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RNAAnalysis.ipf
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
#include ":ChopRNAPulls"
#include "::Force-Ramp-Utilities:BoxCarAveraging"
#include "::Force-Ramp-Utilities:SelectFR"
#include "::AR-Data:MeasurementTimeline"
#include "::MarkovFitter:DriftMarkovApp"
#include "::General-Igor-Utilities:SaveWavesUtil"
#include "::RNA-Pulling:RNAWLCAnalysis"
#include "::RuptureForce:RuptureForceApp"
Function InitRNAAnalysis()
// Make new data folders
NewDataFolder/O root:RNAPulling:Analysis
NewDataFolder/O root:RNAPulling:Analysis:RampAnalysis
// Set RNAAnalysis Parms Path
String PathIn=FunctionPath("")
NewPath/Q/O RNAAnalysisParms ParseFilePath(1, PathIn, ":", 1, 0) +"Parms"
// Load Settings Wave
SetDataFolder root:RNAPulling:Analysis
LoadWave/H/Q/O/P=RNAAnalysisParms "AnalysisSettings.ibw"
SetDataFolder root:RNAPulling:Analysis:RampAnalysis
LoadWave/H/Q/O/P=RNAAnalysisParms "RampFitSettings.ibw"
LoadWave/H/Q/O/P=RNAAnalysisParms "RampAnalysisSettings.ibw"
// Adjust Analysis Settings Wave
Wave AnalysisSettings=root:RNAPulling:Analysis:AnalysisSettings
AnalysisSettings=1
Wave LastRNAPullSettings=root:RNAPulling:RNAPullingSettings
AnalysisSettings[%NumRNAPulls]=LastRNAPullSettings[%Iteration]
// Make filtering settings wave
Make/O/N=(AnalysisSettings[%NumRNAPulls],2) root:RNAPulling:Analysis:RSFilterSettings
Wave RSFilterSettings=root:RNAPulling:Analysis:RSFilterSettings
RSFilterSettings=1
SetDimLabel 1,0, BoxCarNum, RSFilterSettings
SetDimLabel 1,1, Decimation, RSFilterSettings
// Make filtering settings wave
Make/O/N=(AnalysisSettings[%NumRNAPulls]) root:RNAPulling:Analysis:RSForceOffset,root:RNAPulling:Analysis:RSSepOffset
InitRNAPullingOffsets()
// Determine the number of times the rna pulling program ran
Wave Settings=root:RNAPulling:Analysis:Settings
Wave/T SettingsStr=root:RNAPulling:Analysis:SettingsStr
AnalysisSettings[%NumSteps]=NumStepsOrRamps(Settings,SettingsStr)
// Load waves for first time RNA Pulling program ran
LoadAllWavesForIndex(0)
// Load the first ramp/step on the for the first time the RNA pulling program ran
LoadRorS(0,0)
// Make Unfold and Refold Ramp Settings Waves
Wave RampFitSettings=root:RNAPulling:Analysis:RampAnalysis:RampFitSettings
SetDataFolder root:RNAPulling:Analysis:RampAnalysis
Duplicate/O RampFitSettings, UnfoldRFFitSettings, RefoldRFFitSettings
End
Function InitRNAPullingOffsets()
Wave RSForceOffset=root:RNAPulling:Analysis:RSForceOffset
Wave RSSepOffset=root:RNAPulling:Analysis:RSSepOffset
Variable NumRS=DimSize(RSForceOffset,0)
Variable RSCounter=22
For(RSCounter=22;RSCounter<NumRS;RSCounter+=1)
If(WaveExists($"root:FRU:preprocessing:Offsets"))
Wave/T SettingsStr=$"root:RNAPulling:SavedData:SettingsStr"+num2str(RSCounter)
String FRName=SettingsStr[%NearestForcePull]
Wave FRUOffsets=root:FRU:preprocessing:Offsets
RSForceOffset[RSCounter]=FRUOffsets[%$FRName][%Offset_Force]
RSSepOffset[RSCounter]=FRUOffsets[%$FRName][%Offset_Sep]
EndIf
EndFor
End
// Use this function on handle (also known as bridge) constructs to estimate the psf as a function of force
Function EstimatePSFCurrentMI(MasterIndex,StartStep,EndStep,[RNAAnalysisDF])
Variable MasterIndex,StartStep,EndStep
String RNAAnalysisDF
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
Wave ForceWave_smth=$RNAAnalysisDF+"ForceRorS_Smth"
Wave Extension_smth=$RNAAnalysisDF+"SepRorS_Smth"
Variable NumSteps=EndStep-StartStep+1
Make/O/N=(NumSteps) $RNAAnalysisDF+"PSF_Force",$RNAAnalysisDF+"PSF_Width",$RNAAnalysisDF+"PSF_Extension",$RNAAnalysisDF+"PSF_ExtensionWidth"
Wave PSF_Force=$RNAAnalysisDF+"PSF_Force"
Wave PSF_Width=$RNAAnalysisDF+"PSF_Width"
Wave PSF_Extension=$RNAAnalysisDF+"PSF_Extension"
Wave PSF_ExtensionWidth=$RNAAnalysisDF+"PSF_ExtensionWidth"
Variable StepCounter=StartStep
For(StepCounter=StartStep;StepCounter<EndStep+1;StepCounter+=1)
LoadRorS(MasterIndex,StepCounter)
WaveStats/Q ForceWave_smth
Variable Counter=StepCounter-StartStep
PSF_Force[Counter]=V_avg
PSF_Width[Counter]=V_sdev
WaveStats/Q Extension_smth
PSF_Extension[Counter]=V_avg
PSF_ExtensionWidth[Counter]=V_sdev
EndFor
Display PSF_Width vs PSF_Force
CurveFit/M=2/W=0 line, PSF_Width/X=PSF_Force/D
Display PSF_ExtensionWidth vs PSF_Force
CurveFit/M=2/W=0 line, PSF_ExtensionWidth/X=PSF_Force/D
End
Function UpdateNFPFromTimeline()
InitRNAPullingOffsets()
Wave RSForceOffset=root:RNAPulling:Analysis:RSForceOffset
Wave RSSepOffset=root:RNAPulling:Analysis:RSSepOffset
Variable NumRS=DimSize(RSForceOffset,0)
Variable RSCounter=0
For(RSCounter=0;RSCounter<NumRS;RSCounter+=1)
String Name="RNAPulling"+num2str(RSCounter)
String NFP=NearestARForceRamp(Name)
Wave/T SettingsStr=$"root:RNAPulling:SavedData:SettingsStr"+num2str(RSCounter)
SettingsStr[%NearestForcePull]=NFP
Wave FRUOffsets=root:FRU:preprocessing:Offsets
UpdateRNAPullingOffsets(RSCounter,FRUOffsets[%$NFP][%Offset_Force],FRUOffsets[%$NFP][%Offset_Sep])
EndFor
End
Function UpdateRNAPullingOffsets(MasterIndex,NewForceOffset,NewSepOffset,[RampDF])
Variable MasterIndex,NewForceOffset,NewSepOffset
String RampDF
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
Wave RSForceOffset=root:RNAPulling:Analysis:RSForceOffset
Wave RSSepOffset=root:RNAPulling:Analysis:RSSepOffset
If(!(NewForceOffset==RSForceOffset[MasterIndex]))
// Adjust Ramp fits and rupture forces if we have them.
