+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-/**
- * This file contains the implementation of the UserParameter functions
- * Mark Larkin Dec 8 2005
- *
- * Modified: 17 January 2008 Paul McGettigan added in the O aminoacid residue to handle Pyrrolysine
- */
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-#include <stdio.h>
-#include <string>
-#include <cstdlib>
-#include <exception>
-#include <iostream>
-#include <limits>
-#include <climits>
-#include <iomanip>
-#include <fstream>
-#include "UserParameters.h"
-#include "clustalw_version.h"
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
-namespace clustalw
-{
-using namespace std;
-
-UserParameters::UserParameters(bool log)
-{
- // FIXME: huge parts should be merged/replaced with
- // setParamsToDefault (which is not used at all)
-
- gapPos1 = NUMRES - 2; /* code for gaps inserted by clustalw */
- gapPos2 = NUMRES - 1; /* code for gaps already in alignment */
-
- //revisionLevel = CLU_SHORT_VERSION_STRING;
- revisionLevel = CLUSTALW_VERSION;
- interactive = false;
-
- seqName = "";
- DNAGapOpen = 15.0;
- DNAGapExtend = 6.66;
- AAGapOpen = 10.0;
- AAGapExtend = 0.2;
- gapDist = 4;
- outputOrder = ALIGNED; // Note: All macros should be replaced by const
- divergenceCutoff = 30;
-
- hydResidues = "GPSNDQEKR";
- noWeights = false;
- negMatrix = false;
- noHydPenalties = false;
- noVarPenalties = true;
- noPrefPenalties = false;
- useEndGaps = false;
- endGapPenalties = false;
- resetAlignmentsNew = false;
- resetAlignmentsAll = false;
- outputStructPenalties = OUTSECST;
- structPenalties1 = NONE;
- structPenalties2 = NONE;
- useSS1 = true;
- useSS2 = true;
- helixPenalty = 4;
- strandPenalty = 4;
- loopPenalty = 1;
- helixEndMinus = 3;
- helixEndPlus = 0;
- strandEndMinus = 1;
- strandEndPlus = 1;
- helixEndPenalty = 2;
- strandEndPenalty = 2;
- useAmbiguities = false;
- DNAPWGapOpen = 15.0;
- DNAPWGapExtend = 6.66;
- AAPWGapOpen = 10.0;
- AAPWGapExtend = 0.1;
-
- quickPairAlign = false;
- transitionWeight = 0.5;
- DNAKtup = 2;
- DNAWindowGap = 5;
- DNASignif = 4;
- DNAWindow = 4;
- AAKtup = 1;
- AAWindowGap = 3;
- AASignif = 5;
- AAWindow = 5;
- percent = true;
- tossgaps = false;
- kimura = false;
- bootNumTrials = 1000;
- bootRanSeed = 111;
- debug = 0;
- explicitDNAFlag = false;
- lowercase = true;
- clSeqNumbers = false;
- seqRange = false;
- outputClustal = true;
- outputGcg = false;
- outputPhylip = false;
- outputNbrf = false;
- outputGde = false;
- outputNexus = false;
- outputFasta = false;
- showAlign = true;
- saveParameters = false;
- outputTreeClustal = false;
- outputTreePhylip = true;
- outputTreeDistances = false;
- outputTreeNexus = false;
- outputPim = false;
- bootstrapFormat = BS_BRANCH_LABELS;
- profile1Name = ""; // Initialise to blank strings
- profile2Name = "";
- empty = true;
- profile1Empty = true;
- profile2Empty = true;
- outfileName = "";
- //profile1NumSeqs = 0; // MARK: Set to default before used.
- useTreeFile = false;
- newTreeFile = false;
- useTree1File = false;
- useTree2File = false;
- newTree1File = false;
- newTree2File = false;
- aminoAcidCodes = "ABCDEFGHIKLMNOPQRSTUVWXYZ-";
- maxAA = aminoAcidCodes.length() - 2;
-
- // Some variables need the alignment to be read in before they can be set.
