Roslin Bioinformatics - VIPER

Saving Reports and Cleaned Data

Sections

Saving Images

The VIPER menu-bar provides a screenshot button, labeled 'Grab' which can be used for saving PNG format screenshots of the whole application as visible on screen at the time. 'Grab' will also save PNG files for any additional currently open windows, such as the 'Detail View' of a family, the 'Pedigree Chart View' of a family or any table that has been 'unpinned' from the main window.

Grab Button without Batik

If the user has Batik (version 1.7) binaries and dependencies available on the application classpath they should see further buttons to allow images to be saved in SVG and PDF format. (Dependencies listed below).

Grab Button with Batik

The images named according to current date and time and are saved to directories in the user's home directory (~/screenshotPNG, ~/screenshotSVG, ~/screenshotPDF).

Saving Cleaned Genotype Data

At any point in the analysis the 'Save Masked Pedigree Genotype' button on the top menu can be used to save the current state of the data as separate genotype and pedigree output files, from which the filtered and masked datapoints have been removed (deleted markers, completely masked individuals, deleted individual genotypes and deleted parental relationships). An additional log file details which datapoints have been removed. The user is given the choice of which directory to save these time-stamped files.

Analysis can proceed as normal after saving output, or the user may navigate back to an earlier checkpoint in the 'History' pane. Saved pedigree and genotype files may be used as input data files for VIPER, allowing the user to recommence a workflow after a break.

Optional Batik dependencies

        • batik-extension-1.7.jar
        • batik-awt-util-1.7.jar
        • batik-bridge-1.7.jar
        • batik-anim-1.7.jar
        • batik-script-1.7.jar
        • batik-js-1.7.jar
        • xalan-2.6.0.jar
        • batik-css-1.7.jar
        • batik-dom-1.7.jar
        • batik-ext-1.7.jar
        • batik-gvt-1.7.jar
        • batik-parser-1.7.jar
        • batik-svg-dom-1.7.jar
        • batik-util-1.7.jar
        • xml-apis-1.3.04.jar
        • xml-apis-ext-1.3.04.jar
        • batik-svggen-1.7.jar
        • batik-transcoder-1.7.jar
        • fop-0.94.jar
        • xmlgraphics-commons-1.2.jar
        • commons-logging-1.0.4.jar
        • commons-io-1.1.jar
        • avalon-framework-api-4.3.1.jar
        • avalon-framework-impl-4.3.1.jar
        • batik-xml-1.7.jar
        • batik-codec-1.7.jar

As Maven Dependencies

        <dependency>
            <groupId>org.apache.xmlgraphics</groupId>
            <artifactId>batik-extension</artifactId>
            <version>1.7</version>
        </dependency>
        <dependency>
            <groupId>org.apache.xmlgraphics</groupId>
            <artifactId>batik-svggen</artifactId>
            <version>1.7</version>
        </dependency>
        <dependency>
            <groupId>org.apache.xmlgraphics</groupId>
            <artifactId>batik-transcoder</artifactId>
            <version>1.7</version>
        </dependency>
        <dependency>
            <groupId>org.apache.xmlgraphics</groupId>
            <artifactId>batik-codec</artifactId>
            <version>1.7</version>
        </dependency>