If(RFAnalysisQ(MasterIndex))
Variable ForceDiff=+NewForceOffset-RSForceOffset[MasterIndex]
// First update y-intercept for fits
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Variable NumRamps=DimSize(UnfoldSettings,1)
Variable RampCounter=0
For(RampCounter=0;RampCounter<NumRamps;RampCounter+=1)
UnfoldSettings[%Fit1YIntercept][RampCounter]+=ForceDiff
UnfoldSettings[%Fit2YIntercept][RampCounter]+=ForceDiff
RefoldSettings[%Fit1YIntercept][RampCounter]+=ForceDiff
RefoldSettings[%Fit2YIntercept][RampCounter]+=ForceDiff
EndFor
// Now update the rupture forces
Wave UnfoldRF=$RampDF+"UnfoldRF_"+num2str(MasterIndex)
Wave RefoldRF=$RampDF+"RefoldRF_"+num2str(MasterIndex)
UnfoldRF+=ForceDiff
RefoldRF+=ForceDiff
EndIf
RSForceOffset[MasterIndex]=NewForceOffset
EndIf
If(NewSepOffset!=RSSepOffset[MasterIndex])
RSSepOffset[MasterIndex]=NewSepOffset
EndIf
End
// Init a rupture force analysis for a given master index
Function InitRFAnalysis(MasterIndex,[LoadWaves,RNAAnalysisDF,RampDF])
Variable MasterIndex,LoadWaves
String RNAAnalysisDF,RampDF
If(ParamIsDefault(LoadWaves))
LoadWaves=0
EndIf
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
If(LoadWaves)
LoadAllWavesForIndex(MasterIndex)
EndIf
// Initial guesses on ramp analysis for this master index
// Get Wave Paths
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
String UnfoldSettingsName=RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
String RefoldSettingsName=RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Duplicate/O UnfoldRFFitSettings,$UnfoldSettingsName,$RefoldSettingsName
Wave UnfoldSettings=$UnfoldSettingsName
Wave RefoldSettings=$RefoldSettingsName
// How many ramps for this master index
Wave Settings=$RNAAnalysisDF+"Settings"
Wave/T SettingsStr=$RNAAnalysisDF+"SettingsStr"
Variable NumRamps=NumStepsOrRamps(Settings,SettingsStr)
// Resize the settings wave for the master index with the number of ramps
Redimension/N=(-1,NumRamps) UnfoldSettings
Redimension/N=(-1,NumRamps) RefoldSettings
// Do first pass at rupture force analysis for unfolding and refolding
// Guess the RF fits settings for all ramps in this master index
GuessRFFitSettingsMI(MasterIndex)
// Estimate RF for all unfold and refold events in this master index
MeasureRFByMI(MasterIndex,"BothRuptures")
End
Function RFAnalysisQ(MasterIndex,[RampDF])
Variable MasterIndex
String RampDF
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
String RampAnalysisName=RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Return WaveExists($RampAnalysisName)
End
// Show the ramp analysis for a given ramp
Function DisplayRampAnalysis(MasterIndex,RampIndex,[LoadWaves,RNAAnalysisDF,RampDF,LoadFitSettings])
Variable MasterIndex,RampIndex,LoadWaves,LoadFitSettings
String RNAAnalysisDF,RampDF
If(ParamIsDefault(LoadWaves))
LoadWaves=0
EndIf
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
If(ParamIsDefault(LoadFitSettings))
LoadFitSettings=1
EndIf
If(LoadWaves)
LoadAllWavesForIndex(MasterIndex)
LoadRorS(MasterIndex,RampIndex)
EndIf
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
Wave RefoldRFFitSettings=$RampDF+"RefoldRFFitSettings"
Wave ForceRorS=$RNAAnalysisDF+"ForceRorS"
Wave ForceRorS_Smth=$RNAAnalysisDF+"ForceRorS_Smth"
If(LoadFitSettings)
UnfoldRFFitSettings=UnfoldSettings[p][RampIndex]
RefoldRFFitSettings=RefoldSettings[p][RampIndex]
EndIf
Duplicate/O/R=(UnfoldRFFitSettings[%Fit1StartTime],UnfoldRFFitSettings[%Fit2EndTime]) ForceRorS_Smth $RampDF+"UnfoldFit1"
Duplicate/O/R=(UnfoldRFFitSettings[%Fit1StartTime],UnfoldRFFitSettings[%Fit2EndTime]) ForceRorS_Smth $RampDF+"UnfoldFit2"
Duplicate/O/R=(RefoldRFFitSettings[%Fit1StartTime],RefoldRFFitSettings[%Fit2EndTime]) ForceRorS_Smth $RampDF+"RefoldFit1"
Duplicate/O/R=(RefoldRFFitSettings[%Fit1StartTime],RefoldRFFitSettings[%Fit2EndTime]) ForceRorS_Smth $RampDF+"RefoldFit2"
Wave UnfoldFit1=$RampDF+"UnfoldFit1"
Wave UnfoldFit2=$RampDF+"UnfoldFit2"
Wave RefoldFit1=$RampDF+"RefoldFit1"
Wave RefoldFit2=$RampDF+"RefoldFit2"
UnfoldFit1=UnfoldRFFitSettings[%Fit1LR]*x+UnfoldRFFitSettings[%Fit1YIntercept]
UnfoldFit2=UnfoldRFFitSettings[%Fit2LR]*x+UnfoldRFFitSettings[%Fit2YIntercept]
RefoldFit1=RefoldRFFitSettings[%Fit1LR]*x+RefoldRFFitSettings[%Fit1YIntercept]
RefoldFit2=RefoldRFFitSettings[%Fit2LR]*x+RefoldRFFitSettings[%Fit2YIntercept]
WaveStats/Q ForceRorS
Variable MaxForce=V_max
Variable MinForce=V_min
SetDataFolder $RampDF
Make/O/N=2 UnfoldFit1Start,UnfoldFit1End,UnfoldFit2Start,UnfoldFit2End,RefoldFit1Start,RefoldFit1End,RefoldFit2Start,RefoldFit2End,ForceMinMax,RF,RFTime
ForceMinMax={MaxForce,MinForce}
UnfoldFit1Start=UnfoldRFFitSettings[%Fit1StartTime]
UnfoldFit1End=UnfoldRFFitSettings[%Fit1EndTime]
UnfoldFit2Start=UnfoldRFFitSettings[%Fit2StartTime]
UnfoldFit2End=UnfoldRFFitSettings[%Fit2EndTime]
