Will describe an array in softSOFTtext format "ArrayType.Surface Type", "!Platform_support" => "ArrayType.Substrate Type", "!Platform_technology" => "ArrayType.Technology Type", "!Platform_manufacture_protocol" => "ArrayType.Spotting Method", "!Platform_manufacturer" => "ArrayType.Manufacturer.Name", "!Platform_distribution" => "ArrayType.Manufacturer.Origin", "!Platform_title" => "Name", "^PLATFORM" => "Name", "!Platform_organism" => "ArrayType.Species.Standard Ontology.Value", "!Platform_web_link" => "ArrayType.Manufacturer.Website" ); $required = array( "^PLATFORM", "!Platform_title", "!Platform_distribution", "!Platform_technology", "!Platform_organism", "!Platform_manufacturer", "!Platform_manufacture_protocol", "!Platform_support", "!Platform_coating", "!Platform_web_link" ); $protocols = array ("!Platform_manufacture_protocol"); // note only obvious equivalents are translated here... // or else the value will be kept as in maxdLoad2 $translations = array ( "!Platform_technology" => array ( "spotted DNA/cDNA" => "spotted_ds_DNA_features", "spotted oligonucleotide" => "spotted_ss_oligo_features", "in situ oligonucleotide" => "in_situ_oligo_features", "antibody" => "spotted_antibody_features", "RT-PCR" => "spotted_ss_PCR_amplicon_features" ), "!Platform_distribution" => array ( "commercial" => "Commercial", "non-commercial" => "Non-commercial" ) ); // assumes linkedResults come from only one original entry... shoddy! foreach ($input as $linkedKey => $linkedResult) { $newInput = $linkedResult; } $ArrayType = $newInput["ArrayType"]; //print_r($ArrayType["Name"]); $columns = array_keys($ArrayType); $foundArrayTypeID = false; foreach ($ArrayType["Name"] as $id => $name) { //print "\n '$name' == '$ArrayTypeName' \n"; if ($name == $ArrayTypeName) { $ArrayTypeID = $id; $foundArrayTypeID = true; } } if ($foundArrayTypeID != true) { throw new exception ("Sorry, but the ArrayType ID was not found for $ArrayTypeName."); } $string = ""; foreach ($required as $req) { $reqMapped = $map[$req]; if (! in_array($reqMapped, $columns) ) { throw new exception ("'ArrayType.$reqMapped' not found ... though this field may not required by maxdLoad2, it is essential for GEO export. It's the equivalent field to GEO's '$req'. Please annotate this database with this field."); } else { $value = $ArrayType[$reqMapped][$ArrayTypeID]; if (isset($translations[$req]) ) { $string .= "\n" . $req . " = " . array_search ($value, $translations[$req]); } elseif (in_array($req, $protocols) ) { $split = explode("\u000A", $value); foreach ($split as $n => $s) { $string .= "\n" . $req . " = " . ($n+1) . ". " . $s; } } else { $string .= "\n" . $req . " = " . $value; } } } $output = $string; //print "'" . $output . "'"; //die(); ]]> $linkedResult) { $newInput = $linkedResult; } $maxGeneNumber = 0; $tableString = ""; $input2sort = $newInput["Feature"]["Name"]; ksort($input2sort); foreach ($input2sort as $id => $name) { $tableString .= "\n" . $id . "\t" . $name; $reporters =& $newInput['Feature']['Reporter->'][$id]; if (count($reporters) > 0) { foreach ($reporters as $reporterId => $reporterName) { $tableString .= "\t" . $reporterName; $genes =& $newInput['Reporter']['Gene->'][$reporterId]; $geneCount = count($genes); if ($geneCount > $maxGeneNumber) { $maxGeneNumber = $geneCount; } if ($geneCount > 0) { foreach ($genes as $geneId => $geneName) { $tableString .= "\t" . $geneName; } } } } } $headerString = "\nID\tFeature\tReporter$maxGeneNumer"; //$output = "\n" . $maxGeneNumber; $headerCommentString = "\n#ID = the feature ID"; $headerCommentString .= "\n#Feature = the name of the Feature"; $headerCommentString .= "\n#Reporter = the name of the Reporter"; for ($i=1;$i<=$maxGeneNumber;$i++) { $headerString .= "\tSCO_ACC (#$i)"; $headerCommentString .= "\n#SCO_ACC (#$i) = the $GeneDatabaseName accession of a gene picked up by the probe LINK_PRE:\"$GeneAccessionLinkPre\" "; } $output = $headerCommentString . "\n!platform_table_begin" . $headerString . $tableString . "\n!platform_table_end"; ]]> link ArrayType Gene yes array 02