │ ├── colour_defs.js │ │ │ ├── consensus.js │ │ │ ├── defines.js │ │ │ ├── download.js │ │ │ ├── index.js │ │ │ ├── lib │ │ │ ├── FileSaver.min.js │ │ │ ├── bootstrap-switch.min.js │ │ │ ├── bootstrap.min.js │ │ │ ├── canvasToBlob.js │ │ │ ├── crossfilter.min.js │ │ │ ├── d3.tip.v0.6.3.js │ │ │ ├── d3min.js │ │ │ ├── dropdown.js │ │ │ ├── html5shiv.js │ │ │ ├── jquery-2.2.4.min.js │ │ │ ├── jquery.min.js │ │ │ ├── lodash.min.js │ │ │ ├── moderniser.js │ │ │ └── respond.min.js │ │ │ ├── phylo_tree_actions.js │ │ │ ├── phylo_tree_draw.js │ │ │ ├── phylo_tree_options.js │ │ │ ├── phylo_tree_taxa.js │ │ │ └── tree │ │ │ ├── controller.js │ │ │ ├── defines.js │ │ │ ├── model.js │ │ │ └── view.js │ │ └── templates │ │ ├── account.html │ │ ├── confirm_registration.html │ │ ├── error.html │ │ ├── feature_log.html │ │ ├── forgot_password.html │ │ ├── fragments │ │ ├── about.html │ │ ├── alerts.html │ │ ├── download_form.html │ │ ├── errors.html │ │ ├── feature_log.html │ │ ├── footer.html │ │ ├── form.html │ │ ├── head_include.html │ │ ├── header.html │ │ ├── help.html │ │ ├── login_modal.html │ │ ├── nav.html │ │ ├── results.html │ │ ├── results_modal.html │ │ ├── tutorial.html │ │ ├── user.html │ │ ├── workshop.html │ │ └── workshop_tps.html │ │ ├── guide.html │ │ ├── index.html │ │ ├── login.html │ │ ├── ml.html │ │ ├── processing.html │ │ ├── register.html │ │ ├── reset_password_confirmation.html │ │ ├── set_password.html │ │ ├── tutorial.html │ │ └── tutorial_tps.html └── test │ └── java │ └── com │ └── asr │ └── grasp │ ├── BaseTest.java │ ├── ErrorMessageTest.java │ ├── ReconstructionControllerTest.java │ ├── SeqControllerTest.java │ ├── TaxaControllerTest.java │ ├── TestPropertiesExample.java │ ├── TestPropertiesOverride.java │ ├── TreeControllerTest.java │ └── UserControllerTest.java └── update-jar /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.gitignore -------------------------------------------------------------------------------- /.mvn/wrapper/maven-wrapper.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.mvn/wrapper/maven-wrapper.jar -------------------------------------------------------------------------------- /.mvn/wrapper/maven-wrapper.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.mvn/wrapper/maven-wrapper.properties -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/.travis.yml -------------------------------------------------------------------------------- /DockerPostgres/docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/DockerPostgres/docker-compose.yml -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/README.md -------------------------------------------------------------------------------- /archive.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/archive.sh -------------------------------------------------------------------------------- /docker-compose.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/docker-compose.yml -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/start.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/docs/start.md -------------------------------------------------------------------------------- /generate-war: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/generate-war -------------------------------------------------------------------------------- /grasp/docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/docs/index.md -------------------------------------------------------------------------------- /grasp/mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/mkdocs.yml -------------------------------------------------------------------------------- /grasp/site/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/404.html -------------------------------------------------------------------------------- /grasp/site/css/fonts/Roboto-Slab-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/Roboto-Slab-Bold.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/Roboto-Slab-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/Roboto-Slab-Bold.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/Roboto-Slab-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/Roboto-Slab-Regular.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/Roboto-Slab-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/Roboto-Slab-Regular.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /grasp/site/css/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /grasp/site/css/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /grasp/site/css/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-bold-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-bold-italic.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-bold-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-bold-italic.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-bold.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-bold.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-normal-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-normal-italic.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-normal-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-normal-italic.woff2 -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-normal.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-normal.woff -------------------------------------------------------------------------------- /grasp/site/css/fonts/lato-normal.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/fonts/lato-normal.woff2 -------------------------------------------------------------------------------- /grasp/site/css/theme.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/theme.css -------------------------------------------------------------------------------- /grasp/site/css/theme_extra.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/css/theme_extra.css -------------------------------------------------------------------------------- /grasp/site/img/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/img/favicon.ico -------------------------------------------------------------------------------- /grasp/site/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/index.html -------------------------------------------------------------------------------- /grasp/site/js/html5shiv.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/js/html5shiv.min.js -------------------------------------------------------------------------------- /grasp/site/js/jquery-3.6.0.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/js/jquery-3.6.0.min.js -------------------------------------------------------------------------------- /grasp/site/js/theme.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/js/theme.js -------------------------------------------------------------------------------- /grasp/site/js/theme_extra.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/js/theme_extra.js -------------------------------------------------------------------------------- /grasp/site/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/search.html -------------------------------------------------------------------------------- /grasp/site/search/lunr.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/search/lunr.js -------------------------------------------------------------------------------- /grasp/site/search/main.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/search/main.js -------------------------------------------------------------------------------- /grasp/site/search/search_index.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/search/search_index.json -------------------------------------------------------------------------------- /grasp/site/search/worker.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/search/worker.js -------------------------------------------------------------------------------- /grasp/site/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/sitemap.xml -------------------------------------------------------------------------------- /grasp/site/sitemap.xml.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/grasp/site/sitemap.xml.gz -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /mvnw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/mvnw -------------------------------------------------------------------------------- /mvnw.cmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/mvnw.cmd -------------------------------------------------------------------------------- /pom-dev.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/pom-dev.xml -------------------------------------------------------------------------------- /pom-release.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/pom-release.xml -------------------------------------------------------------------------------- /pom-test.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/pom-test.xml -------------------------------------------------------------------------------- /pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/pom.xml -------------------------------------------------------------------------------- /run-dev: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/run-dev -------------------------------------------------------------------------------- /run-test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/run-test -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/ASRThread.