RefoldFit1Start=RefoldRFFitSettings[%Fit1StartTime]
RefoldFit1End=RefoldRFFitSettings[%Fit1EndTime]
RefoldFit2Start=RefoldRFFitSettings[%Fit2StartTime]
RefoldFit2End=RefoldRFFitSettings[%Fit2EndTime]
Wave UnfoldRFMI=$RampDF+"UnfoldRF_"+num2str(MasterIndex)
Wave UnfoldRFTimeMI=$RampDF+"UnfoldRFTime_"+num2str(MasterIndex)
Wave RefoldRFMI=$RampDF+"RefoldRF_"+num2str(MasterIndex)
Wave RefoldRFTimeMI=$RampDF+"RefoldRFTime_"+num2str(MasterIndex)
RF={UnfoldRFMI[RampIndex],RefoldRFMI[RampIndex]}
RFTime={UnfoldRFTimeMI[RampIndex],RefoldRFTimeMI[RampIndex]}
DoWindow/F RNARampAnalysis
If(V_flag==0)
Display/K=1/N=RNARampAnalysis ForceRorS
AppendToGraph/C=(0,15872,65280) ForceRorS_smth
ModifyGraph rgb(ForceRorS)=(48896,59904,65280)
AppendToGraph/C=(0,0,0) UnfoldFit1
AppendToGraph/C=(0,0,0) UnfoldFit2
AppendToGraph/C=(0,0,0) RefoldFit1
AppendToGraph/C=(0,0,0) RefoldFit2
AppendToGraph/C=(0,0,0) ForceMinMax vs UnfoldFit1Start
AppendToGraph/C=(0,0,0) ForceMinMax vs UnfoldFit1End
AppendToGraph/C=(0,0,0) ForceMinMax vs UnfoldFit2Start
AppendToGraph/C=(0,0,0) ForceMinMax vs UnfoldFit2End
AppendToGraph/C=(0,0,0) ForceMinMax vs RefoldFit1Start
AppendToGraph/C=(0,0,0) ForceMinMax vs RefoldFit1End
AppendToGraph/C=(0,0,0) ForceMinMax vs RefoldFit2Start
AppendToGraph/C=(0,0,0) ForceMinMax vs RefoldFit2End
AppendToGraph/C=(65000,0,0) RF vs RFTime
ModifyGraph mode(RF)=3,marker(RF)=42
Label left "Force (pN)"
ModifyGraph tickUnit=1
SetWindow RNARampAnalysis hook(RNADisplayHook)=RNADisplayHookFunction
EndIf
End
Function RNADisplayHookFunction(s)
STRUCT WMWinHookStruct &s
Variable hookResult = 0 // 0 if we do not handle event, 1 if we handle it.
Wave AnalysisSettings=root:RNAPulling:Analysis:AnalysisSettings
String RampDF="root:RNAPulling:Analysis:RampAnalysis:"
String RNAAnalysisDF="root:RNAPulling:Analysis:"
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
Wave RefoldRFFitSettings=$RampDF+"RefoldRFFitSettings"
Wave RF=$RampDF+"RF"
Wave RFTime=$RampDF+"RFTime"
If(RFAnalysisQ(AnalysisSettings[%MasterIndex]))
Wave UnfoldRFMI=$RampDF+"UnfoldRF_"+num2str(AnalysisSettings[%MasterIndex])
Wave UnfoldRFTimeMI=$RampDF+"UnfoldRFTime_"+num2str(AnalysisSettings[%MasterIndex])
Wave RefoldRFMI=$RampDF+"RefoldRF_"+num2str(AnalysisSettings[%MasterIndex])
Wave RefoldRFTimeMI=$RampDF+"RefoldRFTime_"+num2str(AnalysisSettings[%MasterIndex])
Wave RampAnalysisSettings=$RampDF+"RampAnalysisSettings"
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(AnalysisSettings[%MasterIndex])
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(AnalysisSettings[%MasterIndex])
EndIf
Wave ForceRorS=$RNAAnalysisDF+"ForceRorS"
Wave ForceRorS_Smth=$RNAAnalysisDF+"ForceRorS_Smth"
Wave Settings=$RNAAnalysisDF+"Settings"
Variable LeftClick=(s.eventmod & 2^0)!=0
Variable RightClick=(s.eventmod & 2^4)!=0
Variable ControlButton=(s.eventmod & 2^3)!=0
Variable ShiftButton=(s.eventmod & 2^1)!=0
Variable MouseTime=AxisValFromPixel("RNARampAnalysis","bottom",s.mouseloc.h)
Variable MouseForce=AxisValFromPixel("RNARampAnalysis","left",s.mouseloc.v)
switch(s.eventCode)
case 3: // Mouse down event
If(LeftClick&&ControlButton)
Variable NewUnfoldRF=MouseTime*UnfoldRFFitSettings[%Fit1LR]+UnfoldRFFitSettings[%Fit1YIntercept]
RF[0]=NewUnfoldRF
RFTime[0]=MouseTime
UnfoldRFMI[AnalysisSettings[%SubIndex]]=NewUnfoldRF
UnfoldRFTimeMI[AnalysisSettings[%SubIndex]]=MouseTime
hookResult=1
EndIf
If(RightClick&&ControlButton)
Variable NewRefoldRF=MouseTime*RefoldRFFitSettings[%Fit1LR]+RefoldRFFitSettings[%Fit1YIntercept]
RF[1]=NewRefoldRF
RFTime[1]=MouseTime
RefoldRFMI[AnalysisSettings[%SubIndex]]=NewRefoldRF
RefoldRFTimeMI[AnalysisSettings[%SubIndex]]=MouseTime
hookResult=1
EndIf
break
case 11: // Keyboard event
switch (s.keycode)
case 28: // Left Arrow
AnalysisSettings[%SubIndex]-=1
If(AnalysisSettings[%SubIndex]<0)
AnalysisSettings[%SubIndex]=0
EndIf
LoadRorS(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex])
DisplayRampAnalysis(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex],LoadFitSettings=1)
hookResult = 1
break
case 29: // Right Arrow
AnalysisSettings[%SubIndex]+=1
If(AnalysisSettings[%SubIndex]>=AnalysisSettings[%NumSteps])
AnalysisSettings[%SubIndex]=AnalysisSettings[%NumSteps]-1
EndIf
LoadRorS(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex])
DisplayRampAnalysis(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex],LoadFitSettings=1)
hookResult = 1
break
case 30: // Up Arrow
hookResult = 1
break
case 31: // Down Arrow
hookResult = 1
break
endswitch
break
case 22: // Mouse Wheel
If(!ControlButton&&!ShiftButton)
AnalysisSettings[%SubIndex]+=s.wheelDy
If(AnalysisSettings[%SubIndex]<0)
AnalysisSettings[%SubIndex]=0
EndIf
If(AnalysisSettings[%SubIndex]>=AnalysisSettings[%NumSteps])
AnalysisSettings[%SubIndex]=AnalysisSettings[%NumSteps]-1
