Java Web Start version?

That's the thing. We don't have a source file, and we don't want to create one. We want to pass the code to the jnlp file as a URI.

Also, the problem is not just multiline source. I can remove all the return characters from the MRV so that the code consists of a single line, and it still doesn't load. 

I was refering to SMILES and one-letter peptide notations as single-line formats.

MView needs a file to load from in case of other formats. With Applet, it was possible to load up files like this without generating at least a temporary file to load from. I don't think it's possible to do so in WebStart.

Peter

Maybe I'm misunderstanding what you're saying, but we currently launch the MarvinView applet with molecules in MOL and MRV formats with the following code. So it appears to me that MarvinView does indeed accept molecules in MRV and MOL format. Although I agree that the Web Start verson appears not to do.

/* Method for initiating MarvinView in a jsp page. Requires an

 * HTML element with ID = elementId.  */

function startMView(width, height, mol, displayFlags, mviewNum, elementId,

        qdNum, marvinVersion) {

    "use strict";

    var isQDatum = !isNaN(qdNum) && qdNum >= 0,

        appletBld = new String.builder(),

        molParts = (mol + ' ').split('<\/MDocument>'),

        numMols = molParts.length - 1;

    if (numMols === 0) numMols = 1;

    var numCols = (numMols > 2 ? 2 : numMols),

        newWidth = width * numCols,

        numRows;

    if (newWidth < 0) newWidth *= -1;

    else if (newWidth > 300) newWidth = 300;

    if (isQDatum) {

        appletBld.append('<table><tr><td class="boldtext" ' +

                    'style="text-align:right;font-style:italic;">' +

                    'MarvinView&trade;' +

                    '<input type="hidden" id="mviewNumOfQD').

                append(qdNum).

                append('" value="').

                append(mviewNum).

                append('" /><\/td><\/tr><tr><td class="whiteTable">');

    } // if is qDatum

    // multidocument structure to display in table?

    mview_name = 'marvinView' + mviewNum;

    mview_begin('/nosession/' + marvinVersion, newWidth, height);

    if (numMols > 1) {

        numRows = (numMols + (numMols % 2)) / 2;

        mview_param('rows', numRows);

        mview_param('cols', numCols);

        mview_param('border', 1);

    } // if there's more than one molecule to display

    mview_param('mol', mol);

    mview_param('molbg', '#FFFFFF');

    mview_param('rendering', 'wireframe');

    mview_param('valenceErrorVisible', 'true');

    mview_param('valencePropertyVisible', 'false');

    mview_param('implicitH', getHVisibility(displayFlags));

    mview_param('viewCarbonVisibility', getCVisibility(displayFlags));

    mview_param('lonePairsVisible', getLonePairsVisible(displayFlags));

    mview_param('atomPropertiesVisible', 'false');

    mview_param('chiralitySupport', getRSLabelsVisible(displayFlags));

    mview_param('atomMappingVisible', getAtomMapping(displayFlags));

    // if (width < 0) mview_param('tabScale', 30);

    appletBld.append(mview_end_to_string());

    if (isQDatum) {

        appletBld.append('<\/td><\/tr><\/table>');

    }

    setInnerHTML(elementId, appletBld.toString());

} // startMView()

Yes, we've written a wrapper around MView that gave this functionality. Unfortunately, that wrapper can't be used in case of WebStart.

We don't plan on adding this feature to WebStart and suggest to use Marvin JS instead of Marvin Sketch and embedded images instead of Marvin View.

Peter

We already use embedded images as a first choice. We currently allow the user to launch MarvinView when the user wants to manipulate the image, e.g. by rotating it in 3D or by displaying R/S labels. Unfortunately, the fact that the browsers will soon stop supporting Java plugins will make this feature untenable.

Also unfortunately, we can't use Marvin JS because it allows the user to edit the figure. There is currently no view-only version of Marvin JS. I and others have repeatedly asked for one, but the Marvin JS team will not commit to it.

Hi Bob,

I've mingled around on this issue on the weekend and found out that it's possible to use MView JWS with MRV as a parameter like this:

<application-desc main-class="chemaxon.marvin.View">
        <argument><![CDATA[<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_16_02_15.xsd" version="ChemAxon file format v16.02.15, generated by v16.3.14.0">
<MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C O C C N C" x3="-0.2970198534459908 -0.6024338000811952 0.08700386259096181 -0.13261713155340665 0.655147926289708 0.44685032294569726 1.1352289739103467" y3="1.0584811084039731 1.2624620223880887 0.2646849463893985 0.36948860793278454 -0.7455864806318447 -0.6319356697711274 -1.6659666758932636" z3="6.077805993696732 4.58278999318484 3.805679226982109 2.385173607447284 1.6702540933141925 0.21075050165387246 -0.5838332991106883"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"></bond><bond id="b2" atomRefs2="a2 a3" order="1"></bond><bond id="b3" atomRefs2="a3 a4" order="1"></bond><bond id="b4" atomRefs2="a4 a5" order="1"></bond><bond id="b5" atomRefs2="a5 a6" order="1"></bond><bond id="b6" atomRefs2="a6 a7" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument>
</cml>]]></argument>
    </application-desc>

Best regards,

Peter

Thanks for continuing to investigate this. Unfortunately, it's not working for me. Java launches, but I get an error message, Unable to launch the application.

java.lang.NullPointerException

	at com.sun.javaws.Main.launchApp(Unknown Source)

	at com.sun.javaws.Main.continueInSecureThread(Unknown Source)

	at com.sun.javaws.Main.access$000(Unknown Source)

	at com.sun.javaws.Main$1.run(Unknown Source)

	at java.lang.Thread.run(Thread.java:745)

My code:

    var param = new String.builder().

            append(pathToRoot).

            append('includes/mview-jnlp.jsp?argument=<![CDATA[').

            append(mol).

            append(']]>').

            toString();

    deployJava.launchWebStartApplication(param);

It works fine when mol is SMILES, but not when it is MRV. I tried the MRV that you showed above. Can you see anything I'm doing wrong?

You can only use the CDATA element inside the jnlp file and can't use it inside an URL.

You'll have to dynamically generate the whole jnlp file and pass that to the browser to load in.

BRs

Peter

Edit: Have you tried applying URL escaping on the mol string? Newlines and whitespaces have to be handled in a special way in URLs.

I did try using encodeURIComponent() on the structure code, including the <?[CDATA[ part, but it didn't help.

So either I write the MRV to a file, and pass the file's URL to a JSP page that generates the JNLP dynamically, or I write the JNLP page to a file. Either way, I write to a file, which is what I would like to avoid, if possible.

The worst thing about all this is that I was hoping that Chrome would run MarvinView if it was delivered via Java Web Start instead of as an applet, but it doesn't appear to do. So I'm not sure what all this effort has gained me.