pdbToPqrMain.js

var pdbFile;
var job;

var SERVICEURI;

function setIndex( id ,  val ) {
    document.getElementById( id ).selectedIndex =  val ;
}

function init( ) {
    try{

if( selfInfo != null ) {       
		var p = selfInfo.wsdl_uri;
                var k  = p.lastIndexOf( "?" );
		if( k > -1 ) {
		    SERVICEURI  = p.substring( 0,  k );
		} else SERVICEURI = p; 
		
		document.getElementById( "pdb2pqr-desc" ).value = "PDB2PQR: " + SERVICEURI;
        }

}catch( e ){ alert( e ); }

}

function shutdown() {
}

/***** Job Running/Creating *****/

function run( ) {

try{
	if( pdbFile == null ) {
	    alert( "Error: select PDB file first" );
	    return;
	}

updateStatusMessage( "" );
	updateOutputDisplay( "reset" );
	updateProgress( "reset" );

var env = createInput( );

if( jobManager != null )
	{
	    job = jobManager.createJob( );
	}
	else job = new Job( );

job.open( SERVICEURI , true, "opal" , "Pdb2Pqr");
	job.addListener(  "onjoblaunched" , responseHandler) ;
	job.addListener(  "onjobquery" , responseHandler) ;
	job.addListener(  "onjobcompletion" , responseHandler) ;
	job.addListener(  "onjoberror" , responseHandler) ;
	job.addListener(  "onjobaborted" , responseHandler) ;
	job.addNamespace( "default" , "http://nbcr.sdsc.edu/opal/types" );

var rv;
	if( jobManager != null ) {
	    rv = jobManager.addJob( job );
	    if( rv )
		job.launch( env );
	}
	else
		job.launch( env );

disableInput( );

}catch( e ){  trace( "runPdb2pqr: " + e ); alert( "runPdb2pqr: " + e ); }

}

function createInput( ) {

var argList = "";

if( document.getElementById( "debump" ).checked )
	    argList += "--nodebump "
		
	if( document.getElementById( "hydrogens" ).checked )
	    argList += "--noopt "

if( document.getElementById( "propka" ).checked ) {
	    argList += "--with-ph=" + document.getElementById( "ph_val" ).value + " ";
	}
                     
	argList += "--ff=" + document.getElementById( "forcefield" ).selectedItem.value + " ";
	argList +=  pdbFile.getLeaf( )+ " ";
	argList +=  pdbFile.getLeaf( ).substring( 0 , pdbFile.getLeaf( ).lastIndexOf( ".pdb" ) ) + ".pqr" + " ";

pdbFile.open( "r" );
	var content = pdbFile.readBase64( );

var msg = new Array( 14 );
	msg[1] = '<launchJobInput xmlns="http://nbcr.sdsc.edu/opal/types">' + '\n';
	msg[2] = '<argList>' ;
	msg[3] = argList;
	msg[4] = '</argList>' + '\n';
	msg[5] = '<inputFile>' ;
	msg[6] = '<name>';
	msg[7] =  pdbFile.leaf;
	msg[8] = "</name>";
	msg[9] = '<contents>';
	msg[10] =  content;
	msg[11] = "</contents>";
	msg[12] = '</inputFile>' ;
	msg[13] = '</launchJobInput>';

return msg.join( "" );
}

/***** Job Handling *****/

function responseHandler( type , responseState ) {
    try{
	    if( type == "onjobquery" ) {

updateStatusMessage( job.getStatusMessage( ) );

}
	    else if( type == "onjoblaunched" ) {

updateProgress( "start" );
		updateStatusMessage( job.getStatusMessage( ) );

}
	    else if( type == "onjobcompletion" ) {

enableInput();
		updateStatusMessage( job.getStatusMessage( ) );
		updateProgress( "finished" );
		updateOutputDisplay( "set",  responseState.responseText );

}
	    else if( (type == "onjobaborted")   || (type == "onjoberror") ) {

enableInput();
		updateProgress( "finished" );
		updateStatusMessage( job.getStatusMessage( ) );

