fixed mzml to IMSRawDataFile import
package io.github.mzmine.modules.io.rawdataimport.fileformats.mzml_msdk;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.logging.Logger;
import com.google.common.collect.Range;
import io.github.msdk.datamodel.MsScan;
import io.github.mzmine.datamodel.IMSRawDataFile;
@@ -40,6 +32,14 @@ import io.github.mzmine.project.impl.IMSRawDataFileImpl;
import io.github.mzmine.taskcontrol.AbstractTask;
import io.github.mzmine.taskcontrol.TaskStatus;
import io.github.mzmine.util.ExceptionUtils;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.logging.Logger;
/**
* This class reads mzML 1.0 and 1.1.0 files (http://www.psidev.info/index.php?q=node/257) using the
@@ -142,7 +142,7 @@ public class MSDKmzMLReadTask extends AbstractTask {
final List<Double> mobilities = new ArrayList<>();
final List<BuildingImsMsMsInfo> buildingImsMsMsInfos = new ArrayList<>();
Set<ImsMsMsInfo> finishedImsMsMsInfos = null;
- final IMSRawDataFile newImsFile = (IMSRawDataFile) file;
+ final IMSRawDataFile newImsFile = (IMSRawDataFile) newMZmineFile;
for (MsScan scan : file.getScans()) {
MzMLMsScan mzMLScan = (MzMLMsScan) scan;