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/ASRThread.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/GraspApplication.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/GraspApplication.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/GraspConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/GraspConfig.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/ASRController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/ASRController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/ConsensusController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/ConsensusController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/EmailController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/EmailController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/ReconstructionController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/ReconstructionController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/SaveController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/SaveController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/SeqController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/SeqController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/TaxaController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/TaxaController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/TreeController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/TreeController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/controller/UserController.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/controller/UserController.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/BaseModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/BaseModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/ColumnEntry.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/ColumnEntry.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/GroupsModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/GroupsModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/InferenceModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/InferenceModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/QueryEntry.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/QueryEntry.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/ReconstructionsModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/ReconstructionsModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/SeqModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/SeqModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/ShareGroupsModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/ShareGroupsModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/ShareUsersModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/ShareUsersModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/TaxaModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/TaxaModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/TreeModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/TreeModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/model/UsersModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/model/UsersModel.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/ASRObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/ASRObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/EmailObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/EmailObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/GeneralObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/GeneralObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/ReconstructionObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/ReconstructionObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/ShareObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/ShareObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/objects/UserObject.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/objects/UserObject.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/utils/Defines.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/utils/Defines.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/utils/NaturalOrderComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/utils/NaturalOrderComparator.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/validator/LoginValidator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/validator/LoginValidator.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/validator/UserValidator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/validator/UserValidator.java -------------------------------------------------------------------------------- /src/main/java/com/asr/grasp/view/AccountView.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/java/com/asr/grasp/view/AccountView.java -------------------------------------------------------------------------------- /src/main/resources/application-example.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/application-example.properties -------------------------------------------------------------------------------- /src/main/resources/application.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/application.properties -------------------------------------------------------------------------------- /src/main/resources/data/app/CYP2U1_10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/CYP2U1_10.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/CYP2U1_10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/CYP2U1_10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/clifton.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/clifton.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/clifton.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/clifton.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/cyp2u1.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/cyp2u1.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/cyp2u1.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/cyp2u1.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/default.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/default.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/default.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/default.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/hudson.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/hudson.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/hudson.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/hudson.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/tawfik.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tawfik.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/tawfik.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tawfik.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/GRASPTutorial.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/GRASPTutorial.fasta -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/GRASPTutorial_Final.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/GRASPTutorial_Final.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/GRASPTutorial_Final.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/GRASPTutorial_Final.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/tpswb_v5.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/tpswb_v5.aln -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/tpswb_v5.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/tpswb_v5.zip -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/tpswb_v5r.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/tpswb_v5r.nwk -------------------------------------------------------------------------------- /src/main/resources/data/app/tutorial/tutorial.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/app/tutorial/tutorial.zip -------------------------------------------------------------------------------- /src/main/resources/data/test/0_10_dhad_28102018.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/0_10_dhad_28102018.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/0_10_dhad_28102018.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/0_10_dhad_28102018.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/10.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/10_20_dhad_28102018.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/10_20_dhad_28102018.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/10_20_dhad_28102018.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/10_20_dhad_28102018.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/20_40_dhad_28102018.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/20_40_dhad_28102018.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/20_40_dhad_28102018.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/20_40_dhad_28102018.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_10.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_10_no_spaces.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_10_no_spaces.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_10_no_spaces.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_10_no_spaces.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_just_IDs_10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_just_IDs_10.