Vladmodels Tanya Y157 01 Brar: Top

Local installation is more robust than Java Webstart.

The essential file is strap.jar (2.3 MByte) which can be started with the command java -jar strap.jar or by double click. A small helper file strap.bat (Windows), strap.command (Mac) or strap.sh (Linux) moves the jar file to the Strap folder $HOME/.StrapAlign/. It identifies existing Java installations. If needed, it will download and install Java for Windows, Mac or Linux on x86 platforms (50 to 80 MByte). For downloading Java, the script has the capability to detect web proxies. Finally it will start strap.jar. The same script file is used for installation and for running. Any Web-proxy will be automatically identified within Strap.

Start Strap either

from the desktop or the Downloads folder by double click or right-click Open ...
or from the command prompt:
- Protein or alignment files can be given as program parameters. In this case the user should change into the project directory before starting Strap.
- Wild cards under Mac, Unix and Linux
- Command line options -D... or -X... or JVM_... are passed to the Java Virtual Machine. For example -Xmx500M would set the memory to 500 MByte.

Installation for

Vladmodels Tanya Y157 01 Brar: Top

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Strap will detect Web proxy settings automatically by probing a bunch of web addresses with different settings. It will report success or failure.

If proxy detection fails or to speed up the start of Strap: Assume, the proxy host is proxy.organization.com and the port is 8080. Rename the script file to.

        "PH=proxy.organization.com PP=8080 more text if you like"

PH= and PP= must be upper case. The separating spaces are important. There must be no space at the equals sign.

To change settings, edit the script file strap.

OutOfMemoryError: The parameter in the form -Xmx200M sets the maximum memory limit to 200 MByte. Increase in case of OutOfMemoryError.
The absolute path to /bin/java.exe.
Macintosh screen menu bar: Modify the file strap.command with the text editor: Add -Dapple.laf.useScreenMenuBar=true after the Java command.

Strap offers some utilities. They are activated with certain command line parameters.

Protein/alignment file conversion: Use command line options -toFasta, -toMultipleFasta, -toClustal.
Strap can be used as a text viewer for very large files with advanced search text highlighting. Use the command line option -textViewer.
Strap can be used to manage pubmed abstracts and PDF full text. Text pattern highlighting allows text mining by eye in large amounts of pubmed abstracts. Use the command line option -pubmed.

Vladmodels Tanya Y157 01 Brar: Top

Jar-files are zip archives. The source code is contained in strap.jar and can be compiled with javac. However, it has passed a preprocessing step making it hard to read.
The original source code is available here: Source code