- // I am putting the default as protein. Note: this should not make a difference
- // as they are not used before they have been set a value again!!
-
- gapOpen = AAGapOpen;
- gapExtend = AAGapExtend;
- PWGapOpen = AAPWGapOpen;
- PWGapExtend = AAPWGapExtend;
-
- gapPos1 = NUMRES - 2;
- gapPos2 = NUMRES - 1;
- profileNum = 0;
- menuFlag = false; // MARK: I set to default value.
- DNAFlag = false; // MARK: I set to default value.
- distanceTree = true; // MARK: I set to default value.
- ktup = AAKtup;
- window = AAWindow;
- windowGap = AAWindowGap;
- signif = AASignif;
- rangeFrom = -1;
- rangeTo = -1;
- rangeFromToSet = false;
- QTscorePlotScale = 5;
- QTresExceptionCutOff = 5;
-
- QTseqWeightCalculated = false;
- QTminLenLowScoreSegment = 1;
- QTlowScoreDNAMarkingScale = 5;
-
- // Set defaults for iteration variables.
- numIterations = 3;
- doRemoveFirstIteration = NONE;
- maxAllowedSeqLength = INT_MAX;
-
- clusterAlgorithm = NJ;
- displayInfo = true;
- helpFlag = false;
- fullHelpFlag = false;
- quiet = false;
-
-}
-
-// FIXME:never used
-void UserParameters::setParamsToDefault()
-{
- DNAGapOpen = 15.0;
- DNAGapExtend = 6.66;
- AAGapOpen = 10.0;
- AAGapExtend = 0.2;
- gapDist = 4;
- outputOrder = ALIGNED;
- divergenceCutoff = 30;
-
- hydResidues = "GPSNDQEKR";
- noWeights = false;
- negMatrix = false;
- noHydPenalties = false;
- noVarPenalties = true;
- noPrefPenalties = false;
- useEndGaps = false;
- endGapPenalties = false;
- resetAlignmentsNew = false;
- resetAlignmentsAll = false;
- outputStructPenalties = OUTSECST;
- structPenalties1 = NONE;
- structPenalties2 = NONE;
- useSS1 = true;
- useSS2 = true;
- helixPenalty = 4;
- strandPenalty = 4;
- loopPenalty = 1;
- helixEndMinus = 3;
- helixEndPlus = 0;
- strandEndMinus = 1;
- strandEndPlus = 1;
- helixEndPenalty = 2;
- strandEndPenalty = 2;
- useAmbiguities = false;
- DNAPWGapOpen = 15.0;
- DNAPWGapExtend = 6.66;
- AAPWGapOpen = 10.0;
- AAPWGapExtend = 0.1;
- quickPairAlign = false;
- transitionWeight = 0.5;
- DNAKtup = 2;
- DNAWindowGap = 5;
- DNASignif = 4;
- DNAWindow = 4;
- AAKtup = 1;
- AAWindowGap = 3;
- AASignif = 5;
- AAWindow = 5;
- percent = true;
- tossgaps = false;
- kimura = false;
- bootNumTrials = 1000;
- bootRanSeed = 111;
- debug = 0;
- lowercase = true;
- clSeqNumbers = false;
- seqRange = false;
- outputClustal = true;
- outputGcg = false;
- outputPhylip = false;
- outputNbrf = false;
- outputGde = false;
- outputNexus = false;
- outputFasta = false;
- outputTreeClustal = false;
- outputTreePhylip = true;
- outputTreeDistances = false;
- outputTreeNexus = false;
- outputPim = false;
- bootstrapFormat = BS_BRANCH_LABELS;
- useTreeFile = false;
- newTreeFile = false;
- useTree1File = false;
- useTree2File = false;
- newTree1File = false;
- newTree2File = false;
- rangeFrom = -1;
- rangeTo = -1;
- rangeFromToSet = false;
- QTscorePlotScale = 5;
- QTresExceptionCutOff = 5;
-
- QTminLenLowScoreSegment = 1;
- QTlowScoreDNAMarkingScale = 5;
- distanceTree = true; // MARK: I set to default value.