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/CYP2U1_just_IDs_10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/CYP2U1_just_IDs_10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/Edge_parsimony_example_10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Edge_parsimony_example_10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/Edge_parsimony_example_with_non_bi_directional_transition_10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Edge_parsimony_example_with_non_bi_directional_transition_10.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/Name_test_with_no_error_9.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Name_test_with_no_error_9.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/Name_test_with_no_error_9.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Name_test_with_no_error_9.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/Name_test_with_one_error_10.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Name_test_with_one_error_10.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/Name_test_with_one_error_10.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Name_test_with_one_error_10.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/Nexus_simple_6.nexus: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Nexus_simple_6.nexus -------------------------------------------------------------------------------- /src/main/resources/data/test/Nexus_with_labels_and_annotations_64.nexus: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/Nexus_with_labels_and_annotations_64.nexus -------------------------------------------------------------------------------- /src/main/resources/data/test/input_test_aln_diff_length_4.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/input_test_aln_diff_length_4.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/input_test_aln_diff_length_4.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/input_test_aln_diff_length_4.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/input_test_diff_names.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/input_test_diff_names.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/input_test_diff_names.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/input_test_diff_names.nwk -------------------------------------------------------------------------------- /src/main/resources/data/test/resources_explanation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/resources_explanation.md -------------------------------------------------------------------------------- /src/main/resources/data/test/tawfik.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/tawfik.aln -------------------------------------------------------------------------------- /src/main/resources/data/test/tawfik.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/data/test/tawfik.nwk -------------------------------------------------------------------------------- /src/main/resources/database/create_grasp_schema.sql: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/database/create_grasp_schema.sql -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar.md5: -------------------------------------------------------------------------------- 1 | b15403abf4ca015995a41d1f4862ba2a -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar.sha1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.jar.sha1 -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.pom: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.pom -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.pom.md5: -------------------------------------------------------------------------------- 1 | 5ac7e9a1299c62c686c599b883477d66 -------------------------------------------------------------------------------- /src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.pom.sha1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/grasp-repo/com/asr/bnkit/1.0/bnkit-1.0.pom.sha1 -------------------------------------------------------------------------------- /src/main/resources/lib/bnkit.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/lib/bnkit.jar -------------------------------------------------------------------------------- /src/main/resources/lib/bnkit_20190911.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/lib/bnkit_20190911.jar -------------------------------------------------------------------------------- /src/main/resources/lib/bnkit_20191109.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/lib/bnkit_20191109.jar -------------------------------------------------------------------------------- /src/main/resources/lib/bnkit_20200430.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/lib/bnkit_20200430.jar -------------------------------------------------------------------------------- /src/main/resources/lib/bnkit_28112018.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/lib/bnkit_28112018.jar -------------------------------------------------------------------------------- /src/main/resources/logback-spring.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/logback-spring.xml -------------------------------------------------------------------------------- /src/main/resources/messages.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/messages.properties -------------------------------------------------------------------------------- /src/main/resources/public/css/asr.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/asr.css -------------------------------------------------------------------------------- /src/main/resources/public/css/bootstrap_override.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/bootstrap_override.css -------------------------------------------------------------------------------- /src/main/resources/public/css/lib/bootstrap-switch.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/lib/bootstrap-switch.min.css -------------------------------------------------------------------------------- /src/main/resources/public/css/lib/bootstrap.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/lib/bootstrap.min.css -------------------------------------------------------------------------------- /src/main/resources/public/css/lib/font-awesome.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/lib/font-awesome.min.css -------------------------------------------------------------------------------- /src/main/resources/public/css/lib/phyd3.min.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/lib/phyd3.min.css -------------------------------------------------------------------------------- /src/main/resources/public/css/phylotree.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/css/phylotree.css -------------------------------------------------------------------------------- /src/main/resources/public/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /src/main/resources/public/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /src/main/resources/public/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /src/main/resources/public/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /src/main/resources/public/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /src/main/resources/public/fonts/glyphicons-halflings-regular.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/glyphicons-halflings-regular.eot -------------------------------------------------------------------------------- /src/main/resources/public/fonts/glyphicons-halflings-regular.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/glyphicons-halflings-regular.svg -------------------------------------------------------------------------------- /src/main/resources/public/fonts/glyphicons-halflings-regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/glyphicons-halflings-regular.ttf -------------------------------------------------------------------------------- /src/main/resources/public/fonts/glyphicons-halflings-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/glyphicons-halflings-regular.woff -------------------------------------------------------------------------------- /src/main/resources/public/fonts/glyphicons-halflings-regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/fonts/glyphicons-halflings-regular.woff2 -------------------------------------------------------------------------------- /src/main/resources/public/images/GRASP_MSA.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/GRASP_MSA.png -------------------------------------------------------------------------------- /src/main/resources/public/images/GRASP_POAGs.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/GRASP_POAGs.png -------------------------------------------------------------------------------- /src/main/resources/public/images/bg_tmp.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/bg_tmp.jpeg -------------------------------------------------------------------------------- /src/main/resources/public/images/dark_edge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/dark_edge.png -------------------------------------------------------------------------------- /src/main/resources/public/images/dark_light_edges.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/dark_light_edges.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/dark_light_edges.