EndIf
LoadRorS(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex])
DisplayRampAnalysis(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex],LoadFitSettings=1)
hookResult = 1
EndIf
If(ControlButton||ShiftButton)
Variable UnfoldTime=UnfoldRFFitSettings[%RampEndTime]-UnfoldRFFitSettings[%RampStartTime]
Variable RefoldTime=RefoldRFFitSettings[%RampEndTime]-RefoldRFFitSettings[%RampStartTime]
// Determine which interval we are trying to change and then change it by 5% of the ramp interval
Variable UnfoldChange=s.wheelDy*(0.02*UnfoldTime)
Variable RefoldChange=s.wheelDY*(0.02*UnfoldTime)
If((MouseTime>UnfoldRFFitSettings[%Fit1StartTime])&&(MouseTime<UnfoldRFFitSettings[%Fit1EndTime]))
If(ControlButton)
UnfoldRFFitSettings[%Fit1StartTime]+=UnfoldChange
Else
UnfoldRFFitSettings[%Fit1EndTime]+=UnfoldChange
EndIf
EndIf
If((MouseTime>UnfoldRFFitSettings[%Fit2StartTime])&&(MouseTime<UnfoldRFFitSettings[%Fit2EndTime]))
If(ControlButton)
UnfoldRFFitSettings[%Fit2StartTime]+=UnfoldChange
Else
UnfoldRFFitSettings[%Fit2EndTime]+=UnfoldChange
EndIf
EndIf
If((MouseTime>RefoldRFFitSettings[%Fit1StartTime])&&(MouseTime<RefoldRFFitSettings[%Fit1EndTime]))
If(ControlButton)
RefoldRFFitSettings[%Fit1StartTime]+=RefoldChange
Else
RefoldRFFitSettings[%Fit1EndTime]+=RefoldChange
EndIf
EndIf
If((MouseTime>RefoldRFFitSettings[%Fit2StartTime])&&(MouseTime<RefoldRFFitSettings[%Fit2EndTime]))
If(ControlButton)
RefoldRFFitSettings[%Fit2StartTime]+=RefoldChange
Else
RefoldRFFitSettings[%Fit2EndTime]+=RefoldChange
EndIf
EndIf
ApplyRFFit(UnfoldRFFitSettings,RefoldRFFitSettings,ForceRorS)
Variable NumSettings=DimSize(UnfoldRFFitSettings,0)
Variable SettingsCounter=0
For(SettingsCounter=0;SettingsCounter<NumSettings;SettingsCounter+=1)
UnfoldSettings[SettingsCounter][AnalysisSettings[%SubIndex]]=UnfoldRFFitSettings[SettingsCounter]
RefoldSettings[SettingsCounter][AnalysisSettings[%SubIndex]]=RefoldRFFitSettings[SettingsCounter]
EndFor
MeasureBothRF(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex],"BothRuptures",LoadWaves=1)
DisplayRampAnalysis(AnalysisSettings[%MasterIndex],AnalysisSettings[%SubIndex],LoadFitSettings=1)
hookResult = 1
Endif
break
endswitch
return hookResult // If non-zero, we handled event and Igor will ignore it.
End
Function MeasureRFByMI(MasterIndex,Method,[LoadWaves,RNAAnalysisDF,RampDF])
Variable MasterIndex,LoadWaves
String RNAAnalysisDF,RampDF,Method
If(ParamIsDefault(LoadWaves))
LoadWaves=0
EndIf
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
Wave RefoldRFFitSettings=$RampDF+"RefoldRFFitSettings"
If(LoadWaves)
LoadAllWavesForIndex(MasterIndex)
EndIf
Wave Settings=$RNAAnalysisDF+"Settings"
Wave/T SettingsStr=$RNAAnalysisDF+"SettingsStr"
Variable NumRamps=NumStepsOrRamps(Settings,SettingsStr)
Make/O/N=(NumRamps) $RampDF+"UnfoldRF_"+num2str(MasterIndex)
Make/O/N=(NumRamps) $RampDF+"UnfoldRFTime_"+num2str(MasterIndex)
Make/O/N=(NumRamps) $RampDF+"RefoldRF_"+num2str(MasterIndex)
Make/O/N=(NumRamps) $RampDF+"RefoldRFTime_"+num2str(MasterIndex)
Variable RampCounter=0
For(RampCounter=0;RampCounter<NumRamps;RampCounter+=1)
LoadRorS(MasterIndex,RampCounter)
MeasureBothRF(MasterIndex,RampCounter,Method,LoadWaves=1,RNAAnalysisDF=RNAAnalysisDF,RampDF=RampDF)
EndFor
End
Function MeasureBothRF(MasterIndex,RampIndex,Method,[LoadWaves,RNAAnalysisDF,RampDF])
Variable MasterIndex,RampIndex,LoadWaves
String RNAAnalysisDF,RampDF,Method
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
Wave RefoldRFFitSettings=$RampDF+"RefoldRFFitSettings"
If(ParamIsDefault(LoadWaves))
LoadWaves=0
EndIf
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
If(LoadWaves)
//LoadAllWavesForIndex(MasterIndex)
UnfoldRFFitSettings=UnfoldSettings[p][RampIndex]
RefoldRFFitSettings=RefoldSettings[p][RampIndex]
EndIf
Wave ForceWave=$RNAAnalysisDF+"ForceRorS"
Wave ForceWave_smth=$RNAAnalysisDF+"ForceRorS_Smth"
Wave UnfoldRFMI=$RampDF+"UnfoldRF_"+num2str(MasterIndex)
Wave UnfoldRFTimeMI=$RampDF+"UnfoldRFTime_"+num2str(MasterIndex)
Wave RefoldRFMI=$RampDF+"RefoldRF_"+num2str(MasterIndex)
Wave RefoldRFTimeMI=$RampDF+"RefoldRFTime_"+num2str(MasterIndex)
If(StringMatch("TargetTime",Method))
ApplyRFFit(UnfoldRFFitSettings,RefoldRFFitSettings,ForceWave)
Duplicate/O MeasureRF(ForceWave_smth,UnfoldRFFitSettings,Method=Method,TargetRuptureTime=UnfoldRFTimeMI[RampIndex]) $RampDF+"UnfoldRF"
Duplicate/O MeasureRF(ForceWave_smth,RefoldRFFitSettings,Method=Method,TargetRuptureTime=RefoldRFTimeMI[RampIndex]) $RampDF+"RefoldRF"
Variable NumSettings=DimSize(UnfoldRFFitSettings,0)
Variable SettingsCounter=0
For(SettingsCounter=0;SettingsCounter<NumSettings;SettingsCounter+=1)
UnfoldSettings[SettingsCounter][RampIndex]=UnfoldRFFitSettings[SettingsCounter]
RefoldSettings[SettingsCounter][RampIndex]=RefoldRFFitSettings[SettingsCounter]
