Artemis | free genome viewer and annotation tool | Genomics library

 by   sanger-pathogens Java Version: v18.2.0 License: Non-SPDX

kandi X-RAY | Artemis Summary

kandi X-RAY | Artemis Summary

Artemis is a Java library typically used in Artificial Intelligence, Genomics applications. Artemis has no bugs, it has no vulnerabilities, it has build file available and it has low support. However Artemis has a Non-SPDX License. You can download it from GitHub.

The Artemis Software includes:. Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. DNAPlotter generates images of circular and linear DNA maps. BamView is a standalone BAM/CRAM file viewer. For further information and details on how to download the Artemis software, please see the Artemis GitHub page.

            kandi-support Support

              Artemis has a low active ecosystem.
              It has 161 star(s) with 65 fork(s). There are 15 watchers for this library.
              It had no major release in the last 12 months.
              There are 18 open issues and 31 have been closed. On average issues are closed in 47 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of Artemis is v18.2.0

            kandi-Quality Quality

              Artemis has 0 bugs and 0 code smells.

            kandi-Security Security

              Artemis has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              Artemis code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              Artemis 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.

            kandi-Reuse Reuse

              Artemis releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 473049 lines of code, 16168 functions and 1471 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Artemis and discovered the below as its top functions. This is intended to give you an instant insight into Artemis implemented functionality, and help decide if they suit your requirements.
            • Create the menu
            • Configure the plot
            • Define the options options
            • Update the BAM panel
            • Create the components for this feature edit component
            • Read FASTA file
            • Transfer the annotation data to the feature editor
            • Read BLASTP file with significant alignments
            • Main method for testing
            • Combine gene features
            • Create the menu for deletion
            • Constructs all the menus and sets up the main window
            • Construct the main panel
            • Popup the menu
            • Calculate the features
            • Show properties
            • Returns a subset of the sub sequence
            • Add menu items to the menu items
            • Returns a subset of the values in the range
            • Adds the find and replace option
            • Creates the menu for the gene editor
            • Make the menus for this component
            • Create the popup menu
            • Returns the range of this sequence
            • Returns a subset of the values
            • Get the range of this sequence
            Get all kandi verified functions for this library.

            Artemis Key Features

            No Key Features are available at this moment for Artemis.

            Artemis Examples and Code Snippets

            No Code Snippets are available at this moment for Artemis.

            Community Discussions


            Spring Boot connection to SQL Server in Windows Authentication mode
            Asked 2022-Apr-17 at 23:55

            I am new in Spring Boot, I am trying to connect to SQL Server in Windows Authentication mode and here is my database configuration:



            Answered 2022-Apr-17 at 23:55

            I found the solution and it was only to use

            integratedSecurity = false;

            instead of

            integratedSecurity = true;

            so in this case connection string will be:

   DatabaseName spring.datasource.url=jdbc:sqlserver://;DatabaseName=${};integratedSecurity = false;.

            Why to use integratedSecurity = false? The reason is here:

            "Integrated Security When false, User ID and Password are specified in the connection. When true, the current Windows account credentials are used for authentication."



            ActiveMQ Artemis cluster on Docker Swarm
            Asked 2022-Mar-18 at 13:53

            I am trying to setup simple cluster of 2 ActiveMQ Artemis brokers within Docker Swarm environment.

            Stack configuration



            Answered 2022-Mar-18 at 13:53

            The connector named "netty_connector" shouldn't use This is the address that will be sent to other nodes in the cluster to tell them how to connect back to the node who sent it. The address will be meaningless in that context. It needs to be the actual IP address or hostname where the broker is listening for network connections.



            How can I fix this issue in R with webscraping?
            Asked 2022-Mar-09 at 12:46

            I am trying to pull across data from within over 800 links and putting it onto a table. I have tried using chrome selector gadget but cannot work out how to get it to loop. I must have spent 40 hours and keep getting error codes. I need to pull the same information from li:nth-child(8) , li:nth-child(8) strong and another couple text boxes of information. I have tried following a YouTube video and I just changed the names and links but otherwise maintained consistency and it just will not work.