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/dark_light_edges.png -------------------------------------------------------------------------------- /src/main/resources/public/images/dashed_edge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/dashed_edge.png -------------------------------------------------------------------------------- /src/main/resources/public/images/download_pane.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/download_pane.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/download_pane.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/download_pane.png -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/dark_light_edges.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/dark_light_edges.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/download_pane.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/download_pane.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/graph_view.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/graph_view.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/graph_view_marginal.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/graph_view_marginal.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/home_page.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/home_page.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/merged_graph.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/merged_graph.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/msa_pie_chart.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/msa_pie_chart.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/phylo_tree.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/phylo_tree.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/phylo_tree_right_click.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/phylo_tree_right_click.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/edit/taxonomic_annotation.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/edit/taxonomic_annotation.ai -------------------------------------------------------------------------------- /src/main/resources/public/images/graph_view.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/graph_view.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/graph_view.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/graph_view.png -------------------------------------------------------------------------------- /src/main/resources/public/images/graph_view_marginal.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/graph_view_marginal.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/graph_view_marginal.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/graph_view_marginal.png -------------------------------------------------------------------------------- /src/main/resources/public/images/home_page.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/home_page.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/home_page.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/home_page.png -------------------------------------------------------------------------------- /src/main/resources/public/images/light_edge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/light_edge.png -------------------------------------------------------------------------------- /src/main/resources/public/images/loading.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/loading.gif -------------------------------------------------------------------------------- /src/main/resources/public/images/loading_licenced.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/loading_licenced.gif -------------------------------------------------------------------------------- /src/main/resources/public/images/loadingbw.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/loadingbw.gif -------------------------------------------------------------------------------- /src/main/resources/public/images/merged_graph.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/merged_graph.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/merged_graph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/merged_graph.png -------------------------------------------------------------------------------- /src/main/resources/public/images/msa_pie_chart.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/msa_pie_chart.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/msa_pie_chart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/msa_pie_chart.png -------------------------------------------------------------------------------- /src/main/resources/public/images/phylo_tree.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/phylo_tree.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/phylo_tree.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/phylo_tree.png -------------------------------------------------------------------------------- /src/main/resources/public/images/phylo_tree_right_click.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/phylo_tree_right_click.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/phylo_tree_right_click.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/phylo_tree_right_click.png -------------------------------------------------------------------------------- /src/main/resources/public/images/taxonomic_annotation.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/taxonomic_annotation.jpg -------------------------------------------------------------------------------- /src/main/resources/public/images/taxonomic_annotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/taxonomic_annotation.png -------------------------------------------------------------------------------- /src/main/resources/public/images/thick_edge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/thick_edge.png -------------------------------------------------------------------------------- /src/main/resources/public/images/tree_howtoroot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tree_howtoroot.png -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4.aln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4.aln -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4.aln.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4.aln.png -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4.nwk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4.nwk -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4.nwk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4.nwk.png -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4_pos17.nwk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4_pos17.nwk.png -------------------------------------------------------------------------------- /src/main/resources/public/images/tutorial4_pos6.nwk.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/images/tutorial4_pos6.nwk.png -------------------------------------------------------------------------------- /src/main/resources/public/js/actions.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/actions.js -------------------------------------------------------------------------------- /src/main/resources/public/js/annot.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/annot.js -------------------------------------------------------------------------------- /src/main/resources/public/js/asr.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/asr.js -------------------------------------------------------------------------------- /src/main/resources/public/js/colour_defs.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/colour_defs.js -------------------------------------------------------------------------------- /src/main/resources/public/js/consensus.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/consensus.js -------------------------------------------------------------------------------- /src/main/resources/public/js/defines.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/defines.js -------------------------------------------------------------------------------- /src/main/resources/public/js/download.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/download.js -------------------------------------------------------------------------------- /src/main/resources/public/js/index.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/index.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/FileSaver.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/FileSaver.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/bootstrap-switch.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/bootstrap-switch.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/bootstrap.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/bootstrap.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/canvasToBlob.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/canvasToBlob.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/crossfilter.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/crossfilter.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/d3.tip.v0.6.3.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/d3.tip.v0.6.3.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/d3min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/d3min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/dropdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/dropdown.