-
- numIterations = 3;
-
- if(getDNAFlag())
- {
- setDNAParams();
- }
- else
- {
- setProtParams();
- }
-
- clusterAlgorithm = NJ;
- displayInfo = true;
- helpFlag = false;
- fullHelpFlag = false;
- quiet = false;
- doRemoveFirstIteration = NONE;
- maxAllowedSeqLength = INT_MAX;
-}
-
-/*
- * The function createParameterOutput is used to put all the user parameters in
- * a file. It is used for testing and for saving parameters.
- *
- *
- * FIXME: AW: Some parameters are missing here (e.g. the new ones like
- * clustering, etc)
- *
- */
-void UserParameters::createParameterOutput(void)
-{
- string parname, temp;
- string path;
- string message;
-
- utilityObject->getPath(seqName, &path);
- parname = path + "par";
- if(menuFlag)
- {
- message = "\nEnter a name for the parameter output file [" + parname + "]";
- utilityObject->getStr(message, temp);
- if(temp != "")
- {
- parname = temp;
- }
- }
-
- ofstream outfile;
- outfile.open(parname.c_str(), ofstream::out);
-
- if(!outfile)
- {
- return; // Failed to open
- }
-
- outfile << "clustalw \\\n";
- if (!empty && profile1Empty)
- {
- outfile << "-infile=" << seqName << " \\\n";
- }
- if (!profile1Empty)
- {
- outfile << "-profile1=" << profile1Name << "\\\n";
- }
- if (!profile2Empty)
- {
- outfile << "-profile2=" << profile2Name << " \\\n";
- }
- if (DNAFlag == true)
- {
- outfile << "-type=dna \\\n";
- }
- else
- {
- outfile << "-type=protein \\\n";
- }
- if (quickPairAlign)
- {
- outfile << "-quicktree \\\n";
- outfile << "-ktuple=" << ktup << " \\\n";
- outfile << "-window=" << window << " \\\n";
- outfile << "-pairgap=" << windowGap << " \\\n";
- outfile << "-topdiags=" << signif << " \\\n";
- if (percent)
- {
- outfile << "-score=percent \\\n";
- }
- else
- {
- outfile << "-score=absolute \\\n";
- }
- }
- else
- {
- if (!DNAFlag)
- {
- //outfile << "-pwmatrix=" << pwMatrixName << " \\\n";
- outfile << "-pwgapopen=" << fixed << setprecision(2) << AAPWGapOpen
- << " \\\n";
- outfile << "-pwgapext=" << AAPWGapExtend << " \\\n";
- }
- else
- {
- outfile << "-pwgapopen=" << fixed << setprecision(2) << PWGapOpen << " \\\n";
- outfile << "-pwgapext=" << PWGapExtend << " \\\n";
- }
- }
-
- if (!DNAFlag)
- {
- //outfile << "-matrix=" << matrixName << " \\\n";
- outfile << "-gapopen=" << fixed << setprecision(2) << AAGapOpen << " \\\n";
- outfile << "-gapext=" << AAGapExtend << " \\\n";
- }
- else
- {
- outfile << "-gapopen=" << fixed << setprecision(2) << DNAGapOpen << " \\\n";
- outfile << "-gapext=" << DNAGapExtend << " \\\n";
- }
-
- outfile << "-maxdiv=" << divergenceCutoff << " \\\n";
- if (!useEndGaps)
- {
- outfile << "-endgaps \\\n";
- }
-
- if (!DNAFlag)
- {
- if (negMatrix)
- {
- outfile << "-negative \\\n";
- }
- if (noPrefPenalties)
- {
- outfile << "-nopgap \\\n";
- }
- if (noHydPenalties)
- {
- outfile << "-nohgap \\\n";
- }
- if (noVarPenalties)
- {
- outfile << "-novgap \\\n";
- }
- outfile << "-hgapresidues=" << hydResidues << " \\\n";
- outfile << "-gapdist=" << gapDist << " \\\n";
- }
- else
- {
- outfile << "-transweight=" << transitionWeight << " \\\n";
- }
-
- if (outputGcg)
- {
- outfile << "-output=gcg \\\n";
- }
- else if (outputGde)
- {
- outfile << "-output=gde \\\n";
- }
- else if (outputNbrf)
- {
- outfile << "-output=pir \\\n";
- }
- else if (outputPhylip)
- {
- outfile << "-output=phylip \\\n";
- }
- else if (outputNexus)
- {
- outfile << "-output=nexus \\\n";
- }
- if (outfileName[0]!=EOS)
- {
- outfile << "-outfile=" << outfileName << " \\\n";
- }
- if (outputOrder==ALIGNED)
- {
- outfile << "-outorder=aligned \\\n";
- }
- else
- {
- outfile << "-outorder=input \\\n";
- }
- if (outputGde)
- {
- if (lowercase)
- {
- outfile << "-case=lower \\\n";
- }
- else
- {
- outfile << "-case=upper \\\n";
- }
- }
-
-
- outfile << "-interactive\n";
-
- outfile.close();
-
-}
-
-/*
- * The function resIndex returns the index of the character c in the string t.
