Quameter/peak symmetry

.gitignore

@@ -360,7 +360,8 @@ ASALocalRun/
 # NVidia Nsight GPU debugger configuration file
 *.nvuser
 
-/build-nt-x86
+build-nt-x86
+/src_subset
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@@ -379,7 +380,8 @@ Version.cpp
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+/artifact_xml
 
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@@ -399,9 +402,12 @@ Version.cpp
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+/pwiz_aux/msrc/utility/vendor_api/Bruker/**.SxS.manifest
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+/pwiz_aux/msrc/utility/vendor_api/thermo/x64
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@@ -419,45 +425,48 @@ SkylineTester Results
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+/pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/Properties/AssemblyInfo.cs
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-/pwiz_aux/msrc/utility/vendor_api/ABI/SCIEX.Apis.Data.v1.xml
+/SearchControlLog.txt
+
+# created by WIFF2 SDK in working directory
+/UserSettings.data
+/UserSettings.data-journal
+
+# created by TeamCity for Skyline versions that need PrositConfig.xml
+/pwiz_tools/Skyline/Model/Prosit/
+
+# created by older versions of the code in the working directory
+/Enolase_repeats_AQv1.4.2*
+/PressureTrace1*
+/7600ZenoTOFMSMS*
+/swath.api*
+/timstof_prm_scheduler.prmsqlite
+
+# created by tc-perftests.bat
+/perfTestNames.txt
+/tutorialTestNames.txt
+/tests.txt

pwiz_tools/Bumbershoot/quameter/crawdad/CrawPeak.cpp

@@ -1,21 +1,21 @@
-/*
- * Original author: Greg Finney <gfinney .at. u.washington.edu>,
- *                  MacCoss Lab, Department of Genome Sciences, UW
- *
- * Copyright 2009 University of Washington - Seattle, WA
- * 
- * 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.
- */
+/*
+ * Original author: Greg Finney <gfinney .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2009 University of Washington - Seattle, WA
+ * 
+ * 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.
+ */
 #include "CrawPeak.h"
 #include "CrawPeakMethod.h"
 #include <math.h>
@@ -43,12 +43,17 @@ namespace crawpeaks {
       return peak_area / bg_area;
    }
 
+   // BEG KEESH MAYO ASYMM METRIC
    SlimCrawPeak::SlimCrawPeak( int start_idx, int stop_idx, int peak_idx, 
-			     const std::vector<float> & raw ,std::vector<float> & scratch , int mz_idx  ) : 
+			     const std::vector<float> & raw ,std::vector<float> & scratch , int mz_idx,
+                 int start01_idx, int stop01_idx) :
     start_rt_idx(start_idx) , 
     stop_rt_idx(stop_idx) , 
     peak_rt_idx(peak_idx) , 
-    mz_idx(mz_idx) 
+    mz_idx(mz_idx),
+    start01_rt_idx(start01_idx),
+    stop01_rt_idx(stop01_idx)
+   // END KEESH MAYO ASYMM METRIC
    {
      init();
 
@@ -66,7 +71,7 @@ void SlimCrawPeak::init() {
     raw_area = bg_area = peak_area = bgslope = peak_height = raw_height = -1.0f;
     fwhm = -1;
     this->fwhm_calculated_ok = false;
-  }
+ }
 
 void CrawPeak::init() {
   stddev_mean_above_baseline = -1.0f;
@@ -77,10 +82,13 @@ void CrawPeak::init() {
 int SlimCrawPeak::delcnt = 0;
 #endif
 
+// BEG KEESH MAYO ASYMM METRIC
 CrawPeak::CrawPeak(  int start_idx, int stop_idx, int peak_idx, 
-		  const std::vector<float> & raw , std::vector<float> & scratch,  int mz_idx 
+		  const std::vector<float> & raw , std::vector<float> & scratch,  int mz_idx,
+          int start01_idx, int stop01_idx
                  ) :
-    SlimCrawPeak( start_idx, stop_idx, peak_idx, raw, scratch, mz_idx ) {
+    SlimCrawPeak( start_idx, stop_idx, peak_idx, raw, scratch, mz_idx,  start01_idx, stop01_idx) {
+ // END KEESH MAYO ASYMM METRIC
   init();     
   intensities.resize(this->len);
   background_vals.resize(this->len);
@@ -219,10 +227,10 @@ void CrawPeak::calc_baseline_stats( )  {
   }
 