EndFor
Else
Duplicate/O MeasureRF(ForceWave_smth,UnfoldRFFitSettings,Method=Method) $RampDF+"UnfoldRF"
Duplicate/O MeasureRF(ForceWave_smth,RefoldRFFitSettings,Method=Method) $RampDF+"RefoldRF"
EndIf
Wave UnfoldRF=$RampDF+"UnfoldRF"
Wave RefoldRF=$RampDF+"RefoldRF"
UnfoldRFMI[RampIndex]=UnfoldRF[%RuptureForce]
UnfoldRFTimeMI[RampIndex]=UnfoldRF[%RuptureTime]
RefoldRFMI[RampIndex]=RefoldRF[%RuptureForce]
RefoldRFTimeMI[RampIndex]=RefoldRF[%RuptureTime]
End
Function/Wave MeasureRF(ForceWave_smth,RFFitSettings,[Method,TargetRuptureTime])
Wave ForceWave_smth,RFFitSettings
String Method
Variable TargetRuptureTime
If(ParamIsDefault(Method))
Method="JustFirstRupture"
EndIf
If(ParamIsDefault(TargetRuptureTime))
TargetRuptureTime=0
EndIf
If(StringMatch(Method,"TargetTime"))
// Now estimate start of the other state
// Wave RF1=EstimateRF(ForceWave_smth,RFFitSettings[%Fit1LR],RFFitSettings[%Fit1YIntercept],RFFitSettings[%Fit1StartTime],RFFitSettings[%RampEndTime],RFStatsName="RF1",FirstLastTarget="TargetTime",TargetTime=TargetRuptureTime)
// Else
// Wave RF1=EstimateRF(ForceWave_smth,RFFitSettings[%Fit1LR],RFFitSettings[%Fit1YIntercept],RFFitSettings[%Fit1StartTime],RFFitSettings[%RampEndTime],RFStatsName="RF1",FirstLastTarget="Last")
EndIF
// Do the initial estimate of RF
If(StringMatch(Method,"BothRuptures"))
// Now estimate start of the other state
// Wave RF2=EstimateRF(ForceWave_smth,RFFitSettings[%Fit2LR],RFFitSettings[%Fit2YIntercept],RFFitSettings[%RampStartTime],RFFitSettings[%Fit2EndTime],RFStatsName="RF2",FirstLastTarget="First")
//
// // Now check for consistency
// Variable RFIsGood=RF2[%RuptureTime]>RF1[%RuptureTime]
//
// If(!RFIsGood)
// EstimateRF(ForceWave_smth,RFFitSettings[%Fit1LR],RFFitSettings[%Fit1YIntercept],RFFitSettings[%Fit1StartTime],RFFitSettings[%RampEndTime],RFStatsName="RF1",FirstLastTarget="Target",TargetCrossing=RF2[%RuptureTime])
// EndIf
EndIF
// Return RF1
End
// Guess RF fit settings for all ramps of a given master index
Function GuessRFFitSettingsMI(MasterIndex,[UnfoldStartFraction,UnfoldEndFraction,RefoldStartFraction,RefoldEndFraction,RampDF,RNAAnalysisDF])
Variable MasterIndex,UnfoldStartFraction,UnfoldEndFraction,RefoldStartFraction,RefoldEndFraction
String RNAAnalysisDF,RampDF
If(ParamIsDefault(RNAAnalysisDF))
RNAAnalysisDF="root:RNAPulling:Analysis:"
EndIf
If(ParamIsDefault(RampDF))
RampDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
If(ParamIsDefault(UnfoldStartFraction))
UnfoldStartFraction=0.5
EndIf
If(ParamIsDefault(UnfoldEndFraction))
UnfoldEndFraction=0.2
EndIf
If(ParamIsDefault(RefoldStartFraction))
RefoldStartFraction=0.2
EndIf
If(ParamIsDefault(RefoldEndFraction))
RefoldEndFraction=0.5
EndIf
Wave UnfoldRFFitSettings=$RampDF+"UnfoldRFFitSettings"
Wave RefoldRFFitSettings=$RampDF+"RefoldRFFitSettings"
Wave UnfoldSettings=$RampDF+"UnfoldRFFitSettings_"+num2str(MasterIndex)
Wave RefoldSettings=$RampDF+"RefoldRFFitSettings_"+num2str(MasterIndex)
Variable NumRamps=DimSize(UnfoldSettings,1)
Variable RampIndex=0
LoadRorS(MasterIndex,RampIndex)
Wave ForceWave=$RNAAnalysisDF+"ForceRorS"
Wave ForceWave_smth=$RNAAnalysisDF+"ForceRorS_Smth"
Wave RNAPullingSettings=$RNAAnalysisDF+"Settings"
For(RampIndex=0;RampIndex<NumRamps;RampIndex+=1)
LoadRorS(MasterIndex,RampIndex)
GuessRFFitSettings(UnfoldRFFitSettings,RefoldRFFitSettings,ForceWave,ForceWave_smth,RNAPullingSettings,UnfoldStartFraction=UnfoldStartFraction,UnfoldEndFraction=UnfoldEndFraction,RefoldStartFraction=RefoldStartFraction,RefoldEndFraction=RefoldEndFraction)
Variable NumSettings=DimSize(UnfoldRFFitSettings,0)
Variable SettingsCounter=0
For(SettingsCounter=0;SettingsCounter<NumSettings;SettingsCounter+=1)
UnfoldSettings[SettingsCounter][RampIndex]=UnfoldRFFitSettings[SettingsCounter]
RefoldSettings[SettingsCounter][RampIndex]=RefoldRFFitSettings[SettingsCounter]
EndFor
EndFor
End
Function ApplyRFFit(UnfoldSettings,RefoldSettings,ForceWave)
Wave UnfoldSettings,RefoldSettings,ForceWave
// Fit a line to the 4 main segments associated with unfolded and refolded states
// Wave LRFitUnfold1=LR(ForceWave,UnfoldSettings[%Fit1StartTime],UnfoldSettings[%Fit1EndTime],LRFitName="LRFitUnfold1",SpecifyEndTime=1)
// Wave LRFitUnfold2=LR(ForceWave,UnfoldSettings[%Fit2StartTime],UnfoldSettings[%Fit2EndTime],LRFitName="LRFitUnfold2",SpecifyEndTime=1)
// Wave LRFitRefold1=LR(ForceWave,RefoldSettings[%Fit1StartTime],RefoldSettings[%Fit1EndTime],LRFitName="LRFitRefold1",SpecifyEndTime=1)
// Wave LRFitRefold2=LR(ForceWave,RefoldSettings[%Fit2StartTime],RefoldSettings[%Fit2EndTime],LRFitName="LRFitRefold2",SpecifyEndTime=1)
// // Set Unfold Fit Settings
// UnfoldSettings[%Fit1LR]=LRFitUnfold1[%LoadingRate]
// UnfoldSettings[%Fit1YIntercept]=LRFitUnfold1[%YIntercept]