- *
- */
-int UserParameters::resIndex(string t, char c)
-{
- register int i;
-
- for (i = 0; t[i] && t[i] != c; i++)
- ;
- if (t[i])
- {
- return (i);
- }
- else
- {
- return -1;
- }
-}
-
-void UserParameters::setDNAMultiGap()
-{
- gapOpen = DNAGapOpen;
- gapExtend = DNAGapExtend;
-}
-
-void UserParameters::setProtMultiGap()
-{
- gapOpen = AAGapOpen;
- gapExtend = AAGapExtend;
-}
-
-void UserParameters::setDNAParams()
-{
- gapOpen = DNAGapOpen;
- gapExtend = DNAGapExtend;
- PWGapOpen = DNAPWGapOpen;
- PWGapExtend = DNAPWGapExtend;
- ktup = DNAKtup;
- window = DNAWindow;
- signif = DNASignif;
- windowGap = DNAWindowGap;
-}
-
-void UserParameters::setProtParams()
-{
- gapOpen = AAGapOpen;
- gapExtend = AAGapExtend;
- PWGapOpen = AAPWGapOpen;
- PWGapExtend = AAPWGapExtend;
- ktup = AAKtup;
- window = AAWindow;
- signif = AASignif;
- windowGap = AAWindowGap;
-}
-
-void UserParameters::setPWParamToProtein()
-{
- PWGapOpen = AAPWGapOpen;
- PWGapExtend = AAPWGapExtend;
- ktup = AAKtup;
- window = AAWindow;
- signif = AASignif;
- windowGap = AAWindowGap;
-}
-
-void UserParameters::setPWParamToDNA()
-{
- PWGapOpen = DNAPWGapOpen;
- PWGapExtend = DNAPWGapExtend;
- ktup = DNAKtup;
- window = DNAWindow;
- signif = DNASignif;
- windowGap = DNAWindowGap;
-}
-
-void UserParameters::setPWProteinParam()
-{
- AAPWGapOpen = PWGapOpen;
- AAPWGapExtend = PWGapExtend;
- AAKtup = ktup;
- AAWindow = window;
- AASignif = signif;
- AAWindowGap = windowGap;
-}
-
-void UserParameters::setPWDNAParam()
-{
- DNAPWGapOpen = PWGapOpen;
- DNAPWGapExtend = PWGapExtend;
- DNAKtup = ktup;
- DNAWindow = window;
- DNASignif = signif;
- DNAWindowGap = windowGap;
-}
-/*
- * The rest of the functions are get, set and toggle functions for the variables.