 
-
+  
   std::string SlimCrawPeak::as_string_header() const { 
     return std::string("mz\tstart_idx\tpeak_idx\tstop_idx\tfwhm");
-  }
+  } 
    std::string SlimCrawPeak::as_string() const {
        char tmpstr[256];
        sprintf(tmpstr,"%d\t%d\t%d\t%d\t%d\t%2.2f",mz_idx,start_rt_idx,peak_rt_idx,stop_rt_idx,fwhm);
@@ -279,7 +287,7 @@ void CrawPeak::calc_baseline_stats( )  {
 /* ---- suppeaklocated ---- */
 
 CrawPeakLocated::CrawPeakLocated( int lh_valley, int rh_valley,
-			       int peak_loc, const std::vector<float> &chrom , std::vector<float> & scratch, int mz_idx ) : 
+			       int peak_loc, const std::vector<float> &chrom , std::vector<float> & scratch, int mz_idx ) :
   CrawPeak( lh_valley, rh_valley, peak_loc, chrom, scratch, mz_idx ) {
 }
 

pwiz_tools/Bumbershoot/quameter/crawdad/CrawPeak.h

@@ -76,6 +76,11 @@ public :
   float peak_height;
   float raw_height;
 
+  // BEG KEESH MAYO ASYMM METRIC
+  int start01_rt_idx, stop01_rt_idx;
+  // END KEESH MAYO ASYMM METRIC
+
+
   //CrawPeakMethod sup_method;
   virtual void init();
 
@@ -106,8 +111,11 @@ public :
 
   void calc_fwhm();
 
+  // BEG KEESH MAYO ASYMM METRIC
+  SlimCrawPeak(  int start_idx, int stop_idx, int peak_idx, const std::vector<float> & raw , std::vector<float> & scratch, int mz_idx = -1, 
+      int start01_idx = -1, int stop01_idx = -1);
+  // END KEESH MAYO ASYMM METRIC
 
-  SlimCrawPeak(  int start_idx, int stop_idx, int peak_idx, const std::vector<float> & raw , std::vector<float> & scratch, int mz_idx = -1 );
   ~SlimCrawPeak() {
     #ifdef DEBUG
     delcnt++;
@@ -149,6 +157,10 @@ class CrawPeak : public SlimCrawPeak {
   CrawPeak() {
     //sup_method = method;
     start_rt_idx = stop_rt_idx = peak_rt_idx = mz_idx = -1;
+    // BEG KEESH MAYO ASYMM METRIC
+    start01_rt_idx = stop01_rt_idx = -1;
+    // END KEESH MAYO ASYMM METRIC
+
     init();
   }
 
@@ -160,9 +172,11 @@ class CrawPeak : public SlimCrawPeak {
 */
 
   ///Constructor taking start,stop,peak,mz indices, and a vector of intensities
+  // BEG KEESH MAYO ASYMM METRIC
   CrawPeak(  int start_idx, int stop_idx, int peak_idx, 
-	   const std::vector<float> & raw, std::vector<float> & scratch ,int mz_idx = -1 );
-
+	   const std::vector<float> & raw, std::vector<float> & scratch ,int mz_idx = -1,
+       int start01_idx = -1, int stop01_idx = -1);
+  // END KEESH MAYO ASYMM METRIC
   virtual void init();
 
 

pwiz_tools/Bumbershoot/quameter/crawdad/CrawPeakAnnotator.cpp

@@ -515,6 +515,47 @@ void CrawPeakAnnotator::calc_fwhm( SlimCrawPeak & peak ) {
    peak.fwhm = rh_hm - lh_hm;
 }
 
