Commit f5b755f2 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 7.407

parent fc205afe

core/dvtditr.c

+21 −0
Original line number Diff line number Diff line
@@ -481,6 +481,8 @@ int main( int argc, char *argv[] ) 


	nkozo = 0;







	if( njob < 2 ) 

	{

		seq = AllocateCharMtx( 2, nlenmax*1+1 );
@@ -501,6 +503,25 @@ int main( int argc, char *argv[] ) 
	}





	if( nlenmax < 1 )

	{

		seq = AllocateCharMtx( njob, nlenmax*1+1 );

    	name = AllocateCharMtx( njob, B+1 );

//	    nlen = AllocateIntVec( 2 ); 

		readData_pointer( infp, name, nlen, seq );

		fclose( infp );

		initFiles();

		for( i=0; i<njob; i++ ) strcpy( seq[i], "" );

		writeData_pointer( prep_g, njob, name, nlen, seq );

		reporterr( "Warning: No sequence found.\n", njob ); 

		FreeCharMtx( seq );

		FreeCharMtx( name );

//		free( nlen );

		closeFiles();

		exit( 0 );

	}





	if( subalignment )

	{

		readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );

core/mafft.bat

+9 −0
Original line number Diff line number Diff line 
@echo off

setlocal enabledelayedexpansion

cls

for /f "usebackq tokens=*" %%i IN (`cd`) DO @set current_dir=%%i

if /i "%current_dir%" == "%windir%" (

  set mafft_working_dir="%~dp0"

) else (

  set mafft_working_dir="%current_dir%"

)

pushd "%mafft_working_dir%"



echo; 1>&2

echo Preparing environment to run MAFFT on Windows. 1>&2
@@ -21,4 +29,5 @@ REM temporary folder. 


"%ROOTDIR%\usr\bin\bash" "%ROOTDIRWBS%\usr\bin\mafft" %*



popd

exit /b

core/mafft.tmpl

+4 −2
Original line number Diff line number Diff line 
#! /bin/bash 

er=0;

myself=`dirname "$0"`/`basename "$0"`; export myself

version="v7.402 (2018/May/23)"; export version

version="v7.407 (2018/Jul/23)"; export version

LANG=C; export LANG

os=`uname`

progname=`basename "$0"`
@@ -2625,6 +2625,8 @@ BEGIN { 
	prefix = ENVIRON["prefix"];

	version = ENVIRON["version"];

	myself = ENVIRON["myself"];

	pwd = ENVIRON["mafft_working_dir"];  # from mafft.bat on windows

	if( pwd == "" ) pwd = ENVIRON["PWD"];

	while( 1 )

	{

		options = ""
@@ -2642,7 +2644,7 @@ BEGIN { 
		while( 1 )

		{

			printf( "\n" ) > "/dev/tty";

			printf( "Input file? (fasta format)\n@ " ) > "/dev/tty";

			printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty";

			res = getline < "/dev/tty";

			close( "/dev/tty" )

			if( res == 0 || NF == 0 )

core/mltaln.h

+1 −1
Original line number Diff line number Diff line
@@ -35,7 +35,7 @@ 






#define VERSION "7.402"

#define VERSION "7.407"

#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )



#define FFT_THRESHOLD  80

readme

+1 −1
Original line number Diff line number Diff line 
-----------------------------------------------------------------------

  MAFFT: a multiple sequence alignment program

  version 7.402, 2018/May/23

  version 7.407, 2018/Jul/23



  http://mafft.cbrc.jp/alignment/software/

  katoh@ifrec.osaka-u.ac.jp