- */
-
-string UserParameters::getRevisionLevel()
-{
- return revisionLevel;
-}
-
-void UserParameters::setRevisionLevel(string value)
-{
- revisionLevel = value;
-}
-
-void UserParameters::setInteractive(bool value)
-{
- interactive = value;
-}
-
-void UserParameters::setGapOpen(float value)
-{
- gapOpen = value;
-}
-
-void UserParameters::setGapExtend(float value)
-{
- gapExtend = value;
-}
-
-void UserParameters::setPWGapOpen(float value)
-{
- PWGapOpen = value;
-}
-
-void UserParameters::setPWGapExtend(float value)
-{
- PWGapExtend = value;
-}
-
-void UserParameters::setMaxAA(int value)
-{
- maxAA = value;
-}
-
-void UserParameters::setGapPos1(int value)
-{
- gapPos1 = value;
-}
-
-void UserParameters::setGapPos2(int value)
-{
- gapPos2 = value;
-}
-
-void UserParameters::setProfileNum(int value)
-{
- profileNum = value;
-}
-
-void UserParameters::setMenuFlag(bool value)
-{
- menuFlag = value;
-}
-
-void UserParameters::setDNAFlag(bool value)
-{
- if(value == true)
- {
- setDNAParams();
- }
- else
- {
- setProtParams();
- }
- DNAFlag = value;
-}
-
-void UserParameters::setDistanceTree(bool value)
-{
- distanceTree = value;
-}
-
-void UserParameters::setSeqName(string value)
-{
- seqName = value;
-}
-
-void UserParameters::setDNAGapOpen(float value)
-{
- DNAGapOpen = value;
-}
-
-void UserParameters::setDNAGapExtend(float value)
-{
- DNAGapExtend = value;
-}
-
-void UserParameters::setProteinGapOpen(float value)
-{
- AAGapOpen = value;
-}
-
-void UserParameters::setProteinGapExtend(float value)
-{
- AAGapExtend = value;
-}
-
-void UserParameters::setGapDist(int value)
-{
- gapDist = value;
-}
-
-void UserParameters::setOutputOrder(int value)
-{
- outputOrder = value;
-}
-
-void UserParameters::toggleOutputOrder()
-{
- if (outputOrder == INPUT)
- {
- outputOrder = ALIGNED;
- }
- else
- {
- outputOrder = INPUT;
- }
-}
-
-void UserParameters::setDivergenceCutoff(int value)
-{
- divergenceCutoff = value;
-}
-
-void UserParameters::setHydResidues(string value)
-{
- //hydResidues = value;
- char hydResidue;
- string tempHydRes = "";
- int inputStringLength = value.length();
- if(inputStringLength > 0)
- {
- // NOTE this was causing an error, but I fixed it. Was giving an
- // out of range error.
- for (int i = 0; i < MAXHYDRESIDUES && i < inputStringLength; i++)
- {
- hydResidue = toupper(value.at(i));
-
- if (isalpha(hydResidue))
- {
- tempHydRes += hydResidue;
- }
- else // Not Alphabetic character!
- {
- break;
- }
- }
- if(tempHydRes.size() > 0)
- {
- hydResidues = tempHydRes;
- }
- }
-}
-
-void UserParameters::setNoWeights(bool value)
-{
- noWeights = value;
-}
-
-void UserParameters::setUseNegMatrix(bool value)
-{
- negMatrix = value;
-}
-
-void UserParameters::toggleUseNegMatrix()
-{
- negMatrix ^= true;
-}
-
-void UserParameters::setNoHydPenalties(bool value)
-{
- noHydPenalties = value;
-}
-
-void UserParameters::toggleNoHydPenalties()
-{
- noHydPenalties ^= true;
-}
-
-void UserParameters::setNoVarPenalties(bool value)
-{
- noVarPenalties = value;
-}
-
-void UserParameters::setNoPrefPenalties(bool value)
-{
- noPrefPenalties = value;
-}
-
-void UserParameters::toggleNoPrefPenalties()
-{
