se.lth.immun.mzml.Scan.scala Maven / Gradle / Ivy
package se.lth.immun.mzml
import se.lth.immun.xml.XmlReader
import se.lth.immun.xml.XmlWriter
import scala.collection.mutable.ArrayBuffer
object Scan {
import MzML._
def fromFile(r:XmlReader) = {
var x = new Scan
x.externalSpectrumID = r.readOptional(EXTERNAL_SPECTRUM_ID)
x.instrumentConfigurationRef = r.readOptional(INSTRUMENT_CONFIGURATION_REF)
x.sourceFileRef = r.readOptional(SOURCE_FILE_REF)
x.spectrumRef = r.readOptional(SPECTRUM_REF)
var e = r.top
r.next
while (r.in(e))
r.top.name match {
case CV_PARAM =>
x.cvParams += CvParam.fromFile(r)
case USER_PARAM =>
x.userParams += UserParam.fromFile(r)
case REFERENCEABLE_PARAM_GROUP_REF => {
x.paramGroupRefs += r.readAttribute(REF)
r.next
}
case SCAN_WINDOW_LIST => {
r.next
while (r.was(SCAN_WINDOW))
x.scanWindows += ScanWindow.fromFile(r)
}
case _ => r.skipThis
}
x
}
}
class Scan {
var externalSpectrumID:Option[String] = None
var instrumentConfigurationRef:Option[String] = None
var sourceFileRef:Option[String] = None
var spectrumRef:Option[String] = None
var cvParams = new ArrayBuffer[CvParam]
var userParams = new ArrayBuffer[UserParam]
var paramGroupRefs = new ArrayBuffer[String]
var scanWindows = new ArrayBuffer[ScanWindow]
def write(w:XmlWriter) = {
import MzML._
w.startElement(SCAN)
w.writeOptional(EXTERNAL_SPECTRUM_ID, externalSpectrumID)
w.writeOptional(INSTRUMENT_CONFIGURATION_REF, instrumentConfigurationRef)
w.writeOptional(SOURCE_FILE_REF, sourceFileRef)
w.writeOptional(SPECTRUM_REF, spectrumRef)
for (x <- paramGroupRefs) ReferenceableParamGroupRef.write(w, x)
for (x <- cvParams) x.write(w)
for (x <- userParams) x.write(w)
if (!scanWindows.isEmpty) {
w.startListElement(SCAN_WINDOW_LIST, scanWindows)
for (x <- scanWindows) x.write(w)
w.endElement
}
w.endElement
}
}