Commit 3ef1bdb2 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.6.8+dfsg

parent 0f96be77

CMakeLists.txt

+14 −14
Original line number Diff line number Diff line
@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE) 
# The version number.

set (iqtree_VERSION_MAJOR 1)

set (iqtree_VERSION_MINOR 6)

set (iqtree_VERSION_PATCH "7.1")

set (iqtree_VERSION_PATCH "8")



set(BUILD_SHARED_LIBS OFF)

alignment/alignment.cpp

+17 −1
Original line number Diff line number Diff line
@@ -3177,7 +3177,17 @@ void Alignment::createBootstrapAlignment(int *pattern_freq, const char *spec, in 
    if (Params::getInstance().jackknife_prop > 0.0 && spec)

        outError((string)"Unsupported jackknife with " + spec);



    if (!spec) {

    if (spec && strncmp(spec, "SCALE=", 6) == 0) {

        // multi-scale bootstrapping called by AU test

        int orig_nsite = nsite;

        double scale = convert_double(spec+6);

        nsite = (int)round(scale * nsite);

        for (site = 0; site < nsite; site++) {

            int site_id = random_int(orig_nsite, rstream);

            int ptn_id = getPatternID(site_id);

            pattern_freq[ptn_id]++;

        }

    } else if (!spec) {



        int nptn = getNPattern();
@@ -4337,6 +4347,12 @@ void Alignment::getPatternFreq(IntVector &freq) { 
		freq[cnt] = (*it).frequency;

}



void Alignment::getPatternFreq(int *freq) {

    int cnt = 0;

    for (iterator it = begin(); it < end(); it++, cnt++)

        freq[cnt] = (*it).frequency;

}



//added by MA

void Alignment::multinomialProb(Alignment refAlign, double &prob)

{

alignment/alignment.h

+5 −0
Original line number Diff line number Diff line
@@ -332,6 +332,11 @@ public: 
     */

    virtual void getPatternFreq(IntVector &freq);



    /**

     * @param[out] freq vector of site-pattern frequencies

     */

    virtual void getPatternFreq(int *freq);



    /**

            @param i sequence index

            @return sequence name

alignment/superalignment.cpp

+10 −1
Original line number Diff line number Diff line
@@ -776,7 +776,7 @@ void SuperAlignment::getSitePatternIndex(IntVector &pattern_index) { 


void SuperAlignment::getPatternFreq(IntVector &pattern_freq) {

	ASSERT(isSuperAlignment());

	int offset = 0;

	size_t offset = 0;

	if (!pattern_freq.empty()) pattern_freq.resize(0);

	for (vector<Alignment*>::iterator it = partitions.begin(); it != partitions.end(); it++) {

		IntVector freq;
@@ -786,6 +786,15 @@ void SuperAlignment::getPatternFreq(IntVector &pattern_freq) { 
	}

}



void SuperAlignment::getPatternFreq(int *pattern_freq) {

    ASSERT(isSuperAlignment());

    size_t offset = 0;

    for (vector<Alignment*>::iterator it = partitions.begin(); it != partitions.end(); it++) {

        (*it)->getPatternFreq(pattern_freq + offset);

        offset += (*it)->getNPattern();

    }

}



void SuperAlignment::printSiteInfo(const char* filename) {

    try {

        ofstream out(filename);

alignment/superalignment.h

+5 −0
Original line number Diff line number Diff line
@@ -114,6 +114,11 @@ public: 
	*/

	virtual void getPatternFreq(IntVector &pattern_freq);



    /**

     * @param[out] freq vector of site-pattern frequencies

     */

    virtual void getPatternFreq(int *freq);



    /**

        Print all site information to a file

        @param filename output file name