+// BEG KEESH MAYO ASYMM METRIC
+void CrawPeakAnnotator::calc_fw01m(SlimCrawPeak& peak) {
+    std::vector<float>* c = this->get_active_chrom();
+    std::vector<float>& chrom = *c;
+    float lh_height = chrom.at(peak.start_rt_idx);
+    float rh_height = chrom.at(peak.stop_rt_idx);
+    float height = peak.raw_height - std::min(lh_height, rh_height);
+    float one_tenth_max = (float)(peak.raw_height - (0.9 * height));
+    int lh_pt = -1, rh_pt = -1;
+    float lh_hm, rh_hm;
+    for (int i = peak.start_rt_idx; i < peak.peak_rt_idx; i++) {
+        if (chrom[i] <= one_tenth_max && chrom[i + 1] >= one_tenth_max) {
+            lh_pt = i;
+            break;
+        }
+    }
+    for (int i = peak.peak_rt_idx; i < std::min(peak.stop_rt_idx, (int)(chrom.size() - 2)); i++) {
+        if (chrom[i] >= one_tenth_max && chrom[i + 1] <= one_tenth_max) {
+            rh_pt = i;
+            break;
+        }
+    }
+    if (lh_pt == -1) {
+        lh_hm = (float)peak.start_rt_idx;
+    }
+    else {
+        float frac_delta = (one_tenth_max - chrom[lh_pt]) / (chrom[lh_pt + 1] - chrom[lh_pt]);
+        lh_hm = (float)lh_pt + frac_delta;
+    }
+    if (rh_pt == -1) {
+        rh_hm = (float)peak.stop_rt_idx;
+    }
+    else {
+        float frac_delta = (chrom[rh_pt] - one_tenth_max) / (chrom[rh_pt] - chrom[rh_pt + 1]);
+        rh_hm = (float)rh_pt + frac_delta;
+    }
+    peak.start01_rt_idx = (int)lh_hm;
+    peak.stop01_rt_idx = (int)rh_hm;
+}
+// END KEESH MAYO ASYMM METRIC
+
 void CrawPeakAnnotator::refind_peak_peak( SlimCrawPeak & peak ) {
    peak.peak_rt_idx = get_peakloc_in_range( peak.start_rt_idx, peak.stop_rt_idx );
 }

pwiz_tools/Bumbershoot/quameter/crawdad/CrawPeakAnnotator.h

@@ -1,21 +1,21 @@
-/*
- * Original author: Greg Finney <gfinney .at. u.washington.edu>,
- *                  MacCoss Lab, Department of Genome Sciences, UW
- *
- * Copyright 2009 University of Washington - Seattle, WA
- * 
- * 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.
- */
+/*
+ * Original author: Greg Finney <gfinney .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2009 University of Washington - Seattle, WA
+ * 
+ * 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.
+ */
 
 #ifndef _SUPPEAKANNOTATOR_H
 #define _SUPPEAKANNOTATOR_H
@@ -191,6 +191,11 @@ void set_bg_scratch ( int start_idx, int stop_idx );
 
 void calc_fwhm( SlimCrawPeak & peak );
 
+// BEG KEESH MAYO ASYMM METRIC
+// Do we need to duplicat in ProteoWizard\pwiz_tools\Shared\Crawdad\CrawPeakAnnotator.H too?
+void calc_fw01m(SlimCrawPeak& peak);
+// END KEESH MAYO ASYMM METRIC
+
 #if 0
   void set_peak_positions ( SlimCrawPeak & peak ) {
 
@@ -205,7 +210,7 @@ void calc_fwhm( SlimCrawPeak & peak );
     //calls set_peak_areas onpeak member variables
     set_peak_bg_subtracted_area(peak);
     calc_fwhm(peak);
-  };
+    };
 
 
 private :

pwiz_tools/Bumbershoot/quameter/crawdad/CrawPeakFinder.cpp

@@ -597,6 +597,9 @@ void StackCrawPeakFinder::peak_voodoo( int lh_valley, int rh_valley, int peak_lo
      annotator.set_peak_slope(peak);
      annotator.set_peak_bg_subtracted_area ( peak );
      annotator.calc_fwhm(peak);
+     // BEG KEESH MAYO ASYMM METRIC
+     annotator.calc_fw01m(peak);
+     // END KEESH MAYO ASYMM METRIC
      sps.push_back(peak);
 
 }