// UnfoldSettings[%Fit2LR]=LRFitUnfold2[%LoadingRate]
// UnfoldSettings[%Fit2YIntercept]=LRFitUnfold2[%YIntercept]
// // Set Refold Fit Settings
// RefoldSettings[%Fit1LR]=LRFitRefold1[%LoadingRate]
// RefoldSettings[%Fit1YIntercept]=LRFitRefold1[%YIntercept]
// RefoldSettings[%Fit2LR]=LRFitRefold2[%LoadingRate]
// RefoldSettings[%Fit2YIntercept]=LRFitRefold2[%YIntercept]
End
// Guess RF Fit Settings for a single, individual ramp.
Function GuessRFFitSettings(UnfoldSettings,RefoldSettings,ForceWave,ForceWave_smth,RNAPullingSettings,[UnfoldStartFraction,UnfoldEndFraction,RefoldStartFraction,RefoldEndFraction])
Wave UnfoldSettings,RefoldSettings,ForceWave,ForceWave_smth,RNAPullingSettings
Variable UnfoldStartFraction,UnfoldEndFraction,RefoldStartFraction,RefoldEndFraction
If(ParamIsDefault(UnfoldStartFraction))
UnfoldStartFraction=0.5
EndIf
If(ParamIsDefault(UnfoldEndFraction))
UnfoldEndFraction=0.2
EndIf
If(ParamIsDefault(RefoldStartFraction))
RefoldStartFraction=0.25
EndIf
If(ParamIsDefault(RefoldEndFraction))
RefoldEndFraction=0.5
EndIf
// Determine start and stop to all time intervals for analysis
Variable NumPts=DimSize(ForceWave,0)
Variable StartTime=pnt2x(ForceWave,0)
Variable EndTime=pnt2x(ForceWave,NumPts)-RNAPullingSettings[%DwellTime]
Variable FractionInUnfold=0.5 // This only works for equal velocities. Might need to fix later for different unfold/refold ramp speeds.
Variable TurnAroundTime=FractionInUnfold*(EndTime-StartTime)+StartTime
Variable UnfoldTime=TurnAroundTime-StartTime
Variable RefoldTime=EndTime-TurnAroundTime
Variable EndUnfoldFit1=StartTime+UnfoldStartFraction*UnfoldTime
Variable StartUnfoldFit2=TurnAroundTime-UnfoldEndFraction*UnfoldTime
Variable EndRefoldFit1=TurnAroundTime+RefoldStartFraction*RefoldTime
Variable StartRefoldFit2=EndTime-RefoldEndFraction*RefoldTime
// Set Unfold Fit Settings
UnfoldSettings[%RampStartTime]=StartTime
UnfoldSettings[%RampEndTime]=TurnAroundTime
UnfoldSettings[%Fit1StartTime]=StartTime
UnfoldSettings[%Fit1EndTime]=EndUnfoldFit1
UnfoldSettings[%Fit2StartTime]=StartUnfoldFit2
UnfoldSettings[%Fit2EndTime]=TurnAroundTime
// Set Refold Fit Settings
RefoldSettings[%RampStartTime]=TurnAroundTime
RefoldSettings[%RampEndTime]=EndTime
RefoldSettings[%Fit1StartTime]=TurnAroundTime
RefoldSettings[%Fit1EndTime]=EndRefoldFit1
RefoldSettings[%Fit2StartTime]=StartRefoldFit2
RefoldSettings[%Fit2EndTime]=EndTime
// Do fit with settings and save fit parameters to settings wave
ApplyRFFit(UnfoldSettings,RefoldSettings,ForceWave)
End
Function RFbyPullingSpeed([TargetDF])
String TargetDF
If(ParamIsDefault(TargetDF))
TargetDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
SetDataFolder $TargetDF
String UnfoldingWaves=WaveList("UnfoldRF_*", ";","")
String RefoldingWaves=WaveList("RefoldRF_*", ";","")
Variable NumRamps=ItemsInList(UnfoldingWaves)
Make/O/N=(NumRamps) UnfoldingSpeed,UnfoldingIndex,RefoldingSpeed
Variable RampCounter=0
For(RampCounter=0;RampCounter<NumRamps;RampCounter+=1)
String CurrentRampWave=StringFromList(RampCounter,UnfoldingWaves)
Variable MasterIndex=NumberByKey("UnfoldRF", CurrentRampWave, "_")
UnfoldingIndex[RampCounter]=MasterIndex
Wave Settings=$"root:RNAPulling:SavedData:"+"Settings"+num2str(MasterIndex)
UnfoldingSpeed[RampCounter]=Settings[%RetractVelocity]
RefoldingSpeed[RampCounter]=Settings[%ApproachVelocity]
EndFor
GetUniqueValues(UnfoldingSpeed,OutputWaveName="UniqueUnfoldVelocities")
GetUniqueValues(RefoldingSpeed,OutputWaveName="UniqueRefoldVelocities")
Wave UniqueUnfoldVelocities
Wave UniqueRefoldVelocities
Variable NumUniqueV=DimSize(UniqueUnfoldVelocities,0)
Variable UniqueVCounter=0
For(UniqueVCounter=0;UniqueVCounter<NumUniqueV;UniqueVCounter+=1)
Make/N=0/O $TargetDF+"AllUnfoldRF_"+num2str(Floor(UniqueUnfoldVelocities[UniqueVCounter]*1e9))+"nmps"
Make/N=0/O $TargetDF+"AllRefoldRF_"+num2str(Floor(UniqueRefoldVelocities[UniqueVCounter]*1e9))+"nmps"
EndFor
For(RampCounter=0;RampCounter<NumRamps;RampCounter+=1)
Variable UnfoldV=UnfoldingSpeed[RampCounter]
Variable RefoldV=RefoldingSpeed[RampCounter]
Wave AllUnfoldRF=$TargetDF+"AllUnfoldRF_"+num2str(Floor(UnfoldV*1e9))+"nmps"
Duplicate/O $TargetDF+"AllUnfoldRF_"+num2str(Floor(UnfoldV*1e9))+"nmps",TempUnfold
Wave AllRefoldRF=$TargetDF+"AllRefoldRF_"+num2str(Floor(RefoldV*1e9))+"nmps"
Duplicate/O $TargetDF+"AllRefoldRF_"+num2str(Floor(RefoldV*1e9))+"nmps",TempRefold
Wave CurrentUnfoldRF=$StringFromList(RampCounter,UnfoldingWaves)
Wave CurrentRefoldRF=$StringFromList(RampCounter,RefoldingWaves)
Concatenate/NP/O {TempUnfold,CurrentUnfoldRF}, $TargetDF+"AllUnfoldRF_"+num2str(Floor(UnfoldV*1e9))+"nmps"
Concatenate/NP/O {TempRefold,CurrentRefoldRF}, $TargetDF+"AllRefoldRF_"+num2str(Floor(RefoldV*1e9))+"nmps"
EndFor
End
// Function calculate mean rupture force of RNA ramps.