- noPrefPenalties ^= true;
-}
-
-void UserParameters::setUseEndGaps(bool value)
-{
- useEndGaps = value;
-}
-
-void UserParameters::toggleUseEndGaps()
-{
- useEndGaps ^= true;
-}
-
-void UserParameters::setEndGapPenalties(bool value)
-{
- endGapPenalties = value;
-}
-
-void UserParameters::toggleResetAlignmentsNew()
-{
- resetAlignmentsNew ^= true;
-}
-
-void UserParameters::setResetAlignmentsNew(bool value)
-{
- resetAlignmentsNew = value;
-}
-
-void UserParameters::setResetAlignmentsAll(bool value)
-{
- resetAlignmentsAll = value;
-}
-
-void UserParameters::setOutputStructPenalties(int value)
-{
- outputStructPenalties = value;
-}
-
-void UserParameters::setStructPenalties1(int value)
-{
- structPenalties1 = value;
-}
-
-void UserParameters::setStructPenalties2(int value)
-{
- structPenalties2 = value;
-}
-
-void UserParameters::setUseSS1(bool value)
-{
- useSS1 = value;
-}
-
-void UserParameters::toggleUseSS1()
-{
- useSS1 ^= true;
-}
-
-void UserParameters::setUseSS2(bool value)
-{
- useSS2 = value;
-}
-
-void UserParameters::toggleUseSS2()
-{
- useSS2 ^= true;
-}
-
-void UserParameters::setHelixPenalty(int value)
-{
- helixPenalty = value;
-}
-
-void UserParameters::setStrandPenalty(int value)
-{
- strandPenalty = value;
-}
-
-void UserParameters::setLoopPenalty(int value)
-{
- loopPenalty = value;
-}
-
-void UserParameters::setHelixEndMinus(int value)
-{
- helixEndMinus = value;
-}
-
-void UserParameters::setHelixEndPlus(int value)
-{
- helixEndPlus = value;
-}
-
-void UserParameters::setStrandEndMinus(int value)
-{
- strandEndMinus = value;
-}
-
-void UserParameters::setStrandEndPlus(int value)
-{
- strandEndPlus = value;
-}
-
-void UserParameters::setHelixEndPenalty(int value)
-{
- helixEndPenalty = value;
-}
-
-void UserParameters::setStrandEndPenalty(int value)
-{
- strandEndPenalty = value;
-}
-
-void UserParameters::setUseAmbiguities(bool value)
-{
- useAmbiguities = value;
-}
-
-void UserParameters::setDNAPWGapOpenPenalty(float value)
-{
- DNAPWGapOpen = value;
-}
-
-void UserParameters::setDNAPWGapExtendPenalty(float value)
-{
- DNAPWGapExtend = value;
-}
-
-void UserParameters::setProteinPWGapOpenPenalty(float value)
-{
- AAPWGapOpen = value;
-}
-
-void UserParameters::setProteinPWGapExtendPenalty(float value)
-{
- AAPWGapExtend = value;
-}
-
-void UserParameters::toggleQuickPairAlign()
-{
- quickPairAlign ^= true;
-}
-
-void UserParameters::setQuickPairAlign(bool value)
-{
- quickPairAlign = value;
-}
-
-void UserParameters::setTransitionWeight(float value)
-{
- transitionWeight = value;
-}
-
-void UserParameters::setDNAKtup(int value)
-{
- DNAKtup = value;
-}
-
-void UserParameters::setDNAWindowGap(int value)
-{
- DNAWindowGap = value;
-}
-
-void UserParameters::setDNASignif(int value)
-{
- DNASignif = value;
-}
-
-void UserParameters::setDNAWindow(int value)
-{
- DNAWindow = value;
-}
-
-void UserParameters::setAAKtup(int value)
-{
- AAKtup = value;
-}
-
-void UserParameters::setAAWindowGap(int value)
-{
- AAWindowGap = value;
-}
-
-void UserParameters::setAASignif(int value)
-{
- AASignif = value;
-}
-
-void UserParameters::setAAWindow(int value)
-{
- AAWindow = value;
-}
-
