+++ /dev/null
-/*********************************************************************
- * Clustal Omage - Multiple sequence alignment
- *
- * Copyright (C) 2010 University College Dublin
- *
- * Clustal-Omega is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation; either version 2 of the
- * License, or (at your option) any later version.
- *
- * This file is part of Clustal-Omega.
- *
- ********************************************************************/
-
-/*
- * RCS $Id: main.cpp 234 2011-04-13 05:26:16Z andreas $
- */
-
-/*
- * We are using a mix of C and C++, which means that linking has to be
- * done with a C++ compiler. By using this "fake" main c++ function,
- * automake is convinced to use a C++ compiler for linking.
- *
- */
-
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-extern "C" {
-#include "mymain.h"
-#include "clustal/util.h"
-#include "squid/squid.h"
-}
-
-
-/**
- * @brief Convert an old Clustal command line parameter in the form of
- * [-/]param[=value] to new parameter if possible
- *
- * @param[out] iNewArgC_p
- * "argc" which will be incremented for each successfully converted option
- * @param[out] ppcNewArgV_p
- * "argv" to which each successfully converted options will be added
- * (caller has to free)
- * @param[in] pcOldArg
- * The old parameter and value command line option
- *
- */
-void
-ConvertOldCmdLineArg(int *iNewArgC_p, char ***ppcNewArgV_p, char *pcOldArg)
-{
- char *pcOldParam, *pcOldValue, *pcOldArgCopy;
- char zcNotImplementedMsg[] = "WARNING: Invalid old command line option";
-
- pcOldArgCopy = CkStrdup(pcOldArg);
- pcOldParam = strtok(pcOldArgCopy, "=");
- pcOldValue = strtok(NULL, "=");
-
-
- /* go through all options in order of appearance in clustalw2 -help
- *
- */
-
- /* data
- *
- */
- if (STR_NC_EQ("INFILE", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-i");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- } else if (STR_NC_EQ("PROFILE1", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile1");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- } else if (STR_NC_EQ("PROFILE2", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile2");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- /* verbs
- *
- */
-
- /* missing:
- * OPTIONS
- */
-
- } else if (STR_NC_EQ("HELP", &pcOldParam[1])
- || STR_NC_EQ("CHECK", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
-
- } else if (STR_NC_EQ("FULLHELP", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
-
- } else if (STR_NC_EQ("ALIGN", &pcOldParam[1])) {
- char msg[] = "WARNING: The ALIGN option is default in Clustal Omega";
- fprintf(stderr, "%s\n", msg);
-
- /* missing:
- * TREE
- * PIM
- * BOOTSTRAP
- * CONVERT
- */
-
- /* parameters
- *
- */
- } else if (STR_NC_EQ("INTERACTIVE", &pcOldParam[1])) {
- char msg[] = "WARNING: There is no interactive command-line menu in Clustal Omega";
- fprintf(stderr, "%s\n", msg);
- /* trigger help */
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
-
- } else if (STR_NC_EQ("QUICKTREE", &pcOldParam[1])) {
- char msg[] = "WARNING: The QUICKTREE (i.e. k-tuple distance) option is default in Clustal Omega";
- fprintf(stderr, "%s\n", msg);
