--- /dev/null
+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
+ */
+/**
+ * Mark Larkin 9 Dec 2005.
+ * Note that most of the variables in this class are from param.h.
+ *
+ * Change log:
+ * Jan 18th 2006: Changed all of the c style strings into c++ string objects!
+ * Mark 30-1-2007: Added useLEScoringFunction and access functions.
+ * 31-01-07,Nigel Brown(EMBL): Revision string now obtained from clustalw
+ * specific versionw.h and updated from 1.83 to 2.1.
+ */
+
+#ifndef USERPARAMETERS_H
+#define USERPARAMETERS_H
+
+#include <string>
+#include <iostream>
+#include "utils.h"
+#include "general.h"
+#include "clustalw.h"
+
+namespace clustalw
+{
+
+class UserParameters
+{
+ public:
+ /* Functions */
+ UserParameters(bool log = false);
+ void setParamsToDefault();
+ void createParameterOutput();
+ int resIndex(string t,char c);
+ void setDNAMultiGap();
+ void setProtMultiGap();
+ void setDNAParams();
+ void setProtParams();
+ void setPWProteinParam();
+ void setPWDNAParam();
+ void setPWParamToProtein();
+ void setPWParamToDNA();
+ string getRevisionLevel();
+ void setRevisionLevel(string value);
+ bool getInteractive(){return interactive;};
+ void setInteractive(bool value);
+ float getGapOpen(){return gapOpen;};
+ void setGapOpen(float value);
+ float getGapExtend(){return gapExtend;};
+ void setGapExtend(float value);
+ float getPWGapOpen(){return PWGapOpen;};
+ void setPWGapOpen(float value);
+ float getPWGapExtend(){return PWGapExtend;};
+ void setPWGapExtend(float value);
+ float getAAGapOpen(){return AAGapOpen;}
+ void setAAGapOpen(float gap){AAGapOpen = gap;}
+ float getAAGapExtend(){return AAGapExtend;}
+ void setAAGapExtend(float gap){AAGapExtend = gap;}
+ float getAAPWGapOpen(){return AAPWGapOpen;}
+ void setAAPWGapOpen(float gap){AAPWGapOpen = gap;}
+ float getAAPWGapExtend(){return AAPWGapExtend;}
+ void setAAPWGapExtend(float gap){AAPWGapExtend = gap;}
+ int getMaxAA(){return maxAA;};
+ void setMaxAA(int value);
+ int getGapPos1(){return gapPos1;};
+ void setGapPos1(int value);
+ int getGapPos2(){return gapPos2;};
+ void setGapPos2(int value);
+ int getProfileNum(){return profileNum;};
+ void setProfileNum(int value);
+ bool getMenuFlag(){return menuFlag;};
+ void setMenuFlag(bool value);
+ bool getDNAFlag(){return DNAFlag;};
+ void setDNAFlag(bool value);
+ bool getDistanceTree(){return distanceTree;};
+ void setDistanceTree(bool value);
+ string getSeqName(){return seqName;};
+ void setSeqName(string value);
+ float getDNAGapOpen(){return DNAGapOpen;};
+ void setDNAGapOpen(float value);
+ float getDNAGapExtend(){return DNAGapExtend;};
+ void setDNAGapExtend(float value);
+ float getProteinGapOpen(){return AAGapOpen;};
+ void setProteinGapOpen(float value);
+ float getProteinGapExtend(){return AAGapExtend;};
+ void setProteinGapExtend(float value);
+ int getGapDist(){return gapDist;};
+ void setGapDist(int value);
+ int getOutputOrder(){return outputOrder;};
+ void setOutputOrder(int value);
+ void toggleOutputOrder();
+ int getDivergenceCutoff(){return divergenceCutoff;};
+ void setDivergenceCutoff(int value);
+
+
+ string getHydResidues(){return hydResidues;};
+ void setHydResidues(string value);
+ bool getNoWeights(){return noWeights;};
+ void setNoWeights(bool value);
+ bool getUseNegMatrix(){return negMatrix;};
+ void setUseNegMatrix(bool value);
+ void toggleUseNegMatrix();
+ bool getNoHydPenalties(){return noHydPenalties;};
+ void setNoHydPenalties(bool value);
+ void toggleNoHydPenalties();
+ bool getNoVarPenalties(){return noVarPenalties;};
+ void setNoVarPenalties(bool value);
+ bool getNoPrefPenalties(){return noPrefPenalties;};
+ void setNoPrefPenalties(bool value);
+ void toggleNoPrefPenalties();
+ bool getUseEndGaps(){return useEndGaps;};
+ void setUseEndGaps(bool value);
+ void toggleUseEndGaps();