            Answered 2022-Mar-09 at 12:46

            We can use simple for loop,



            Create DLQ per-consumer in ActiveMQ Artemis
            Asked 2022-Mar-04 at 21:15

            I'm consuming messages from an ActiveMQ Artemis topic using JMS. My consumers are connecting directly to the FQQN of their consumer queues. Like this:



            Answered 2022-Mar-04 at 16:18

            It's not possible to configure the broker to auto-create a dead-letter queue whose name contains the name of the queue where the message was originally sent. As noted in the documentation, the dead-letter queue is named according to the address where the message was originally sent along with any configured prefix and/or suffix.

            However, the message itself will have a property named _AMQ_ORIG_QUEUE which will contain the name of the queue where the message was originally routed. This means you can use a consumer with a message selector (e.g. _AMQ_ORIG_QUEUE = 'ConsumerA') so that the consumer will only receive messages which were originally routed to a particular queue. This is functionally equivalent to having a dead-letter queue per-queue.

            For what it's worth, what you're calling the "consumer name" isn't the name of the consumer at all, at least not from the broker's point of view. It's just the name of the queue.

            Ultimately it's just not possible to configure a dead-letter queue per-queue. It's only possible to configure a dead-letter queue per address. This is true whether the resources are create manually (e.g. via broker.xml) or automatically.



            How to provide a custom broker.xml to ActiveMQ Artemis broker instance
            Asked 2022-Feb-17 at 15:39

            How can I provide a custom broker.xml to my instance of ActiveMQ Artemis? The standard implementation generates the config data in the broker instance's etc directory but I wish to mount my own config files.



            Answered 2022-Feb-17 at 15:39

            If you're starting the broker with the artemis run command then you can pass the location of a custom bootstrap.xml, e.g.:



            Readiness fails in the Eclipse Hono pods of the Cloud2Edge package
            Asked 2022-Feb-09 at 06:58

            I am a bit desperate and I hope someone can help me. A few months ago I installed the eclipse cloud2edge package on a kubernetes cluster by following the installation instructions, creating a persistentVolume and running the helm install command with these options.



            Answered 2022-Feb-09 at 06:58

            based on the iconic Failed to create SSL Connection output in the logs, I assume that you have run into the dreaded The demo certificates included in the Hono chart have expired problem.

            The Cloud2Edge package chart is being updated currently ( with the most recent version of the Ditto and Hono charts (which includes fresh certificates that are valid for two more years to come). As soon as that PR is merged and the Eclipse Packages chart repository has been rebuilt, you should be able to do a helm repo update and then (hopefully) succesfully install the c2e package.



            ActiveMQ Artemis data journal folder
            Asked 2022-Feb-03 at 14:42

            I am trying to understand how ActiveMQ Artemis manages the journal files (under data/journal) and when it creates new ones. I read the documentation, but it wasn't clear how the files are create. I have a broker.xml has simple settings (won't be able to share unfortunately). Here are a few:

            • journal min threads - 2
            • journal pool size - 50
            • file size is defaulted to 10MB.

            ActiveMQ Artemis starts, and I see 2 files are already created under /data/journal. I am now running a request that posts a lot of messages in a very short time. These messages are being actively consumed. I am publishing a lot of messages but they are not accumulating as fast because the consumer is consuming them. However, this doesn't cause the files to grow to recreate the space issue.

            As the message volume is going up I don't see the number of files going up. It goes up and stays at 12 files for a long time. I can understand the message # is not sufficient trigger additional files if only the latest journal file is being written to. However, I see all the 11 files have updated timestamps making me think they are being rotated.

            My paging directory is empty.

            I am trying to understand why the journal is not growing despite the message volume.



            Answered 2022-Feb-03 at 14:42

            From what I can tell, message consumption has reached a break-even point with message production so that messages are not accumulating on the broker therefore the journal is not actually growing in size. The journal files are simply being re-used as messages are being added & acknowledged.



