--- /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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