+ bool getEndGapPenalties(){return endGapPenalties;};
+ void setEndGapPenalties(bool value);
+ bool getResetAlignmentsNew(){return resetAlignmentsNew;};
+ void setResetAlignmentsNew(bool value);
+ bool getResetAlignmentsAll(){return resetAlignmentsAll;};
+ void toggleResetAlignmentsNew();
+ void setResetAlignmentsAll(bool value);
+ int getOutputStructPenalties(){return outputStructPenalties;};
+ void setOutputStructPenalties(int value);
+ int getStructPenalties1(){return structPenalties1;};
+ void setStructPenalties1(int value);
+ int getStructPenalties2(){return structPenalties2;};
+ void setStructPenalties2(int value);
+ bool getUseSS1(){return useSS1;};
+ void setUseSS1(bool value);
+ void toggleUseSS1();
+ bool getUseSS2(){return useSS2;};
+ void setUseSS2(bool value);
+ void toggleUseSS2();
+ int getHelixPenalty(){return helixPenalty;};
+ void setHelixPenalty(int value);
+ int getStrandPenalty(){return strandPenalty;};
+ void setStrandPenalty(int value);
+ int getLoopPenalty(){return loopPenalty;};
+ void setLoopPenalty(int value);
+ int getHelixEndMinus(){return helixEndMinus;};
+ void setHelixEndMinus(int value);
+ int getHelixEndPlus(){return helixEndPlus;};
+ void setHelixEndPlus(int value);
+ int getStrandEndMinus(){return strandEndMinus;};
+ void setStrandEndMinus(int value);
+ int getStrandEndPlus(){return strandEndPlus;};
+ void setStrandEndPlus(int value);
+ int getHelixEndPenalty(){return helixEndPenalty;};
+ void setHelixEndPenalty(int value);
+ int getStrandEndPenalty(){return strandEndPenalty;};
+ void setStrandEndPenalty(int value);
+ bool getUseAmbiguities(){return useAmbiguities;};
+ void setUseAmbiguities(bool value);
+ float getDNAPWGapOpenPenalty(){return DNAPWGapOpen;};
+ void setDNAPWGapOpenPenalty(float value);
+ float getDNAPWGapExtendPenalty(){return DNAPWGapExtend;};
+ void setDNAPWGapExtendPenalty(float value);
+ float getProteinPWGapOpenPenalty(){return AAPWGapOpen;};
+ void setProteinPWGapOpenPenalty(float value);
+ float getProteinPWGapExtendPenalty(){return AAPWGapExtend;};
+ void setProteinPWGapExtendPenalty(float value);
+
+ bool getQuickPairAlign(){return quickPairAlign;};
+ void setQuickPairAlign(bool value);
+ void toggleQuickPairAlign(); // Mark new!!!
+ float getTransitionWeight(){return transitionWeight;};
+ void setTransitionWeight(float value);
+ int getDNAKtup(){return DNAKtup;};
+ void setDNAKtup(int value);
+ int getDNAWindowGap(){return DNAWindowGap;};
+ void setDNAWindowGap(int value);
+ int getDNASignif(){return DNASignif;};
+ void setDNASignif(int value);
+ int getDNAWindow(){return DNAWindow;};
+ void setDNAWindow(int value);
+ int getAAKtup(){return AAKtup;};
+ void setAAKtup(int value);
+ int getAAWindowGap(){return AAWindowGap;};
+ void setAAWindowGap(int value);
+ int getAASignif(){return AASignif;};
+ void setAASignif(int value);
+ int getAAWindow(){return AAWindow;};
+ void setAAWindow(int value);
+ bool getPercent(){return percent;};
+ void setPercent(bool value);
+ bool getTossGaps(){return tossgaps;};
+ void setTossGaps(bool value);
+ void toggleTossGaps();
+ bool getKimura(){return kimura;};
+ void setKimura(bool value);
+ void toggleKimura();
+ int getBootNumTrials(){return bootNumTrials;};
+ void setBootNumTrials(int value);
+ unsigned int getBootRanSeed(){return bootRanSeed;};
+ void setBootRanSeed(unsigned int value);
+ int getDebug(){return debug;};
+ void setDebug(int value);
+ bool getExplicitDNAFlag(){return explicitDNAFlag;};
+ void setExplicitDNAFlag(bool value);
+ bool getLowercase(){return lowercase;};
+ void setLowercase(bool value);
+ void toggleLowercase();
+ bool getClSeqNumbers(){return clSeqNumbers;};
+ void setClSeqNumbers(bool value);
+ void toggleClSeqNumbers();
+ bool getSeqRange(){return seqRange;};
+ void setSeqRange(bool value);
+ void toggleSeqRange();