            Apache ActiveMQ Artemis transform TextMessage to ObjectMessage
            Asked 2022-Feb-02 at 17:23

            I have a use case where I need to convert a message from one type to another (i.e. TextMessage -> ObjectMessage).

            I found that when diverting between queues there is an option to transform the message. I have implemented the Transformer interface as instructed in the documentation.



            Answered 2022-Feb-02 at 17:23

            It should technically be possible to convert a javax.jms.TextMessage to a javax.jms.ObjectMessage, but it may be cumbersome. Here are some important things to note:

            • javax.jms.TextMessage, javax.jms.ObjectMessage, and org.apache.activemq.artemis.api.core.Message are all just interfaces. The javax version is what you use on the client and Message is what is used on the broker. The data for each type of message is stored differently in the underlying message implementation.
            • The class for the Java object that you wish to put into the ObjectMessage will need to be on the broker's classpath. This isn't required under normal circumstances as the broker itself will never serialize or deserialize the object.
            • You should really try to avoid ObjectMessage whenever possible. ObjectMessage objects depend on Java serialization to marshal and unmarshal their object payload. This process is generally considered unsafe (and slow!), because a malicious payload can exploit the host system. Lots of CVEs have been created for this. For this reason, most JMS providers force users to explicitly whitelist packages that can be exchanged using ObjectMessage messages. For example, here's the related documentation for ActiveMQ Artemis. There are a number of other issues with using JMS ObjectMessage not related to security that you should read about.

            Granted you understand all that you should be able to convert the message using code something like this:



            how to retrieve the last value of a cell dynamically while parsing each rows of a dataframe?
            Asked 2022-Jan-18 at 13:47

            I'm trying to store the last value of a cell while I parse my dataframe, I can't know what this value will be so I need a dynamic method to do so.

            The desired value is stored in the position [row, 2] of my dataframe, but at each new row it changes. I'd like a way to write the position [index, 2] while using my parsing method.

            So far my code look like that :



            Answered 2022-Jan-18 at 13:47

            Split your rows in two dataframes: df3 for Code=50 and df4 for Code=10 then merge them:



            How to parse a dataframe efficiently, while storing data (specific row, or multiple rows) in others dataframe using a specific pattern?
            Asked 2022-Jan-17 at 08:14

            How to parse data on all rows, and use this row to populate other dataframes with data from multiple rows ?

            I am trying to parse a csv file containing several data entry for training purpose as I am quite new to this technology.

            My data consist in 10 columns, and hunderds of rows. The first column is filled with a code that is either 10, 50, or 90. Example :

            Dataframe 1 :

            0 1 10 Power-220 90 End 10 Power-290 90 End 10 Power-445 90 End 10 Power-390 50 Clotho 50 Kronus 90 End 10 Power-550 50 Ares 50 Athena 50 Artemis 50 Demeter 90 End

            And the list goes on..

            On one hand I want to be able to read the first cell, and to populate another dataframe directly if this is a code 10.

            On the other hand, I'd like to populate another dataframe with all the codes 50s, but I want to be able to get the data from the previous code 10, as it hold the type of Power that is used, and populate a new column on this dataframe.

            The new data frames are supposed to look like this:

            Dataframe 2 :

            0 1 10 Power-220 10 Power-290 10 Power-445 10 Power-390 10 Power-550

            Dataframe 3 :

            0 1 2 50 Clotho Power-390 50 Kronus Power-390 50 Ares Power-550 50 Athena Power-550 50 Artemis Power-550 50 Demeter Power-550

            So far, I was using iterrows, and I've read everywhere that it was a bad idea.. but i'm struggling implementing another method..

            In my code I just create two other dataframes, but I don't know yet a way to retrieve data from the previous cell. I would usually use a classic method, but I think it's rather archaic.



            Answered 2022-Jan-14 at 15:03

            You could simply copy the required rows to another dataframe,


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


            No vulnerabilities reported

            Install Artemis

            Please refer to the relevant documentation in the Documentation section below.


            Artemis GitHub pages: The Artemis user manual is at: The ACT user manual is at: The DNA plotter documentation is at: The BAM View documentation is at:
            Find more information at:

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