--- /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