Commit 48b7c97f authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.6.9+dfsg

parent 3ef1bdb2

CMakeLists.txt

+1 −1
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@@ -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 "8")

set (iqtree_VERSION_PATCH "9")



set(BUILD_SHARED_LIBS OFF)

README.md

+3 −0
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IQ-TREE

=======



[![Build Status](https://travis-ci.org/bqminh/IQ-TREE.svg?branch=master)](https://travis-ci.org/bqminh/IQ-TREE)

[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)



Efficient and versatile phylogenomic software by maximum likelihood <http://www.iqtree.org>



Introduction

alignment/superalignment.cpp

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@@ -1008,6 +1008,9 @@ void SuperAlignment::createBootstrapAlignment(int *pattern_freq, const char *spe 
		// resampling sites within genes

		int offset = 0;

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

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

                (*it)->createBootstrapAlignment(pattern_freq + offset, spec, rstream);

            else

                (*it)->createBootstrapAlignment(pattern_freq + offset, NULL, rstream);

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

		}
@@ -1259,11 +1262,12 @@ Alignment *SuperAlignment::concatenateAlignments(set<int> &ids) { 


Alignment *SuperAlignment::concatenateAlignments() {

    vector<SeqType> seq_types;

    vector<char*> genetic_codes;

    vector<set<int> > ids;

    for (int i = 0; i < partitions.size(); i++) {

        bool found = false;

        for (int j = 0; j < seq_types.size(); j++)

            if (partitions[i]->seq_type == seq_types[j]) {

            if (partitions[i]->seq_type == seq_types[j] && partitions[i]->genetic_code == genetic_codes[j]) {

                ids[j].insert(i);

                found = true;

                break;
@@ -1272,6 +1276,7 @@ Alignment *SuperAlignment::concatenateAlignments() { 
            continue;

        // create a new partition

        seq_types.push_back(partitions[i]->seq_type);

        genetic_codes.push_back(partitions[i]->genetic_code);

        ids.push_back(set<int>());

        ids.back().insert(i);

    }

nclextra/msetsblock.cpp

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@@ -267,6 +267,9 @@ void MSetsBlock::Read(NxsToken &token) 


		else

		{

            errormsg = "Unknown command ";

            errormsg += token.GetToken();

            throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());

			SkippingCommand(token.GetToken());

			do

			{
@@ -284,6 +287,11 @@ void MSetsBlock::Read(NxsToken &token) 


}



void MSetsBlock::SkippingCommand(NxsString commandName) {

    cout << "WARNING: Skipping unknown command " << commandName << endl;

}





CharSet *MSetsBlock::findCharSet(string name) {

	for (vector<CharSet*>::iterator it = charsets.begin(); it != charsets.end(); it++)

		if ((*it)->name == name) return (*it);

nclextra/msetsblock.h

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@@ -95,6 +95,12 @@ public: 
	*/

	virtual void Reset();



    /**

     called when some commands are skipped

     @param commandName command name

     */

    virtual void SkippingCommand(NxsString commandName);



	/**

		@return the number of sets

	*/