+ bool getOutputClustal(){return outputClustal;};
+ void setOutputClustal(bool value);
+ void toggleOutputClustal();
+ bool getOutputGCG(){return outputGcg;};
+ void setOutputGCG(bool value);
+ void toggleOutputGCG();
+ bool getOutputPhylip(){return outputPhylip;};
+ void setOutputPhylip(bool value);
+ void toggleOutputPhylip();
+ bool getOutputNbrf(){return outputNbrf;};
+ void setOutputNbrf(bool value);
+ void toggleOutputNbrf();
+ bool getOutputGde(){return outputGde;};
+ void setOutputGde(bool value);
+ void toggleOutputGde();
+ bool getOutputNexus(){return outputNexus;};
+ void setOutputNexus(bool value);
+ void toggleOutputNexus();
+ bool getOutputFasta(){return outputFasta;};
+ void setOutputFasta(bool value);
+ void toggleOutputFasta();
+ bool getShowAlign(){return showAlign;};
+ void setShowAlign(bool value);
+ void toggleShowAlign();
+ bool getSaveParameters(){return saveParameters;};
+ void setSaveParameters(bool value);
+ void toggleSaveParameters();
+ bool getOutputTreeClustal(){return outputTreeClustal;};
+ void setOutputTreeClustal(bool value);
+ void toggleOutputTreeClustal();
+ bool getOutputTreePhylip(){return outputTreePhylip;};
+ void setOutputTreePhylip(bool value);
+ void toggleOutputTreePhylip();
+ bool getOutputTreeDistances(){return outputTreeDistances;};
+ void setOutputTreeDistances(bool value);
+ void toggleOutputTreeDistances();
+ bool getOutputTreeNexus(){return outputTreeNexus;};
+ void setOutputTreeNexus(bool value);
+ void toggleOutputTreeNexus();
+ bool getOutputPim(){return outputPim;};
+ void setOutputPim(bool value);
+ int getBootstrapFormat(){return bootstrapFormat;};
+ void setBootstrapFormat(int value);
+ void toggleBootstrapFormat();
+ string getProfile1Name(){return profile1Name;};
+ void setProfile1Name(string value);
+ string getProfile2Name(){return profile2Name;};
+ void setProfile2Name(string value);
+ bool getEmpty(){return empty;};
+ void setEmpty(bool value);
+ bool getProfile1Empty(){return profile1Empty;};
+ void setProfile1Empty(bool value);
+ bool getProfile2Empty(){return profile2Empty;};
+ void setProfile2Empty(bool value);
+ string getOutfileName(){return outfileName;};
+ void setOutfileName(string value);
+ bool getUseTreeFile(){return useTreeFile;};
+ void setUseTreeFile(bool value);
+ bool getNewTreeFile(){return newTreeFile;};
+ void setNewTreeFile(bool value);
+ bool getUseTree1File(){return useTree1File;};
+ void setUseTree1File(bool value);
+ bool getUseTree2File(){return useTree2File;};
+ void setUseTree2File(bool value);
+ bool getNewTree1File(){return newTree1File;};
+ void setNewTree1File(bool value);
+ bool getNewTree2File(){return newTree2File;};
+ void setNewTree2File(bool value);
+ string getAminoAcidCodes(){return aminoAcidCodes;};
+ char getAminoAcidCode(int i){return aminoAcidCodes[i];};
+ void setAminoAcidCodes(string value);
+ int getKtup(){return ktup;};
+ void setKtup(int value);
+ int getWindow(){return window;};
+ void setWindow(int value);
+ int getWindowGap(){return windowGap;};
+ void setWindowGap(int value);
+ int getSignif(){return signif;};
+ void setSignif(int value);
+ int getRangeFrom(){return rangeFrom;};
+ int getRangeTo(){return rangeTo;};
+ void setRangeFrom(int from);
+ void setRangeTo(int to);
+ bool getRangeFromToSet(){return rangeFromToSet;};
+ void setRangeFromToSet(bool set){rangeFromToSet = set;};
+ int getQTScorePlotScale();
+ void setQTScorePlotScale(int score);
+ int getQTResExceptionCutOff();
+ void setQTResExceptionCutOff(int cutOff);
+ bool getQTseqWeightCalculated();
+ void setQTseqWeightCalculated(bool calculated);
+ int getQTminLenLowScoreSegment();
+ void setQTminLenLowScoreSegment(int minLen);
+ int getQTlowScoreDNAMarkingScale();
+ void setQTlowScoreDNAMarkingScale(int dnaScale);
+
+
+ // Access functions for the iteration variables.
