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treemachine | Source tree graph database

 by   OpenTreeOfLife Java Version: Current License: Non-SPDX

 by   OpenTreeOfLife Java Version: Current License: Non-SPDX

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kandi X-RAY | treemachine Summary

treemachine is a Java library. treemachine has no bugs, it has no vulnerabilities, it has build file available and it has low support. However treemachine has a Non-SPDX License. You can download it from GitHub.
treemachine-LITE is a pared-down version of the original treemachine which was used to generate synthetic phylogenetic trees for the Open Tree of Life project. Synthetic analyses are now performed by other tools. The role of treemachine-LITE is simply to construct a neo4j database and serve such trees.
Support
Support
Quality
Quality
Security
Security
License
License
Reuse
Reuse

kandi-support Support

  • treemachine has a low active ecosystem.
  • It has 17 star(s) with 6 fork(s). There are 18 watchers for this library.
  • It had no major release in the last 12 months.
  • There are 15 open issues and 173 have been closed. On average issues are closed in 437 days. There are no pull requests.
  • It has a neutral sentiment in the developer community.
  • The latest version of treemachine is current.
treemachine Support
Best in #Java
Average in #Java
treemachine Support
Best in #Java
Average in #Java

quality kandi Quality

  • treemachine has 0 bugs and 0 code smells.
treemachine Quality
Best in #Java
Average in #Java
treemachine Quality
Best in #Java
Average in #Java

securitySecurity

  • treemachine has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
  • treemachine code analysis shows 0 unresolved vulnerabilities.
  • There are 0 security hotspots that need review.
treemachine Security
Best in #Java
Average in #Java
treemachine Security
Best in #Java
Average in #Java

license License

  • treemachine has a Non-SPDX License.
  • Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.
treemachine License
Best in #Java
Average in #Java
treemachine License
Best in #Java
Average in #Java

buildReuse

  • treemachine releases are not available. You will need to build from source code and install.
  • Build file is available. You can build the component from source.
  • Installation instructions are not available. Examples and code snippets are available.
  • treemachine saves you 2870 person hours of effort in developing the same functionality from scratch.
  • It has 6203 lines of code, 330 functions and 56 files.
  • It has high code complexity. Code complexity directly impacts maintainability of the code.
treemachine Reuse
Best in #Java
Average in #Java
treemachine Reuse
Best in #Java
Average in #Java
Top functions reviewed by kandi - BETA

kandi has reviewed treemachine and discovered the below as its top functions. This is intended to give you an instant insight into treemachine implemented functionality, and help decide if they suit your requirements.

  • Gets the graphML representation of a given node .
    • Import JadeTree .
      • Reads a JadeTree from a string .
        • Converts JadeTree to JadeTree .
          • Adds the linked nodes that have been linked to this node .
            • Deletes all the relationships for a given source .
              • todo remove blobs
                • Helper method to extract the synthetic node of a synthetic tree .
                  • Indent the indentation level .
                    • Evaluate the edge - based relationship

                      Get all kandi verified functions for this library.

                      Get all kandi verified functions for this library.

                      treemachine Key Features

                      To compile the command-line version (which you can then use to build a database):. This creates treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar in the target directory (and deletes the server plugin jar if it existed).

                      treemachine Examples and Code Snippets

                      See all related Code Snippets

                      Installing dependencies

                      copy iconCopydownload iconDownload
                      sudo apt-get install maven
                      

                      Command-line version

                      copy iconCopydownload iconDownload
                      sh mvn_cmdline.sh
                      

                      Server plugins

                      copy iconCopydownload iconDownload
                      sh mvn_serverplugins.sh
                      

                      Constructing a DB

                      copy iconCopydownload iconDownload
                      java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar ingestsynth newick_tree json_annotations tsv_taxonomy DB_name
                      

                      Serving a DB with Neo4j

                      copy iconCopydownload iconDownload
                      neo4j-community-1.9.5/bin/neo4j start
                      

                      Running the tests

                      copy iconCopydownload iconDownload
                      cd ws-tests
                      ./run_tests.sh host:apihost=http://localhost:7474 host:translate=true
                      

                      See all related Code Snippets

                      Community Discussions

                      No Community Discussions are available at this moment for treemachine.Refer to stack overflow page for discussions.

                      No Community Discussions are available at this moment for treemachine.Refer to stack overflow page for discussions.

                      Community Discussions, Code Snippets contain sources that include Stack Exchange Network

                      Vulnerabilities

                      No vulnerabilities reported

                      Install treemachine

                      You can download it from GitHub.
                      You can use treemachine like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the treemachine component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

                      Support

                      For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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