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/html5shiv.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/html5shiv.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/jquery-2.2.4.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/jquery-2.2.4.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/jquery.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/jquery.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/lodash.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/lodash.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/moderniser.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/moderniser.js -------------------------------------------------------------------------------- /src/main/resources/public/js/lib/respond.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/lib/respond.min.js -------------------------------------------------------------------------------- /src/main/resources/public/js/phylo_tree_actions.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/phylo_tree_actions.js -------------------------------------------------------------------------------- /src/main/resources/public/js/phylo_tree_draw.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/phylo_tree_draw.js -------------------------------------------------------------------------------- /src/main/resources/public/js/phylo_tree_options.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/phylo_tree_options.js -------------------------------------------------------------------------------- /src/main/resources/public/js/phylo_tree_taxa.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/phylo_tree_taxa.js -------------------------------------------------------------------------------- /src/main/resources/public/js/tree/controller.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/tree/controller.js -------------------------------------------------------------------------------- /src/main/resources/public/js/tree/defines.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/tree/defines.js -------------------------------------------------------------------------------- /src/main/resources/public/js/tree/model.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/tree/model.js -------------------------------------------------------------------------------- /src/main/resources/public/js/tree/view.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/public/js/tree/view.js -------------------------------------------------------------------------------- /src/main/resources/templates/account.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/account.html -------------------------------------------------------------------------------- /src/main/resources/templates/confirm_registration.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/confirm_registration.html -------------------------------------------------------------------------------- /src/main/resources/templates/error.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/error.html -------------------------------------------------------------------------------- /src/main/resources/templates/feature_log.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/feature_log.html -------------------------------------------------------------------------------- /src/main/resources/templates/forgot_password.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/forgot_password.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/about.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/about.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/alerts.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/alerts.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/download_form.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/download_form.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/errors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/errors.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/feature_log.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/feature_log.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/footer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/footer.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/form.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/form.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/head_include.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/head_include.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/header.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/header.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/help.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/help.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/login_modal.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/login_modal.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/nav.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/nav.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/results.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/results.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/results_modal.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/results_modal.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/tutorial.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/tutorial.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/user.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/user.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/workshop.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/workshop.html -------------------------------------------------------------------------------- /src/main/resources/templates/fragments/workshop_tps.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/fragments/workshop_tps.html -------------------------------------------------------------------------------- /src/main/resources/templates/guide.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/guide.html -------------------------------------------------------------------------------- /src/main/resources/templates/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/index.html -------------------------------------------------------------------------------- /src/main/resources/templates/login.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/login.html -------------------------------------------------------------------------------- /src/main/resources/templates/ml.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/ml.html -------------------------------------------------------------------------------- /src/main/resources/templates/processing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/processing.html -------------------------------------------------------------------------------- /src/main/resources/templates/register.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/register.html -------------------------------------------------------------------------------- /src/main/resources/templates/reset_password_confirmation.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/reset_password_confirmation.html -------------------------------------------------------------------------------- /src/main/resources/templates/set_password.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/set_password.html -------------------------------------------------------------------------------- /src/main/resources/templates/tutorial.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/tutorial.html -------------------------------------------------------------------------------- /src/main/resources/templates/tutorial_tps.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/main/resources/templates/tutorial_tps.html -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/BaseTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/BaseTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/ErrorMessageTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/ErrorMessageTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/ReconstructionControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/ReconstructionControllerTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/SeqControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/SeqControllerTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/TaxaControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/TaxaControllerTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/TestPropertiesExample.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/TestPropertiesExample.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/TestPropertiesOverride.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/TestPropertiesOverride.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/TreeControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/TreeControllerTest.java -------------------------------------------------------------------------------- /src/test/java/com/asr/grasp/UserControllerTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/src/test/java/com/asr/grasp/UserControllerTest.java -------------------------------------------------------------------------------- /update-jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bodenlab/GRASP/HEAD/update-jar --------------------------------------------------------------------------------