+++ /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
-
git://source.jalview.org / jabaws.git / blobdiff