Function RNAMeanRF([Mode,TargetDF])
String Mode,TargetDF
If(ParamIsDefault(Mode))
Mode="ByRampSpeed"
EndIf
If(ParamIsDefault(TargetDF))
TargetDF="root:RNAPulling:Analysis:RampAnalysis:"
EndIf
SetDataFolder $TargetDF
String UnfoldingWaves,RefoldingWaves
StrSwitch(Mode)
case "ByIndex":
UnfoldingWaves=WaveList("UnfoldRF_*", ";","")
RefoldingWaves=WaveList("RefoldRF_*", ";","")
break
case "ByRampSpeed":
UnfoldingWaves=WaveList("AllUnfoldRF_*", ";","")
RefoldingWaves=WaveList("AllRefoldRF_*", ";","")
break
EndSwitch
Variable NumWaves=ItemsInList(UnfoldingWaves)
Variable WaveCounter=0
Make/O/D/N=(NumWaves) $"RFError"+Mode,$"UFError"+Mode,$"UF"+Mode,$"RF"+Mode,$"RF"+Mode+"Velocity",$"RF"+Mode+"TimeToLastCFR"
Wave UnfoldForce=$"UF"+Mode
Wave RefoldForce=$"RF"+Mode
Wave UnfoldForceError=$"UFError"+Mode
Wave RefoldForceError=$"RFError"+Mode
Wave Velocity=$"RF"+Mode+"Velocity"
Wave TimeToLastCFR=$"RF"+Mode+"TimeToLastCFR"
For(WaveCounter=0;WaveCounter<NumWaves;WaveCounter+=1)
SetDataFolder $TargetDF
Wave CurrentUnfoldRF=$StringFromList(WaveCounter,UnfoldingWaves)
Wave CurrentRefoldRF=$StringFromList(WaveCounter,RefoldingWaves)
WaveStats/Q CurrentUnfoldRF
UnfoldForce[WaveCounter]=V_avg
UnfoldForceError[WaveCounter]=V_sdev
WaveStats/Q CurrentRefoldRF
RefoldForce[WaveCounter]=V_avg
RefoldForceError[WaveCounter]=V_sdev
StrSwitch(Mode)
case "ByIndex":
Variable Index=Nan
sscanf StringFromList(WaveCounter,UnfoldingWaves), "UnfoldRF_%f", Index
Wave Settings=$"root:RNAPulling:SavedData:Settings"+num2str(Index)
Velocity[WaveCounter]=Settings[%RetractVelocity]
TimeToLastCFR[WaveCounter]=TimeSincePreviousCFR("RNAPulling"+num2str(Index))
break
case "ByRampSpeed":
Variable CurrentPullingSpeed=Nan
sscanf StringFromList(WaveCounter,UnfoldingWaves), "AllUnfoldRF_%f", CurrentPullingSpeed
Velocity[WaveCounter]=CurrentPullingSpeed
TimeToLastCFR[WaveCounter]=NaN
break
EndSwitch
EndFor
End
Function LoadRorS(MasterIndex,RSIndex,[TargetDF])
Variable MasterIndex,RSIndex
String TargetDF
If(ParamIsDefault(TargetDF))
TargetDF="root:RNAPulling:Analysis:"
EndIf
Wave Settings=$TargetDF+"Settings"
Wave/T SettingsStr=$TargetDF+"SettingsStr"
Wave DefV=$TargetDF+"DefV"
Wave ZSensor=$TargetDF+"ZSensor"
Wave ZSetPoint=$TargetDF+"ZSetPoint"
Wave RorSForce=$TargetDF+"RorSForce"
Wave RorSSep=$TargetDF+"RorSSep"
String ForcePath=TargetDF+"ForceRorS"
String SepPath=TargetDF+"SepRorS"
Wave RorSForce_smth=$TargetDF+"RorSForce_smth"
Wave RorSSep_smth=$TargetDF+"RorSSep_smth"
String ForcesmthPath=TargetDF+"ForceRorS_smth"
String SepsmthPath=TargetDF+"SepRorS_smth"
GetIndividualRoS(MasterIndex,RSIndex,DefV,ZSensor,ZSetPoint,Settings,SettingsStr)
GetIndividualRoS(MasterIndex,RSIndex,RorSForce,RorSSep,ZSetPoint,Settings,SettingsStr,DefVName=ForcePath,ZSensorName=SepPath)
GetIndividualRoS(MasterIndex,RSIndex,RorSForce_smth,RorSSep_smth,ZSetPoint,Settings,SettingsStr,DefVName=ForcesmthPath,ZSensorName=SepsmthPath)
End
// Get an individual ramp or step from the RNA Pulling data
Function GetIndividualRoS(MasterIndex,RSIndex,DefV,ZSensor,ZSetPoint,RNAPullingSettings,RNAPullingSettingsStr,[DefVName,ZSensorName])
Variable MasterIndex,RSIndex
Wave DefV,ZSensor,RNAPullingSettings,ZSetPoint
Wave/T RNAPullingSettingsStr
String DefVName,ZSensorName
If(ParamIsDefault(DefVName))
DefVName="root:RNAPulling:Analysis:DefVRorS"
EndIf
If(ParamIsDefault(ZSensorName))
ZSensorName="root:RNAPulling:Analysis:ZSensorRorS"
EndIf
Variable StartIndex,EndIndex=0
StrSwitch(RNAPullingSettingsStr[%CurrentMode])
case "LocalRamp":
Variable TotalTime=deltax(ZSetPoint)*DimSize(ZSetPoint,0)
Variable TimePerRamp=TotalTime/NumStepsOrRamps(RNAPullingSettings,RNAPullingSettingsStr)