-
- } else if (STR_NC_EQ("TYPE", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-t");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- /* NEGATIVE */
-
- } else if (STR_NC_EQ("OUTFILE", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
-
- } else if (STR_NC_EQ("OUTPUT", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- /* missing:
- * OUTORDER
- * CASE
- * SEQNOS
- * SEQNO_RANGE
- * RANGE
- */
-
- } else if (STR_NC_EQ("MAXSEQLEN", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--maxseqlen");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- } else if (STR_NC_EQ("QUIET", &pcOldParam[1])) {
- char msg[] = "WARNING: The QUIET option is default in Clustal Omega";
- fprintf(stderr, "%s\n", msg);
-
- /* missing:
- * STATS
- */
-
- /* fast pariwise alignment
- *
- */
-
- /* missing:
- * KTUPLE
- * TOPDIAGS
- * WINDOW
- * PAIRGAP
- * SCORE
- */
-
- /* slow pairwise alignments
- *
- */
-
- /* missing:
- * PWMATRIX
- * PWDNAMATRIX
- * PWGAPOPEN
- * PWGAPEXT
- */
-
- /* multiple alignments
- *
- */
- } else if (STR_NC_EQ("NEWTREE", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-out");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- } else if (STR_NC_EQ("USETREE", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-in");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-
- /* missing:
- * MATRIX
- * DNAMATRIX
- * GAPOPEN
- * GAPEXT
- * ENDGAPS
- * GAPDIST
- * NOGAP
- * NOHGAP
- * HGAPRESIDUES
- * MAXDIV
- * TYPE already handled above
- * TRANSWEIGHT
- * ITERATION
- * NUMITER
- * NOWEIGHTS
- */
-
- /* profile alignments
- *
- */
-
- /* missing:
- * PROFILE
- * NEWTREE1
- * NEWTREE2
- * USETREE1
- * USETREE2
- */
-
- /* sequence to profile alignments
- *
- */
- } else if (STR_NC_EQ("SEQUENCES", &pcOldParam[1])) {
- fprintf(stderr, "WARNING: %s: %s\n", zcNotImplementedMsg, pcOldArg);
-
- /* SEQUENCES and NEWTREE already handled above */
-
- /* structure alignments
- *
- */
-
- /* missing:
- * NOSECSTR1
- * NOSECSTR2
- * SECSTROUT
- * HELIXGAP
- * STRANDGAP
- * LOOPGAP
- * TERMINALGAP
- * HELIXENDIN
- * HELIXENDOUT
- * STRANDENDIN
- * STRANDENDOUT
- */
-
- /* trees
- *
- */
-
- /* missing:
- * OUTPUTTREE
- * SEED
- * KIMURA
- * TOSSGAPS
- * BOOTLABELS
- */
-#if 0
- } else if (STR_NC_EQ("CLUSTERING", &pcOldParam[1])) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-c");
- if (NULL != pcOldValue)
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
-#endif
-
- } else {
- fprintf(stderr,
- "WARNING: Unsupported old command line option '%s' will be ignored\n",
- pcOldArg);
- }
-
- /* FIXME: if not outfile was given, than the old default was to create a
- * filename based on the input filename but with its extension replaced by
- * aln. If the input already had the extension aln then the input was
- * overwritten. What to do here? Strictly mimic the old behaviour?
- */
-
- free(pcOldArgCopy);
-}
-/* end ConvertOldCmdLineArg */
-
-
-
-/**
- * @brief Convert old command line usage to new one. Mix of old and
- * new style will be tolerated
- *
- * @param[out] iNewArgC_p
- * The updated "argc"
- * @param[out] ppcNewArgV_p
- * The updated "argv". Caller has to free.
