+ def filelist = []
+ file.eachLine {
+ line ->
+ filelist += line
+ }
+ def list = fileTree(dir: j2sDir, includes: filelist)
+
+ def jsfile = "${outputDir}/core${name}.js"
+ def zjsfile = "${outputDir}/core${name}.z.js"
+
+ jalviewjsCoreClasslists += [
+ 'jsfile': jsfile,
+ 'zjsfile': zjsfile,
+ 'list': list,
+ 'name': name
+ ]
+
+ inputs.file(file)
+ inputs.files(list)
+ outputs.file(jsfile)
+ outputs.file(zjsfile)
+ }
+
+ // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
+ def stevesoftClasslistName = "_stevesoft"
+ def stevesoftClasslist = [
+ 'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+ 'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
+ 'name': stevesoftClasslistName
+ ]
+ jalviewjsCoreClasslists += stevesoftClasslist
+ inputs.files(stevesoftClasslist['list'])
+ outputs.file(stevesoftClasslist['jsfile'])
+ outputs.file(stevesoftClasslist['zjsfile'])
+
+ // _all core
+ def allClasslistName = "_all"
+ def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+ allJsFiles += fileTree(
+ dir: libJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+ "**/org/jmol/export/JSExporter.js"
+ ]
+ )
+ allJsFiles += fileTree(
+ dir: swingJ2sDir,
+ include: "**/*.js",
+ excludes: [
+ // these exlusions are files that the closure-compiler produces errors for. Should fix them
+ "**/sun/misc/Unsafe.js",
+ "**/swingjs/jquery/jquery-editable-select.js",
+ "**/swingjs/jquery/j2sComboBox.js",
+ "**/sun/misc/FloatingDecimal.js"
+ ]
+ )
+ def allClasslist = [
+ 'jsfile': "${outputDir}/core${allClasslistName}.js",
+ 'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+ 'list': allJsFiles,
+ 'name': allClasslistName
+ ]
+ // not including this version of "all" core at the moment
+ //jalviewjsCoreClasslists += allClasslist
+ inputs.files(allClasslist['list'])
+ outputs.file(allClasslist['jsfile'])
+ outputs.file(allClasslist['zjsfile'])
+
+ doFirst {
+ def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+ logOutFile.getParentFile().mkdirs()
+ logOutFile.createNewFile()
+ logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+
+ jalviewjsCoreClasslists.each {
+ jalviewjsCallCore(it.name, it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+ }
+ }
+
+}
+
+
+def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inputFile, String outputFile) {
+ copy {
+ from inputFile
+ into file(outputFile).getParentFile()
+ rename { filename ->
+ if (filename.equals(inputFile.getName())) {
+ return file(outputFile).getName()
+ }
+ return null
+ }
+ filter(ReplaceTokens,
+ beginToken: '_',
+ endToken: '_',
+ tokens: [
+ 'MAIN': '"'+main_class+'"',
+ 'CODE': "null",
+ 'NAME': jalviewjsJalviewTemplateName+" [core ${coreName}]",
+ 'COREKEY': jalviewjs_core_key,
+ 'CORENAME': coreName
+ ]
+ )
+ }
+}
+
+
+task jalviewjsPublishCoreTemplates {
+ dependsOn jalviewjsBuildAllCores
+ def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
+ def inputFile = file(inputFileName)
+ def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+
+ def outputFiles = []
+ jalviewjsCoreClasslists.each { cl ->
+ def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+ cl['outputfile'] = outputFile
+ outputFiles += outputFile
+ }
+
+ doFirst {
+ jalviewjsCoreClasslists.each { cl ->
+ jalviewjsPublishCoreTemplate(cl.name, jalviewjsJalviewTemplateName, inputFile, cl.outputfile)
+ }
+ }
+ inputs.file(inputFile)
+ outputs.files(outputFiles)
+}
+
+
+task jalviewjsSyncCore (type: Sync) {
+ dependsOn jalviewjsBuildAllCores
+ dependsOn jalviewjsPublishCoreTemplates
+ def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
+ def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+
+ from inputFiles
+ into outputDir
+ def outputFiles = []
+ rename { filename ->
+ outputFiles += "${outputDir}/${filename}"
+ null
+ }
+ preserve {
+ include "**"
+ }
+ outputs.files outputFiles
+ inputs.files inputFiles
+}
+
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
+ dependsOn jalviewjsTranspile
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
+task jalviewjsSyncTransferSiteJs(type: Sync) {
+ from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+ include "**/*.*"
+ into "${jalviewDir}/${jalviewjsSiteDir}"
+ preserve {
+ include "**"
+ }
+}
+
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+
+jalviewjsSyncAllLibs.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+
+
+task jalviewjsPrepareSite {
+ group "JalviewJS"
+ description "Prepares the website folder including unzipping files and copying resources"
+ dependsOn jalviewjsSyncAllLibs
+ dependsOn jalviewjsSyncResources
+ dependsOn jalviewjsSyncSiteResources
+ dependsOn jalviewjsSyncBuildProperties
+ dependsOn jalviewjsSyncCore
+}
+
+
+task jalviewjsBuildSite {
+ group "JalviewJS"
+ description "Builds the whole website including transpiled code"
+ dependsOn jalviewjsCopyTransferSiteJs
+ dependsOn jalviewjsPrepareSite
+}
+
+
+task cleanJalviewjsTransferSite {
+ doFirst {
+ delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"