-void UserParameters::setPercent(bool value)
-{
- percent = value;
-}
-
-void UserParameters::toggleTossGaps()
-{
- tossgaps ^= true;
-}
-
-void UserParameters::setTossGaps(bool value)
-{
- tossgaps = value;
-}
-
-void UserParameters::setKimura(bool value)
-{
- kimura = value;
-}
-
-void UserParameters::toggleKimura()
-{
- kimura ^= true;
-}
-
-void UserParameters::setBootNumTrials(int value)
-{
- bootNumTrials = value;
-}
-
-void UserParameters::setBootRanSeed(unsigned int value)
-{
- bootRanSeed = value;
-}
-
-void UserParameters::setDebug(int value)
-{
- debug = value;
-}
-
-void UserParameters::setExplicitDNAFlag(bool value)
-{
- explicitDNAFlag = value;
-}
-
-void UserParameters::setLowercase(bool value)
-{
- lowercase = value;
-}
-
-void UserParameters::toggleLowercase()
-{
- lowercase ^= true;
-}
-
-void UserParameters::setClSeqNumbers(bool value)
-{
- clSeqNumbers = value;
-}
-
-void UserParameters::toggleClSeqNumbers()
-{
- clSeqNumbers ^= true;
-}
-
-void UserParameters::setSeqRange(bool value)
-{
- seqRange = value;
-}
-
-void UserParameters::toggleSeqRange()
-{
- seqRange ^= true;
-}
-
-void UserParameters::setOutputClustal(bool value)
-{
- outputClustal = value;
-}
-
-void UserParameters::toggleOutputClustal()
-{
- outputClustal ^= true;
-}
-
-void UserParameters::setOutputGCG(bool value)
-{
- outputGcg = value;
-}
-
-void UserParameters::toggleOutputGCG()
-{
- outputGcg ^= true;
-}
-
-void UserParameters::setOutputPhylip(bool value)
-{
- outputPhylip = value;
-}
-
-void UserParameters::toggleOutputPhylip()
-{
- outputPhylip ^= true;
-}
-
-void UserParameters::setOutputNbrf(bool value)
-{
- outputNbrf = value;
-}
-
-void UserParameters::toggleOutputNbrf()
-{
- outputNbrf ^= true;
-}
-
-void UserParameters::setOutputGde(bool value)
-{
- outputGde = value;
-}
-
-void UserParameters::toggleOutputGde()
-{
- outputGde ^= true;
-}
-
-void UserParameters::setOutputNexus(bool value)
-{
- outputNexus = value;
-}
-
-void UserParameters::toggleOutputNexus()
-{
- outputNexus ^= true;
-}
-
-void UserParameters::setOutputFasta(bool value)
-{
- outputFasta = value;
-}
-
-void UserParameters::toggleOutputFasta()
-{
- outputFasta ^= true;
-}
-
-void UserParameters::setShowAlign(bool value)
-{
- showAlign = value;
-}
-
-void UserParameters::toggleShowAlign()
-{
- showAlign ^= true;
-}
-
-void UserParameters::setSaveParameters(bool value)
-{
- saveParameters = value;
-}
-
-void UserParameters::toggleSaveParameters()
-{
- saveParameters ^= true;
-}
-
-void UserParameters::setOutputTreeClustal(bool value)
-{
- outputTreeClustal = value;
-}
-
-void UserParameters::toggleOutputTreeClustal()
-{
- outputTreeClustal ^= true;
-}
-
-void UserParameters::setOutputTreePhylip(bool value)
-{
- outputTreePhylip = value;
-}
-
-void UserParameters::toggleOutputTreePhylip()
-{
- outputTreePhylip ^= true;
-}
-
-void UserParameters::setOutputTreeDistances(bool value)
-{
- outputTreeDistances = value;
-}
-
-void UserParameters::toggleOutputTreeDistances()
-{
- outputTreeDistances ^= true;
-}
-
-void UserParameters::setOutputTreeNexus(bool value)
-{
- outputTreeNexus = value;
-}
-
-void UserParameters::toggleOutputTreeNexus()
-{
- outputTreeNexus ^= true;