- * @param[in] argc
- * Original "argc"
- * @param[in] argv
- * Original argv
- *
- * @note old style parameters look like this:
- * [/-]param[=value]
- * new style parameters:
- * -p [value]
- * --param [value]
- *
- */
-void
-ConvertOldCmdline(int *iNewArgC_p, char ***ppcNewArgV_p, int argc, char **argv)
-{
- bool bOldCmdlineDetected = false;
- int i; /* aux */
-
- /* we can have at most 2*argc converted arguments, plus the few
- * that we set by default (.e.g --force)
- */
- (*ppcNewArgV_p) = (char **) CKCALLOC(argc*2+10, sizeof(char*));
-
- /* copy first arg which is program name */
- (*ppcNewArgV_p)[0] = CkStrdup(argv[0]);
- *iNewArgC_p = 1;
-
- for (i=1; i<argc; i++) {
- bool bNewStyle = false;
-
- if (strlen(argv[i])<=2) {
- /* e.g. -i (param) or just numbers (value) */
- bNewStyle = true;
-
- } else if (strlen(argv[i])>2) {
- if (argv[i][0] == '-' && argv[i][1] == '-') {
- /* new style long opts */
- bNewStyle = true;
-
- } else if (argv[i][0]=='/' && (NULL!=strchr(&argv[i][1], '/'))) {
- /* Slash used to be a valid replacement for dash in
- * Clustal<=2, but could also be file in new style. If
- * we find at least two slashes, one at the beginning,
- * it should be a filename and therefore new style */
- bNewStyle = true;
-
- } else if (argv[i][0] != '/' && argv[i][0] != '-') {
- /* old style opts always start with slash or dash */
- bNewStyle = true;
-
- }
- }
-
- /* copy and continue if new style arg or attempt to convert
- * old style arg
- */
- if (bNewStyle) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(argv[i]);
- } else {
- ConvertOldCmdLineArg(iNewArgC_p, ppcNewArgV_p, argv[i]);
- /*LOG_DEBUG("old command line arg: %s", argv[i]);*/
- bOldCmdlineDetected = true;
- }
- }
-
- if (bOldCmdlineDetected) {
- bool bOutfileOptSet = FALSE;
- bool bOutFormatOptSet = FALSE;
-
-
- /* old clustal used to write to a file called in.aln by
- * default. set if not
- * explicitely requested otherwisee
- */
- for (i=0; i<*iNewArgC_p; i++) {
- const char *pcOpt = "-o";
- if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
- if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
- bOutfileOptSet = TRUE;
- break;
- }
- }
- }
- if (FALSE == bOutfileOptSet) {
-#ifdef TOO_LAZY_TO_IMPLEMENT_JUST_USING_DEFAULT_NAME_INSTEAD
- char *pcDotPos = NULL;
- char *pcInfileOpt = NULL;
-
- /* get infile arg and find last dot in it. if found replace
- * everything after with "aln", otherwise just add "aln"
- */
- for (i=0; i<*iNewArgC_p; i++) {
- const char *pcOpt = "-i";
- if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
- if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
- if (*iNewArgC_p<= i+1) {
- fprintf(stderr,
- "Oups...error while trying to convert old commandline (%s).\n",
- "No more arguments left after -i");
- exit(1);
- }
- pcInfileOpt = (*ppcNewArgV_p)[i+1];
- break;
- }
- }
- }
- if (NULL == pcInfileOpt) {
- fprintf(stderr,
- "Oups...error while trying to convert old commandline (%s)\n",
- "No infile opt found");
- exit(1);
- }
-
- fprintf(stderr, "FIXME: unfinished\n");
- exit(1);
-#endif
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("clustal.aln");
- }
-
-
- /* old clustal used the clustal format by default. set if not
- * explicitely requested otherwisee
- */
- for (i=0; i<*iNewArgC_p; i++) {
- const char *pcOpt = "--outfmt";
- if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
- if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
- bOutFormatOptSet = TRUE;
- break;
- }
- }
- }
- if (FALSE == bOutFormatOptSet) {
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt=clustal");
- }
-
-
- /* old clustal was verbose by default
- */
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-v");
-
- /* old clustal used to overwrite files by default
- */
- (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--force");
-
- fprintf(stderr,
- "WARNING: Your old-style command-line options were converted to: ");
- for (i=0; i<*iNewArgC_p; i++) {
- fprintf(stderr, " %s", (*ppcNewArgV_p)[i]);
- }
- fprintf(stderr, "\n");
- }
-
-}
-/* end ConvertOldCmdline */
-
-
-
-int
-main(int argc, char **argv)
-{
- int new_argc = 0;
- char **new_argv = NULL;
- int i; /* aux */
-
- ConvertOldCmdline(&new_argc, &new_argv, argc, argv);
-
- MyMain(new_argc, new_argv);
-
- for (i=0; i<new_argc; i++) {
- free(new_argv[i]);
- }
- free(new_argv);
-
- return 0;
-}
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