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- Jalview installer user interface mode not supported windows how to#
- Jalview installer user interface mode not supported windows code#
setValue ( "20" ) List arguments = new ArrayList () arguments. getArgument ( "GAPOPEN" ) gapopenpenalty. setValue ( "PAM300" ) Argument gapopenpenalty = options. getRunnerOptions () Argument matrix = options. Methods and classes mentioned in the excerpt are available from the JABAWS client library.
Jalview installer user interface mode not supported windows how to#
The next section describes how to check the status of the calculation. This is done to prevent excessive load on the server. While this may be ok with your local server, our public server (will not let you hold the connection for longer than 10 minutes.
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This is to avoid keeping the connection to the server on hold for a prolonged periods of time. In general, you should make sure that the calculation has been completed before attempting retrieving results. This line will block the execution until the result is available. Line three retrieves the alignment from a web service. Line two submits them to web service represented by msaws proxy. getResult ( jobId ) Line one loads FASTA sequence from the file. align ( fastalist ) Alignment alignment = msaws. readFasta ( new FileInputStream ( file )) String jobId = msaws. Framework exclude the web services layer. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Use Ant “Compile” or “Complile_with_debug” tasks to perform the staged compilation.Ī client package contains only classes from data model layer and a simple web services client. Any violation of the layer boundaries results in the compilation failure.
Jalview installer user interface mode not supported windows code#
The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. It depends on the engines and the data model, but know nothing about the web services.įinally, the upper layer contains the web services, that depend on all the layers below. The third layer consists of the wrappers for the native executables and classes to handle their configuration. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above. Thus currently code on this layer contain two engines. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster.
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The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. At the same time classes on this layer does not have any dependencies on the layers above. So, to be able to use JABAWS one needs to have these classes. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So the JABAWS project is split into 4 layers. The web services folder is the bottom layer and depends on all the other source code. The Engine level depends on the datamodel to compile etc. For example, the datamodel is the top level folder so it has no other dependencies on other JABAWS code. Each source folder depends on the upper folders for compilation.