-}
-
-void UserParameters::setOutputPim(bool value)
-{
- outputPim = value;
-}
-
-void UserParameters::setBootstrapFormat(int value)
-{
- bootstrapFormat = value;
-}
-
-void UserParameters::toggleBootstrapFormat()
-{
- if (bootstrapFormat == BS_NODE_LABELS)
- {
- bootstrapFormat = BS_BRANCH_LABELS;
- }
- else
- {
- bootstrapFormat = BS_NODE_LABELS;
- }
-}
-
-void UserParameters::setProfile1Name(string value)
-{
- profile1Name = value;
-}
-
-void UserParameters::setProfile2Name(string value)
-{
- profile2Name = value;
-}
-
-void UserParameters::setEmpty(bool value)
-{
- empty = value;
-}
-
-void UserParameters::setProfile1Empty(bool value)
-{
- profile1Empty = value;
-}
-
-void UserParameters::setProfile2Empty(bool value)
-{
- profile2Empty = value;
-}
-
-void UserParameters::setOutfileName(string value)
-{
- outfileName = value;
-}
-
-/*void UserParameters::setProfile1NumSeqs(int value)
-{
- profile1NumSeqs = value;
-}*/ // MARK CHANGE Jan 10
-
-void UserParameters::setUseTreeFile(bool value)
-{
- useTreeFile = value;
-}
-
-void UserParameters::setNewTreeFile(bool value)
-{
- newTreeFile = value;
-}
-
-void UserParameters::setUseTree1File(bool value)
-{
- useTree1File = value;
-}
-
-void UserParameters::setUseTree2File(bool value)
-{
- useTree2File = value;
-}
-
-void UserParameters::setNewTree1File(bool value)
-{
- newTree1File = value;
-}
-
-void UserParameters::setNewTree2File(bool value)
-{
- newTree2File = value;
-}
-
-void UserParameters::setAminoAcidCodes(string value)
-{
- aminoAcidCodes = value;
-}
-
-void UserParameters::setKtup(int value)
-{
- ktup = value;
-}
-
-void UserParameters::setWindow(int value)
-{
- window = value;
-}
-
-void UserParameters::setWindowGap(int value)
-{
- windowGap = value;
-}
-
-void UserParameters::setSignif(int value)
-{
- signif = value;
-}
-
-void UserParameters::setRangeFrom(int from)
-{
- rangeFrom = from;
- rangeFromToSet = true;
-}
-
-void UserParameters::setRangeTo(int to)
-{
- rangeTo = to;
- rangeFromToSet = true;
-}
-
-int UserParameters::getQTScorePlotScale()
-{
- return QTscorePlotScale;
-}
-
-void UserParameters::setQTScorePlotScale(int score)
-{
- QTscorePlotScale = score;
-}
-
-int UserParameters::getQTResExceptionCutOff()
-{
- return QTresExceptionCutOff;
-}
-
-void UserParameters::setQTResExceptionCutOff(int cutOff)
-{
- QTresExceptionCutOff = cutOff;
-}
-
-bool UserParameters::getQTseqWeightCalculated()
-{
- return QTseqWeightCalculated;
-}
-
-void UserParameters::setQTseqWeightCalculated(bool calculated)
-{
- QTseqWeightCalculated = calculated;
-}
-
-int UserParameters::getQTminLenLowScoreSegment()
-{
- return QTminLenLowScoreSegment;
-}
-
-void UserParameters::setQTminLenLowScoreSegment(int minLen)
-{
- QTminLenLowScoreSegment = minLen;
-}
-
-int UserParameters::getQTlowScoreDNAMarkingScale()
-{
- return QTlowScoreDNAMarkingScale;
-}
-
-void UserParameters::setQTlowScoreDNAMarkingScale(int dnaScale)
-{
- QTlowScoreDNAMarkingScale = dnaScale;
-}
-
-bool UserParameters::IterationIsEnabled()
-{
- if (doRemoveFirstIteration == clustalw::NONE)
- return false;
- else
- return true;
-}
-}
-
-
-
-
git://source.jalview.org / jabaws.git / blobdiff