}

}catch( e ){  trace( "PDB2PQR: " + e ); alert( "PDB2PQR: " + e ); }

}

function updateOutputDisplay( mode , txt ) {

try{
	    if( mode == "reset" ) {
                var outRows = geid( "output-rows" );

while( outRows.hasChildNodes() == true ) {
                    outRows.removeChild( outRows.firstChild );
                }

return;
            }
            else if( mode == "set" ) {

var doc = new DOMParser().parseFromString(txt, 'text/xml');

var outRows = geid( "output-rows" );
                var outVars = [ "stdOut" , "stdErr" , "outputFile" ];

for( var k = 0; k < outVars.length; k++ ) {

var nodes = xPathSearch( doc, '//' + outVars[ k ] );
                    var name;
                    var url;

for( var i = 0; i < nodes.length; i++ ) {

var row = document.createElement("row");
                        var lbl = document.createElement("label");
                        var btn = document.createElement("button");
                        var btn2 = document.createElement("button");

try{
                                if( nodes[ i ].nodeName == "outputFile"  ) {
                                    name = nodes[ i ].firstChild.lastChild.nodeValue;
                                    url = nodes[ i ].lastChild.firstChild.nodeValue;
                                }
                                else {
                                    name = outVars[ k ];
                                    url = nodes[ i ].firstChild.nodeValue;
                                }

}catch( e ){ }

lbl.setAttribute( "value" , name );
                        var btn = document.createElement("button");
                        btn.setAttribute( "label" , "Open..." );
                        btn.setAttribute( "oncommand" , 'openExternalURI("'  + url +'")' );

btn2.setAttribute( "v" ,  url );
                        btn2.setAttribute( "label" , "Save..." );
                        btn2.setAttribute( "oncommand" , 'saveOutputFile(event);');
                        btn2.setAttribute(  "ondraggesture", "nsDragAndDrop.startDrag(event,outputFileObserver);" );

row.appendChild( lbl );
                        row.appendChild( btn );
                        row.appendChild( btn2 );
                        outRows.appendChild( row );
                    }

setIndex("pdb2pqr-content-tabpanels" , 1 );
                     setIndex("pdb2pqr-content-tabs" , 1 );
                }

}

}catch( e ){  trace( "updateOutputDisplay: " + e ); alert( "updateOutputDisplay: " + e ); }

}

function updateStatusMessage( msg ) {

document.getElementById("status-message").value = msg;
}

function updateProgress( action ) {

if( action == "reset" ) {
            document.getElementById("progress-meter").setAttribute( "mode" , "determined");
            document.getElementById("progress-meter").value =  0;
    }
    else if( action == "start" ) {
            document.getElementById("progress-meter").setAttribute( "mode" , "undetermined");
    }
    else if( action == "finished" ) {
            document.getElementById("progress-meter").setAttribute( "mode" , "determined");
            document.getElementById("progress-meter").value =  100;
    }

}

function enableInput( ) {
    document.getElementById( "run-btn" ).removeAttribute( "disabled" );
}

function disableInput( ) {
    document.getElementById( "run-btn" ).setAttribute( "disabled" , "true");
}

/***** User Interaction *****/

function togglePropka(  ) {
    if( document.getElementById( "propka" ).checked ) {
	document.getElementById( "ph" ).removeAttribute( "hidden" );
	document.getElementById( "ph_val" ).removeAttribute( "hidden" );
    }
    else {
	document.getElementById( "ph" ).setAttribute( "hidden" , "true" );
	document.getElementById( "ph_val" ).setAttribute( "hidden" , "true" );
    }

}

function selectPdb( mode, path ) {
    try{

var filepath;

if( mode == "drag" ) {
	   filepath = path; 
	}
	else {
	    var fp =  showFilePicker( "modeOpen" , "Select PDB"    ); 
	    if( fp == null )
		return;
	    else filepath = fp.filePath;	    
	}

pdbFile = new File( filepath );

document.getElementById( "pdb-txt" ).value = pdbFile.getLeaf( );

}catch( e ){  trace( "PDB2PQR: " + e ); alert( "PDB2PQR: " + e ); }
}

function saveOutputFile( event ) {

var url =  event.explicitOriginalTarget.getAttribute( "v" );
   var fileName = url.substring( url.lastIndexOf( "/" ) + 1 );

var rv = showFilePicker( "modeSave" , "Save Output File", null, fileName    );
   downloadWithManager( url, new File( rv.file) );

}

/***** Drag & Drop *****/

var dropObserver = {

getSupportedFlavours : function () {
    var flavours = new FlavourSet();
    flavours.appendFlavour("text/unicode");
    return flavours;
  },

onDragOver: function (evt,flavour,session)
  {

if( evt.explicitOriginalTarget.tagName.indexOf( "textbox" ) != -1 )
        session.canDrop = false;
  },

onDrop: function (evt,dropdata,session){
    var dest = evt.currentTarget.tagName;

if( dest == "textbox" )
	return;

if (dropdata.data!=""){
	    var data =  getFilepathFromURL( dropdata.data );
	    selectPdb( "drag" , data );
	}
    }

};

var outputFileObserver = {
         onDragStart: function (evt,transferData,action){

var path = evt.target.getAttribute( 'v' );

transferData.data=new TransferData();
             transferData.data.addDataForFlavour("text/unicode",path);
       }
     };