+ void setNumIterations(int num){numIterations = num;}
+ int getNumIterations(){return numIterations;}
+ void setDoRemoveFirstIteration(int doIter){doRemoveFirstIteration = doIter;}
+ int getDoRemoveFirstIteration(){return doRemoveFirstIteration;}
+ bool IterationIsEnabled();
+
+ void setClusterAlgorithm(int clust){clusterAlgorithm = clust;}
+ int getClusterAlgorithm(){return clusterAlgorithm;}
+
+ void setDisplayInfo(bool display){displayInfo = display;}
+ bool getDisplayInfo(){return displayInfo;}
+ bool getHelpFlag() {return helpFlag;}
+ void setHelpFlag(bool b) {helpFlag = b;}
+ bool getFullHelpFlag() {return fullHelpFlag;}
+ void setFullHelpFlag(bool b) {fullHelpFlag = b;}
+ void setMaxAllowedSeqLength(int num){maxAllowedSeqLength = num;}
+ int getMaxAllowedSeqLength(){return maxAllowedSeqLength;}
+
+ bool ResetGapsIsEnabled() {return (resetAlignmentsNew || resetAlignmentsAll);};
+
+ /* Attributes */
+
+ private:
+ /* Functions */
+
+
+ /* Attributes */
+
+ string revisionLevel;
+ bool interactive;
+ float gapOpen;
+ float gapExtend;
+ float PWGapOpen;
+ float PWGapExtend;
+ int maxAA;
+ int gapPos1;
+ int gapPos2;
+ int profileNum;
+ bool menuFlag;
+ bool DNAFlag;
+ bool distanceTree;
+ string seqName;
+ float DNAGapOpen;
+ float DNAGapExtend;
+ float AAGapOpen;
+ float AAGapExtend;
+ int gapDist;
+ int outputOrder;
+ int divergenceCutoff;
+ string hydResidues;
+ bool noWeights;
+ bool negMatrix;
+ bool noHydPenalties;
+ bool noVarPenalties;
+ bool noPrefPenalties;
+ bool useEndGaps;
+ bool endGapPenalties;
+ bool resetAlignmentsNew;
+ bool resetAlignmentsAll;
+ int outputStructPenalties;
+ int structPenalties1;
+ int structPenalties2;
+ bool useSS1;
+ bool useSS2;
+ int helixPenalty;
+ int strandPenalty;
+ int loopPenalty;
+ int helixEndMinus;
+ int helixEndPlus;
+ int strandEndMinus;
+ int strandEndPlus;
+ int helixEndPenalty;
+ int strandEndPenalty;
+ bool useAmbiguities;
+ float DNAPWGapOpen;
+ float DNAPWGapExtend;
+ float AAPWGapOpen;
+ float AAPWGapExtend;
+
+ bool quickPairAlign;
+ float transitionWeight;
+ int DNAKtup;
+ int DNAWindowGap;
+ int DNASignif;
+ int DNAWindow;
+ int AAKtup;
+ int AAWindowGap;
+ int AASignif;
+ int AAWindow;
+ bool percent;
+ bool tossgaps;
+ bool kimura;
+ int bootNumTrials;
+ unsigned int bootRanSeed;
+ int debug;
+ bool explicitDNAFlag;
+ bool lowercase; /* Flag for GDE output - set on comm. line*/
+ bool clSeqNumbers;
+ bool seqRange;
+ bool outputClustal;
+ bool outputGcg;
+ bool outputPhylip;
+ bool outputNbrf;
+ bool outputGde;
+ bool outputNexus;
+ bool outputFasta;
+ bool showAlign;
+ bool saveParameters;
+ bool outputTreeClustal;
+ bool outputTreePhylip;
+ bool outputTreeDistances;
+ bool outputTreeNexus;
+ bool outputPim;
+ int bootstrapFormat;
+ string profile1Name;
+ string profile2Name;
+ bool empty;
+ bool profile1Empty;
+ bool profile2Empty;
+ string outfileName;
+ //int profile1NumSeqs; MARK CHANGE Jan 10
+ bool useTreeFile;
+ bool newTreeFile;
+ bool useTree1File;
+ bool useTree2File;
+ bool newTree1File;
+ bool newTree2File;
+ string aminoAcidCodes;
+ int ktup;
+ int window;
+ int windowGap;
+ int signif;
+
+ int rangeFrom;
+ int rangeTo;
+ bool rangeFromToSet;
+
+ int QTscorePlotScale;
+ int QTresExceptionCutOff;
+ bool QTseqWeightCalculated;
+ int QTminLenLowScoreSegment;
+ int QTlowScoreDNAMarkingScale;
+
+
+ // New variables for iteration
+ int numIterations;
+ int doRemoveFirstIteration;
+
+ int clusterAlgorithm;
+ bool displayInfo;
+ bool helpFlag;
+ bool fullHelpFlag;
+ bool quiet;
+
+ int maxAllowedSeqLength;
+};
+}
+#endif
+
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