StartIndex=RSIndex*TimePerRamp
EndIndex=(RSIndex+1)*TimePerRamp
break
case "Steps":
StartIndex=GetStepStartTime(RNAPullingSettings,RSIndex)
EndIndex=StartIndex+RNAPullingSettings[%TimePerStep]
break
EndSwitch
Duplicate/O/R=(StartIndex,EndIndex) DefV, $DefVName
Duplicate/O/R=(StartIndex,EndIndex) ZSensor, $ZSensorName
End
Function MakeStartEndIndexRorS(MasterIndex,ZSetPoint,RNAPullingSettings,RNAPullingSettingsStr,[StartIndexName,EndIndexName,UnfoldStartName,UnfoldEndName,RefoldStartName,RefoldEndName])
Variable MasterIndex
Wave ZSetPoint,RNAPullingSettings
Wave/T RNAPullingSettingsStr
String StartIndexName,EndIndexName,UnfoldStartName,UnfoldEndName,RefoldStartName,RefoldEndName
If(ParamIsDefault(StartIndexName))
StartIndexName="root:RNAPulling:Analysis:StartIndex"
EndIf
If(ParamIsDefault(EndIndexName))
EndIndexName="root:RNAPulling:Analysis:EndIndex"
EndIf
If(ParamIsDefault(UnfoldStartName))
UnfoldStartName="root:RNAPulling:Analysis:UnfoldStart"
EndIf
If(ParamIsDefault(UnfoldEndName))
UnfoldEndName="root:RNAPulling:Analysis:UnfoldEnd"
EndIf
If(ParamIsDefault(RefoldStartName))
RefoldStartName="root:RNAPulling:Analysis:RefoldStart"
EndIf
If(ParamIsDefault(RefoldEndName))
RefoldEndName="root:RNAPulling:Analysis:RefoldEnd"
EndIf
Variable RSIndex=0
Variable NumRS=NumStepsOrRamps(RNAPullingSettings,RNAPullingSettingsStr)
Make/O/D/N=(NumRS) $StartIndexName,$EndIndexName,$UnfoldStartName,$UnfoldEndName,$RefoldStartName,$RefoldEndName
Wave StartIndex=$StartIndexName
Wave EndIndex=$EndIndexName
Wave UnfoldStart=$UnfoldStartName
Wave UnfoldEnd=$UnfoldEndName
Wave RefoldStart=$RefoldStartName
Wave RefoldEnd=$RefoldEndName
For(RSIndex=0;RSIndex<NumRS;RSIndex+=1)
StrSwitch(RNAPullingSettingsStr[%CurrentMode])
case "LocalRamp":
Variable TotalTime=deltax(ZSetPoint)*DimSize(ZSetPoint,0)
Variable TimePerRamp=TotalTime/NumStepsOrRamps(RNAPullingSettings,RNAPullingSettingsStr)
StartIndex[RSIndex]=RSIndex*TimePerRamp
EndIndex[RSIndex]=(RSIndex+1)*TimePerRamp
UnfoldStart[RSIndex]=RSIndex*TimePerRamp
UnfoldEnd[RSIndex]=(RSIndex+0.5)*TimePerRamp
RefoldStart[RSIndex]=(RSIndex+0.5)*TimePerRamp
RefoldEnd[RSIndex]=(RSIndex+1)*TimePerRamp
break
case "Steps":
StartIndex[RSIndex]=GetStepStartTime(RNAPullingSettings,RSIndex)
EndIndex[RSIndex]=StartIndex+RNAPullingSettings[%TimePerStep]
UnfoldStart[RSIndex]=NaN
UnfoldEnd[RSIndex]=NaN
RefoldStart[RSIndex]=NaN
RefoldEnd[RSIndex]=NaN
break
EndSwitch
EndFor
End
Function AllRNADisplays([TargetDF])
String TargetDF
If(ParamIsDefault(TargetDF))
TargetDF="root:RNAPulling:Analysis:"
EndIf
DisplayRNAPull("ForceVsSep",TargetDF=TargetDF)
DisplayRNAPull("ForceVsSep_RorS",TargetDF=TargetDF)
DisplayRNAPull("ForceRorS",TargetDF=TargetDF)
DisplayRNAPull("RorSForce",TargetDF=TargetDF)
End
Function DisplayRNAPull(DisplayType,[TargetDF])
String DisplayType,TargetDF
If(ParamIsDefault(TargetDF))
TargetDF="root:RNAPulling:Analysis:"
EndIf
Wave DefV=$TargetDF+"DefV"
Wave ZSensor=$TargetDF+"ZSensor"
Wave SelectedForce_Ret=$TargetDF+"SelectedForce_Ret"
Wave SelectedSep_Ret=$TargetDF+"SelectedSep_Ret"
Wave RorSForce=$TargetDF+"RorSForce"
Wave RorSSep=$TargetDF+"RorSSep"
Wave RorSForce_smth=$TargetDF+"RorSForce_smth"
Wave RorSSep_smth=$TargetDF+"RorSSep_smth"
Wave ForceRorS=$TargetDF+"ForceRorS"
Wave SepRorS=$TargetDF+"SepRorS"
Wave ForceRorS_smth=$TargetDF+"ForceRorS_smth"
Wave SepRorS_smth=$TargetDF+"SepRorS_smth"
StrSwitch(DisplayType)
case "ForceVsSep":
DoWindow/F RNAAnalysis_ForceVsSep
If(V_flag==0)
Display/K=1/N=RNAAnalysis_ForceVsSep RorSForce vs RorSSep
AppendToGraph SelectedForce_Ret vs SelectedSep_Ret
ModifyGraph rgb(RorSForce)=(48896,59904,65280)