v1.1.1 Added check for overlap of MS2 isolation window with MS1 scan …

…range.
chhh · Nov 7, 2016 · e10f6ea · e10f6ea
1 parent 9c0772b
commit e10f6ea
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Showing 3 changed files with 41 additions and 20 deletions.
diff --git a/MSFileToolbox/src/umich/ms/datatypes/scancollection/ScanCollectionHelper.java b/MSFileToolbox/src/umich/ms/datatypes/scancollection/ScanCollectionHelper.java
@@ -112,9 +112,30 @@ public static void finalizeScanCollection(IScanCollection scans) throws FilePars
 
                         Integer thisMsLevel = curScan.getMsLevel();
                         Integer chldMsLevel = childScan.getMsLevel();
-                        if (precursor.getParentScanNum() == null
-                                && thisMsLevel != null && chldMsLevel != null && thisMsLevel + 1 == chldMsLevel) {
-                            precursor.setParentScanNum(curScanNum);
+                        if (precursor.getParentScanNum() == null && thisMsLevel != null && chldMsLevel != null && thisMsLevel + 1 == chldMsLevel) {
+
+                            Double pLo = precursor.getMzRangeStart();
+                            Double pHi = precursor.getMzRangeEnd();
+                            Double sLo = curScan.getScanMzWindowLower();
+                            Double sHi = curScan.getScanMzWindowUpper();
+                            if (pLo != null && pHi != null && sLo != null && sHi != null) {
+                                // if we know precursor isolation window and the scan's m/z scan range
+                                // they must overlap
+                                if (pLo <= sHi && sLo <= pHi) {
+                                    // they overlap!
+                                    if (pLo.equals(pHi)) { // it's a single point
+                                        precursor.setParentScanNum(curScanNum);
+                                    } else {
+                                        final double minOverlap = 0.75;
+                                        double overlap = Math.min(pHi, sHi) - Math.max(pLo, sLo);
+                                        precursor.setParentScanNum(curScanNum);
+                                    }
+                                }
+
+                            } else {
+                                // otherwise blindly add it
+                                precursor.setParentScanNum(curScanNum);
+                            }
                         }
 
                         // this else condition seems to not hold when some scans were cut out from mzXML file with ProteoWizrd.

diff --git a/MSFileToolbox/src/umich/ms/fileio/filetypes/LCMSDataSource.java b/MSFileToolbox/src/umich/ms/fileio/filetypes/LCMSDataSource.java
@@ -1,18 +1,18 @@
-/* 
- * Copyright 2016 Dmitry Avtonomov.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+/* 
+ * Copyright 2016 Dmitry Avtonomov.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package umich.ms.fileio.filetypes;
 
 import java.util.List;
@@ -163,5 +163,5 @@ public interface LCMSDataSource<T extends Index<?>> {
      * @throws umich.ms.fileio.exceptions.FileParsingException
      * @throws IllegalArgumentException
      */
-    public List<IScan> parse(List<Integer> scanNums) throws FileParsingException;
+    List<IScan> parse(List<Integer> scanNums) throws FileParsingException;
 }
diff --git a/MSFileToolbox/src/umich/ms/msfiletoolbox/MsftbxInfo.java b/MSFileToolbox/src/umich/ms/msfiletoolbox/MsftbxInfo.java
@@ -20,5 +20,5 @@
  * @author Dmitry Avtonomov
  */
 public class MsftbxInfo {
-    public static final String version = "1.1.0";
+    public static final String version = "1.1.1";
 }